Menu
▾
▴
treebase-guts — Commit and tracker messages
You can subscribe to this list here.
| 2009 |
Jan
|
Feb
|
Mar
(1) |
Apr
(14) |
May
(36) |
Jun
(148) |
Jul
(33) |
Aug
(2) |
Sep
(17) |
Oct
(42) |
Nov
(137) |
Dec
(88) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 2010 |
Jan
(89) |
Feb
(80) |
Mar
(217) |
Apr
(76) |
May
(5) |
Jun
(39) |
Jul
(35) |
Aug
(4) |
Sep
(7) |
Oct
(14) |
Nov
(12) |
Dec
(9) |
| 2011 |
Jan
(6) |
Feb
(4) |
Mar
(11) |
Apr
(55) |
May
(90) |
Jun
(39) |
Jul
(15) |
Aug
(15) |
Sep
(23) |
Oct
(12) |
Nov
(17) |
Dec
(20) |
| 2012 |
Jan
(22) |
Feb
(63) |
Mar
|
Apr
(1) |
May
(6) |
Jun
(3) |
Jul
(1) |
Aug
(1) |
Sep
|
Oct
|
Nov
|
Dec
|
| 2013 |
Jan
(3) |
Feb
(6) |
Mar
|
Apr
|
May
|
Jun
(4) |
Jul
(1) |
Aug
(1) |
Sep
|
Oct
|
Nov
|
Dec
|
| 2014 |
Jan
|
Feb
|
Mar
|
Apr
(7) |
May
|
Jun
|
Jul
|
Aug
|
Sep
|
Oct
|
Nov
|
Dec
|
|
From: <rv...@us...> - 2009-12-16 10:52:46
|
Revision: 393
http://treebase.svn.sourceforge.net/treebase/?rev=393&view=rev
Author: rvos
Date: 2009-12-16 10:52:28 +0000 (Wed, 16 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/jama/
trunk/treebase-core/lib/mesquite/jama/aJamaIntro/
trunk/treebase-core/lib/mesquite/jama/aJamaIntro/aJamaIntro.class
trunk/treebase-core/lib/mesquite/jama/aJamaIntro/index.html
trunk/treebase-core/lib/mesquite/jama/aJamaIntro/splash.gif
trunk/treebase-core/lib/mesquite/jama/explanation.txt
trunk/treebase-core/lib/mesquite/jsci/
trunk/treebase-core/lib/mesquite/jsci/aJSciIntro/
trunk/treebase-core/lib/mesquite/jsci/aJSciIntro/aJSciIntro.class
trunk/treebase-core/lib/mesquite/jsci/aJSciIntro/index.html
trunk/treebase-core/lib/mesquite/jsci/aJSciIntro/splash.gif
trunk/treebase-core/lib/mesquite/jsci/explanation.txt
trunk/treebase-core/lib/mesquite/lib/
trunk/treebase-core/lib/mesquite/lib/AImagePanel.class
trunk/treebase-core/lib/mesquite/lib/ANTextField.class
trunk/treebase-core/lib/mesquite/lib/Abortable.class
trunk/treebase-core/lib/mesquite/lib/AdjustableTree.class
trunk/treebase-core/lib/mesquite/lib/AlertDialog.class
trunk/treebase-core/lib/mesquite/lib/AnnotPanelOwner.class
trunk/treebase-core/lib/mesquite/lib/Annotatable.class
trunk/treebase-core/lib/mesquite/lib/AnnotationsPanel.class
trunk/treebase-core/lib/mesquite/lib/AntMarcher.class
trunk/treebase-core/lib/mesquite/lib/Arguments.class
trunk/treebase-core/lib/mesquite/lib/Associable.class
trunk/treebase-core/lib/mesquite/lib/AssociableWithSpecs.class
trunk/treebase-core/lib/mesquite/lib/Attachable.class
trunk/treebase-core/lib/mesquite/lib/AttachedNote.class
trunk/treebase-core/lib/mesquite/lib/AttachedNotesVector.class
trunk/treebase-core/lib/mesquite/lib/Author.class
trunk/treebase-core/lib/mesquite/lib/AutoSavedLister.class
trunk/treebase-core/lib/mesquite/lib/BannerPanel.class
trunk/treebase-core/lib/mesquite/lib/Binomial.class
trunk/treebase-core/lib/mesquite/lib/Bits.class
trunk/treebase-core/lib/mesquite/lib/BitsSpecsSet.class
trunk/treebase-core/lib/mesquite/lib/ButtonWaitThread.class
trunk/treebase-core/lib/mesquite/lib/CRecord.class
trunk/treebase-core/lib/mesquite/lib/CardPanel.class
trunk/treebase-core/lib/mesquite/lib/ChangeAuthority.class
trunk/treebase-core/lib/mesquite/lib/ChangeEvent.class
trunk/treebase-core/lib/mesquite/lib/ChangeHistory.class
trunk/treebase-core/lib/mesquite/lib/ChartBkgdExtra.class
trunk/treebase-core/lib/mesquite/lib/ChartExtra.class
trunk/treebase-core/lib/mesquite/lib/ChartField.class
trunk/treebase-core/lib/mesquite/lib/ChartListener.class
trunk/treebase-core/lib/mesquite/lib/ChartScroll.class
trunk/treebase-core/lib/mesquite/lib/ChartScrollPane.class
trunk/treebase-core/lib/mesquite/lib/ChartTool.class
trunk/treebase-core/lib/mesquite/lib/ChartWindow.class
trunk/treebase-core/lib/mesquite/lib/Charter.class
trunk/treebase-core/lib/mesquite/lib/ChecklistBox.class
trunk/treebase-core/lib/mesquite/lib/ChecklistDialog.class
trunk/treebase-core/lib/mesquite/lib/ChecklistScrollPane.class
trunk/treebase-core/lib/mesquite/lib/CircleSymbol.class
trunk/treebase-core/lib/mesquite/lib/Clade.class
trunk/treebase-core/lib/mesquite/lib/Clades.class
trunk/treebase-core/lib/mesquite/lib/ClassVector.class
trunk/treebase-core/lib/mesquite/lib/ClockPanel.class
trunk/treebase-core/lib/mesquite/lib/ColorDialog.class
trunk/treebase-core/lib/mesquite/lib/ColorDistribution.class
trunk/treebase-core/lib/mesquite/lib/ColorEvent.class
trunk/treebase-core/lib/mesquite/lib/ColorEventVector.class
trunk/treebase-core/lib/mesquite/lib/ColorPickerPanel.class
trunk/treebase-core/lib/mesquite/lib/ColorRecord.class
trunk/treebase-core/lib/mesquite/lib/Colorable.class
trunk/treebase-core/lib/mesquite/lib/CommandChecker.class
trunk/treebase-core/lib/mesquite/lib/CommandCommunicator.class
trunk/treebase-core/lib/mesquite/lib/CommandRecord.class
trunk/treebase-core/lib/mesquite/lib/CommandRecordHolder.class
trunk/treebase-core/lib/mesquite/lib/CommandThread.class
trunk/treebase-core/lib/mesquite/lib/Commandable.class
trunk/treebase-core/lib/mesquite/lib/CommandableOwner.class
trunk/treebase-core/lib/mesquite/lib/CompatibilityChecker.class
trunk/treebase-core/lib/mesquite/lib/CompatibilityTest.class
trunk/treebase-core/lib/mesquite/lib/ConsoleThread.class
trunk/treebase-core/lib/mesquite/lib/ConsoleWindow.class
trunk/treebase-core/lib/mesquite/lib/ContentArea.class
trunk/treebase-core/lib/mesquite/lib/ContentLedgeContainer.class
trunk/treebase-core/lib/mesquite/lib/ContentSideContainer.class
trunk/treebase-core/lib/mesquite/lib/Context.class
trunk/treebase-core/lib/mesquite/lib/ControlP.class
trunk/treebase-core/lib/mesquite/lib/CurrentColorPanel.class
trunk/treebase-core/lib/mesquite/lib/Debugg.class
trunk/treebase-core/lib/mesquite/lib/DialogGraphicsPanel.class
trunk/treebase-core/lib/mesquite/lib/DirFilenameFilter.class
trunk/treebase-core/lib/mesquite/lib/Doomable.class
trunk/treebase-core/lib/mesquite/lib/Double2DArray.class
trunk/treebase-core/lib/mesquite/lib/DoubleArray.class
trunk/treebase-core/lib/mesquite/lib/DoubleClickList.class
trunk/treebase-core/lib/mesquite/lib/DoubleClickListener.class
trunk/treebase-core/lib/mesquite/lib/DoubleField.class
trunk/treebase-core/lib/mesquite/lib/DoubleMiniScroll.class
trunk/treebase-core/lib/mesquite/lib/DoubleSliderWindow.class
trunk/treebase-core/lib/mesquite/lib/DoubleSqMatrixFields.class
trunk/treebase-core/lib/mesquite/lib/DragRectangle.class
trunk/treebase-core/lib/mesquite/lib/ETContentArea.class
trunk/treebase-core/lib/mesquite/lib/EmployeeNeed.class
trunk/treebase-core/lib/mesquite/lib/EmployeeVector.class
trunk/treebase-core/lib/mesquite/lib/EmployerEmployee.class
trunk/treebase-core/lib/mesquite/lib/EnterButton.class
trunk/treebase-core/lib/mesquite/lib/EnterTextField.class
trunk/treebase-core/lib/mesquite/lib/Evaluator.class
trunk/treebase-core/lib/mesquite/lib/ExplTextArea.class
trunk/treebase-core/lib/mesquite/lib/Explainable.class
trunk/treebase-core/lib/mesquite/lib/ExplanationArea.class
trunk/treebase-core/lib/mesquite/lib/ExplanationControl.class
trunk/treebase-core/lib/mesquite/lib/ExponentialDistribution.class
trunk/treebase-core/lib/mesquite/lib/ExporterDialog.class
trunk/treebase-core/lib/mesquite/lib/ExtensibleDialog$ConstrJEP.class
trunk/treebase-core/lib/mesquite/lib/ExtensibleDialog.class
trunk/treebase-core/lib/mesquite/lib/ExtensibleExplDialog.class
trunk/treebase-core/lib/mesquite/lib/ExtensibleListDialog.class
trunk/treebase-core/lib/mesquite/lib/FileBlock.class
trunk/treebase-core/lib/mesquite/lib/FileDirtier.class
trunk/treebase-core/lib/mesquite/lib/FileElement.class
trunk/treebase-core/lib/mesquite/lib/FillableMesquiteSymbol.class
trunk/treebase-core/lib/mesquite/lib/Fittable.class
trunk/treebase-core/lib/mesquite/lib/FrameTabsPanel.class
trunk/treebase-core/lib/mesquite/lib/FunctionExplainable.class
trunk/treebase-core/lib/mesquite/lib/FunctionExplanation.class
trunk/treebase-core/lib/mesquite/lib/GraphicsUtil.class
trunk/treebase-core/lib/mesquite/lib/GroupLabel.class
trunk/treebase-core/lib/mesquite/lib/HNode.class
trunk/treebase-core/lib/mesquite/lib/HPanel.class
trunk/treebase-core/lib/mesquite/lib/HSWindow.class
trunk/treebase-core/lib/mesquite/lib/HTMLDescribable.class
trunk/treebase-core/lib/mesquite/lib/HTMLSidePanel.class
trunk/treebase-core/lib/mesquite/lib/HeaderPanel.class
trunk/treebase-core/lib/mesquite/lib/HelpSearchManager$ManualPage.class
trunk/treebase-core/lib/mesquite/lib/HelpSearchManager.class
trunk/treebase-core/lib/mesquite/lib/HelpSearchStrip.class
trunk/treebase-core/lib/mesquite/lib/HorizontalLine.class
trunk/treebase-core/lib/mesquite/lib/Hyperlink.class
trunk/treebase-core/lib/mesquite/lib/Identifiable.class
trunk/treebase-core/lib/mesquite/lib/Illustratable.class
trunk/treebase-core/lib/mesquite/lib/ImageHeaderPanel.class
trunk/treebase-core/lib/mesquite/lib/ImageLabel.class
trunk/treebase-core/lib/mesquite/lib/ImageOwner.class
trunk/treebase-core/lib/mesquite/lib/ImagePanel.class
trunk/treebase-core/lib/mesquite/lib/ImagePanelListener.class
trunk/treebase-core/lib/mesquite/lib/Incrementable.class
trunk/treebase-core/lib/mesquite/lib/InfoBar.class
trunk/treebase-core/lib/mesquite/lib/InfoPanel.class
trunk/treebase-core/lib/mesquite/lib/Integer2DArray.class
trunk/treebase-core/lib/mesquite/lib/IntegerArray.class
trunk/treebase-core/lib/mesquite/lib/IntegerField.class
trunk/treebase-core/lib/mesquite/lib/IntegerSqMatrixFields.class
trunk/treebase-core/lib/mesquite/lib/InterContentArea.class
trunk/treebase-core/lib/mesquite/lib/Journal.class
trunk/treebase-core/lib/mesquite/lib/KIListener.class
trunk/treebase-core/lib/mesquite/lib/KeyAdapterToConsumeKeys.class
trunk/treebase-core/lib/mesquite/lib/LabelsAtNodes.class
trunk/treebase-core/lib/mesquite/lib/LeakFinder.class
trunk/treebase-core/lib/mesquite/lib/Legend.class
trunk/treebase-core/lib/mesquite/lib/LegendHolder.class
trunk/treebase-core/lib/mesquite/lib/LightLabel.class
trunk/treebase-core/lib/mesquite/lib/LightLabelsAtNodes.class
trunk/treebase-core/lib/mesquite/lib/LinearValueToPixel.class
trunk/treebase-core/lib/mesquite/lib/ListDialog.class
trunk/treebase-core/lib/mesquite/lib/Listable.class
trunk/treebase-core/lib/mesquite/lib/ListableVector.class
trunk/treebase-core/lib/mesquite/lib/Listenable.class
trunk/treebase-core/lib/mesquite/lib/Listened.class
trunk/treebase-core/lib/mesquite/lib/LogValueToPixel.class
trunk/treebase-core/lib/mesquite/lib/LogWindow.class
trunk/treebase-core/lib/mesquite/lib/Logger.class
trunk/treebase-core/lib/mesquite/lib/Long2DArray.class
trunk/treebase-core/lib/mesquite/lib/LongArray.class
trunk/treebase-core/lib/mesquite/lib/LongField.class
trunk/treebase-core/lib/mesquite/lib/MDPHelperThread.class
trunk/treebase-core/lib/mesquite/lib/MDPShowThread.class
trunk/treebase-core/lib/mesquite/lib/MDPanel.class
trunk/treebase-core/lib/mesquite/lib/MHTMLControl.class
trunk/treebase-core/lib/mesquite/lib/MRPopup.class
trunk/treebase-core/lib/mesquite/lib/MainThread.class
trunk/treebase-core/lib/mesquite/lib/MarchingAnts.class
trunk/treebase-core/lib/mesquite/lib/MenuItemsSpecsVector.class
trunk/treebase-core/lib/mesquite/lib/MenuOwner.class
trunk/treebase-core/lib/mesquite/lib/Mesquite3DIntPoint.class
trunk/treebase-core/lib/mesquite/lib/MesquiteBoolean.class
trunk/treebase-core/lib/mesquite/lib/MesquiteButton.class
trunk/treebase-core/lib/mesquite/lib/MesquiteCMenuItemSpec.class
trunk/treebase-core/lib/mesquite/lib/MesquiteChart.class
trunk/treebase-core/lib/mesquite/lib/MesquiteCheckMenuItem.class
trunk/treebase-core/lib/mesquite/lib/MesquiteColorTable.class
trunk/treebase-core/lib/mesquite/lib/MesquiteCommand.class
trunk/treebase-core/lib/mesquite/lib/MesquiteCursor.class
trunk/treebase-core/lib/mesquite/lib/MesquiteDialog.class
trunk/treebase-core/lib/mesquite/lib/MesquiteDialogParent.class
trunk/treebase-core/lib/mesquite/lib/MesquiteDouble.class
trunk/treebase-core/lib/mesquite/lib/MesquiteDroppedFileHandler.class
trunk/treebase-core/lib/mesquite/lib/MesquiteEvent.class
trunk/treebase-core/lib/mesquite/lib/MesquiteException.class
trunk/treebase-core/lib/mesquite/lib/MesquiteFile.class
trunk/treebase-core/lib/mesquite/lib/MesquiteFileDialog.class
trunk/treebase-core/lib/mesquite/lib/MesquiteFrame$MWCE.class
trunk/treebase-core/lib/mesquite/lib/MesquiteFrame$MWWE.class
trunk/treebase-core/lib/mesquite/lib/MesquiteFrame.class
trunk/treebase-core/lib/mesquite/lib/MesquiteHTMLWindow.class
trunk/treebase-core/lib/mesquite/lib/MesquiteImage.class
trunk/treebase-core/lib/mesquite/lib/MesquiteInteger.class
trunk/treebase-core/lib/mesquite/lib/MesquiteLabel.class
trunk/treebase-core/lib/mesquite/lib/MesquiteListTable.class
trunk/treebase-core/lib/mesquite/lib/MesquiteListWindow.class
trunk/treebase-core/lib/mesquite/lib/MesquiteListener.class
trunk/treebase-core/lib/mesquite/lib/MesquiteLong.class
trunk/treebase-core/lib/mesquite/lib/MesquiteMacro.class
trunk/treebase-core/lib/mesquite/lib/MesquiteMenu.class
trunk/treebase-core/lib/mesquite/lib/MesquiteMenuBar.class
trunk/treebase-core/lib/mesquite/lib/MesquiteMenuItem.class
trunk/treebase-core/lib/mesquite/lib/MesquiteMenuItemSpec.class
trunk/treebase-core/lib/mesquite/lib/MesquiteMenuSpec.class
trunk/treebase-core/lib/mesquite/lib/MesquiteMessage.class
trunk/treebase-core/lib/mesquite/lib/MesquiteModule.class
trunk/treebase-core/lib/mesquite/lib/MesquiteModuleInfo.class
trunk/treebase-core/lib/mesquite/lib/MesquiteNumber.class
trunk/treebase-core/lib/mesquite/lib/MesquitePDFFile.class
trunk/treebase-core/lib/mesquite/lib/MesquitePackageRecord.class
trunk/treebase-core/lib/mesquite/lib/MesquitePanel.class
trunk/treebase-core/lib/mesquite/lib/MesquiteParameter.class
trunk/treebase-core/lib/mesquite/lib/MesquitePopup.class
trunk/treebase-core/lib/mesquite/lib/MesquitePrintJob$P2.class
trunk/treebase-core/lib/mesquite/lib/MesquitePrintJob$P2Text.class
trunk/treebase-core/lib/mesquite/lib/MesquitePrintJob.class
trunk/treebase-core/lib/mesquite/lib/MesquiteProject.class
trunk/treebase-core/lib/mesquite/lib/MesquiteScrollbar.class
trunk/treebase-core/lib/mesquite/lib/MesquiteSet.class
trunk/treebase-core/lib/mesquite/lib/MesquiteString.class
trunk/treebase-core/lib/mesquite/lib/MesquiteSubmenu.class
trunk/treebase-core/lib/mesquite/lib/MesquiteSubmenuSpec.class
trunk/treebase-core/lib/mesquite/lib/MesquiteSymbol.class
trunk/treebase-core/lib/mesquite/lib/MesquiteTextWindow.class
trunk/treebase-core/lib/mesquite/lib/MesquiteThread.class
trunk/treebase-core/lib/mesquite/lib/MesquiteTimer.class
trunk/treebase-core/lib/mesquite/lib/MesquiteTool.class
trunk/treebase-core/lib/mesquite/lib/MesquiteTree.class
trunk/treebase-core/lib/mesquite/lib/MesquiteTrunk.class
trunk/treebase-core/lib/mesquite/lib/MesquiteWindow.class
trunk/treebase-core/lib/mesquite/lib/MesquiteXMLPreferencesModule.class
trunk/treebase-core/lib/mesquite/lib/MesquiteXMLUtilities.class
trunk/treebase-core/lib/mesquite/lib/MessagePanel.class
trunk/treebase-core/lib/mesquite/lib/MiniControl.class
trunk/treebase-core/lib/mesquite/lib/MiniNumberEditor.class
trunk/treebase-core/lib/mesquite/lib/MiniScroll.class
trunk/treebase-core/lib/mesquite/lib/MiniScrollButton.class
trunk/treebase-core/lib/mesquite/lib/MiniSlider.class
trunk/treebase-core/lib/mesquite/lib/MiniSliderWithText.class
trunk/treebase-core/lib/mesquite/lib/MiniStringEditor.class
trunk/treebase-core/lib/mesquite/lib/ModuleInfoWindow.class
trunk/treebase-core/lib/mesquite/lib/ModulesInfoVector.class
trunk/treebase-core/lib/mesquite/lib/MousePanel.class
trunk/treebase-core/lib/mesquite/lib/MqFilterInputStream.class
trunk/treebase-core/lib/mesquite/lib/NameReference.class
trunk/treebase-core/lib/mesquite/lib/NexusBlock.class
trunk/treebase-core/lib/mesquite/lib/NexusBlockEditableRaw.class
trunk/treebase-core/lib/mesquite/lib/NexusBlockTest.class
trunk/treebase-core/lib/mesquite/lib/NexusCommandTest.class
trunk/treebase-core/lib/mesquite/lib/NexusWritable.class
trunk/treebase-core/lib/mesquite/lib/Notification.class
trunk/treebase-core/lib/mesquite/lib/NumSpecsSet.class
trunk/treebase-core/lib/mesquite/lib/Number2DArray.class
trunk/treebase-core/lib/mesquite/lib/NumberArray.class
trunk/treebase-core/lib/mesquite/lib/Object2DArray.class
trunk/treebase-core/lib/mesquite/lib/ObjectArray.class
trunk/treebase-core/lib/mesquite/lib/ObjectContainer.class
trunk/treebase-core/lib/mesquite/lib/ObjectR.class
trunk/treebase-core/lib/mesquite/lib/ObjectSpecsSet.class
trunk/treebase-core/lib/mesquite/lib/Optimizer.class
trunk/treebase-core/lib/mesquite/lib/OuterContentArea.class
trunk/treebase-core/lib/mesquite/lib/OutputFileProcessor.class
trunk/treebase-core/lib/mesquite/lib/OwnedByModule.class
trunk/treebase-core/lib/mesquite/lib/PanelOfCards.class
trunk/treebase-core/lib/mesquite/lib/PanelsAtNodes.class
trunk/treebase-core/lib/mesquite/lib/ParametersDialog.class
trunk/treebase-core/lib/mesquite/lib/ParametersExplorable.class
trunk/treebase-core/lib/mesquite/lib/ParseUtil.class
trunk/treebase-core/lib/mesquite/lib/Parser.class
trunk/treebase-core/lib/mesquite/lib/PathHolder.class
trunk/treebase-core/lib/mesquite/lib/PendingCommand.class
trunk/treebase-core/lib/mesquite/lib/PhoneHomeRecord.class
trunk/treebase-core/lib/mesquite/lib/PhoneHomeUtil.class
trunk/treebase-core/lib/mesquite/lib/PoCPanel.class
trunk/treebase-core/lib/mesquite/lib/PopUpPanel.class
trunk/treebase-core/lib/mesquite/lib/PopUpPanelOfCards.class
trunk/treebase-core/lib/mesquite/lib/Prioritizable.class
trunk/treebase-core/lib/mesquite/lib/Priority.class
trunk/treebase-core/lib/mesquite/lib/ProgressIndicator.class
trunk/treebase-core/lib/mesquite/lib/ProgressPanel.class
trunk/treebase-core/lib/mesquite/lib/ProgressWindow.class
trunk/treebase-core/lib/mesquite/lib/ProgressWindowThread.class
trunk/treebase-core/lib/mesquite/lib/ProjectRead.class
trunk/treebase-core/lib/mesquite/lib/ProjectReadThread.class
trunk/treebase-core/lib/mesquite/lib/Projects.class
trunk/treebase-core/lib/mesquite/lib/PropertyNamesProvider.class
trunk/treebase-core/lib/mesquite/lib/PuppetThread.class
trunk/treebase-core/lib/mesquite/lib/Puppeteer.class
trunk/treebase-core/lib/mesquite/lib/QueryDialogs.class
trunk/treebase-core/lib/mesquite/lib/RadioButtons.class
trunk/treebase-core/lib/mesquite/lib/RandomBetween.class
trunk/treebase-core/lib/mesquite/lib/Renamable.class
trunk/treebase-core/lib/mesquite/lib/ResizableLegend.class
trunk/treebase-core/lib/mesquite/lib/RotatedRectangle.class
trunk/treebase-core/lib/mesquite/lib/ScrollTextField.class
trunk/treebase-core/lib/mesquite/lib/Selectionable.class
trunk/treebase-core/lib/mesquite/lib/ShellScriptUtil.class
trunk/treebase-core/lib/mesquite/lib/ShellScriptWatcher.class
trunk/treebase-core/lib/mesquite/lib/Short2DArray.class
trunk/treebase-core/lib/mesquite/lib/ShortArray.class
trunk/treebase-core/lib/mesquite/lib/Showable.class
trunk/treebase-core/lib/mesquite/lib/SingleLineTextArea.class
trunk/treebase-core/lib/mesquite/lib/SingleLineTextField.class
trunk/treebase-core/lib/mesquite/lib/SliderWindow.class
trunk/treebase-core/lib/mesquite/lib/Snapshot.class
trunk/treebase-core/lib/mesquite/lib/SpecialListName.class
trunk/treebase-core/lib/mesquite/lib/SpecsSet.class
trunk/treebase-core/lib/mesquite/lib/SpecsSetVector.class
trunk/treebase-core/lib/mesquite/lib/StreamGobbler.class
trunk/treebase-core/lib/mesquite/lib/StringArray.class
trunk/treebase-core/lib/mesquite/lib/StringInABox.class
trunk/treebase-core/lib/mesquite/lib/StringIntegerDialog.class
trunk/treebase-core/lib/mesquite/lib/StringIntegerListDlog.class
trunk/treebase-core/lib/mesquite/lib/StringLister.class
trunk/treebase-core/lib/mesquite/lib/StringUtil.class
trunk/treebase-core/lib/mesquite/lib/SymbolGraphicsPanel.class
trunk/treebase-core/lib/mesquite/lib/SymbolsVector.class
trunk/treebase-core/lib/mesquite/lib/SystemWindow.class
trunk/treebase-core/lib/mesquite/lib/TCMPanel.class
trunk/treebase-core/lib/mesquite/lib/TDLegendWithColors.class
trunk/treebase-core/lib/mesquite/lib/Taxa.class
trunk/treebase-core/lib/mesquite/lib/TaxaBitsSet.class
trunk/treebase-core/lib/mesquite/lib/TaxaBlock.class
trunk/treebase-core/lib/mesquite/lib/TaxaDisplay.class
trunk/treebase-core/lib/mesquite/lib/TaxaDisplayActive.class
trunk/treebase-core/lib/mesquite/lib/TaxaDisplayBkgdExtra.class
trunk/treebase-core/lib/mesquite/lib/TaxaDisplayDrawnExtra.class
trunk/treebase-core/lib/mesquite/lib/TaxaDisplayExtra.class
trunk/treebase-core/lib/mesquite/lib/TaxaDrawing.class
trunk/treebase-core/lib/mesquite/lib/TaxaGroup.class
trunk/treebase-core/lib/mesquite/lib/TaxaGroupVector.class
trunk/treebase-core/lib/mesquite/lib/TaxaInclusionSet.class
trunk/treebase-core/lib/mesquite/lib/TaxaPartition.class
trunk/treebase-core/lib/mesquite/lib/TaxaSelectionSet.class
trunk/treebase-core/lib/mesquite/lib/TaxaSpecsSet.class
trunk/treebase-core/lib/mesquite/lib/TaxaStringsSet.class
trunk/treebase-core/lib/mesquite/lib/TaxaTool.class
trunk/treebase-core/lib/mesquite/lib/TaxaTreeDisplay.class
trunk/treebase-core/lib/mesquite/lib/Taxon.class
trunk/treebase-core/lib/mesquite/lib/TaxonPair.class
trunk/treebase-core/lib/mesquite/lib/TaxonUtility.class
trunk/treebase-core/lib/mesquite/lib/TextCanvas.class
trunk/treebase-core/lib/mesquite/lib/TextContentArea.class
trunk/treebase-core/lib/mesquite/lib/TextRotator.class
trunk/treebase-core/lib/mesquite/lib/TextTree.class
trunk/treebase-core/lib/mesquite/lib/ThermoPanel.class
trunk/treebase-core/lib/mesquite/lib/ToolKeyListener.class
trunk/treebase-core/lib/mesquite/lib/ToolPalette.class
trunk/treebase-core/lib/mesquite/lib/TranslationTable.class
trunk/treebase-core/lib/mesquite/lib/Tree.class
trunk/treebase-core/lib/mesquite/lib/TreeContext.class
trunk/treebase-core/lib/mesquite/lib/TreeContextListener.class
trunk/treebase-core/lib/mesquite/lib/TreeDecorator.class
trunk/treebase-core/lib/mesquite/lib/TreeDisplay.class
trunk/treebase-core/lib/mesquite/lib/TreeDisplayActive.class
trunk/treebase-core/lib/mesquite/lib/TreeDisplayBkgdExtra.class
trunk/treebase-core/lib/mesquite/lib/TreeDisplayDrawnExtra.class
trunk/treebase-core/lib/mesquite/lib/TreeDisplayExtra.class
trunk/treebase-core/lib/mesquite/lib/TreeDisplayLegend.class
trunk/treebase-core/lib/mesquite/lib/TreeDrawing.class
trunk/treebase-core/lib/mesquite/lib/TreeReference.class
trunk/treebase-core/lib/mesquite/lib/TreeTool.class
trunk/treebase-core/lib/mesquite/lib/TreeUtil.class
trunk/treebase-core/lib/mesquite/lib/TreeVector.class
trunk/treebase-core/lib/mesquite/lib/Trees.class
trunk/treebase-core/lib/mesquite/lib/TwoIntegersDialog.class
trunk/treebase-core/lib/mesquite/lib/TwoStringsDialog.class
trunk/treebase-core/lib/mesquite/lib/UndoInstructions.class
trunk/treebase-core/lib/mesquite/lib/UndoReference.class
trunk/treebase-core/lib/mesquite/lib/Undoer.class
trunk/treebase-core/lib/mesquite/lib/ValueToPixel.class
trunk/treebase-core/lib/mesquite/lib/WaitPanel.class
trunk/treebase-core/lib/mesquite/lib/WindowButton.class
trunk/treebase-core/lib/mesquite/lib/WithStringDetails.class
trunk/treebase-core/lib/mesquite/lib/WizardInfoPanel.class
trunk/treebase-core/lib/mesquite/lib/WorkaroundThread.class
trunk/treebase-core/lib/mesquite/lib/ZipUtil.class
trunk/treebase-core/lib/mesquite/lib/characters/
trunk/treebase-core/lib/mesquite/lib/characters/AdjustableDistribution.class
trunk/treebase-core/lib/mesquite/lib/characters/CLikelihoodCalculator.class
trunk/treebase-core/lib/mesquite/lib/characters/CModelEstimator.class
trunk/treebase-core/lib/mesquite/lib/characters/CentralModelListener.class
trunk/treebase-core/lib/mesquite/lib/characters/CharBitsSet.class
trunk/treebase-core/lib/mesquite/lib/characters/CharHistoryContainer.class
trunk/treebase-core/lib/mesquite/lib/characters/CharInclusionSet.class
trunk/treebase-core/lib/mesquite/lib/characters/CharNumSet.class
trunk/treebase-core/lib/mesquite/lib/characters/CharObjectSpecsSet.class
trunk/treebase-core/lib/mesquite/lib/characters/CharSelectionSet.class
trunk/treebase-core/lib/mesquite/lib/characters/CharSort.class
trunk/treebase-core/lib/mesquite/lib/characters/CharSpecsSet.class
trunk/treebase-core/lib/mesquite/lib/characters/CharWeightSet.class
trunk/treebase-core/lib/mesquite/lib/characters/CharacterData.class
trunk/treebase-core/lib/mesquite/lib/characters/CharacterDistribution.class
trunk/treebase-core/lib/mesquite/lib/characters/CharacterHistory.class
trunk/treebase-core/lib/mesquite/lib/characters/CharacterModel.class
trunk/treebase-core/lib/mesquite/lib/characters/CharacterPartition.class
trunk/treebase-core/lib/mesquite/lib/characters/CharacterState.class
trunk/treebase-core/lib/mesquite/lib/characters/CharacterStateTest.class
trunk/treebase-core/lib/mesquite/lib/characters/CharacterStates.class
trunk/treebase-core/lib/mesquite/lib/characters/CharacterStatesHolder.class
trunk/treebase-core/lib/mesquite/lib/characters/CharacterSubmodel.class
trunk/treebase-core/lib/mesquite/lib/characters/CharactersBlock.class
trunk/treebase-core/lib/mesquite/lib/characters/CharactersGroup.class
trunk/treebase-core/lib/mesquite/lib/characters/CharactersGroupVector.class
trunk/treebase-core/lib/mesquite/lib/characters/CodonPositionsSet.class
trunk/treebase-core/lib/mesquite/lib/characters/DefaultReference.class
trunk/treebase-core/lib/mesquite/lib/characters/MAdjustableDistribution.class
trunk/treebase-core/lib/mesquite/lib/characters/MCharactersDistribution.class
trunk/treebase-core/lib/mesquite/lib/characters/MCharactersHistory.class
trunk/treebase-core/lib/mesquite/lib/characters/MCharactersStates.class
trunk/treebase-core/lib/mesquite/lib/characters/MCharactersStatesHolder.class
trunk/treebase-core/lib/mesquite/lib/characters/ModelCompatibilityInfo.class
trunk/treebase-core/lib/mesquite/lib/characters/ModelSet.class
trunk/treebase-core/lib/mesquite/lib/characters/ModelVector.class
trunk/treebase-core/lib/mesquite/lib/characters/ProbabilityModel.class
trunk/treebase-core/lib/mesquite/lib/characters/ProbabilityModelSet.class
trunk/treebase-core/lib/mesquite/lib/characters/SlicedCharacterHistory.class
trunk/treebase-core/lib/mesquite/lib/characters/StoredCharacterHistory.class
trunk/treebase-core/lib/mesquite/lib/characters/TaxaInfo.class
trunk/treebase-core/lib/mesquite/lib/characters/WholeCharacterModel.class
trunk/treebase-core/lib/mesquite/lib/duties/
trunk/treebase-core/lib/mesquite/lib/duties/AnalyticalDrawTree.class
trunk/treebase-core/lib/mesquite/lib/duties/BooleanForCharacter.class
trunk/treebase-core/lib/mesquite/lib/duties/BooleanForItem.class
trunk/treebase-core/lib/mesquite/lib/duties/BooleanForTaxon.class
trunk/treebase-core/lib/mesquite/lib/duties/BooleanForTree.class
trunk/treebase-core/lib/mesquite/lib/duties/BooleanForTreeIncr.class
trunk/treebase-core/lib/mesquite/lib/duties/BooleanForTreeM.class
trunk/treebase-core/lib/mesquite/lib/duties/BranchLengthsAlterer.class
trunk/treebase-core/lib/mesquite/lib/duties/BranchLengthsAltererMult.class
trunk/treebase-core/lib/mesquite/lib/duties/BrowseHierarchy.class
trunk/treebase-core/lib/mesquite/lib/duties/CellColorer.class
trunk/treebase-core/lib/mesquite/lib/duties/CharHistorySource.class
trunk/treebase-core/lib/mesquite/lib/duties/CharMapper.class
trunk/treebase-core/lib/mesquite/lib/duties/CharMatrixFiller.class
trunk/treebase-core/lib/mesquite/lib/duties/CharMatrixManager.class
trunk/treebase-core/lib/mesquite/lib/duties/CharMatrixObedSource.class
trunk/treebase-core/lib/mesquite/lib/duties/CharMatrixOneSource.class
trunk/treebase-core/lib/mesquite/lib/duties/CharMatrixSource.class
trunk/treebase-core/lib/mesquite/lib/duties/CharModelCurator.class
trunk/treebase-core/lib/mesquite/lib/duties/CharSelectCoordinator.class
trunk/treebase-core/lib/mesquite/lib/duties/CharSourceCoord.class
trunk/treebase-core/lib/mesquite/lib/duties/CharSourceCoordObed.class
trunk/treebase-core/lib/mesquite/lib/duties/CharSpecsSetManager.class
trunk/treebase-core/lib/mesquite/lib/duties/CharStatesForNodes.class
trunk/treebase-core/lib/mesquite/lib/duties/CharSubmodelCurator.class
trunk/treebase-core/lib/mesquite/lib/duties/CharTableAssistantI.class
trunk/treebase-core/lib/mesquite/lib/duties/CharacterModelSource.class
trunk/treebase-core/lib/mesquite/lib/duties/CharacterObedSource.class
trunk/treebase-core/lib/mesquite/lib/duties/CharacterOneSource.class
trunk/treebase-core/lib/mesquite/lib/duties/CharacterSelector.class
trunk/treebase-core/lib/mesquite/lib/duties/CharacterSimulator.class
trunk/treebase-core/lib/mesquite/lib/duties/CharacterSource.class
trunk/treebase-core/lib/mesquite/lib/duties/CharactersManager.class
trunk/treebase-core/lib/mesquite/lib/duties/CharsStatesForNodes.class
trunk/treebase-core/lib/mesquite/lib/duties/ChartAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/Consenser.class
trunk/treebase-core/lib/mesquite/lib/duties/CuratorWithSettings.class
trunk/treebase-core/lib/mesquite/lib/duties/DataAlterer.class
trunk/treebase-core/lib/mesquite/lib/duties/DataAltererCon.class
trunk/treebase-core/lib/mesquite/lib/duties/DataColumnNamesAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/DataMatcher.class
trunk/treebase-core/lib/mesquite/lib/duties/DataSearcher.class
trunk/treebase-core/lib/mesquite/lib/duties/DataUtility.class
trunk/treebase-core/lib/mesquite/lib/duties/DataWSelectionAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/DataWindowAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/DataWindowAssistantA.class
trunk/treebase-core/lib/mesquite/lib/duties/DataWindowAssistantI.class
trunk/treebase-core/lib/mesquite/lib/duties/DataWindowMaker.class
trunk/treebase-core/lib/mesquite/lib/duties/DefaultsAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/DisplayCharsStsAtNodes.class
trunk/treebase-core/lib/mesquite/lib/duties/DisplayNumbersAtNodes.class
trunk/treebase-core/lib/mesquite/lib/duties/DisplayStatesAtNodes.class
trunk/treebase-core/lib/mesquite/lib/duties/DistanceBetween2Trees.class
trunk/treebase-core/lib/mesquite/lib/duties/DrawChart.class
trunk/treebase-core/lib/mesquite/lib/duties/DrawNamesTaxaDisplay.class
trunk/treebase-core/lib/mesquite/lib/duties/DrawNamesTreeDisplay.class
trunk/treebase-core/lib/mesquite/lib/duties/DrawTaxa.class
trunk/treebase-core/lib/mesquite/lib/duties/DrawTaxaCoordinator.class
trunk/treebase-core/lib/mesquite/lib/duties/DrawTree.class
trunk/treebase-core/lib/mesquite/lib/duties/DrawTreeCoordinator.class
trunk/treebase-core/lib/mesquite/lib/duties/EditRawNexusBlock.class
trunk/treebase-core/lib/mesquite/lib/duties/EditingCurator.class
trunk/treebase-core/lib/mesquite/lib/duties/ElementManager.class
trunk/treebase-core/lib/mesquite/lib/duties/EmployeeTree.class
trunk/treebase-core/lib/mesquite/lib/duties/ExternalTreeSearcher.class
trunk/treebase-core/lib/mesquite/lib/duties/FileAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/FileAssistantC.class
trunk/treebase-core/lib/mesquite/lib/duties/FileAssistantCH.class
trunk/treebase-core/lib/mesquite/lib/duties/FileAssistantCP.class
trunk/treebase-core/lib/mesquite/lib/duties/FileAssistantCS.class
trunk/treebase-core/lib/mesquite/lib/duties/FileAssistantN.class
trunk/treebase-core/lib/mesquite/lib/duties/FileAssistantT.class
trunk/treebase-core/lib/mesquite/lib/duties/FileCoordinator.class
trunk/treebase-core/lib/mesquite/lib/duties/FileElementManager.class
trunk/treebase-core/lib/mesquite/lib/duties/FileInit.class
trunk/treebase-core/lib/mesquite/lib/duties/FileInitEarlyLoad.class
trunk/treebase-core/lib/mesquite/lib/duties/FileInterpreter.class
trunk/treebase-core/lib/mesquite/lib/duties/FileInterpreterI.class
trunk/treebase-core/lib/mesquite/lib/duties/FileInterpreterITree.class
trunk/treebase-core/lib/mesquite/lib/duties/GeneralFileMaker.class
trunk/treebase-core/lib/mesquite/lib/duties/HistogramAssistantA.class
trunk/treebase-core/lib/mesquite/lib/duties/ItemsBiplotter.class
trunk/treebase-core/lib/mesquite/lib/duties/ItemsCharter.class
trunk/treebase-core/lib/mesquite/lib/duties/ItemsSource.class
trunk/treebase-core/lib/mesquite/lib/duties/ManageModelSet.class
trunk/treebase-core/lib/mesquite/lib/duties/ManagerAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/MatrixCharter.class
trunk/treebase-core/lib/mesquite/lib/duties/MatrixSourceCoord.class
trunk/treebase-core/lib/mesquite/lib/duties/MatrixSourceCoordObed.class
trunk/treebase-core/lib/mesquite/lib/duties/MesquiteInit.class
trunk/treebase-core/lib/mesquite/lib/duties/ModelsetNexusCommandTest.class
trunk/treebase-core/lib/mesquite/lib/duties/NexusFileInterpreter.class
trunk/treebase-core/lib/mesquite/lib/duties/NodeChooser.class
trunk/treebase-core/lib/mesquite/lib/duties/NodeLocs.class
trunk/treebase-core/lib/mesquite/lib/duties/NodeLocsCircle.class
trunk/treebase-core/lib/mesquite/lib/duties/NodeLocsFree.class
trunk/treebase-core/lib/mesquite/lib/duties/NodeLocsPlot.class
trunk/treebase-core/lib/mesquite/lib/duties/NodeLocsVH.class
trunk/treebase-core/lib/mesquite/lib/duties/NumFor2CharHistAndTree.class
trunk/treebase-core/lib/mesquite/lib/duties/NumForCharHistAndTree.class
trunk/treebase-core/lib/mesquite/lib/duties/NumForCharTreeDep.class
trunk/treebase-core/lib/mesquite/lib/duties/NumForCharTreeIndep.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberFor2CharAndTree.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberFor2Characters.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberFor2Taxa.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberFor2TaxaIncr.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberFor2Trees.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForCharAndTaxon.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForCharAndTree.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForCharAndTreeM.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForCharacter.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForCharacterIncr.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForItem.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForMatrix.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForMatrixAndTree.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForNode.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForTaxon.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForTaxonIncr.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForTree.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForTreeBlock.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForTreeIncr.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForTreeM.class
trunk/treebase-core/lib/mesquite/lib/duties/NumberForTreeWContext.class
trunk/treebase-core/lib/mesquite/lib/duties/NumbersForNodes.class
trunk/treebase-core/lib/mesquite/lib/duties/NumbersForNodesAndChar.class
trunk/treebase-core/lib/mesquite/lib/duties/NumbersForNodesAndHistory.class
trunk/treebase-core/lib/mesquite/lib/duties/NumbersForNodesAndMatrix.class
trunk/treebase-core/lib/mesquite/lib/duties/NumbersForNodesIncr.class
trunk/treebase-core/lib/mesquite/lib/duties/NumbersForNodesWith2Char.class
trunk/treebase-core/lib/mesquite/lib/duties/OneTreeSource.class
trunk/treebase-core/lib/mesquite/lib/duties/PackageIntro.class
trunk/treebase-core/lib/mesquite/lib/duties/PackageIntroInterface.class
trunk/treebase-core/lib/mesquite/lib/duties/ParametersExplorer.class
trunk/treebase-core/lib/mesquite/lib/duties/ReadFileFromString.class
trunk/treebase-core/lib/mesquite/lib/duties/ScattergramAssistantA.class
trunk/treebase-core/lib/mesquite/lib/duties/ScriptingManager.class
trunk/treebase-core/lib/mesquite/lib/duties/SpecsSetManager.class
trunk/treebase-core/lib/mesquite/lib/duties/TSrcCompatibilityTest.class
trunk/treebase-core/lib/mesquite/lib/duties/TWindowMaker.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaDisplayAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaDisplayAssistantA.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaDisplayAssistantAD.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaDisplayAssistantD.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaDisplayAssistantDI.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaDisplayAssistantI.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaDisplayAssistantMA.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaManager.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaPartitionSource.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaSelectCoordinator.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaSource.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaTableAssistantI.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaWindowAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaWindowAssistantC.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaWindowAssistantI.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaWindowAssistantN.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxaWindowMaker.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxonNameAlterer.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxonPairSource.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxonSelector.class
trunk/treebase-core/lib/mesquite/lib/duties/TaxonSource.class
trunk/treebase-core/lib/mesquite/lib/duties/TextDisplayer.class
trunk/treebase-core/lib/mesquite/lib/duties/TraceCharacterInit.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeAlterer.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeAltererMult.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeBlockFiller.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeBlockSource.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeDisplayAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeDisplayAssistantA.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeDisplayAssistantAD.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeDisplayAssistantAO.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeDisplayAssistantD.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeDisplayAssistantDI.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeDisplayAssistantI.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeDisplayAssistantMA.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeInferer.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeSearcher.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeSimulate.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeSource.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeSourceDefinite.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeSwapper.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeTransformer.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeTransformerMult.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeUtility.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeWindowAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeWindowAssistantA.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeWindowAssistantC.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeWindowAssistantI.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeWindowAssistantN.class
trunk/treebase-core/lib/mesquite/lib/duties/TreeWindowMaker.class
trunk/treebase-core/lib/mesquite/lib/duties/TreesManager.class
trunk/treebase-core/lib/mesquite/lib/duties/UtilitiesAssistant.class
trunk/treebase-core/lib/mesquite/lib/duties/WholeCharModelCurator.class
trunk/treebase-core/lib/mesquite/lib/duties/WindowHolder.class
trunk/treebase-core/lib/mesquite/lib/system/
trunk/treebase-core/lib/mesquite/lib/system/SystemUtil.class
trunk/treebase-core/lib/mesquite/lib/table/
trunk/treebase-core/lib/mesquite/lib/table/AutoScrollThread.class
trunk/treebase-core/lib/mesquite/lib/table/CMTable.class
trunk/treebase-core/lib/mesquite/lib/table/ColumnNamesPanel.class
trunk/treebase-core/lib/mesquite/lib/table/ControlStrip.class
trunk/treebase-core/lib/mesquite/lib/table/CornerPanel.class
trunk/treebase-core/lib/mesquite/lib/table/EditorPanel.class
trunk/treebase-core/lib/mesquite/lib/table/EditorTextField$FListener.class
trunk/treebase-core/lib/mesquite/lib/table/EditorTextField$KListener.class
trunk/treebase-core/lib/mesquite/lib/table/EditorTextField.class
trunk/treebase-core/lib/mesquite/lib/table/MatrixPanel.class
trunk/treebase-core/lib/mesquite/lib/table/MesquiteTable.class
trunk/treebase-core/lib/mesquite/lib/table/RowNamesPanel.class
trunk/treebase-core/lib/mesquite/lib/table/TableMarchingAnts.class
trunk/treebase-core/lib/mesquite/lib/table/TableScroll.class
trunk/treebase-core/lib/mesquite/lib/table/TableTool.class
trunk/treebase-core/lib/mesquite/lib/table/TableWindow.class
trunk/treebase-core/lib/mesquite/lists/
trunk/treebase-core/lib/mesquite/lists/BooleanForCharList/
trunk/treebase-core/lib/mesquite/lists/BooleanForCharList/BooleanForCharList.class
trunk/treebase-core/lib/mesquite/lists/BooleanForTreeList/
trunk/treebase-core/lib/mesquite/lists/BooleanForTreeList/BooleanForTreeList.class
trunk/treebase-core/lib/mesquite/lists/CharInclSetList/
trunk/treebase-core/lib/mesquite/lists/CharInclSetList/CharInclSetList.class
trunk/treebase-core/lib/mesquite/lists/CharInclSetListNum/
trunk/treebase-core/lib/mesquite/lists/CharInclSetListNum/CharInclSetListNum.class
trunk/treebase-core/lib/mesquite/lists/CharListAnnotPanel/
trunk/treebase-core/lib/mesquite/lists/CharListAnnotPanel/CharListAnnotPanel.class
trunk/treebase-core/lib/mesquite/lists/CharListCodonPos/
trunk/treebase-core/lib/mesquite/lists/CharListCodonPos/CharListCodonPos.class
trunk/treebase-core/lib/mesquite/lists/CharListInclusion/
trunk/treebase-core/lib/mesquite/lists/CharListInclusion/CharListInclusion.class
trunk/treebase-core/lib/mesquite/lists/CharListPartition/
trunk/treebase-core/lib/mesquite/lists/CharListPartition/CharListPartition.class
trunk/treebase-core/lib/mesquite/lists/CharListUniqueID/
trunk/treebase-core/lib/mesquite/lists/CharListUniqueID/CharListUniqueID.class
trunk/treebase-core/lib/mesquite/lists/CharListWeights/
trunk/treebase-core/lib/mesquite/lists/CharListWeights/CharListWeights.class
trunk/treebase-core/lib/mesquite/lists/CharNumForList/
trunk/treebase-core/lib/mesquite/lists/CharNumForList/CharNumForList.class
trunk/treebase-core/lib/mesquite/lists/CharPartitionList/
trunk/treebase-core/lib/mesquite/lists/CharPartitionList/CharPartitionList.class
trunk/treebase-core/lib/mesquite/lists/CharSetList/
trunk/treebase-core/lib/mesquite/lists/CharSetList/CharSetList.class
trunk/treebase-core/lib/mesquite/lists/CharSetListNum/
trunk/treebase-core/lib/mesquite/lists/CharSetListNum/CharSetListNum.class
trunk/treebase-core/lib/mesquite/lists/CharacterList/
trunk/treebase-core/lib/mesquite/lists/CharacterList/CharacterList.class
trunk/treebase-core/lib/mesquite/lists/CharacterList/CharacterListWindow.class
trunk/treebase-core/lib/mesquite/lists/CharacterStats/
trunk/treebase-core/lib/mesquite/lists/CharacterStats/CharacterStats.class
trunk/treebase-core/lib/mesquite/lists/CodePosSetsList/
trunk/treebase-core/lib/mesquite/lists/CodePosSetsList/CodePosSetsList.class
trunk/treebase-core/lib/mesquite/lists/DatasetList/
trunk/treebase-core/lib/mesquite/lists/DatasetList/DatasetList.class
trunk/treebase-core/lib/mesquite/lists/DatasetsListClass/
trunk/treebase-core/lib/mesquite/lists/DatasetsListClass/DatasetsListClass.class
trunk/treebase-core/lib/mesquite/lists/DatasetsListNumChars/
trunk/treebase-core/lib/mesquite/lists/DatasetsListNumChars/DatasetsListNumChars.class
trunk/treebase-core/lib/mesquite/lists/DatasetsListTaxa/
trunk/treebase-core/lib/mesquite/lists/DatasetsListTaxa/DatasetsListTaxa.class
trunk/treebase-core/lib/mesquite/lists/DefaultCharOrder/
trunk/treebase-core/lib/mesquite/lists/DefaultCharOrder/DefaultCharOrder.class
trunk/treebase-core/lib/mesquite/lists/DefaultTaxaOrder/
trunk/treebase-core/lib/mesquite/lists/DefaultTaxaOrder/DefaultTaxaOrder.class
trunk/treebase-core/lib/mesquite/lists/ModelsList/
trunk/treebase-core/lib/mesquite/lists/ModelsList/ModelsList.class
trunk/treebase-core/lib/mesquite/lists/ModelsList/ModelsListWindow.class
trunk/treebase-core/lib/mesquite/lists/ModelsListDatatype/
trunk/treebase-core/lib/mesquite/lists/ModelsListDatatype/ModelsListDatatype.class
trunk/treebase-core/lib/mesquite/lists/ModelsListParadigm/
trunk/treebase-core/lib/mesquite/lists/ModelsListParadigm/ModelsListParadigm.class
trunk/treebase-core/lib/mesquite/lists/ModelsListType/
trunk/treebase-core/lib/mesquite/lists/ModelsListType/ModelsListType.class
trunk/treebase-core/lib/mesquite/lists/ModelsListWhole/
trunk/treebase-core/lib/mesquite/lists/ModelsListWhole/ModelsListWhole.class
trunk/treebase-core/lib/mesquite/lists/NexusBlockList/
trunk/treebase-core/lib/mesquite/lists/NexusBlockList/NexusBlockList.class
trunk/treebase-core/lib/mesquite/lists/NumForCharMatrixList/
trunk/treebase-core/lib/mesquite/lists/NumForCharMatrixList/NumForCharMatrixList.class
trunk/treebase-core/lib/mesquite/lists/NumForTaxaList/
trunk/treebase-core/lib/mesquite/lists/NumForTaxaList/NumForTaxaList.class
trunk/treebase-core/lib/mesquite/lists/NumForTreeList/
trunk/treebase-core/lib/mesquite/lists/NumForTreeList/NumForTreeList.class
trunk/treebase-core/lib/mesquite/lists/NumForTreeblockList/
trunk/treebase-core/lib/mesquite/lists/NumForTreeblockList/NumForTreeblockList.class
trunk/treebase-core/lib/mesquite/lists/TaxaListUniqueID/
trunk/treebase-core/lib/mesquite/lists/TaxaListUniqueID/TaxaListUniqueID.class
trunk/treebase-core/lib/mesquite/lists/TaxaPartListNumGroups/
trunk/treebase-core/lib/mesquite/lists/TaxaPartListNumGroups/TaxaPartListNumGroups.class
trunk/treebase-core/lib/mesquite/lists/TaxaPartitionList/
trunk/treebase-core/lib/mesquite/lists/TaxaPartitionList/TaxaPartitionList.class
trunk/treebase-core/lib/mesquite/lists/TaxaSetListNum/
trunk/treebase-core/lib/mesquite/lists/TaxaSetListNum/TaxaSetListNum.class
trunk/treebase-core/lib/mesquite/lists/TaxablockList/
trunk/treebase-core/lib/mesquite/lists/TaxablockList/TaxablockList.class
trunk/treebase-core/lib/mesquite/lists/TaxablockListNumber/
trunk/treebase-core/lib/mesquite/lists/TaxablockListNumber/TaxablockListNumber.class
trunk/treebase-core/lib/mesquite/lists/TaxonList/
trunk/treebase-core/lib/mesquite/lists/TaxonList/TaxonList.class
trunk/treebase-core/lib/mesquite/lists/TaxonList/TaxonListWindow.class
trunk/treebase-core/lib/mesquite/lists/TaxonListAnnotPanel/
trunk/treebase-core/lib/mesquite/lists/TaxonListAnnotPanel/TaxonListAnnotPanel.class
trunk/treebase-core/lib/mesquite/lists/TaxonListArchivedName/
trunk/treebase-core/lib/mesquite/lists/TaxonListArchivedName/TaxonListArchivedName.class
trunk/treebase-core/lib/mesquite/lists/TaxonListCurrPartition/
trunk/treebase-core/lib/mesquite/lists/TaxonListCurrPartition/TaxonListCurrPartition.class
trunk/treebase-core/lib/mesquite/lists/TaxonSetList/
trunk/treebase-core/lib/mesquite/lists/TaxonSetList/TaxonSetList.class
trunk/treebase-core/lib/mesquite/lists/TreeListAttachment/
trunk/treebase-core/lib/mesquite/lists/TreeListAttachment/TreeListAttachment.class
trunk/treebase-core/lib/mesquite/lists/TreeListPolyAssumption/
trunk/treebase-core/lib/mesquite/lists/TreeListPolyAssumption/TreeListPolyAssumption.class
trunk/treebase-core/lib/mesquite/lists/TreeListPolys/
trunk/treebase-core/lib/mesquite/lists/TreeListPolys/TreeListPolys.class
trunk/treebase-core/lib/mesquite/lists/TreeListRooted/
trunk/treebase-core/lib/mesquite/lists/TreeListRooted/TreeListRooted.class
trunk/treebase-core/lib/mesquite/lists/TreeblockList/
trunk/treebase-core/lib/mesquite/lists/TreeblockList/TreeblockList.class
trunk/treebase-core/lib/mesquite/lists/TreeblocksListNumber/
trunk/treebase-core/lib/mesquite/lists/TreeblocksListNumber/TreeblocksListNumber.class
trunk/treebase-core/lib/mesquite/lists/TreeblocksListTaxa/
trunk/treebase-core/lib/mesquite/lists/TreeblocksListTaxa/TreeblocksListTaxa.class
trunk/treebase-core/lib/mesquite/lists/TreesList/
trunk/treebase-core/lib/mesquite/lists/TreesList/TreesList.class
trunk/treebase-core/lib/mesquite/lists/TreesList/TreesListWindow.class
trunk/treebase-core/lib/mesquite/lists/WeightSetList/
trunk/treebase-core/lib/mesquite/lists/WeightSetList/WeightSetList.class
trunk/treebase-core/lib/mesquite/lists/explanation.txt
trunk/treebase-core/lib/mesquite/lists/lib/
trunk/treebase-core/lib/mesquite/lists/lib/CharInclSetListAsst.class
trunk/treebase-core/lib/mesquite/lists/lib/CharListAssistant.class
trunk/treebase-core/lib/mesquite/lists/lib/CharListAssistantI.class
trunk/treebase-core/lib/mesquite/lists/lib/CharListModel.class
trunk/treebase-core/lib/mesquite/lists/lib/CharListPartitionUtil.class
trunk/treebase-core/lib/mesquite/lists/lib/CharSetListAsst.class
trunk/treebase-core/lib/mesquite/lists/lib/DataSetsListAssistant.class
trunk/treebase-core/lib/mesquite/lists/lib/DataSpecsListWindow.class
trunk/treebase-core/lib/mesquite/lists/lib/DataSpecssetList.class
trunk/treebase-core/lib/mesquite/lists/lib/DatasetsListUtility.class
trunk/treebase-core/lib/mesquite/lists/lib/GroupDialog.class
trunk/treebase-core/lib/mesquite/lists/lib/LTCellAnnotation.class
trunk/treebase-core/lib/mesquite/lists/lib/ListAssistant.class
trunk/treebase-core/lib/mesquite/lists/lib/ListLVModule.class
trunk/treebase-core/lib/mesquite/lists/lib/ListModule.class
trunk/treebase-core/lib/mesquite/lists/lib/ListTable.class
trunk/treebase-core/lib/mesquite/lists/lib/ListWindow.class
trunk/treebase-core/lib/mesquite/lists/lib/ListableVectorWindow.class
trunk/treebase-core/lib/mesquite/lists/lib/ModelSetListAsst.class
trunk/treebase-core/lib/mesquite/lists/lib/ModelsListAssistant.class
trunk/treebase-core/lib/mesquite/lists/lib/TaxaBlocksListAssistant.class
trunk/treebase-core/lib/mesquite/lists/lib/TaxaBlocksListUtility.class
trunk/treebase-core/lib/mesquite/lists/lib/TaxaListAssistantI.class
trunk/treebase-core/lib/mesquite/lists/lib/TaxaPartListAssistant.class
trunk/treebase-core/lib/mesquite/lists/lib/TaxaSetListAssistant.class
trunk/treebase-core/lib/mesquite/lists/lib/TaxaSpecsListWindow.class
trunk/treebase-core/lib/mesquite/lists/lib/TaxaSpecssetList.class
trunk/treebase-core/lib/mesquite/lists/lib/TaxonListAssistant.class
trunk/treebase-core/lib/mesquite/lists/lib/TreeBlockListUtility.class
trunk/treebase-core/lib/mesquite/lists/lib/TreeListAssistant.class
trunk/treebase-core/lib/mesquite/lists/lib/TreeListUtility.class
trunk/treebase-core/lib/mesquite/lists/lib/TreeblocksListAssistant.class
trunk/treebase-core/lib/mesquite/mb/
trunk/treebase-core/lib/mesquite/mb/BestBayesTree/
trunk/treebase-core/lib/mesquite/mb/BestBayesTree/BestBayesTree.class
trunk/treebase-core/lib/mesquite/mb/ExportForMrBayes/
trunk/treebase-core/lib/mesquite/mb/ExportForMrBayes/ExportForMrBayes.class
trunk/treebase-core/lib/mesquite/mb/MrBayesScore/
trunk/treebase-core/lib/mesquite/mb/MrBayesScore/MrBayesScore.class
trunk/treebase-core/lib/mesquite/mb/TreesFromMrBayes/
trunk/treebase-core/lib/mesquite/mb/TreesFromMrBayes/TreesFromMrBayes.class
trunk/treebase-core/lib/mesquite/minimal/
trunk/treebase-core/lib/mesquite/minimal/BasicFileCoordinator/
trunk/treebase-core/lib/mesquite/minimal/BasicFileCoordinator/BasicFileCoordinator.class
trunk/treebase-core/lib/mesquite/minimal/BasicFileCoordinator/BasicPanel.class
trunk/treebase-core/lib/mesquite/minimal/BasicFileCoordinator/FileRead.class
trunk/treebase-core/lib/mesquite/minimal/BasicFileCoordinator/ProjectWindow.class
trunk/treebase-core/lib/mesquite/minimal/BasicFileCoordinator/index.html
trunk/treebase-core/lib/mesquite/minimal/BasicFileCoordinator/splash.gif
trunk/treebase-core/lib/mesquite/minimal/BasicFileCoordinator/splash.gif copy
trunk/treebase-core/lib/mesquite/minimal/BasicFileCoordinator/splashSmall.gif
trunk/treebase-core/lib/mesquite/minimal/Defaults/
trunk/treebase-core/lib/mesquite/minimal/Defaults/Defaults.class
trunk/treebase-core/lib/mesquite/minimal/DrawHierarchy/
trunk/treebase-core/lib/mesquite/minimal/DrawHierarchy/DrawHierarchy.class
trunk/treebase-core/lib/mesquite/minimal/DrawHierarchy/FieldPanel.class
trunk/treebase-core/lib/mesquite/minimal/DrawHierarchy/HierarchyPanel.class
trunk/treebase-core/lib/mesquite/minimal/DrawHierarchy/NodeLabel.class
trunk/treebase-core/lib/mesquite/minimal/DrawHierarchy/SupplementLabel.class
trunk/treebase-core/lib/mesquite/minimal/IDsDefaults/
trunk/treebase-core/lib/mesquite/minimal/IDsDefaults/IDsDefaults.class
trunk/treebase-core/lib/mesquite/minimal/InterpretNEXUS/
trunk/treebase-core/lib/mesquite/minimal/InterpretNEXUS/InterpretNEXUS.class
trunk/treebase-core/lib/mesquite/minimal/ManageForeignBlocks/
trunk/treebase-core/lib/mesquite/minimal/ManageForeignBlocks/ForeignBlock.class
trunk/treebase-core/lib/mesquite/minimal/ManageForeignBlocks/ManageForeignBlocks.class
trunk/treebase-core/lib/mesquite/minimal/ManageMesquiteBlock/
trunk/treebase-core/lib/mesquite/minimal/ManageMesquiteBlock/ManageMesquiteBlock.class
trunk/treebase-core/lib/mesquite/minimal/ManageMesquiteBlock/MesquiteBlock.class
trunk/treebase-core/lib/mesquite/minimal/ManageMesquiteBlock/MesquiteBlockTest.class
trunk/treebase-core/lib/mesquite/minimal/ManageTaxa/
trunk/treebase-core/lib/mesquite/minimal/ManageTaxa/ManageTaxa.class
trunk/treebase-core/lib/mesquite/minimal/ManageTaxa/TAXANexusCommandTest.class
trunk/treebase-core/lib/mesquite/minimal/ManageTaxa/TaxaBlockTest.class
trunk/treebase-core/lib/mesquite/minimal/NEXUSDefaults/
trunk/treebase-core/lib/mesquite/minimal/NEXUSDefaults/NEXUSDefaults.class
trunk/treebase-core/lib/mesquite/minimal/OpenURL/
trunk/treebase-core/lib/mesquite/minimal/OpenURL/OpenURL.class
trunk/treebase-core/lib/mesquite/minimal/ShowEmployeeTree/
trunk/treebase-core/lib/mesquite/minimal/ShowEmployeeTree/EmployeeTreeWindow.class
trunk/treebase-core/lib/mesquite/minimal/ShowEmployeeTree/ShowEmployeeTree.class
trunk/treebase-core/lib/mesquite/minimal/StoredTaxa/
trunk/treebase-core/lib/mesquite/minimal/StoredTaxa/StoredTaxa.class
trunk/treebase-core/lib/mesquite/minimal/Utilities/
trunk/treebase-core/lib/mesquite/minimal/Utilities/Utilities.class
trunk/treebase-core/lib/mesquite/minimal/WindowBabysitter/
trunk/treebase-core/lib/mesquite/minimal/WindowBabysitter/WindowBabysitter.class
trunk/treebase-core/lib/mesquite/minimal/explanation.txt
trunk/treebase-core/lib/mesquite/molec/
trunk/treebase-core/lib/mesquite/molec/AAHydrophobicity/
trunk/treebase-core/lib/mesquite/molec/AAHydrophobicity/AAHydrophobicity.class
trunk/treebase-core/lib/mesquite/molec/AASize/
trunk/treebase-core/lib/mesquite/molec/AASize/AASize.class
trunk/treebase-core/lib/mesquite/molec/AminoAcidProperties/
trunk/treebase-core/lib/mesquite/molec/AminoAcidProperties/AminoAcidProperties.class
trunk/treebase-core/lib/mesquite/molec/AssignGeneticCode/
trunk/treebase-core/lib/mesquite/molec/AssignGeneticCode/AssignGeneticCode.class
trunk/treebase-core/lib/mesquite/molec/BLASTSearch/
trunk/treebase-core/lib/mesquite/molec/BLASTSearch/BLASTSearch.class
trunk/treebase-core/lib/mesquite/molec/CharListGenCodeModels/
trunk/treebase-core/lib/mesquite/molec/CharListGenCodeModels/CharListGenCodeModels.class
trunk/treebase-core/lib/mesquite/molec/CharacterGCBias/
trunk/treebase-core/lib/mesquite/molec/CharacterGCBias/CharacterGCBias.class
trunk/treebase-core/lib/mesquite/molec/CodesetList/
trunk/treebase-core/lib/mesquite/molec/CodesetList/CodesetList.class
trunk/treebase-core/lib/mesquite/molec/CollapseEdges/
trunk/treebase-core/lib/mesquite/molec/CollapseEdges/CollapseEdges.class
trunk/treebase-core/lib/mesquite/molec/ColorByAA/
trunk/treebase-core/lib/mesquite/molec/ColorByAA/ColorByAA.class
trunk/treebase-core/lib/mesquite/molec/ColorByNumber/
trunk/treebase-core/lib/mesquite/molec/ColorByNumber/CbNCompatibilityTest.class
trunk/treebase-core/lib/mesquite/molec/ColorByNumber/ColorByNumber.class
trunk/treebase-core/lib/mesquite/molec/CompareBasesWithTaxon/
trunk/treebase-core/lib/mesquite/molec/CompareBasesWithTaxon/CompareBasesWithTaxon.class
trunk/treebase-core/lib/mesquite/molec/CurrentGenCodeModels/
trunk/treebase-core/lib/mesquite/molec/CurrentGenCodeModels/CurrentGenCodeModels.class
trunk/treebase-core/lib/mesquite/molec/FetchGenBank/
trunk/treebase-core/lib/mesquite/molec/FetchGenBank/FetchGenBank.class
trunk/treebase-core/lib/mesquite/molec/FillCharSelection/
trunk/treebase-core/lib/mesquite/molec/FillCharSelection/FillCharSelection.class
trunk/treebase-core/lib/mesquite/molec/FindSequence/
trunk/treebase-core/lib/mesquite/molec/FindSequence/FindSequence.class
trunk/treebase-core/lib/mesquite/molec/GCAsNumber/
trunk/treebase-core/lib/mesquite/molec/GCAsNumber/GCAsNumber.class
trunk/treebase-core/lib/mesquite/molec/GapsToMissing/
trunk/treebase-core/lib/mesquite/molec/GapsToMissing/GapsToMissing.class
trunk/treebase-core/lib/mesquite/molec/InitializeGenCode/
trunk/treebase-core/lib/mesquite/molec/InitializeGenCode/InitializeGenCode.class
trunk/treebase-core/lib/mesquite/molec/LowercaseEnds/
trunk/treebase-core/lib/mesquite/molec/LowercaseEnds/LowercaseEnds.class
trunk/treebase-core/lib/mesquite/molec/MaintainClipMatch/
trunk/treebase-core/lib/mesquite/molec/MaintainClipMatch/MaintainClipMatch.class
trunk/treebase-core/lib/mesquite/molec/ManageCodeSets/
trunk/treebase-core/lib/mesquite/molec/ManageCodeSets/ManageCodeSets.class
trunk/treebase-core/lib/mesquite/molec/ManageCodeSets/TypesetNexusCommandTest.class
trunk/treebase-core/lib/mesquite/molec/MatchingSequence/
trunk/treebase-core/lib/mesquite/molec/MatchingSequence/MatchingSequence.class
trunk/treebase-core/lib/mesquite/molec/MeanValueLinked/
trunk/treebase-core/lib/mesquite/molec/MeanValueLinked/MeanValueLinked.class
trunk/treebase-core/lib/mesquite/molec/MissingToGaps/
trunk/treebase-core/lib/mesquite/molec/MissingToGaps/MissingToGaps.class
trunk/treebase-core/lib/mesquite/molec/NucleotideComplement/
trunk/treebase-core/lib/mesquite/molec/NucleotideComplement/NucleotideComplement.class
trunk/treebase-core/lib/mesquite/molec/NumLowerCase/
trunk/treebase-core/lib/mesquite/molec/NumLowerCase/NumLowerCase.class
trunk/treebase-core/lib/mesquite/molec/NumberPolyInTaxon/
trunk/treebase-core/lib/mesquite/molec/NumberPolyInTaxon/NumberPolyInTaxon.class
trunk/treebase-core/lib/mesquite/m...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-16 10:14:42
|
Revision: 392
http://treebase.svn.sourceforge.net/treebase/?rev=392&view=rev
Author: rvos
Date: 2009-12-16 10:14:30 +0000 (Wed, 16 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/charts/
trunk/treebase-core/lib/mesquite/charts/CharacterValuesChart/
trunk/treebase-core/lib/mesquite/charts/CharacterValuesChart/CharacterValuesChart.class
trunk/treebase-core/lib/mesquite/charts/CharsScattergram/
trunk/treebase-core/lib/mesquite/charts/CharsScattergram/CharsScattergram.class
trunk/treebase-core/lib/mesquite/charts/Histogram/
trunk/treebase-core/lib/mesquite/charts/Histogram/Histogram.class
trunk/treebase-core/lib/mesquite/charts/Histogram/HistogramCharter.class
trunk/treebase-core/lib/mesquite/charts/Histogram/LittlePanel.class
trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/
trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ChartMessages.class
trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ItemValuesChart.class
trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ItemsChartWindow.class
trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/
trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/ItemsBiplot.class
trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/ItemsBiplotWindow.class
trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/TChartMessages.class
trunk/treebase-core/lib/mesquite/charts/MatrixValuesChart/
trunk/treebase-core/lib/mesquite/charts/MatrixValuesChart/MatrixValuesChart.class
trunk/treebase-core/lib/mesquite/charts/NodesScattergram/
trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodeLabeller.class
trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodeScattergramWindow.class
trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodesScattergram.class
trunk/treebase-core/lib/mesquite/charts/Notes/
trunk/treebase-core/lib/mesquite/charts/Notes/Chart Notes.txt
trunk/treebase-core/lib/mesquite/charts/Scattergram/
trunk/treebase-core/lib/mesquite/charts/Scattergram/Scattergram.class
trunk/treebase-core/lib/mesquite/charts/Scattergram/ScattergramCharter.class
trunk/treebase-core/lib/mesquite/charts/Scattergram/ScattergramColorLegend.class
trunk/treebase-core/lib/mesquite/charts/ShowMean/
trunk/treebase-core/lib/mesquite/charts/ShowMean/ShowMean.class
trunk/treebase-core/lib/mesquite/charts/ShowMean/ShowMeanExtra.class
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/001.gif
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/01.gif
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/05.gif
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/ShowPercentile.class
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/ShowPercentileExtra.class
trunk/treebase-core/lib/mesquite/charts/ShowPercentile/manual.html
trunk/treebase-core/lib/mesquite/charts/ShowYEqualsX/
trunk/treebase-core/lib/mesquite/charts/ShowYEqualsX/ShowYEqualsX.class
trunk/treebase-core/lib/mesquite/charts/ShowYEqualsX/ShowYEqualsXExtra.class
trunk/treebase-core/lib/mesquite/charts/TaxaScattergram/
trunk/treebase-core/lib/mesquite/charts/TaxaScattergram/TaxaScattergram.class
trunk/treebase-core/lib/mesquite/charts/TaxonPairValuesChart/
trunk/treebase-core/lib/mesquite/charts/TaxonPairValuesChart/TaxonPairValuesChart.class
trunk/treebase-core/lib/mesquite/charts/TaxonPairsScattergram/
trunk/treebase-core/lib/mesquite/charts/TaxonPairsScattergram/TaxonPairsScattergram.class
trunk/treebase-core/lib/mesquite/charts/TaxonValuesChart/
trunk/treebase-core/lib/mesquite/charts/TaxonValuesChart/TaxonValuesChart.class
trunk/treebase-core/lib/mesquite/charts/TreeBlockValues/
trunk/treebase-core/lib/mesquite/charts/TreeBlockValues/TreeBlockValues.class
trunk/treebase-core/lib/mesquite/charts/TreeValuesChart/
trunk/treebase-core/lib/mesquite/charts/TreeValuesChart/TreeValuesChart.class
trunk/treebase-core/lib/mesquite/charts/TreesScattergram/
trunk/treebase-core/lib/mesquite/charts/TreesScattergram/TreesScattergram.class
trunk/treebase-core/lib/mesquite/charts/explanation.txt
trunk/treebase-core/lib/mesquite/coalesce/
trunk/treebase-core/lib/mesquite/coalesce/CoalescenceWMigration/
trunk/treebase-core/lib/mesquite/coalesce/CoalescenceWMigration/CoalescenceWMigration.class
trunk/treebase-core/lib/mesquite/coalesce/CoalescentTrees/
trunk/treebase-core/lib/mesquite/coalesce/CoalescentTrees/CoalescentTrees.class
trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescSim/
trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescSim/ContainedCoalescSim.class
trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescence/
trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescence/ContainedCoalescence.class
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalMultLoci/
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalMultLoci/DeepCoalMultLoci.class
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesG/
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesG/DeepCoalescencesG.class
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesSp/
trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesSp/DeepCoalescencesSp.class
trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsG/
trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsG/DuplicationsExtinctionsG.class
trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsSp/
trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsSp/DuplicationsExtinctionsSp.class
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/32insertNode.gif
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/64insertNode.gif
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/InsertNode.class
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/InsertToolExtra.class
trunk/treebase-core/lib/mesquite/coalesce/InsertNode/insertNode.gif
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/32adjustWidths.gif
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/64adjustWidths.gif
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/LineageWidth.class
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/WidthsToolExtra.class
trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/adjustWidths.gif
trunk/treebase-core/lib/mesquite/coalesce/NeutralCoalescence/
trunk/treebase-core/lib/mesquite/coalesce/NeutralCoalescence/NeutralCoalescence.class
trunk/treebase-core/lib/mesquite/coalesce/RecCoalescenceHistory/
trunk/treebase-core/lib/mesquite/coalesce/RecCoalescenceHistory/RecCoalescenceHistory.class
trunk/treebase-core/lib/mesquite/coalesce/RecCoalescenceHistory/RerootStore.class
trunk/treebase-core/lib/mesquite/coalesce/SlatkinMaddisonS/
trunk/treebase-core/lib/mesquite/coalesce/SlatkinMaddisonS/SlatkinMaddisonS.class
trunk/treebase-core/lib/mesquite/coalesce/TreeDepth/
trunk/treebase-core/lib/mesquite/coalesce/TreeDepth/TreeDepth.class
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/aCoalescencePkgIntro.class
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/index.html
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/splash.gif
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/splash.gif copy
trunk/treebase-core/lib/mesquite/coalesce/aCoalescencePkgIntro/splashSmall.gif
trunk/treebase-core/lib/mesquite/coalesce/explanation.txt
trunk/treebase-core/lib/mesquite/coalesce/lib/
trunk/treebase-core/lib/mesquite/coalesce/lib/CoalescedNode.class
trunk/treebase-core/lib/mesquite/coalesce/lib/Coalescer.class
trunk/treebase-core/lib/mesquite/coalesce/lib/CoalescerObed.class
trunk/treebase-core/lib/mesquite/coalesce/lib/ContainedTreeSim.class
trunk/treebase-core/lib/mesquite/coalesce/lib/GeneTreeFit.class
trunk/treebase-core/lib/mesquite/coalesce/lib/SpeciesTreeFit.class
trunk/treebase-core/lib/mesquite/coalesce/macros/
trunk/treebase-core/lib/mesquite/coalesce/macros/s_by_depth
trunk/treebase-core/lib/mesquite/cont/
trunk/treebase-core/lib/mesquite/cont/AddItem/
trunk/treebase-core/lib/mesquite/cont/AddItem/AddItem.class
trunk/treebase-core/lib/mesquite/cont/AddNoise/
trunk/treebase-core/lib/mesquite/cont/AddNoise/AddNoise.class
trunk/treebase-core/lib/mesquite/cont/AddToStates/
trunk/treebase-core/lib/mesquite/cont/AddToStates/AddToStates.class
trunk/treebase-core/lib/mesquite/cont/ContCharFrTaxonValue/
trunk/treebase-core/lib/mesquite/cont/ContCharFrTaxonValue/ContCharFrTaxonValue.class
trunk/treebase-core/lib/mesquite/cont/ContinuousStatesT/
trunk/treebase-core/lib/mesquite/cont/ContinuousStatesT/ContinuousStatesT.class
trunk/treebase-core/lib/mesquite/cont/LogTransform/
trunk/treebase-core/lib/mesquite/cont/LogTransform/LogTransform.class
trunk/treebase-core/lib/mesquite/cont/ManageContChars/
trunk/treebase-core/lib/mesquite/cont/ManageContChars/ManageContChars.class
trunk/treebase-core/lib/mesquite/cont/ManageGeogChars/
trunk/treebase-core/lib/mesquite/cont/ManageGeogChars/ManageGeogChars.class
trunk/treebase-core/lib/mesquite/cont/MapContinuous/
trunk/treebase-core/lib/mesquite/cont/MapContinuous/MapContinuous.class
trunk/treebase-core/lib/mesquite/cont/MeanValue/
trunk/treebase-core/lib/mesquite/cont/MeanValue/MeanValue.class
trunk/treebase-core/lib/mesquite/cont/MultiplyStates/
trunk/treebase-core/lib/mesquite/cont/MultiplyStates/MultiplyStates.class
trunk/treebase-core/lib/mesquite/cont/NodeLocs2DPlot/
trunk/treebase-core/lib/mesquite/cont/NodeLocs2DPlot/NodeLocs2DPlot.class
trunk/treebase-core/lib/mesquite/cont/NodeLocs2DPlot/NodeLocs2DPlotExtra.class
trunk/treebase-core/lib/mesquite/cont/NodeLocs2DPlot/NodeLocs2DPlotLegend.class
trunk/treebase-core/lib/mesquite/cont/PlotTree/
trunk/treebase-core/lib/mesquite/cont/PlotTree/PlotTree.class
trunk/treebase-core/lib/mesquite/cont/PlotTree/PlotTreeDrawing.class
trunk/treebase-core/lib/mesquite/cont/RandomFillCont/
trunk/treebase-core/lib/mesquite/cont/RandomFillCont/RandomFillCont.class
trunk/treebase-core/lib/mesquite/cont/RandomFillUniform/
trunk/treebase-core/lib/mesquite/cont/RandomFillUniform/RandomFillUniform.class
trunk/treebase-core/lib/mesquite/cont/RemoveItem/
trunk/treebase-core/lib/mesquite/cont/RemoveItem/RemoveItem.class
trunk/treebase-core/lib/mesquite/cont/RenameItem/
trunk/treebase-core/lib/mesquite/cont/RenameItem/RenameItem.class
trunk/treebase-core/lib/mesquite/cont/Standardize/
trunk/treebase-core/lib/mesquite/cont/Standardize/Standardize.class
trunk/treebase-core/lib/mesquite/cont/explanation.txt
trunk/treebase-core/lib/mesquite/cont/lib/
trunk/treebase-core/lib/mesquite/cont/lib/BasicStatPak.class
trunk/treebase-core/lib/mesquite/cont/lib/ContColorTable.class
trunk/treebase-core/lib/mesquite/cont/lib/ContDataAlterer.class
trunk/treebase-core/lib/mesquite/cont/lib/ContDataSearcher.class
trunk/treebase-core/lib/mesquite/cont/lib/ContDataUtility.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousAdjustable.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousData.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousDistribution.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousEmbedded.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousHistory.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousState.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousStateTest.class
trunk/treebase-core/lib/mesquite/cont/lib/ContinuousStates.class
trunk/treebase-core/lib/mesquite/cont/lib/EigenAnalysis.class
trunk/treebase-core/lib/mesquite/cont/lib/GeogDataSearcher.class
trunk/treebase-core/lib/mesquite/cont/lib/GeogDataUtility.class
trunk/treebase-core/lib/mesquite/cont/lib/GeographicAdjustable.class
trunk/treebase-core/lib/mesquite/cont/lib/GeographicData.class
trunk/treebase-core/lib/mesquite/cont/lib/GeographicState.class
trunk/treebase-core/lib/mesquite/cont/lib/GeographicStateTest.class
trunk/treebase-core/lib/mesquite/cont/lib/GeographicStates.class
trunk/treebase-core/lib/mesquite/cont/lib/ItemContainer.class
trunk/treebase-core/lib/mesquite/cont/lib/MContinuousAdjustable.class
trunk/treebase-core/lib/mesquite/cont/lib/MContinuousDistribution.class
trunk/treebase-core/lib/mesquite/cont/lib/MContinuousEmbedded.class
trunk/treebase-core/lib/mesquite/cont/lib/MContinuousHistory.class
trunk/treebase-core/lib/mesquite/cont/lib/MContinuousStates.class
trunk/treebase-core/lib/mesquite/cont/lib/MGeographicStates.class
trunk/treebase-core/lib/mesquite/cont/lib/ManageContCharsA.class
trunk/treebase-core/lib/mesquite/cont/lib/SquaredReconstructor.class
trunk/treebase-core/lib/mesquite/correl/
trunk/treebase-core/lib/mesquite/correl/CorrelationViewer/
trunk/treebase-core/lib/mesquite/correl/CorrelationViewer/CorrelPanel.class
trunk/treebase-core/lib/mesquite/correl/CorrelationViewer/CorrelationViewer.class
trunk/treebase-core/lib/mesquite/correl/Pagel94/
trunk/treebase-core/lib/mesquite/correl/Pagel94/Pagel94.class
trunk/treebase-core/lib/mesquite/correl/aCorrelPackageIntro/
trunk/treebase-core/lib/mesquite/correl/aCorrelPackageIntro/aCorrelPackageIntro.class
trunk/treebase-core/lib/mesquite/correl/aCorrelPackageIntro/splash.gif
trunk/treebase-core/lib/mesquite/correl/aCorrelPackageIntro/splash.psd
trunk/treebase-core/lib/mesquite/correl/lib/
trunk/treebase-core/lib/mesquite/correl/lib/CLogger.class
trunk/treebase-core/lib/mesquite/correl/lib/ComplexMatrix.class
trunk/treebase-core/lib/mesquite/correl/lib/MultipleProbCategCharModel.class
trunk/treebase-core/lib/mesquite/correl/lib/MultipleProbabilityModel.class
trunk/treebase-core/lib/mesquite/correl/lib/Pagel94Calculator.class
trunk/treebase-core/lib/mesquite/correl/lib/PagelMatrixModel$StuckSearchException.class
trunk/treebase-core/lib/mesquite/correl/lib/PagelMatrixModel.class
trunk/treebase-core/lib/mesquite/correl/notes/
trunk/treebase-core/lib/mesquite/correl/notes/PEM Notes
trunk/treebase-core/lib/mesquite/correl/notes/Pagel94Hominids.nex
trunk/treebase-core/lib/mesquite/correl/notes/Pagel94test.nex
trunk/treebase-core/lib/mesquite/correl/notes/Pagel94test.ppy
trunk/treebase-core/lib/mesquite/correl/notes/Putzer method
trunk/treebase-core/lib/mesquite/correl/notes/disc2.nex
trunk/treebase-core/lib/mesquite/correl/notes/disc2.ppy
trunk/treebase-core/lib/mesquite/correl/notes/omphalina.nex
trunk/treebase-core/lib/mesquite/correl/notes/omphalina.ppy
trunk/treebase-core/lib/mesquite/distance/
trunk/treebase-core/lib/mesquite/distance/AverageOfDistances/
trunk/treebase-core/lib/mesquite/distance/AverageOfDistances/AverageOfDistances.class
trunk/treebase-core/lib/mesquite/distance/AverageOfDistances/AvgDistances.class
trunk/treebase-core/lib/mesquite/distance/ClusterAnalysis/
trunk/treebase-core/lib/mesquite/distance/ClusterAnalysis/ClusterAnalysis.class
trunk/treebase-core/lib/mesquite/distance/DistanceContainedTaxa/
trunk/treebase-core/lib/mesquite/distance/DistanceContainedTaxa/ContainedDistances.class
trunk/treebase-core/lib/mesquite/distance/DistanceContainedTaxa/DistanceContainedTaxa.class
trunk/treebase-core/lib/mesquite/distance/F81Distance/
trunk/treebase-core/lib/mesquite/distance/F81Distance/F81Distance.class
trunk/treebase-core/lib/mesquite/distance/F81Distance/F81TD.class
trunk/treebase-core/lib/mesquite/distance/F84Distance/
trunk/treebase-core/lib/mesquite/distance/F84Distance/F84Distance.class
trunk/treebase-core/lib/mesquite/distance/F84Distance/F84TD.class
trunk/treebase-core/lib/mesquite/distance/JukesCantorDistance/
trunk/treebase-core/lib/mesquite/distance/JukesCantorDistance/JukesCantorDistance.class
trunk/treebase-core/lib/mesquite/distance/JukesCantorDistance/JukesCantorTD.class
trunk/treebase-core/lib/mesquite/distance/K2PDistance/
trunk/treebase-core/lib/mesquite/distance/K2PDistance/K2PDistance.class
trunk/treebase-core/lib/mesquite/distance/K2PDistance/K2PTD.class
trunk/treebase-core/lib/mesquite/distance/NodeCountDist/
trunk/treebase-core/lib/mesquite/distance/NodeCountDist/NodeCountDist$NodeCountTD.class
trunk/treebase-core/lib/mesquite/distance/NodeCountDist/NodeCountDist.class
trunk/treebase-core/lib/mesquite/distance/Notes/
trunk/treebase-core/lib/mesquite/distance/Notes/Distance Notes
trunk/treebase-core/lib/mesquite/distance/PDistance/
trunk/treebase-core/lib/mesquite/distance/PDistance/PDistance.class
trunk/treebase-core/lib/mesquite/distance/PDistance/PTD.class
trunk/treebase-core/lib/mesquite/distance/PatristicDistance/
trunk/treebase-core/lib/mesquite/distance/PatristicDistance/PatristicDistance.class
trunk/treebase-core/lib/mesquite/distance/PatristicDistance/PatristicTD.class
trunk/treebase-core/lib/mesquite/distance/SharedHistoryDistance/
trunk/treebase-core/lib/mesquite/distance/SharedHistoryDistance/SharedHistoryDistance$SharedHistoryTD.class
trunk/treebase-core/lib/mesquite/distance/SharedHistoryDistance/SharedHistoryDistance.class
trunk/treebase-core/lib/mesquite/distance/SharedProportionalDistance/
trunk/treebase-core/lib/mesquite/distance/SharedProportionalDistance/SharedProportionalDistance$SharedProportionTD.class
trunk/treebase-core/lib/mesquite/distance/SharedProportionalDistance/SharedProportionalDistance.class
trunk/treebase-core/lib/mesquite/distance/SingleLinkage/
trunk/treebase-core/lib/mesquite/distance/SingleLinkage/SingleLinkage.class
trunk/treebase-core/lib/mesquite/distance/TaxaDistFromMatrixSrc/
trunk/treebase-core/lib/mesquite/distance/TaxaDistFromMatrixSrc/TaxaDistFromMatrixSrc.class
trunk/treebase-core/lib/mesquite/distance/TaxonDistance/
trunk/treebase-core/lib/mesquite/distance/TaxonDistance/TaxonDistance.class
trunk/treebase-core/lib/mesquite/distance/UPGMA/
trunk/treebase-core/lib/mesquite/distance/UPGMA/UPGMA.class
trunk/treebase-core/lib/mesquite/distance/UncorrectedDistance/
trunk/treebase-core/lib/mesquite/distance/UncorrectedDistance/SimpleTD.class
trunk/treebase-core/lib/mesquite/distance/UncorrectedDistance/UncorrectedDistance.class
trunk/treebase-core/lib/mesquite/distance/explanation.txt
trunk/treebase-core/lib/mesquite/distance/lib/
trunk/treebase-core/lib/mesquite/distance/lib/DNATaxaDistFromMatrix.class
trunk/treebase-core/lib/mesquite/distance/lib/DNATaxaDistFromMatrixFreq.class
trunk/treebase-core/lib/mesquite/distance/lib/DNATaxaDistance.class
trunk/treebase-core/lib/mesquite/distance/lib/GeoTaxaDistFromMatrix.class
trunk/treebase-core/lib/mesquite/distance/lib/GeoTaxaDistance.class
trunk/treebase-core/lib/mesquite/distance/lib/IncTaxaDistanceSource.class
trunk/treebase-core/lib/mesquite/distance/lib/MolecularTaxaDistance.class
trunk/treebase-core/lib/mesquite/distance/lib/PairsChartMessages.class
trunk/treebase-core/lib/mesquite/distance/lib/PairsWindow.class
trunk/treebase-core/lib/mesquite/distance/lib/TaxaDistFromMatrix.class
trunk/treebase-core/lib/mesquite/distance/lib/TaxaDistance.class
trunk/treebase-core/lib/mesquite/distance/lib/TaxaDistanceSource.class
trunk/treebase-core/lib/mesquite/distance/lib/TreeClusterer.class
trunk/treebase-core/lib/mesquite/diverse/
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihood/
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihood/BiSSELikelihood.class
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihoodCalculator/
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihoodCalculator/BiSSELikelihoodCalculator.class
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihoodCalculator/SpecExtincCategModel.class
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihoodRatio/
trunk/treebase-core/lib/mesquite/diverse/BiSSELikelihoodRatio/BiSSELikelihoodRatio.class
trunk/treebase-core/lib/mesquite/diverse/BiSSETreeCharSim/
trunk/treebase-core/lib/mesquite/diverse/BiSSETreeCharSim/BiSSETreeCharSim.class
trunk/treebase-core/lib/mesquite/diverse/BirthDeathTrees/
trunk/treebase-core/lib/mesquite/diverse/BirthDeathTrees/BirthDeathTrees.class
trunk/treebase-core/lib/mesquite/diverse/CharAssocDivViewer/
trunk/treebase-core/lib/mesquite/diverse/CharAssocDivViewer/CADPanel.class
trunk/treebase-core/lib/mesquite/diverse/CharAssocDivViewer/CharAssocDivViewer.class
trunk/treebase-core/lib/mesquite/diverse/CharIndepDivViewer/
trunk/treebase-core/lib/mesquite/diverse/CharIndepDivViewer/CADPanel.class
trunk/treebase-core/lib/mesquite/diverse/CharIndepDivViewer/CharIndepDivViewer.class
trunk/treebase-core/lib/mesquite/diverse/ContCharSpeciation/
trunk/treebase-core/lib/mesquite/diverse/ContCharSpeciation/ContCharSpeciation.class
trunk/treebase-core/lib/mesquite/diverse/DivCategCharMLCalculator/
trunk/treebase-core/lib/mesquite/diverse/DivCategCharMLCalculator/DivCategCharMLCalculator.class
trunk/treebase-core/lib/mesquite/diverse/DivCategCharMLCalculator/DiversificationCategModel.class
trunk/treebase-core/lib/mesquite/diverse/DiversCategCharLikelihood/
trunk/treebase-core/lib/mesquite/diverse/DiversCategCharLikelihood/DiversCategCharLikelihood.class
trunk/treebase-core/lib/mesquite/diverse/EvolveTreesDiversChars/
trunk/treebase-core/lib/mesquite/diverse/EvolveTreesDiversChars/EvolveTreesDiversChars.class
trunk/treebase-core/lib/mesquite/diverse/LineagesThroughTime/
trunk/treebase-core/lib/mesquite/diverse/LineagesThroughTime/LinPanel.class
trunk/treebase-core/lib/mesquite/diverse/LineagesThroughTime/LineagesThroughTime.class
trunk/treebase-core/lib/mesquite/diverse/LineagesThroughTime/LineagesWindow.class
trunk/treebase-core/lib/mesquite/diverse/SisterDiversification/
trunk/treebase-core/lib/mesquite/diverse/SisterDiversification/SisterDiversification.class
trunk/treebase-core/lib/mesquite/diverse/SpecExtincLikelihood/
trunk/treebase-core/lib/mesquite/diverse/SpecExtincLikelihood/SpecExtincLikelihood.class
trunk/treebase-core/lib/mesquite/diverse/SpecExtincMLCalculator/
trunk/treebase-core/lib/mesquite/diverse/SpecExtincMLCalculator/SpecExtincMLCalculator.class
trunk/treebase-core/lib/mesquite/diverse/SpecExtincMLCalculator/SpecExtincModel.class
trunk/treebase-core/lib/mesquite/diverse/aDiverseIntro/
trunk/treebase-core/lib/mesquite/diverse/aDiverseIntro/aDiverseIntro.class
trunk/treebase-core/lib/mesquite/diverse/aDiverseIntro/splash.gif
trunk/treebase-core/lib/mesquite/diverse/aDiverseIntro/splash.psd
trunk/treebase-core/lib/mesquite/diverse/lib/
trunk/treebase-core/lib/mesquite/diverse/lib/DEQNumSolver.class
trunk/treebase-core/lib/mesquite/diverse/lib/DESystem.class
trunk/treebase-core/lib/mesquite/diverse/lib/NumForCharAndTreeDivers.class
trunk/treebase-core/lib/mesquite/diverse/lib/NumberForTreeDivers.class
trunk/treebase-core/lib/mesquite/diverse/lib/RK4Solver.class
trunk/treebase-core/lib/mesquite/diverse/lib/RKF45Solver.class
trunk/treebase-core/lib/mesquite/diverse/lib/SpecExtincRatioDiffCategModel.class
trunk/treebase-core/lib/mesquite/diverse/lib/TreeCharSimulate.class
trunk/treebase-core/lib/mesquite/dmanager/
trunk/treebase-core/lib/mesquite/dmanager/FuseTaxaMatrices/
trunk/treebase-core/lib/mesquite/dmanager/FuseTaxaMatrices/FuseTaxaMatrices.class
trunk/treebase-core/lib/mesquite/dmanager/TaxaListImportSource/
trunk/treebase-core/lib/mesquite/dmanager/TaxaListImportSource/TaxaListImportSource.class
trunk/treebase-core/lib/mesquite/genesis/
trunk/treebase-core/lib/mesquite/genesis/CodePosRatesCurator/
trunk/treebase-core/lib/mesquite/genesis/CodePosRatesCurator/CodePosRatesCurator.class
trunk/treebase-core/lib/mesquite/genesis/EvolveDNAChars/
trunk/treebase-core/lib/mesquite/genesis/EvolveDNAChars/EDCCategoricalStateTest.class
trunk/treebase-core/lib/mesquite/genesis/EvolveDNAChars/EvolveDNAChars.class
trunk/treebase-core/lib/mesquite/genesis/GammaCurator/
trunk/treebase-core/lib/mesquite/genesis/GammaCurator/GammaCurator.class
trunk/treebase-core/lib/mesquite/genesis/GammaInvarCurator/
trunk/treebase-core/lib/mesquite/genesis/GammaInvarCurator/GammaInvarCurator.class
trunk/treebase-core/lib/mesquite/genesis/InitDNASubmodels/
trunk/treebase-core/lib/mesquite/genesis/InitDNASubmodels/InitDNASubmodels.class
trunk/treebase-core/lib/mesquite/genesis/InvarCurator/
trunk/treebase-core/lib/mesquite/genesis/InvarCurator/InvarCurator.class
trunk/treebase-core/lib/mesquite/genesis/RateMatrixGTRCurator/
trunk/treebase-core/lib/mesquite/genesis/RateMatrixGTRCurator/RateMatrixGTRCurator.class
trunk/treebase-core/lib/mesquite/genesis/RateMatrixTiTvCurator/
trunk/treebase-core/lib/mesquite/genesis/RateMatrixTiTvCurator/RateMatrixTiTvCurator.class
trunk/treebase-core/lib/mesquite/genesis/SimDNAModelCurator/
trunk/treebase-core/lib/mesquite/genesis/SimDNAModelCurator/SimDNAModelCurator.class
trunk/treebase-core/lib/mesquite/genesis/StateFreqDNAEmpCurator/
trunk/treebase-core/lib/mesquite/genesis/StateFreqDNAEmpCurator/StateFreqDNAEmpCurator.class
trunk/treebase-core/lib/mesquite/genesis/StateFreqUserDNACurator/
trunk/treebase-core/lib/mesquite/genesis/StateFreqUserDNACurator/StateFreqUserDNACurator.class
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/aGenesisIntro.class
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/composite.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/gamma.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/genesisTest.html
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/gtr.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/index.html
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/splash.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/splashSmall.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/testimages/
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/testimages/gamma.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/testimages/gtrra.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/testimages/gtrrb.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/testimages/gtrrc.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/testimages/gtrrd.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/testimages/gtrre.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/testimages/titv.gif
trunk/treebase-core/lib/mesquite/genesis/aGenesisIntro/testimages/tree.gif
trunk/treebase-core/lib/mesquite/genesis/explanation.txt
trunk/treebase-core/lib/mesquite/genesis/lib/
trunk/treebase-core/lib/mesquite/genesis/lib/CharRateMatrixModelSet.class
trunk/treebase-core/lib/mesquite/genesis/lib/CharRatesCodePos.class
trunk/treebase-core/lib/mesquite/genesis/lib/CharRatesCurator.class
trunk/treebase-core/lib/mesquite/genesis/lib/CharRatesEqual.class
trunk/treebase-core/lib/mesquite/genesis/lib/CharRatesGamma.class
trunk/treebase-core/lib/mesquite/genesis/lib/CharRatesGammaInvar.class
trunk/treebase-core/lib/mesquite/genesis/lib/CharRatesInvar.class
trunk/treebase-core/lib/mesquite/genesis/lib/CharRatesModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/CharRatesModelInfo.class
trunk/treebase-core/lib/mesquite/genesis/lib/CharRatesModelSet.class
trunk/treebase-core/lib/mesquite/genesis/lib/CompositProbCategModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/ProbSubModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/ProbSubModelCurator.class
trunk/treebase-core/lib/mesquite/genesis/lib/ProbSubmodelEdit.class
trunk/treebase-core/lib/mesquite/genesis/lib/ProbabilityDNAModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/RateMatrixCatModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/RateMatrixCatModelInfo.class
trunk/treebase-core/lib/mesquite/genesis/lib/RateMatrixCurator.class
trunk/treebase-core/lib/mesquite/genesis/lib/RateMatrixDNAModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/RateMatrixEqualDNAModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/RateMatrixGTRModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/RateMatrixTiTvModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/SimulationDNAModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/StateFreqCurator.class
trunk/treebase-core/lib/mesquite/genesis/lib/StateFreqDNAEmpir.class
trunk/treebase-core/lib/mesquite/genesis/lib/StateFreqDNAEqual.class
trunk/treebase-core/lib/mesquite/genesis/lib/StateFreqDNAModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/StateFreqDNASpecif.class
trunk/treebase-core/lib/mesquite/genesis/lib/StateFreqModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/StateFreqModelSet.class
trunk/treebase-core/lib/mesquite/genesis/lib/StateFreqUserCurator.class
trunk/treebase-core/lib/mesquite/genesis/lib/StateFreqUserDNAModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/StateFreqUserModel.class
trunk/treebase-core/lib/mesquite/genesis/lib/SubmodelInfo.class
trunk/treebase-core/lib/mesquite/iText/
trunk/treebase-core/lib/mesquite/iText/aiTextIntro/
trunk/treebase-core/lib/mesquite/iText/aiTextIntro/aiTextIntro.class
trunk/treebase-core/lib/mesquite/iText/aiTextIntro/index.html
trunk/treebase-core/lib/mesquite/iText/aiTextIntro/splash.ai
trunk/treebase-core/lib/mesquite/iText/aiTextIntro/splash.gif
trunk/treebase-core/lib/mesquite/iText/explanation.txt
trunk/treebase-core/lib/mesquite/io/
trunk/treebase-core/lib/mesquite/io/ExportCharStateInfo/
trunk/treebase-core/lib/mesquite/io/ExportCharStateInfo/ExportCharStateInfo.class
trunk/treebase-core/lib/mesquite/io/ExportDistanceMatrix/
trunk/treebase-core/lib/mesquite/io/ExportDistanceMatrix/ExportDistanceMatrix.class
trunk/treebase-core/lib/mesquite/io/ExportFusedMatrixNEXUS/
trunk/treebase-core/lib/mesquite/io/ExportFusedMatrixNEXUS/ExportFusedMatrixNEXUS.class
trunk/treebase-core/lib/mesquite/io/ExportNEXUSTreeFile/
trunk/treebase-core/lib/mesquite/io/ExportNEXUSTreeFile/ExportNEXUSTreeFile.class
trunk/treebase-core/lib/mesquite/io/InterpretClustalDNA/
trunk/treebase-core/lib/mesquite/io/InterpretClustalDNA/InterpretClustalDNA.class
trunk/treebase-core/lib/mesquite/io/InterpretClustalProtein/
trunk/treebase-core/lib/mesquite/io/InterpretClustalProtein/InterpretClustalProtein.class
trunk/treebase-core/lib/mesquite/io/InterpretFastaDNA/
trunk/treebase-core/lib/mesquite/io/InterpretFastaDNA/InterpretFastaDNA.class
trunk/treebase-core/lib/mesquite/io/InterpretFastaProtein/
trunk/treebase-core/lib/mesquite/io/InterpretFastaProtein/InterpretFastaProtein.class
trunk/treebase-core/lib/mesquite/io/InterpretGenBankDNA/
trunk/treebase-core/lib/mesquite/io/InterpretGenBankDNA/InterpretGenBankDNA.class
trunk/treebase-core/lib/mesquite/io/InterpretGenBankProt/
trunk/treebase-core/lib/mesquite/io/InterpretGenBankProt/InterpretGenBankProt.class
trunk/treebase-core/lib/mesquite/io/InterpretNBRFDNA/
trunk/treebase-core/lib/mesquite/io/InterpretNBRFDNA/InterpretNBRFDNA.class
trunk/treebase-core/lib/mesquite/io/InterpretNBRFProtein/
trunk/treebase-core/lib/mesquite/io/InterpretNBRFProtein/InterpretNBRFProtein.class
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/HennigCCODE.class
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/HennigCNAMES.class
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/HennigCOMMENTS.class
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/HennigDREAD.class
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/HennigNonaCommand.class
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/HennigQUOTE.class
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/HennigTREAD.class
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/HennigXDREAD.class
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/HennigXREAD.class
trunk/treebase-core/lib/mesquite/io/InterpretNonaHennig/InterpretNonaHennig.class
trunk/treebase-core/lib/mesquite/io/InterpretPOYDNA/
trunk/treebase-core/lib/mesquite/io/InterpretPOYDNA/InterpretPOYDNA.class
trunk/treebase-core/lib/mesquite/io/InterpretPhylipCat/
trunk/treebase-core/lib/mesquite/io/InterpretPhylipCat/InterpretPhylipCat.class
trunk/treebase-core/lib/mesquite/io/InterpretPhylipDNA/
trunk/treebase-core/lib/mesquite/io/InterpretPhylipDNA/InterpretPhylipDNA.class
trunk/treebase-core/lib/mesquite/io/InterpretPhylipProtein/
trunk/treebase-core/lib/mesquite/io/InterpretPhylipProtein/InterpretPhylipProtein.class
trunk/treebase-core/lib/mesquite/io/InterpretPhylipTrees/
trunk/treebase-core/lib/mesquite/io/InterpretPhylipTrees/InterpretPhylipTrees.class
trunk/treebase-core/lib/mesquite/io/InterpretSimpleCat/
trunk/treebase-core/lib/mesquite/io/InterpretSimpleCat/InterpretSimpleCat.class
trunk/treebase-core/lib/mesquite/io/InterpretSimpleCont/
trunk/treebase-core/lib/mesquite/io/InterpretSimpleCont/InterpretSimpleCont.class
trunk/treebase-core/lib/mesquite/io/InterpretSimpleDNA/
trunk/treebase-core/lib/mesquite/io/InterpretSimpleDNA/InterpretSimpleDNA.class
trunk/treebase-core/lib/mesquite/io/InterpretSimpleGeog/
trunk/treebase-core/lib/mesquite/io/InterpretSimpleGeog/InterpretSimpleGeog.class
trunk/treebase-core/lib/mesquite/io/InterpretSimpleProtein/
trunk/treebase-core/lib/mesquite/io/InterpretSimpleProtein/InterpretSimpleProtein.class
trunk/treebase-core/lib/mesquite/io/InterpretTabbedCat/
trunk/treebase-core/lib/mesquite/io/InterpretTabbedCat/InterpretTabbedCat.class
trunk/treebase-core/lib/mesquite/io/InterpretTabbedConts/
trunk/treebase-core/lib/mesquite/io/InterpretTabbedConts/InterpretTabbedConts.class
trunk/treebase-core/lib/mesquite/io/aIOIntro/
trunk/treebase-core/lib/mesquite/io/aIOIntro/aIOIntro.class
trunk/treebase-core/lib/mesquite/io/explanation.txt
trunk/treebase-core/lib/mesquite/io/lib/
trunk/treebase-core/lib/mesquite/io/lib/DistanceMatrixExporterDialog.class
trunk/treebase-core/lib/mesquite/io/lib/InterpretClustal.class
trunk/treebase-core/lib/mesquite/io/lib/InterpretFasta.class
trunk/treebase-core/lib/mesquite/io/lib/InterpretGenBank.class
trunk/treebase-core/lib/mesquite/io/lib/InterpretNBRF.class
trunk/treebase-core/lib/mesquite/io/lib/InterpretPhylip.class
trunk/treebase-core/lib/mesquite/io/lib/InterpretSimple.class
trunk/treebase-core/lib/mesquite/io/lib/PhylipExporterDialog.class
trunk/treebase-core/lib/mesquite/io/putThisInMesquite_Folder-mesquite-io.zip
trunk/treebase-core/lib/mesquite/io/xExportSimpleNexus/
trunk/treebase-core/lib/mesquite/io/xExportSimpleNexus/xExportSimpleNexus.class
Added: trunk/treebase-core/lib/mesquite/charts/CharacterValuesChart/CharacterValuesChart.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/CharacterValuesChart/CharacterValuesChart.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/CharsScattergram/CharsScattergram.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/CharsScattergram/CharsScattergram.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/Histogram/Histogram.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/Histogram/Histogram.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/Histogram/HistogramCharter.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/Histogram/HistogramCharter.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/Histogram/LittlePanel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/Histogram/LittlePanel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ChartMessages.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ChartMessages.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ItemValuesChart.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ItemValuesChart.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ItemsChartWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ItemValuesChart/ItemsChartWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/ItemsBiplot.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/ItemsBiplot.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/ItemsBiplotWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/ItemsBiplotWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/TChartMessages.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ItemsBiplot/TChartMessages.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/MatrixValuesChart/MatrixValuesChart.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/MatrixValuesChart/MatrixValuesChart.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodeLabeller.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodeLabeller.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodeScattergramWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodeScattergramWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodesScattergram.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/NodesScattergram/NodesScattergram.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/Notes/Chart Notes.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/charts/Notes/Chart Notes.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/charts/Notes/Chart Notes.txt 2009-12-16 10:14:30 UTC (rev 392)
@@ -0,0 +1,8 @@
+Notes for mesquite.charts
+----------------------------------
+
+- rewrite entire charting undercode into separate components:
+ - generation and storage of data (one, two, three... values per item)
+ - modules for display of charts that would allow much more flexibility in presentation
+
+-color by codon positions
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/charts/Scattergram/Scattergram.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/Scattergram/Scattergram.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/Scattergram/ScattergramCharter.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/Scattergram/ScattergramCharter.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/Scattergram/ScattergramColorLegend.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/Scattergram/ScattergramColorLegend.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ShowMean/ShowMean.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ShowMean/ShowMean.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ShowMean/ShowMeanExtra.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ShowMean/ShowMeanExtra.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/001.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/001.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/01.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/01.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/05.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/05.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/ShowPercentile.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/ShowPercentile.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/ShowPercentileExtra.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/ShowPercentileExtra.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ShowPercentile/manual.html
===================================================================
--- trunk/treebase-core/lib/mesquite/charts/ShowPercentile/manual.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/charts/ShowPercentile/manual.html 2009-12-16 10:14:30 UTC (rev 392)
@@ -0,0 +1,47 @@
+<HTML>
+<!--This file created 14/3/01 8:53 AM by Claris Home Page version 3.0-->
+<HEAD>
+ <TITLE>Show Percentile</TITLE>
+ <META NAME=GENERATOR CONTENT="Claris Home Page 3.0">
+ <X-CLARIS-WINDOW TOP=42 BOTTOM=757 LEFT=4 RIGHT=534>
+ <X-CLARIS-TAGVIEW MODE=minimal>
+<meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
+</HEAD>
+<BODY>
+<H2><TABLE BORDER=4 CELLPADDING=0>
+ <TR>
+ <TD>
+ <H2>Mesquite: Show Percentile</H2>
+ </TD>
+ </TR>
+</TABLE>
+</H2>
+
+<H4>David Maddison & Wayne Maddison</H4>
+
+<P>August 2005</P>
+
+<P>Show Percentile calculates and displays percentile values in histograms.</P>
+<P>For example, the lower (left) tail of the following distribution has the 0.01
+ percentile marked, as exactly 1 of the 100 values is less than or equal to the
+ marked value. </P>
+<P><img src="01.gif" width="468" height="250"></P>
+<P>Show Percentile shows that value that corresponds to the specified percentile.
+ However, if there is no value that exactly corresponds to a percentile, then
+ it shows the value that corresponds most closely to the requested percentile,
+ but that is less than the requested percentile. For example, the nearest two
+ percentiles in this distribution to 0.001 would be either 0.0 (including 0 values)
+ or 0.01 (including 1 value); Show Percentile chooses 0.0, as that is the nearest
+ value that does not exceed the requested percentile:</P>
+<P><img src="001.gif" width="468" height="250"></P>
+<P>The 0.05 lower percentile for this distribution is shown below:</P>
+<P><img src="05.gif" width="468" height="250"></P>
+<P>This might also be the distribution shown if you requested 0.06, as the nearest
+ percentiles for that value are 0.05 or 0.07, and so Show Percentile would choose
+ 0.05. <br>
+</P>
+<P>Full details of the percentiles displayed can be seen by touching the Text
+ tab of the histogram window.</P>
+<P>© David Maddison & Wayne Maddison, 2005</P>
+</BODY>
+</HTML>
Added: trunk/treebase-core/lib/mesquite/charts/ShowYEqualsX/ShowYEqualsX.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ShowYEqualsX/ShowYEqualsX.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/ShowYEqualsX/ShowYEqualsXExtra.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/ShowYEqualsX/ShowYEqualsXExtra.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/TaxaScattergram/TaxaScattergram.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/TaxaScattergram/TaxaScattergram.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/TaxonPairValuesChart/TaxonPairValuesChart.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/TaxonPairValuesChart/TaxonPairValuesChart.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/TaxonPairsScattergram/TaxonPairsScattergram.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/TaxonPairsScattergram/TaxonPairsScattergram.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/TaxonValuesChart/TaxonValuesChart.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/TaxonValuesChart/TaxonValuesChart.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/TreeBlockValues/TreeBlockValues.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/TreeBlockValues/TreeBlockValues.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/TreeValuesChart/TreeValuesChart.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/TreeValuesChart/TreeValuesChart.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/TreesScattergram/TreesScattergram.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charts/TreesScattergram/TreesScattergram.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charts/explanation.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/charts/explanation.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/charts/explanation.txt 2009-12-16 10:14:30 UTC (rev 392)
@@ -0,0 +1,2 @@
+Charting Package
+One of the core Mesquite packages. Provides basic charting facilities (histograms, scatter plots) and some particular charts (histograms and scattergrams for trees, characters, taxa and other objects).
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/coalesce/CoalescenceWMigration/CoalescenceWMigration.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/CoalescenceWMigration/CoalescenceWMigration.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/CoalescentTrees/CoalescentTrees.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/CoalescentTrees/CoalescentTrees.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescSim/ContainedCoalescSim.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescSim/ContainedCoalescSim.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescence/ContainedCoalescence.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/ContainedCoalescence/ContainedCoalescence.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/DeepCoalMultLoci/DeepCoalMultLoci.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/DeepCoalMultLoci/DeepCoalMultLoci.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesG/DeepCoalescencesG.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesG/DeepCoalescencesG.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesSp/DeepCoalescencesSp.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/DeepCoalescencesSp/DeepCoalescencesSp.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsG/DuplicationsExtinctionsG.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsG/DuplicationsExtinctionsG.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsSp/DuplicationsExtinctionsSp.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/DuplicationsExtinctionsSp/DuplicationsExtinctionsSp.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/InsertNode/32insertNode.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/InsertNode/32insertNode.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/InsertNode/64insertNode.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/InsertNode/64insertNode.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/InsertNode/InsertNode.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/InsertNode/InsertNode.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/InsertNode/InsertToolExtra.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/InsertNode/InsertToolExtra.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/InsertNode/insertNode.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/InsertNode/insertNode.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/32adjustWidths.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/32adjustWidths.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/64adjustWidths.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/64adjustWidths.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/LineageWidth.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/LineageWidth.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/WidthsToolExtra.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/WidthsToolExtra.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/adjustWidths.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/coalesce/LineageWidth/adjustWidths.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/coalesce/NeutralCoalescence/NeutralCoalescence.class
===========...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-16 10:03:24
|
Revision: 391
http://treebase.svn.sourceforge.net/treebase/?rev=391&view=rev
Author: rvos
Date: 2009-12-16 10:03:18 +0000 (Wed, 16 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/charMatrices/CharReferenceStrip.zip
trunk/treebase-core/lib/mesquite/charMatrices/Wand/
trunk/treebase-core/lib/mesquite/charMatrices/Wand/32magicWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/Wand/64magicWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/Wand/Wand.class
trunk/treebase-core/lib/mesquite/charMatrices/Wand/magicWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/WandChar/
trunk/treebase-core/lib/mesquite/charMatrices/WandChar/32charWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/WandChar/64charWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/WandChar/WandChar.class
trunk/treebase-core/lib/mesquite/charMatrices/WandChar/charWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/
trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/32taxaWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/64taxaWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/WandTaxon.class
trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/taxaWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/explanation.txt
Added: trunk/treebase-core/lib/mesquite/charMatrices/CharReferenceStrip.zip
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/CharReferenceStrip.zip
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/Wand/32magicWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/Wand/32magicWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/Wand/64magicWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/Wand/64magicWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/Wand/Wand.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/Wand/Wand.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/Wand/magicWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/Wand/magicWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/WandChar/32charWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/WandChar/32charWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/WandChar/64charWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/WandChar/64charWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/WandChar/WandChar.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/WandChar/WandChar.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/WandChar/charWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/WandChar/charWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/32taxaWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/32taxaWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/64taxaWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/64taxaWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/WandTaxon.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/WandTaxon.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/taxaWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/WandTaxon/taxaWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/explanation.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/charMatrices/explanation.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/charMatrices/explanation.txt 2009-12-16 10:03:18 UTC (rev 391)
@@ -0,0 +1,2 @@
+Character Matrix Editing Package
+One of the core Mesquite packages. Provides the spreadsheet editors for character matrices, including the standard editing tools.
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-16 09:56:01
|
Revision: 390
http://treebase.svn.sourceforge.net/treebase/?rev=390&view=rev
Author: rvos
Date: 2009-12-16 09:55:53 +0000 (Wed, 16 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/charMatrices/SaveMatrixCopies/
trunk/treebase-core/lib/mesquite/charMatrices/SaveMatrixCopies/SaveMatrixCopies.class
trunk/treebase-core/lib/mesquite/charMatrices/SearchData/
trunk/treebase-core/lib/mesquite/charMatrices/SearchData/SearchData.class
trunk/treebase-core/lib/mesquite/charMatrices/SearchSelect/
trunk/treebase-core/lib/mesquite/charMatrices/SearchSelect/SearchSelect.class
trunk/treebase-core/lib/mesquite/charMatrices/SelectCharsWithProbP/
trunk/treebase-core/lib/mesquite/charMatrices/SelectCharsWithProbP/SelectCharsWithProbP.class
trunk/treebase-core/lib/mesquite/charMatrices/SelectDiffering/
trunk/treebase-core/lib/mesquite/charMatrices/SelectDiffering/SelectDiffering.class
trunk/treebase-core/lib/mesquite/charMatrices/SelectMatchingTaxa/
trunk/treebase-core/lib/mesquite/charMatrices/SelectMatchingTaxa/SelectMatchingTaxa.class
trunk/treebase-core/lib/mesquite/charMatrices/SelectRndCharacters/
trunk/treebase-core/lib/mesquite/charMatrices/SelectRndCharacters/SelectRndCharacters.class
trunk/treebase-core/lib/mesquite/charMatrices/SelectSame/
trunk/treebase-core/lib/mesquite/charMatrices/SelectSame/SelectSame.class
trunk/treebase-core/lib/mesquite/charMatrices/SelectSameVert/
trunk/treebase-core/lib/mesquite/charMatrices/SelectSameVert/SelectSameVert.class
trunk/treebase-core/lib/mesquite/charMatrices/SelectVariableCharacters/
trunk/treebase-core/lib/mesquite/charMatrices/SelectVariableCharacters/SelectVariableCharacters.class
trunk/treebase-core/lib/mesquite/charMatrices/ShuffleStates/
trunk/treebase-core/lib/mesquite/charMatrices/ShuffleStates/ShuffleStates.class
trunk/treebase-core/lib/mesquite/charMatrices/SortChar/
trunk/treebase-core/lib/mesquite/charMatrices/SortChar/32charSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortChar/32revCharSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortChar/64charSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortChar/64revCharSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortChar/SortChar.class
trunk/treebase-core/lib/mesquite/charMatrices/SortChar/charSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortChar/revCharSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/
trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/32revTaxaSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/32taxaSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/64revTaxaSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/64taxaSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/SortTaxa.class
trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/revTaxaSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/taxaSort.gif
trunk/treebase-core/lib/mesquite/charMatrices/SortsInCharList/
trunk/treebase-core/lib/mesquite/charMatrices/SortsInCharList/SortsInCharList.class
trunk/treebase-core/lib/mesquite/charMatrices/SortsManagerChar/
trunk/treebase-core/lib/mesquite/charMatrices/SortsManagerChar/SortingNexusCommandTest.class
trunk/treebase-core/lib/mesquite/charMatrices/SortsManagerChar/SortsManagerChar.class
trunk/treebase-core/lib/mesquite/charMatrices/SprinkleMissing/
trunk/treebase-core/lib/mesquite/charMatrices/SprinkleMissing/SprinkleMissing.class
trunk/treebase-core/lib/mesquite/charMatrices/StoredCharacters/
trunk/treebase-core/lib/mesquite/charMatrices/StoredCharacters/CSMCompatibilityTest.class
trunk/treebase-core/lib/mesquite/charMatrices/StoredCharacters/StoredCharacters.class
trunk/treebase-core/lib/mesquite/charMatrices/StoredMatrices/
trunk/treebase-core/lib/mesquite/charMatrices/StoredMatrices/CSMCompatibilityTest.class
trunk/treebase-core/lib/mesquite/charMatrices/StoredMatrices/StoredMatrices.class
Added: trunk/treebase-core/lib/mesquite/charMatrices/SaveMatrixCopies/SaveMatrixCopies.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SaveMatrixCopies/SaveMatrixCopies.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SearchData/SearchData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SearchData/SearchData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SearchSelect/SearchSelect.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SearchSelect/SearchSelect.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SelectCharsWithProbP/SelectCharsWithProbP.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SelectCharsWithProbP/SelectCharsWithProbP.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SelectDiffering/SelectDiffering.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SelectDiffering/SelectDiffering.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SelectMatchingTaxa/SelectMatchingTaxa.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SelectMatchingTaxa/SelectMatchingTaxa.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SelectRndCharacters/SelectRndCharacters.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SelectRndCharacters/SelectRndCharacters.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SelectSame/SelectSame.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SelectSame/SelectSame.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SelectSameVert/SelectSameVert.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SelectSameVert/SelectSameVert.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SelectVariableCharacters/SelectVariableCharacters.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SelectVariableCharacters/SelectVariableCharacters.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ShuffleStates/ShuffleStates.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ShuffleStates/ShuffleStates.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/32charSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/32charSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/32revCharSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/32revCharSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/64charSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/64charSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/64revCharSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/64revCharSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/SortChar.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/SortChar.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/charSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/charSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/revCharSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortChar/revCharSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/32revTaxaSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/32revTaxaSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/32taxaSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/32taxaSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/64revTaxaSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/64revTaxaSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/64taxaSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/64taxaSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/SortTaxa.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/SortTaxa.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/revTaxaSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/revTaxaSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/taxaSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortTaxa/taxaSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortsInCharList/SortsInCharList.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortsInCharList/SortsInCharList.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortsManagerChar/SortingNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortsManagerChar/SortingNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SortsManagerChar/SortsManagerChar.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SortsManagerChar/SortsManagerChar.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/SprinkleMissing/SprinkleMissing.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/SprinkleMissing/SprinkleMissing.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/StoredCharacters/CSMCompatibilityTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/StoredCharacters/CSMCompatibilityTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/StoredCharacters/StoredCharacters.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/StoredCharacters/StoredCharacters.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/StoredMatrices/CSMCompatibilityTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/StoredMatrices/CSMCompatibilityTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/StoredMatrices/StoredMatrices.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/StoredMatrices/StoredMatrices.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-16 09:30:17
|
Revision: 389
http://treebase.svn.sourceforge.net/treebase/?rev=389&view=rev
Author: rvos
Date: 2009-12-16 09:30:11 +0000 (Wed, 16 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/charMatrices/PercentGaps/
trunk/treebase-core/lib/mesquite/charMatrices/PercentGaps/PercentGaps.class
trunk/treebase-core/lib/mesquite/charMatrices/PercentMissing/
trunk/treebase-core/lib/mesquite/charMatrices/PercentMissing/PercentMissing.class
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeyDown.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeyRight.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeySelector copy.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeySelector.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeyDown.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeyRight.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeySelector copy.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeySelector.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/QuickKeySelector.class
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeyDown.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeyRight.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeySelector copy.gif
trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeySelector.gif
trunk/treebase-core/lib/mesquite/charMatrices/RandomFillCateg/
trunk/treebase-core/lib/mesquite/charMatrices/RandomFillCateg/RandomFillCateg.class
trunk/treebase-core/lib/mesquite/charMatrices/RandomFillWithMissing/
trunk/treebase-core/lib/mesquite/charMatrices/RandomFillWithMissing/RandomFillWithMissing.class
trunk/treebase-core/lib/mesquite/charMatrices/RandomModRespMatrices/
trunk/treebase-core/lib/mesquite/charMatrices/RandomModRespMatrices/RandomModRespMatrices.class
trunk/treebase-core/lib/mesquite/charMatrices/RandomModifMatrix/
trunk/treebase-core/lib/mesquite/charMatrices/RandomModifMatrix/RandomModifMatrix.class
trunk/treebase-core/lib/mesquite/charMatrices/RarefyMatrix/
trunk/treebase-core/lib/mesquite/charMatrices/RarefyMatrix/RarefyMatrix.class
trunk/treebase-core/lib/mesquite/charMatrices/RecodeCateg/
trunk/treebase-core/lib/mesquite/charMatrices/RecodeCateg/RecodeCateg.class
trunk/treebase-core/lib/mesquite/charMatrices/RecodeCateg/RecodeDialog.class
trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleCharacter/
trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleCharacter/ReshuffleCharacter.class
trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleMatrix/
trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleMatrix/ReshuffleMatrix.class
trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleMatrixByPart/
trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleMatrixByPart/ReshuffleMatrixByPart.class
trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleWTaxaByPart/
trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleWTaxaByPart/ReshuffleWTaxaByPart.class
trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleWithinTaxa/
trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleWithinTaxa/ReshuffleWithinTaxa.class
Added: trunk/treebase-core/lib/mesquite/charMatrices/PercentGaps/PercentGaps.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/PercentGaps/PercentGaps.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/PercentMissing/PercentMissing.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/PercentMissing/PercentMissing.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeyDown.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeyDown.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeyRight.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeyRight.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeySelector copy.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeySelector copy.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeySelector.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/32quickKeySelector.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeyDown.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeyDown.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeyRight.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeyRight.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeySelector copy.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeySelector copy.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeySelector.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/64quickKeySelector.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/QuickKeySelector.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/QuickKeySelector.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeyDown.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeyDown.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeyRight.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeyRight.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeySelector copy.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeySelector copy.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeySelector.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/QuickKeySelector/quickKeySelector.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/RandomFillCateg/RandomFillCateg.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/RandomFillCateg/RandomFillCateg.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/RandomFillWithMissing/RandomFillWithMissing.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/RandomFillWithMissing/RandomFillWithMissing.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/RandomModRespMatrices/RandomModRespMatrices.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/RandomModRespMatrices/RandomModRespMatrices.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/RandomModifMatrix/RandomModifMatrix.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/RandomModifMatrix/RandomModifMatrix.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/RarefyMatrix/RarefyMatrix.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/RarefyMatrix/RarefyMatrix.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/RecodeCateg/RecodeCateg.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/RecodeCateg/RecodeCateg.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/RecodeCateg/RecodeDialog.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/RecodeCateg/RecodeDialog.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleCharacter/ReshuffleCharacter.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleCharacter/ReshuffleCharacter.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleMatrix/ReshuffleMatrix.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleMatrix/ReshuffleMatrix.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleMatrixByPart/ReshuffleMatrixByPart.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleMatrixByPart/ReshuffleMatrixByPart.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleWTaxaByPart/ReshuffleWTaxaByPart.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleWTaxaByPart/ReshuffleWTaxaByPart.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleWithinTaxa/ReshuffleWithinTaxa.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ReshuffleWithinTaxa/ReshuffleWithinTaxa.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-16 09:27:07
|
Revision: 388
http://treebase.svn.sourceforge.net/treebase/?rev=388&view=rev
Author: rvos
Date: 2009-12-16 09:26:59 +0000 (Wed, 16 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/charMatrices/DataPainter/
trunk/treebase-core/lib/mesquite/charMatrices/DataPainter/DataPainter.class
trunk/treebase-core/lib/mesquite/charMatrices/DifferenceInNumsForChar/
trunk/treebase-core/lib/mesquite/charMatrices/DifferenceInNumsForChar/DifferenceInNumsForChar.class
trunk/treebase-core/lib/mesquite/charMatrices/Fill/
trunk/treebase-core/lib/mesquite/charMatrices/Fill/Fill.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageAssumptionsBlock/
trunk/treebase-core/lib/mesquite/charMatrices/ManageAssumptionsBlock/AssumptionsBlock.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageAssumptionsBlock/AssumptionsBlockTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageAssumptionsBlock/ManageAssumptionsBlock.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharInclusion/
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharInclusion/CharsetNexusCommandTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharInclusion/ManageCharInclusion.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/CharModelsNexusCmdTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/ForeignModel.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/ManageCharModels.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/ModelNamesLister.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharPartitions/
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharPartitions/ManageCharPartitions.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharPartitions/PartitionNexusCommandTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharWeights/
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharWeights/ManageCharWeights.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharWeights/WtsetNexusCommandTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharacters/
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharacters/CHARNexusCommandTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharacters/CharactersBlockTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharacters/ManageCharacters.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharsets/
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharsets/CharsetNexusCommandTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCharsets/ManageCharsets.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonPositions/
trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonPositions/ManageCodonPositions.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonPositions/PosNexusCommandTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonsBlock/
trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonsBlock/CodonsBlock.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonsBlock/CodonsBlockTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonsBlock/ManageCodonsBlock.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageDATAblock/
trunk/treebase-core/lib/mesquite/charMatrices/ManageDATAblock/DATABlockTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ManageDATAblock/ManageDATAblock.class
trunk/treebase-core/lib/mesquite/charMatrices/MatrixFromClipboard/
trunk/treebase-core/lib/mesquite/charMatrices/MatrixFromClipboard/MFCDialog.class
trunk/treebase-core/lib/mesquite/charMatrices/MatrixFromClipboard/MatrixFromClipboard.class
trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/
trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/MatrixInfoTool.class
trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/matrixInfo.gif
trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/matrixInfo32.gif
trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/matrixInfo64.gif
trunk/treebase-core/lib/mesquite/charMatrices/MatrixSelection/
trunk/treebase-core/lib/mesquite/charMatrices/MatrixSelection/MatrixSelection.class
trunk/treebase-core/lib/mesquite/charMatrices/NoColor/
trunk/treebase-core/lib/mesquite/charMatrices/NoColor/NoColor.class
trunk/treebase-core/lib/mesquite/charMatrices/NumApplicableNonMissing/
trunk/treebase-core/lib/mesquite/charMatrices/NumApplicableNonMissing/NumApplicableNonMissing.class
trunk/treebase-core/lib/mesquite/charMatrices/NumForCharWithChar/
trunk/treebase-core/lib/mesquite/charMatrices/NumForCharWithChar/NumForCharWithChar.class
trunk/treebase-core/lib/mesquite/charMatrices/lib/
trunk/treebase-core/lib/mesquite/charMatrices/lib/DataWindow.class
trunk/treebase-core/lib/mesquite/charMatrices/lib/RandomMatrixModifier.class
trunk/treebase-core/lib/mesquite/charMatrices/lib/SourceModRespectiveMatrix.class
trunk/treebase-core/lib/mesquite/charMatrices/lib/SourceModifiedMatrix.class
Added: trunk/treebase-core/lib/mesquite/charMatrices/DataPainter/DataPainter.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/DataPainter/DataPainter.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/DifferenceInNumsForChar/DifferenceInNumsForChar.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/DifferenceInNumsForChar/DifferenceInNumsForChar.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/Fill/Fill.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/Fill/Fill.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageAssumptionsBlock/AssumptionsBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageAssumptionsBlock/AssumptionsBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageAssumptionsBlock/AssumptionsBlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageAssumptionsBlock/AssumptionsBlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageAssumptionsBlock/ManageAssumptionsBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageAssumptionsBlock/ManageAssumptionsBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharInclusion/CharsetNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharInclusion/CharsetNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharInclusion/ManageCharInclusion.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharInclusion/ManageCharInclusion.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/CharModelsNexusCmdTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/CharModelsNexusCmdTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/ForeignModel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/ForeignModel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/ManageCharModels.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/ManageCharModels.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/ModelNamesLister.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharModels/ModelNamesLister.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharPartitions/ManageCharPartitions.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharPartitions/ManageCharPartitions.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharPartitions/PartitionNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharPartitions/PartitionNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharWeights/ManageCharWeights.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharWeights/ManageCharWeights.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharWeights/WtsetNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharWeights/WtsetNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharacters/CHARNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharacters/CHARNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharacters/CharactersBlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharacters/CharactersBlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharacters/ManageCharacters.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharacters/ManageCharacters.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharsets/CharsetNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharsets/CharsetNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharsets/ManageCharsets.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCharsets/ManageCharsets.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonPositions/ManageCodonPositions.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonPositions/ManageCodonPositions.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonPositions/PosNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonPositions/PosNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonsBlock/CodonsBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonsBlock/CodonsBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonsBlock/CodonsBlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonsBlock/CodonsBlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonsBlock/ManageCodonsBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageCodonsBlock/ManageCodonsBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageDATAblock/DATABlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageDATAblock/DATABlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ManageDATAblock/ManageDATAblock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ManageDATAblock/ManageDATAblock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/MatrixFromClipboard/MFCDialog.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/MatrixFromClipboard/MFCDialog.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/MatrixFromClipboard/MatrixFromClipboard.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/MatrixFromClipboard/MatrixFromClipboard.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/MatrixInfoTool.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/MatrixInfoTool.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/matrixInfo.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/matrixInfo.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/matrixInfo32.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/matrixInfo32.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/matrixInfo64.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/MatrixInfoTool/matrixInfo64.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/MatrixSelection/MatrixSelection.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/MatrixSelection/MatrixSelection.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/NoColor/NoColor.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/NoColor/NoColor.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/NumApplicableNonMissing/NumApplicableNonMissing.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/NumApplicableNonMissing/NumApplicableNonMissing.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/NumForCharWithChar/NumForCharWithChar.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/NumForCharWithChar/NumForCharWithChar.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/lib/DataWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/lib/DataWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/lib/RandomMatrixModifier.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/lib/RandomMatrixModifier.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/lib/SourceModRespectiveMatrix.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/lib/SourceModRespectiveMatrix.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/lib/SourceModifiedMatrix.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/lib/SourceModifiedMatrix.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-16 09:24:35
|
Revision: 387
http://treebase.svn.sourceforge.net/treebase/?rev=387&view=rev
Author: rvos
Date: 2009-12-16 09:24:28 +0000 (Wed, 16 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/charMatrices/
trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/
trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/32addChars.gif
trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/32addTaxa.gif
trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/64addChars.gif
trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/64addTaxa.gif
trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/AddDeleteData.class
trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/addChars.gif
trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/addTaxa.gif
trunk/treebase-core/lib/mesquite/charMatrices/AlterData/
trunk/treebase-core/lib/mesquite/charMatrices/AlterData/AlterData.class
trunk/treebase-core/lib/mesquite/charMatrices/AnnotPanel/
trunk/treebase-core/lib/mesquite/charMatrices/AnnotPanel/AnnotPanel.class
trunk/treebase-core/lib/mesquite/charMatrices/AnnotPanel/annot.gif
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowCoord/
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowCoord/BasicDataWindowCoord.class
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/32colorWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/64colorWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindow.class
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.class
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/CellAnnotation.class
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/ColorLegend.class
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/MatrixTable.class
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/SequenceLedge.class
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/birdsEye.gif
trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/colorWand.gif
trunk/treebase-core/lib/mesquite/charMatrices/BootstrapResample/
trunk/treebase-core/lib/mesquite/charMatrices/BootstrapResample/BootstrapResample.class
trunk/treebase-core/lib/mesquite/charMatrices/CharMatrixCoordIndep/
trunk/treebase-core/lib/mesquite/charMatrices/CharMatrixCoordIndep/CharMatrixCoordIndep.class
trunk/treebase-core/lib/mesquite/charMatrices/CharMatrixCoordObed/
trunk/treebase-core/lib/mesquite/charMatrices/CharMatrixCoordObed/CharMatrixCoordObed.class
trunk/treebase-core/lib/mesquite/charMatrices/CharReferenceStrip/
trunk/treebase-core/lib/mesquite/charMatrices/CharReferenceStrip/CharReferenceStrip.class
trunk/treebase-core/lib/mesquite/charMatrices/CharReferenceStrip/Ledge.class
trunk/treebase-core/lib/mesquite/charMatrices/CharSelCoordinator/
trunk/treebase-core/lib/mesquite/charMatrices/CharSelCoordinator/CharSelCoordinator.class
trunk/treebase-core/lib/mesquite/charMatrices/CharSrcCoordIndep/
trunk/treebase-core/lib/mesquite/charMatrices/CharSrcCoordIndep/CharSrcCoordIndep.class
trunk/treebase-core/lib/mesquite/charMatrices/CharSrcCoordObed/
trunk/treebase-core/lib/mesquite/charMatrices/CharSrcCoordObed/CharSrcCoordObed.class
trunk/treebase-core/lib/mesquite/charMatrices/ColorByCharValue/
trunk/treebase-core/lib/mesquite/charMatrices/ColorByCharValue/CbNCompatibilityTest.class
trunk/treebase-core/lib/mesquite/charMatrices/ColorByCharValue/ColorByCharValue.class
trunk/treebase-core/lib/mesquite/charMatrices/ColorByExcluded/
trunk/treebase-core/lib/mesquite/charMatrices/ColorByExcluded/ColorByExcluded.class
trunk/treebase-core/lib/mesquite/charMatrices/ColorByFootnote/
trunk/treebase-core/lib/mesquite/charMatrices/ColorByFootnote/ColorByFootnote.class
trunk/treebase-core/lib/mesquite/charMatrices/ColorByState/
trunk/treebase-core/lib/mesquite/charMatrices/ColorByState/ColorByState.class
trunk/treebase-core/lib/mesquite/charMatrices/ColorByTaxonValue/
trunk/treebase-core/lib/mesquite/charMatrices/ColorByTaxonValue/ColorByTaxonValue.class
trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/
trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/32color.gif
trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/64color.gif
trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/ColorCells.class
trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/color.gif
trunk/treebase-core/lib/mesquite/charMatrices/CompareMatrices/
trunk/treebase-core/lib/mesquite/charMatrices/CompareMatrices/CompareMatrices.class
trunk/treebase-core/lib/mesquite/charMatrices/ConcatenateMatrices/
trunk/treebase-core/lib/mesquite/charMatrices/ConcatenateMatrices/ConcatenateMatrices.class
trunk/treebase-core/lib/mesquite/charMatrices/aCharMatricesIntro/
trunk/treebase-core/lib/mesquite/charMatrices/aCharMatricesIntro/aCharMatricesIntro.class
trunk/treebase-core/lib/mesquite/charMatrices/charReference/
Added: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/32addChars.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/32addChars.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/32addTaxa.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/32addTaxa.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/64addChars.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/64addChars.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/64addTaxa.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/64addTaxa.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/AddDeleteData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/AddDeleteData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/addChars.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/addChars.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/addTaxa.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/AddDeleteData/addTaxa.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/AlterData/AlterData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/AlterData/AlterData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/AnnotPanel/AnnotPanel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/AnnotPanel/AnnotPanel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/AnnotPanel/annot.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/AnnotPanel/annot.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowCoord/BasicDataWindowCoord.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowCoord/BasicDataWindowCoord.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/32colorWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/32colorWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/64colorWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/64colorWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/BasicDataWindowMaker.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/CellAnnotation.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/CellAnnotation.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/ColorLegend.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/ColorLegend.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/MatrixTable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/MatrixTable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/SequenceLedge.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/SequenceLedge.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/birdsEye.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/birdsEye.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/colorWand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BasicDataWindowMaker/colorWand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/BootstrapResample/BootstrapResample.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/BootstrapResample/BootstrapResample.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/CharMatrixCoordIndep/CharMatrixCoordIndep.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/CharMatrixCoordIndep/CharMatrixCoordIndep.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/CharMatrixCoordObed/CharMatrixCoordObed.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/CharMatrixCoordObed/CharMatrixCoordObed.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/CharReferenceStrip/CharReferenceStrip.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/CharReferenceStrip/CharReferenceStrip.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/CharReferenceStrip/Ledge.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/CharReferenceStrip/Ledge.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/CharSelCoordinator/CharSelCoordinator.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/CharSelCoordinator/CharSelCoordinator.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/CharSrcCoordIndep/CharSrcCoordIndep.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/CharSrcCoordIndep/CharSrcCoordIndep.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/CharSrcCoordObed/CharSrcCoordObed.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/CharSrcCoordObed/CharSrcCoordObed.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ColorByCharValue/CbNCompatibilityTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ColorByCharValue/CbNCompatibilityTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ColorByCharValue/ColorByCharValue.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ColorByCharValue/ColorByCharValue.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ColorByExcluded/ColorByExcluded.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ColorByExcluded/ColorByExcluded.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ColorByFootnote/ColorByFootnote.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ColorByFootnote/ColorByFootnote.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ColorByState/ColorByState.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ColorByState/ColorByState.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ColorByTaxonValue/ColorByTaxonValue.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ColorByTaxonValue/ColorByTaxonValue.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/32color.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/32color.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/64color.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/64color.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/ColorCells.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/ColorCells.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/color.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ColorCells/color.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/CompareMatrices/CompareMatrices.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/CompareMatrices/CompareMatrices.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/ConcatenateMatrices/ConcatenateMatrices.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/ConcatenateMatrices/ConcatenateMatrices.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/charMatrices/aCharMatricesIntro/aCharMatricesIntro.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/charMatrices/aCharMatricesIntro/aCharMatricesIntro.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 18:44:10
|
Revision: 386
http://treebase.svn.sourceforge.net/treebase/?rev=386&view=rev
Author: rvos
Date: 2009-12-15 18:44:03 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/categ/
trunk/treebase-core/lib/mesquite/categ/AmbiguityToPolym/
trunk/treebase-core/lib/mesquite/categ/AmbiguityToPolym/AmbiguityToPolym.class
trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/
trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/ConsensusSequenceStrip.class
trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/consensus.gif
trunk/treebase-core/lib/mesquite/categ/ConsensusStateForChar/
trunk/treebase-core/lib/mesquite/categ/ConsensusStateForChar/ConsensusStateForChar.class
trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/
trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/CategNexusCommandTest.class
trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/ManageCategoricalChars.class
trunk/treebase-core/lib/mesquite/categ/ManageDNARNAChars/
trunk/treebase-core/lib/mesquite/categ/ManageDNARNAChars/ManageDNARNAChars.class
trunk/treebase-core/lib/mesquite/categ/ManageProteinChars/
trunk/treebase-core/lib/mesquite/categ/ManageProteinChars/ManageProteinChars.class
trunk/treebase-core/lib/mesquite/categ/PolymToAmbiguity/
trunk/treebase-core/lib/mesquite/categ/PolymToAmbiguity/PolymToAmbiguity.class
trunk/treebase-core/lib/mesquite/categ/ResolveStateAmbiguity/
trunk/treebase-core/lib/mesquite/categ/ResolveStateAmbiguity/ResolveStateAmbiguity.class
trunk/treebase-core/lib/mesquite/categ/StateFrequency/
trunk/treebase-core/lib/mesquite/categ/StateFrequency/StateFrequency.class
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateAnnotation.class
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesEditor.class
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesTable.class
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesWindow.class
trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/transpose.gif
trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/
trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/Ledge.class
trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/StateNamesStrip.class
trunk/treebase-core/lib/mesquite/categ/explanation.txt
trunk/treebase-core/lib/mesquite/categ/lib/
trunk/treebase-core/lib/mesquite/categ/lib/CategColorTable.class
trunk/treebase-core/lib/mesquite/categ/lib/CategDataAlterer.class
trunk/treebase-core/lib/mesquite/categ/lib/CategDataEditorInit.class
trunk/treebase-core/lib/mesquite/categ/lib/CategDataMatcher.class
trunk/treebase-core/lib/mesquite/categ/lib/CategDataSearcher.class
trunk/treebase-core/lib/mesquite/categ/lib/CategDataUtility.class
trunk/treebase-core/lib/mesquite/categ/lib/CategInternodeEvent.class
trunk/treebase-core/lib/mesquite/categ/lib/CategMatrixManager.class
trunk/treebase-core/lib/mesquite/categ/lib/CategStateForCharacter.class
trunk/treebase-core/lib/mesquite/categ/lib/CategTModel.class
trunk/treebase-core/lib/mesquite/categ/lib/CategTModelEditWindow.class
trunk/treebase-core/lib/mesquite/categ/lib/CategTModelTable.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalData.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalDistribution.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalState.class
trunk/treebase-core/lib/mesquite/categ/lib/CategoricalStates.class
trunk/treebase-core/lib/mesquite/categ/lib/DNACharacterAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/DNACharacterHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/DNAColorTable.class
trunk/treebase-core/lib/mesquite/categ/lib/DNAData.class
trunk/treebase-core/lib/mesquite/categ/lib/DNADataAlterer.class
trunk/treebase-core/lib/mesquite/categ/lib/DNADataAltererCon.class
trunk/treebase-core/lib/mesquite/categ/lib/DNADataSearcher.class
trunk/treebase-core/lib/mesquite/categ/lib/DNADataUtility.class
trunk/treebase-core/lib/mesquite/categ/lib/DNAEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/DNAState.class
trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalDistribution.class
trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalStates.class
trunk/treebase-core/lib/mesquite/categ/lib/MDNAAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/MDNAEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/MDNAHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/MProteinAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/MProteinEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/MProteinHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/MesquiteSequence.class
trunk/treebase-core/lib/mesquite/categ/lib/MolecDataEditorInit.class
trunk/treebase-core/lib/mesquite/categ/lib/MolecularData.class
trunk/treebase-core/lib/mesquite/categ/lib/MolecularDataAlterer.class
trunk/treebase-core/lib/mesquite/categ/lib/MolecularState.class
trunk/treebase-core/lib/mesquite/categ/lib/OffersCategoricalData.class
trunk/treebase-core/lib/mesquite/categ/lib/OffersDNAData.class
trunk/treebase-core/lib/mesquite/categ/lib/OffersProteinData.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinCharacterHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinColorTable.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinData.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinEmbedded.class
trunk/treebase-core/lib/mesquite/categ/lib/ProteinState.class
trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterAdjustable.class
trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterHistory.class
trunk/treebase-core/lib/mesquite/categ/lib/RNAData.class
trunk/treebase-core/lib/mesquite/categ/lib/RNAState.class
trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyCategoricalData.class
trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyDNAData.class
trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyMolecularData.class
trunk/treebase-core/lib/mesquite/categ/lib/RequiresExactlyCategoricalData.class
trunk/treebase-core/lib/mesquite/categ/lib/RequiresProteinData.class
Added: trunk/treebase-core/lib/mesquite/categ/AmbiguityToPolym/AmbiguityToPolym.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/AmbiguityToPolym/AmbiguityToPolym.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/ConsensusSequenceStrip.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/ConsensusSequenceStrip.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/consensus.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/ConsensusSequenceStrip/consensus.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ConsensusStateForChar/ConsensusStateForChar.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/ConsensusStateForChar/ConsensusStateForChar.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/CategNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/CategNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/ManageCategoricalChars.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/ManageCategoricalChars/ManageCategoricalChars.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ManageDNARNAChars/ManageDNARNAChars.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/ManageDNARNAChars/ManageDNARNAChars.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ManageProteinChars/ManageProteinChars.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/ManageProteinChars/ManageProteinChars.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/PolymToAmbiguity/PolymToAmbiguity.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/PolymToAmbiguity/PolymToAmbiguity.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/ResolveStateAmbiguity/ResolveStateAmbiguity.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/ResolveStateAmbiguity/ResolveStateAmbiguity.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateFrequency/StateFrequency.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/StateFrequency/StateFrequency.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateAnnotation.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateAnnotation.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesEditor.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesEditor.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesTable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesTable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/StateNamesWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/transpose.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesEditor/transpose.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/Ledge.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/Ledge.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/StateNamesStrip.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/StateNamesStrip/StateNamesStrip.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/explanation.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/categ/explanation.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/categ/explanation.txt 2009-12-15 18:44:03 UTC (rev 386)
@@ -0,0 +1,2 @@
+Categorical character package
+One of the core Mesquite packages. A package of fundamental modules and libraries for categorical character data. These define key elements of categorical data and manage categorical data matrices.
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategColorTable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategColorTable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategDataAlterer.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategDataAlterer.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategDataEditorInit.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategDataEditorInit.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategDataMatcher.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategDataMatcher.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategDataSearcher.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategDataSearcher.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategDataUtility.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategDataUtility.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategInternodeEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategInternodeEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategMatrixManager.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategMatrixManager.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategStateForCharacter.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategStateForCharacter.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategTModel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategTModel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategTModelEditWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategTModelEditWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategTModelTable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategTModelTable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalAdjustable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalAdjustable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalDistribution.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalDistribution.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalEmbedded.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalEmbedded.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalHistory.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalState.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalState.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalStates.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/CategoricalStates.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/DNACharacterAdjustable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/DNACharacterAdjustable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/DNACharacterHistory.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/DNACharacterHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/DNAColorTable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/DNAColorTable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/DNAData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/DNAData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/DNADataAlterer.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/DNADataAlterer.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/DNADataAltererCon.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/DNADataAltererCon.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/DNADataSearcher.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/DNADataSearcher.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/DNADataUtility.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/DNADataUtility.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/DNAEmbedded.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/DNAEmbedded.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/DNAState.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/DNAState.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalAdjustable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalAdjustable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalDistribution.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalDistribution.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalEmbedded.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalEmbedded.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalHistory.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalStates.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MCategoricalStates.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MDNAAdjustable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MDNAAdjustable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MDNAEmbedded.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MDNAEmbedded.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MDNAHistory.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MDNAHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MProteinAdjustable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MProteinAdjustable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MProteinEmbedded.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MProteinEmbedded.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MProteinHistory.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MProteinHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MesquiteSequence.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MesquiteSequence.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MolecDataEditorInit.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MolecDataEditorInit.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MolecularData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MolecularData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MolecularDataAlterer.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MolecularDataAlterer.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/MolecularState.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/MolecularState.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/OffersCategoricalData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/OffersCategoricalData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/OffersDNAData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/OffersDNAData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/OffersProteinData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/OffersProteinData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinAdjustable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinAdjustable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinCharacterHistory.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinCharacterHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinColorTable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinColorTable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinEmbedded.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinEmbedded.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/ProteinState.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/ProteinState.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterAdjustable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterAdjustable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterHistory.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RNACharacterHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RNAData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RNAData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RNAState.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RNAState.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyCategoricalData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyCategoricalData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyDNAData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyDNAData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyMolecularData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RequiresAnyMolecularData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RequiresExactlyCategoricalData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RequiresExactlyCategoricalData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/categ/lib/RequiresProteinData.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/categ/lib/RequiresProteinData.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 18:42:32
|
Revision: 385
http://treebase.svn.sourceforge.net/treebase/?rev=385&view=rev
Author: rvos
Date: 2009-12-15 18:42:23 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/batchArch/
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/BatchTemplateManager.class
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ChooseTemplateDLOG.class
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditFileSpecificsDLOG.class
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditTemplatesDLOG.class
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ManageTemplatesDLOG.class
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/manual.html
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/NONA.template
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/aPAUPTestConstPars.template
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/basicPAUP.template
trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/simple.template
trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/
trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartFromInstructions.class
trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartInstrItemsSource.class
trunk/treebase-core/lib/mesquite/batchArch/ExportMatricesBatch/
trunk/treebase-core/lib/mesquite/batchArch/ExportMatricesBatch/ExportMatricesBatch.class
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/aBatchArchIntro.class
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplate.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplates.html
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/emb1.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/index.html
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/instructions.html
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/oneGear.psd
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/snippetNeeded.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.psd
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash2.psd
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateManager.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateeg.gif
trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/treeNeeded.gif
trunk/treebase-core/lib/mesquite/batchArch/lib/
trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateManager.class
trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateRecord.class
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/BatchTemplateManager.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/BatchTemplateManager.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ChooseTemplateDLOG.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ChooseTemplateDLOG.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditFileSpecificsDLOG.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditFileSpecificsDLOG.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditTemplatesDLOG.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/EditTemplatesDLOG.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ManageTemplatesDLOG.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/ManageTemplatesDLOG.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/manual.html
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/manual.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/manual.html 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,26 @@
+<HTML>
+<!--This file created 14/3/01 8:53 AM by Claris Home Page version 3.0-->
+<HEAD>
+ <TITLE>Batch File Template Manager</TITLE>
+ <META NAME=GENERATOR CONTENT="Claris Home Page 3.0">
+ <X-CLARIS-WINDOW TOP=42 BOTTOM=757 LEFT=4 RIGHT=534>
+ <X-CLARIS-TAGVIEW MODE=minimal>
+<meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
+</HEAD>
+<BODY>
+<H2><TABLE BORDER=4 CELLPADDING=0>
+ <TR>
+ <TD>
+ <H2>Mesquite: Batch File Template Manager</H2>
+ </TD>
+ </TR>
+</TABLE>
+</H2>
+
+<H4>David Maddison & Wayne Maddison</H4>
+
+<P>September 2003</P>
+
+<p> </p><P>© David Maddison & Wayne Maddison, 2003</P>
+</BODY>
+</HTML>
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/NONA.template
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/NONA.template (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/NONA.template 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,8 @@
+#MESQUITEINIT BATCHFILE 1
+name = 'Basic NONA tree search'
+explanation = 'Batch file to request NONA to do basic tree search on each data matrix, saving a tree file for each'
+repeat1 = 'proc <name><number>.ss;^nh 100;^namb=;^nemp;^nsv* <name><number>.tre;^nsv/;^ndata -;^nz;'
+end1 = 'proc/;'
+repeat2 = '<name><number>.tre'
+matrixExportFormat = 'NONA, Hennig86, PiWe, WinClada'
+batchFileName1 = 'batch.ss'
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/aPAUPTestConstPars.template
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/aPAUPTestConstPars.template (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/aPAUPTestConstPars.template 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,10 @@
+#MESQUITEINIT BATCHFILE 1
+ name = 'PAUPConstraintTestParsimony'
+ explanation = 'This template produces a batch file to request PAUP to find the most parsimonious trees that match a constraint, and the most parsimonious ones unconstrained, for each matrix. It asks PAUP to write the results to a score file. '
+ start1 = '#NEXUS^nbegin paup;^n log file=''<name>.log'';^n set autoclose nowarnreset tcompress torder=right;^n defaults hs <snippet>search options</snippet>;'
+ repeat1 = ' execute ''<name><number>.nex'';^n set criterion=parsimony;^n constraint theConstraint= <tree>;^n hs enforce noconverse constraint=theConstraint;^n pscore 1/scorefile=''<name>Score.scr'' append;^n hs noenforce;^n pscore 1/scorefile=''<name>Score.scr'' append;'
+ end1 = ' log stop;^nend;'
+ batchFileName1 = PaupCommands.nex
+ start2 = 'MesquiteInstructions^nnumVariables = 2^nnumFiles = 1^nfile1 = ''itemsPerRecord=8 v1=4 v2=8''^nrecordLabel = ''Replicates''^nformula = ''v1-v2''^nlabel1 = ''Constrained treelength''^nlabel2 = ''Unconstrained treelength'''
+ batchFileName2 = MesquiteInstructions
+ matrixExportFormat = NEXUS_file_interpreter
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/basicPAUP.template
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/basicPAUP.template (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/basicPAUP.template 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,8 @@
+#MESQUITEINIT BATCHFILE 1
+ name = Basic_PAUP_tree_search
+ explanation = 'Batch file to request PAUP to do basic tree search on each data matrix, saving a tree file and consensus tree for each. It will also produce consensus trees of the consensus trees from each search.'
+ start1 = '#NEXUS^nbegin paup;^n set autoclose nowarnreset nowarntree nowarntsave;'
+ repeat1 = 'execute ''<name><number>.nex'';^nhs;^nsavetrees file = ''<name><number>.trees'';^ncontree / strict= yes majrule=no treefile = ''CB<name>'' append = yes;'
+ end1 = 'gettrees file = ''CB<name>'' warntree = no allblocks;^nsavetrees file = ''consensus.trees'';^ncontree / strict= yes treefile = ''StrictConsCons.trees'';^ncontree / strict= no majrule=yes treefile = ''MajRuleConsCons.trees'';^nend;'
+ batchFileName1 = paupCommands.nex
+ matrixExportFormat = NEXUS_file_interpreter
Added: trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/simple.template
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/simple.template (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/BatchTemplateManager/templates/simple.template 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,6 @@
+#MESQUITEINIT BATCHFILE 1
+name = 'Simple List'
+explanation = 'Produces an accessory file consisting of a simple list of the data matrix files'
+repeat1 = '<name><number>.nex'
+matrixExportFormat = 'NEXUS file interpreter'
+batchFileName1 = 'commands.txt'
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartFromInstructions.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartFromInstructions.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartInstrItemsSource.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/ChartFromInstructions/ChartInstrItemsSource.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/ExportMatricesBatch/ExportMatricesBatch.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/ExportMatricesBatch/ExportMatricesBatch.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/aBatchArchIntro.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/aBatchArchIntro.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplate.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplate.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplates.html
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplates.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/batchtemplates.html 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,106 @@
+<HTML>
+<!--This file created 14/3/01 8:53 AM by Claris Home Page version 3.0-->
+<HEAD>
+ <TITLE>Batch Architect: Design of Batch Templates</TITLE>
+ <META NAME=GENERATOR CONTENT="Claris Home Page 3.0">
+ <X-CLARIS-WINDOW TOP=42 BOTTOM=757 LEFT=4 RIGHT=534>
+ <X-CLARIS-TAGVIEW MODE=minimal>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+</HEAD>
+<BODY bgcolor="#FFFFCC">
+<H2><TABLE BORDER=0 CELLPADDING=4>
+ <TR>
+ <TD> <P><img src="splash.gif" width="164" height="64"></P>
+ </TD>
+ <TD>
+ <H2>Batch Architect: Design of Batch Templates</H2>
+ </TD>
+ </TR>
+</TABLE>
+</H2>
+
+<p><a href="index.html">Return to Batch Architect Page</a></p>
+<H4>David Maddison & Wayne Maddison</H4>
+
+<P>The Template Editor for editing Batch File templates appears as follows:</P>
+<P align="center"><img src="batchtemplate.gif" width="348" height="408"></P>
+<P> </P>
+<P>The text entered into the "Text for start of batch file" field will
+ be written once, at the start of the file; the text in "Repeated text,
+ written for each replicate" will be written as many times as there are
+ replicates; the text in "Text for end of batch file" will be written
+ at the end of the file. The following codes included in these fields will be
+ replaced in the batch file as follows:</P>
+<ul>
+ <li><name> will be replaced by the text entered in the "base name"
+ field in the Export Matrices & Batch Files or Export Batch Files dialog
+ boxes.</li>
+ <li><tree> will be replaced by the Newick formatted text description of
+ the tree chosen in the Export Matrices & Batch Files or Export Batch Files
+ dialog boxes.</li>
+ <li><snippet></snippet> surrounding the name of a code snippet will
+ be replaced by the text of the code snippet</li>
+ <li><fileExtension> will be replaced by the extension (with dot, if present;
+ e.g., ".nex", ".ss") that Mesquite will write based upon
+ the matrix format. </li>
+ <li><matrixFormat> will be replaced by the name of the matrix format (e.g.,
+ "NEXUS file")</li>
+ <li><random> numValues=n lowerBound=b1 upperBound=b2 type=double|long
+ withReplacement=yes|no </random> will be replaced by n random numbers
+ chosen with a uniform distribution over the range b1 through b2 inclusive,
+ with replacement or not. The numbers are either real numbers (if type=double
+ is chosen) or integers (type=long). For example, <random>numValues=3
+ lowerBound=1 upperBound=100 type=long withReplacement=no</random> entered
+ in the repeated text field might be replaced by "86 42 23" in one
+ replicate, and "5 73 31" in the next replicate. </li>
+</ul>
+<P>For the field "Repeated text, written for each replicate", the following
+ replacement will also be made:</P>
+<ul>
+ <li><number> will be replaced by the number of the replicate</li>
+</ul>
+<P>For example, consider 5 replicates run with a base name of "matrix"
+ for a template with the following specification:</P>
+<P align="center"><img src="templateeg.gif" width="445" height="270"></P>
+<P>A file called "commands.nex" would be created by Mesquite that would
+ look like this:</P>
+<P> </P>
+<pre> #NEXUS
+ begin paup;
+ set autoclose nowarnreset nowarntree nowarntsave;
+ execute 'matrix1.nex';
+ hs;
+ savetrees file = 'maxtrix1.nex';
+
+ execute 'matrix2.nex';
+ hs;
+ savetrees file = 'matrix2.nex';
+
+ execute 'matrix3.nex';
+ hs;
+ savetrees file = 'matrix3.nex';
+
+ execute 'matrix4.nex';
+ hs;
+ savetrees file = 'matrix4.nex';
+
+ execute 'matrix5.nex';
+ hs;
+ savetrees file = 'matrix5.nex';
+ end;
+</pre>
+<P> </P>
+<P>Up to five separate batch files can be specified for any one Batch File Template.</P>
+<p>The "Format of Matrices" choice will be ignored if matrices are not
+ being exported (e.g., if Export Batch Files was chosen).</p>
+<p> </p>
+
+<P>
+
+<HR>
+
+</P>
+
+<P>© David Maddison & Wayne Maddison, 2003</P>
+</BODY>
+</HTML>
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/emb1.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/emb1.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/index.html
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/index.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/index.html 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,165 @@
+<HTML>
+<!--This file created 14/3/01 8:53 AM by Claris Home Page version 3.0-->
+<HEAD>
+ <TITLE>Batch Architect Package</TITLE>
+ <META NAME=GENERATOR CONTENT="Claris Home Page 3.0">
+ <X-CLARIS-WINDOW TOP=42 BOTTOM=757 LEFT=4 RIGHT=534>
+ <X-CLARIS-TAGVIEW MODE=minimal>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+</HEAD>
+<BODY bgcolor="#FFFFCC">
+<H2>
+ <TABLE BORDER=0 CELLPADDING=4>
+ <TR>
+ <TD>
+<P><img src="splash.gif" width="164" height="64"></P></TD>
+ <TD> <H2>Batch Architect package for the Mesquite system</H2></TD>
+ </TR>
+ </TABLE>
+</H2>
+
+<H4>David Maddison & Wayne Maddison</H4>
+
+<P>August 2005</P>
+
+<P>This package of modules supplies basic importing and exporting
+services to Mesquite.</P>
+
+<UL>
+ <LI><A HREF="#overview">Overview</A></LI>
+ <LI><A HREF="#installation">Installation</A></LI>
+ <LI><A HREF="#features">Features</A>
+ <ul>
+ <li><a href="#embf">Export Matrices & Batch Files</a></li>
+ <li><a href="#ebf">Export Batch Files</a></li>
+ <li><a href="#batchtemplates">Batch Templates</a></li>
+ <li><a href="#codesnippets">Code Snippets</a></li>
+ <li><a href="#chartresults">Chart Results via Instruction File</a></li>
+ </ul>
+ </LI>
+ <LI><A HREF="#examples">Examples</A></LI>
+ <LI><A HREF="#citation">Citation</A></LI>
+</UL>
+
+<H3><A NAME=overview></A>Overview</H3>
+
+<P>This package automates the generation of files with repeated elements as well
+ as the processing of files with repeated records.</P>
+<P>One can ask Mesquite to build a "batch" file that can serve as a
+ command file for another program such as PAUP* that does repetitive analyses.
+ For example, one might simulate 100 matrices under a particular model of evolution,
+ and for each of these matrices, include an entry in a batch file that asks PAUP
+ to analyze that matrix, saving tree files for the matrix. At the same time,
+ another batch file might be created that could be used to ask another program
+ to read in, sequentially, each tree file, and conduct a synthetic analysis on
+ them. </P>
+
+<H3><A NAME=installation></A>Installation</H3>
+
+<P>To install the basic Batch Architect package, the "batchArch" directory must
+ be installed in the "mesquite" directory within "Mesquite Folder". It should
+ be present in a basic Mesquite installation.</P>
+
+<H3><A NAME=features id="features"></A>Features</H3>
+<h4><a name="embf"></a>Export Matrices & Batch Files</h4>
+<p>This feature, in the Batch Architect submenu in the Analysis menu, will export
+ multiple matrices and one or more associated batch files. </p>
+<p>In choosing this feature, you will first be led through as serious of dialog
+ boxes in which you will choose how the matrices are to be created. Following
+ your choosing, the Export Matrices & Batch Files dialog box will be presented:</p>
+<p align="center"><img src="emb1.gif" width="336" height="356"></p>
+<p>In this dialog box you are to specify the base name to be used both for the
+ matrices and in the batch file template system. For example, in the example
+ shown, 10 matrices will be created, with names "SimMatrix1", "SimMatrix2",
+ "SimMatrix3", and so on. </p>
+<p>The file names may have extensions added (e.g., ".nex"), depending
+ upon the matrix format to be used (the matrix format is specified in the batch
+ file template). The extension will be added automatically by Mesquite.</p>
+<p>In this dialog you will most importantly also select the batch template to
+ use. A batch template specifies exactly how the batch file or files produced
+ will be structured. To examine or edit the template, use the Edit Templates
+ button. </p>
+<p>Some batch templates contain code that requires "<a href="#codesnippets">code
+ snippets</a>" to be defined. If code snippets are needed by a template,
+ they will be listed in the dialog box. If some are needed but unavailable, the
+ list will appear in red and note them as unavailable:</p>
+<p align="center"><img src="snippetNeeded.gif" width="320" height="48"> </p>
+<p>You can define or edit snippets uing the Edit Snippets button.</p>
+<p>Some batch templates require a tree to be chosen by the user; if so, and you
+ have not yet chosen a tree, "TREE NEEDED" will appear in red in the
+ box beside the Choose Tree button:</p>
+<p align="center"><img src="treeNeeded.gif" width="248" height="24"></p>
+<p>You can then use the Choose Tree button to choose your tree.</p>
+<h4><a name="ebf"></a>Export Batch Files</h4>
+<p>This is similar to the Export Matrices & Batch Files feature expect that
+ no matrices are exported. This can be used to generate batch files for already
+ existing matrices, for example, or to automate processes other than the analyses
+ of matrices.</p>
+<h4><a name="batchtemplates"></a>Batch Templates</h4>
+<P>Batch templates contain the instructions telling Mesquite how to construct
+ the batch files. They are managed in the Batch Template Manager window, which
+ allow ones to create, duplicate, edit, rename, or delete templates:</P>
+<P align="center"><img src="templateManager.gif" width="275" height="237"></P>
+<P>You can also load templates from template files; this allows you to move templates
+ between copies of Mesquite. For example, if you create a template on one computer,
+ it will be stored as a single text file in the BatchTemplates in the Mesquite_Prefs
+ directory in the Mesquite_Support_Files directory on your disk. You can then
+ move that file to another computer, and load it into Mesquite on that computer
+ using the Load button. </P>
+<P>Selecting a template in the Batch File Template Manager and pressing "View"
+ (if it is a pre-defined template) or "Edit..." (if it is a user-defined
+ template) will bring forth the Batch Template Editor, in which the template
+ can be viewed or edited:</P>
+<P align="center"><img src="batchtemplate.gif" width="348" height="408"></P>
+<P>See the page on <a href="batchtemplates.html">Designing Batch Templates</a>
+ for details on the formats used. Batch templates can be edited using the submenu
+ in Mesquite's Edit menu, or from the Export Matrices & Batch Files or Export
+ Batch Files dialog boxes.</P>
+<P>The pre-defined templates can be viewed and duplicated, but not renamed or
+ edited. Their duplicates can be renamed and edited.</P>
+<h4><a name="codesnippets"></a>Code Snippets</h4>
+<P>Code snippets are designed as file-specific elements that are to be used in
+ place of tagged elements in the batch templates. For example, if in a batch
+ template the following text appeared:</P>
+<pre> exec setParameterValues;
+ <snippet>search command</snippet>
+ display all;</pre>
+<p>then within the Mesquite file you could store a code snippet called "search
+ command" whose contents would be inserted in place of the above text when
+ the batch file was created. If the text of "search command" was</p>
+<pre> hsearch nreps=100 addseq=random swap=tbr;</pre>
+<P>then the batch file, when written, would contain</P>
+<pre> exec setParameterValues;
+ hsearch nreps=100 addseq=random swap=tbr;
+ display all;
+
+</pre>
+<p>Batch templates can be edited using the Batch File Templates submenu in Mesquite's
+ Edit menu, or from the Export Matrices & Batch Files or Export Batch Files
+ dialog boxes.</p>
+<h4><a name="chartresults"></a>Chart Results via Instruction File</h4>
+<P>If you have a text file on disk containing tab-delimited data, you can design
+ a Mesquite Instruction file that will give Mesquite enough information about
+ the data file to allow Mesquite to read it. See <a href="instructions.html">Instructions
+ File Format</a> for details about the way Mesquite Instruction files are to
+ be structured.</P>
+<P>Some of the batch templates distributed with Mesquite have instruction files
+ defined within them.</P>
+<H3><a name=examples></a>Examples</H3>
+<p>See the <a href="../../../docs/mesquite/RandomSimul/RandomSimul.html">Simulations
+ and Randomizations</a> page of the Mesquite manual for examples.</p>
+<H3>Citation</H3>
+
+<P> Maddison, D.R., & W.P. Maddison. 2005. Batch Architect: automation of
+ simulations and replicated analyses. A package of modules for Mesquite. Version
+ 1.06.</P>
+
+<P>
+
+<HR>
+
+</P>
+
+<P>© David Maddison & Wayne Maddison, 2005</P>
+</BODY>
+</HTML>
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/instructions.html
===================================================================
--- trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/instructions.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/instructions.html 2009-12-15 18:42:23 UTC (rev 385)
@@ -0,0 +1,130 @@
+<HTML>
+<!--This file created 14/3/01 8:53 AM by Claris Home Page version 3.0-->
+<HEAD>
+ <TITLE>Batch Architect: Instructions File Format</TITLE>
+ <META NAME=GENERATOR CONTENT="Claris Home Page 3.0">
+ <X-CLARIS-WINDOW TOP=42 BOTTOM=757 LEFT=4 RIGHT=534>
+ <X-CLARIS-TAGVIEW MODE=minimal>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+</HEAD>
+<BODY bgcolor="#FFFFCC">
+<H2>
+ <TABLE BORDER=0 CELLPADDING=4>
+ <TR>
+ <TD> <P><img src="splash.gif" width="164" height="64"></P>
+ </TD>
+ <TD> <H2>Batch Architect: Instruction File Format</H2>
+ </TD>
+ </TR>
+</TABLE>
+</H2>
+
+<p><a href="index.html">Return to Batch Architect Page</a></p>
+<H4>David Maddison & Wayne Maddison</H4>
+
+<P>A Mesquite Instruction File is a text file describing the contents of one or
+ more other text files containing data. The Instruction File gives enough details
+ about the other text files to allow Mesquite to be able to read it. </P>
+<h4>Structure of the data file to be read</h4>
+<P>The data file that is to be described by the Instructions File must consist
+ of a series of records, each record represented by the same number of elements,
+ and each element must be separated by either a tab or a new line or carriage
+ return. For example, you might have a file with various numbers given for each
+ of a series of five trees. The data for each tree might be on a single line,
+ and there might be three numbers per tree. There would thus be five records
+ (corresponding to the five trees), and each record would have exactly three
+ numbers. </P>
+<h4>Instruction File format</h4>
+<P>The format of the instruction file is currently very primitive and simple;
+ eventually, it will be altered to use standard languages such as XML, and allow
+ more flexibility, but for the moment it is formatted as follows.</P>
+<ol>
+ <li> The first line must be "MesquiteInstructions"<br>
+ </li>
+ <li>The second line gives the number of data elements to be read in and stored
+ for each record. Currently the maximum number of elements to
+ be stored is 12. There can be many more elements per record, but if there
+ are more than the maximum number, some of them will not be able to be stored
+ by Mesquite. The form of this line is<br>
+ <br>
+ numVariables = <number of elements to be read and stored><br>
+ </li>
+ <li>The third line describes how many files are to be read. The current maximum
+ is 2. If more than one file is to be read, the two files need not have the
+ same format.<br>
+ </li>
+ <li>The next lines specify the layout of each file to be read, using the format:<br>
+ <br>
+ file1 = 'itemsPerRecord=<number of elements total in each record> v1=<element
+ number of first variable> v2=<element number of second variable>...'<br>
+ <br>
+ For the second file, use <br>
+ <br>
+ file2 = ...<br>
+ </li>
+ <li>An optional line can be included specifying the name to be applied to the
+ records:<br>
+ <br>
+ recordLabel = <label for records><br>
+ </li>
+ <li>An optional line can be included specifying a simple formula to manipulate
+ the data, of the form:<br>
+ <br>
+ formula = 'v1-v2'<br>
+ <br>
+ The formula can consist of nothing more than two variables with one of the
+ standard four operators (+, -, *, /).<br>
+ <br>
+ If a formula is defined, you can label it with<br>
+ <br>
+ formulaLabel = <label for formula><br>
+ </li>
+ <li>Optional lines can then be give naming each of the variables that has been
+ stored:<br>
+ <br>
+ label1 = <label for variable 1><br>
+ label2 = <label for variable 2><br>
+ </li>
+</ol>
+<p>For each of these parts of the description, the <specification> part
+ must consist of a single token; thus, if you wish to label something with multiple
+ words, surround them by single quotes, as in 'Gamma Shape'.</p>
+<h4>Example</h4>
+<P>Imagine that you wished to ask PAUP* to estimate the value of the gamma shape
+ parameter and proportion of invariant characters for a series of trees. The
+ PAUP* commands you might give are:<br>
+</P>
+<pre> lset basefreq=empirical nst=1 pinvar=estimate rates=gamma shape=estimate;
+ lscoreall/scorefile='score';</pre>
+<P>The start of the score file that would be generated would look something like
+ this:</P>
+<pre> Tree -lnL p-inv gamma shape
+ 1 8430.14114160 0.59050567 1.075992
+ 2 8410.59386351 0.57306194 0.991805
+ 3 7922.53719113 0.64386747 1.401232</pre>
+<p>The first step would be to strip the first line out of the score file, to yield:</p>
+<pre> 1 8430.14114160 0.59050567 1.075992
+ 2 8410.59386351 0.57306194 0.991805
+ 3 7922.53719113 0.64386747 1.401232</pre>
+<p>Each record has four items. If you wished Mesquite to read in only the estimate
+ of the porportion of invariable characters and the gamma shape parameters, then
+ you will want Mesquite to read in the third and fourth item in each record.
+ The MesquiteInstructions file for processing this might then be:</p>
+<pre> MesquiteInstructions
+ numVariables = 2
+ numFiles = 1
+ file1 = 'itemsPerRecord=4 v1=3 v2=4'
+ recordLabel = 'Replicates'
+ label1 = 'proportion invariable
+ label2 = 'gamma shape'</pre>
+<p> </p>
+
+<P>
+
+<HR>
+
+</P>
+
+<P>© David Maddison & Wayne Maddison, 2005</P>
+</BODY>
+</HTML>
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/oneGear.psd
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/oneGear.psd
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/snippetNeeded.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/snippetNeeded.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.psd
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash.psd
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash2.psd
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/splash2.psd
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateManager.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateManager.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateeg.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/templateeg.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/treeNeeded.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/aBatchArchIntro/treeNeeded.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateManager.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateManager.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateRecord.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/batchArch/lib/TemplateRecord.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 18:41:17
|
Revision: 384
http://treebase.svn.sourceforge.net/treebase/?rev=384&view=rev
Author: rvos
Date: 2009-12-15 18:41:10 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/basic/
trunk/treebase-core/lib/mesquite/basic/AddToTaxonNames/
trunk/treebase-core/lib/mesquite/basic/AddToTaxonNames/AddToTaxonNames.class
trunk/treebase-core/lib/mesquite/basic/AssignTaxonNames/
trunk/treebase-core/lib/mesquite/basic/AssignTaxonNames/AssignTaxonNames.class
trunk/treebase-core/lib/mesquite/basic/AuthorDefaults/
trunk/treebase-core/lib/mesquite/basic/AuthorDefaults/AuthorDefaults.class
trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/
trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/32centre.gif
trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/64centre.gif
trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/BasicParametersExplorer.class
trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/FieldPanel.class
trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/PEWindow.class
trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/centre.gif
trunk/treebase-core/lib/mesquite/basic/CondenseTaxonNames/
trunk/treebase-core/lib/mesquite/basic/CondenseTaxonNames/CondenseTaxonNames.class
trunk/treebase-core/lib/mesquite/basic/CurrentTaxaPartition/
trunk/treebase-core/lib/mesquite/basic/CurrentTaxaPartition/CurrentTaxaPartition.class
trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/
trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/ExamplesNavigator.class
trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/ExamplesNavigatorWindow.class
trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/FieldPanel.class
trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/LinkBanner.class
trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/LinkPanel.class
trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/TitlePanel.class
trunk/treebase-core/lib/mesquite/basic/GoToWebPage/
trunk/treebase-core/lib/mesquite/basic/GoToWebPage/GoToWebPage.class
trunk/treebase-core/lib/mesquite/basic/GoToWebPage/GoToWebPageWindow.class
trunk/treebase-core/lib/mesquite/basic/ManageArchivedTaxonNames/
trunk/treebase-core/lib/mesquite/basic/ManageArchivedTaxonNames/ManageArchivedTaxonNames.class
trunk/treebase-core/lib/mesquite/basic/ManageArchivedTaxonNames/TSetNexusCommandTest.class
trunk/treebase-core/lib/mesquite/basic/ManageAuthors/
trunk/treebase-core/lib/mesquite/basic/ManageAuthors/AuthorsBlock.class
trunk/treebase-core/lib/mesquite/basic/ManageAuthors/AuthorsBlockTest.class
trunk/treebase-core/lib/mesquite/basic/ManageAuthors/ManageAuthors.class
trunk/treebase-core/lib/mesquite/basic/ManageFileComments/
trunk/treebase-core/lib/mesquite/basic/ManageFileComments/FileCommentBlockTest.class
trunk/treebase-core/lib/mesquite/basic/ManageFileComments/FileCommentsBlock.class
trunk/treebase-core/lib/mesquite/basic/ManageFileComments/FileNoteNexusCommandTest.class
trunk/treebase-core/lib/mesquite/basic/ManageFileComments/ManageFileComments.class
trunk/treebase-core/lib/mesquite/basic/ManageLabelsBlock/
trunk/treebase-core/lib/mesquite/basic/ManageLabelsBlock/LabelsBlock.class
trunk/treebase-core/lib/mesquite/basic/ManageLabelsBlock/LabelsBlockTest.class
trunk/treebase-core/lib/mesquite/basic/ManageLabelsBlock/ManageLabelsBlock.class
trunk/treebase-core/lib/mesquite/basic/ManageNotesBlock/
trunk/treebase-core/lib/mesquite/basic/ManageNotesBlock/ManageNotesBlock.class
trunk/treebase-core/lib/mesquite/basic/ManageNotesBlock/NotesBlock.class
trunk/treebase-core/lib/mesquite/basic/ManageNotesBlock/NotesBlockTest.class
trunk/treebase-core/lib/mesquite/basic/ManageSetsBlock/
trunk/treebase-core/lib/mesquite/basic/ManageSetsBlock/ManageSetsBlock.class
trunk/treebase-core/lib/mesquite/basic/ManageSetsBlock/SETSBlock.class
trunk/treebase-core/lib/mesquite/basic/ManageSetsBlock/SetsBlockTest.class
trunk/treebase-core/lib/mesquite/basic/ManageTaxaPartitions/
trunk/treebase-core/lib/mesquite/basic/ManageTaxaPartitions/ManageTaxaPartitions.class
trunk/treebase-core/lib/mesquite/basic/ManageTaxaPartitions/TPartNexusCommandTest.class
trunk/treebase-core/lib/mesquite/basic/ManageTaxaSets/
trunk/treebase-core/lib/mesquite/basic/ManageTaxaSets/ManageTaxaSets.class
trunk/treebase-core/lib/mesquite/basic/ManageTaxaSets/TSetNexusCommandTest.class
trunk/treebase-core/lib/mesquite/basic/MergeTaxa/
trunk/treebase-core/lib/mesquite/basic/MergeTaxa/MergeTaxa.class
trunk/treebase-core/lib/mesquite/basic/NextProject/
trunk/treebase-core/lib/mesquite/basic/NextProject/NextProject.class
trunk/treebase-core/lib/mesquite/basic/NextProject/NextProjectWindow.class
trunk/treebase-core/lib/mesquite/basic/RawNexusBlockEditor/
trunk/treebase-core/lib/mesquite/basic/RawNexusBlockEditor/RawNexusBlockEditor.class
trunk/treebase-core/lib/mesquite/basic/RemoveFromTaxonNames/
trunk/treebase-core/lib/mesquite/basic/RemoveFromTaxonNames/RemoveFromTaxonNames.class
trunk/treebase-core/lib/mesquite/basic/ReplaceInTaxonNames/
trunk/treebase-core/lib/mesquite/basic/ReplaceInTaxonNames/ReplaceInTaxonNames.class
trunk/treebase-core/lib/mesquite/basic/ShowText/
trunk/treebase-core/lib/mesquite/basic/ShowText/ShowText.class
trunk/treebase-core/lib/mesquite/basic/StoredTaxonPairs/
trunk/treebase-core/lib/mesquite/basic/StoredTaxonPairs/StoredTaxonPairs.class
trunk/treebase-core/lib/mesquite/basic/SuffixTaxonNames/
trunk/treebase-core/lib/mesquite/basic/SuffixTaxonNames/SuffixTaxonNames.class
trunk/treebase-core/lib/mesquite/basic/TaxaSelCoordinator/
trunk/treebase-core/lib/mesquite/basic/TaxaSelCoordinator/TaxaSelCoordinator.class
trunk/treebase-core/lib/mesquite/basic/TextWindowMaker/
trunk/treebase-core/lib/mesquite/basic/TextWindowMaker/TextWindowMaker.class
trunk/treebase-core/lib/mesquite/basic/TruncTaxonNames/
trunk/treebase-core/lib/mesquite/basic/TruncTaxonNames/TruncTaxonNames.class
trunk/treebase-core/lib/mesquite/basic/explanation.txt
Added: trunk/treebase-core/lib/mesquite/basic/AddToTaxonNames/AddToTaxonNames.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/AddToTaxonNames/AddToTaxonNames.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/AssignTaxonNames/AssignTaxonNames.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/AssignTaxonNames/AssignTaxonNames.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/AuthorDefaults/AuthorDefaults.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/AuthorDefaults/AuthorDefaults.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/32centre.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/32centre.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/64centre.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/64centre.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/BasicParametersExplorer.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/BasicParametersExplorer.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/FieldPanel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/FieldPanel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/PEWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/PEWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/centre.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/BasicParametersExplorer/centre.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/CondenseTaxonNames/CondenseTaxonNames.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/CondenseTaxonNames/CondenseTaxonNames.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/CurrentTaxaPartition/CurrentTaxaPartition.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/CurrentTaxaPartition/CurrentTaxaPartition.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/ExamplesNavigator.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/ExamplesNavigator.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/ExamplesNavigatorWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/ExamplesNavigatorWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/FieldPanel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/FieldPanel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/LinkBanner.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/LinkBanner.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/LinkPanel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/LinkPanel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/TitlePanel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ExamplesNavigator/TitlePanel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/GoToWebPage/GoToWebPage.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/GoToWebPage/GoToWebPage.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/GoToWebPage/GoToWebPageWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/GoToWebPage/GoToWebPageWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageArchivedTaxonNames/ManageArchivedTaxonNames.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageArchivedTaxonNames/ManageArchivedTaxonNames.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageArchivedTaxonNames/TSetNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageArchivedTaxonNames/TSetNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageAuthors/AuthorsBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageAuthors/AuthorsBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageAuthors/AuthorsBlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageAuthors/AuthorsBlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageAuthors/ManageAuthors.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageAuthors/ManageAuthors.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageFileComments/FileCommentBlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageFileComments/FileCommentBlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageFileComments/FileCommentsBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageFileComments/FileCommentsBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageFileComments/FileNoteNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageFileComments/FileNoteNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageFileComments/ManageFileComments.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageFileComments/ManageFileComments.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageLabelsBlock/LabelsBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageLabelsBlock/LabelsBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageLabelsBlock/LabelsBlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageLabelsBlock/LabelsBlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageLabelsBlock/ManageLabelsBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageLabelsBlock/ManageLabelsBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageNotesBlock/ManageNotesBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageNotesBlock/ManageNotesBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageNotesBlock/NotesBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageNotesBlock/NotesBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageNotesBlock/NotesBlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageNotesBlock/NotesBlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageSetsBlock/ManageSetsBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageSetsBlock/ManageSetsBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageSetsBlock/SETSBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageSetsBlock/SETSBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageSetsBlock/SetsBlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageSetsBlock/SetsBlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageTaxaPartitions/ManageTaxaPartitions.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageTaxaPartitions/ManageTaxaPartitions.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageTaxaPartitions/TPartNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageTaxaPartitions/TPartNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageTaxaSets/ManageTaxaSets.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageTaxaSets/ManageTaxaSets.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ManageTaxaSets/TSetNexusCommandTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ManageTaxaSets/TSetNexusCommandTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/MergeTaxa/MergeTaxa.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/MergeTaxa/MergeTaxa.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/NextProject/NextProject.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/NextProject/NextProject.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/NextProject/NextProjectWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/NextProject/NextProjectWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/RawNexusBlockEditor/RawNexusBlockEditor.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/RawNexusBlockEditor/RawNexusBlockEditor.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/RemoveFromTaxonNames/RemoveFromTaxonNames.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/RemoveFromTaxonNames/RemoveFromTaxonNames.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ReplaceInTaxonNames/ReplaceInTaxonNames.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ReplaceInTaxonNames/ReplaceInTaxonNames.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/ShowText/ShowText.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/ShowText/ShowText.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/StoredTaxonPairs/StoredTaxonPairs.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/StoredTaxonPairs/StoredTaxonPairs.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/SuffixTaxonNames/SuffixTaxonNames.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/SuffixTaxonNames/SuffixTaxonNames.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/TaxaSelCoordinator/TaxaSelCoordinator.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/TaxaSelCoordinator/TaxaSelCoordinator.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/TextWindowMaker/TextWindowMaker.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/TextWindowMaker/TextWindowMaker.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/TruncTaxonNames/TruncTaxonNames.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/basic/TruncTaxonNames/TruncTaxonNames.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/basic/explanation.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/basic/explanation.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/basic/explanation.txt 2009-12-15 18:41:10 UTC (rev 384)
@@ -0,0 +1,2 @@
+Basic Modules for Mesquite
+One of the core Mesquite packages. A diverse collection of modules that most calculations will need. Included are modules to manage character data and other critical parts of data files and basic calculations modules for trees
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 18:39:43
|
Revision: 383
http://treebase.svn.sourceforge.net/treebase/?rev=383&view=rev
Author: rvos
Date: 2009-12-15 18:39:37 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/assoc/
trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/
trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssocExtra.class
trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssociates.class
trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedLegend.class
trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/WideTreeDrawing.class
trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/
trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepCTreeWindow.class
trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepContTreeWindow.class
trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepTreeExtra.class
trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/
trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationBlockTest.class
trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationsBlock.class
trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/ManageAssociations.class
trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/
trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/DistributionBlockTest.class
trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/ManageDistributionBlock.class
trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/
trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartCompatibilityTest.class
trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartitionFromAssociation.class
trunk/treebase-core/lib/mesquite/assoc/StoredAssociations/
trunk/treebase-core/lib/mesquite/assoc/StoredAssociations/StoredAssociations.class
trunk/treebase-core/lib/mesquite/assoc/TaxaAssociationSpecs.txt
trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/
trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/AssocEditor.class
trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/TaxonListAssoc.class
trunk/treebase-core/lib/mesquite/assoc/aAssocIntro/
trunk/treebase-core/lib/mesquite/assoc/aAssocIntro/aAssocIntro.class
trunk/treebase-core/lib/mesquite/assoc/explanation.txt
trunk/treebase-core/lib/mesquite/assoc/lib/
trunk/treebase-core/lib/mesquite/assoc/lib/AssociationHistory.class
trunk/treebase-core/lib/mesquite/assoc/lib/AssociationSource.class
trunk/treebase-core/lib/mesquite/assoc/lib/AssociationsManager.class
trunk/treebase-core/lib/mesquite/assoc/lib/ReconstructAssociation.class
trunk/treebase-core/lib/mesquite/assoc/lib/SimpleTaxaList.class
trunk/treebase-core/lib/mesquite/assoc/lib/TaxaAssociation.class
trunk/treebase-core/lib/mesquite/assoc/lib/TaxonWithTaxa.class
trunk/treebase-core/lib/mesquite/assoc/macros/
trunk/treebase-core/lib/mesquite/assoc/macros/setupAssocMacro
Added: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssocExtra.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssocExtra.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssociates.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedAssociates.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedLegend.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/ContainedLegend.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/WideTreeDrawing.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/ContainedAssociates/WideTreeDrawing.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepCTreeWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepCTreeWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepContTreeWindow.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepContTreeWindow.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepTreeExtra.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/DepContTreeWindow/DepTreeExtra.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationBlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationBlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationsBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/AssociationsBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/ManageAssociations.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/ManageAssociations/ManageAssociations.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/DistributionBlockTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/DistributionBlockTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/ManageDistributionBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/ManageDistributionBlock/ManageDistributionBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartCompatibilityTest.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartCompatibilityTest.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartitionFromAssociation.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/PartitionFromAssociation/PartitionFromAssociation.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/StoredAssociations/StoredAssociations.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/StoredAssociations/StoredAssociations.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/TaxaAssociationSpecs.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/assoc/TaxaAssociationSpecs.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/assoc/TaxaAssociationSpecs.txt 2009-12-15 18:39:37 UTC (rev 383)
@@ -0,0 +1,96 @@
+Format Specification for TaxaAssociation block of NEXUS file
+W. Maddison January 2003
+
+BEGIN TaxaAssociation;
+[TITLE <name of this association, a token>; [optional but recommended]]
+TAXA <name of first taxa block, a token> , <name of second taxa block, a token>;
+ASSOCIATES
+ <nt1> / <nt2> [<nt2> ...] ,
+ <nt1> / <nt2> [<nt2> ...] ,
+ .
+ .
+ .
+ <nt1> / <nt2> [<nt2> ...]
+
+;
+
+[ASSOCIATES ... ; may be repeated]
+
+END;
+
+
+where nt1 means name of a taxon in first block, nt2 means name of a taxon in first block (these would not, of course, all be the same). The two taxa blocks and their contained taxa must already be defined.
+
+Items may be repeated and there may be more than one ASSOCIATES command. Thus, the following 4 blocks are equivalent, indicating genes a1 and a2 are within species A, b1 and b2 within species B, and c1 and c2 within species C.
+
+=============================================
+BEGIN TaxaAssociation;
+TITLE species_Containing_Genes;
+TAXA species, genes;
+ASSOCIATES
+ A / a1 a2,
+ B / b1 b2,
+ C / c1 c2
+;
+END;
+
+=========
+BEGIN TaxaAssociation;
+TITLE species_Containing_Genes;
+TAXA species, genes;
+ASSOCIATES
+ A / a1,
+ A / a2
+;
+ASSOCIATES
+ B / b1 b2,
+ C / c1 c2
+;
+END;
+
+=========
+BEGIN TaxaAssociation;
+TITLE genes_In_Species;
+TAXA genes , species;
+ASSOCIATES
+ a1 / A ,
+ a2 / A ,
+ b1 / B ,
+ b2 / B ,
+ c1 / C ,
+ c2 / C
+;
+END;
+=========
+BEGIN TaxaAssociation;
+TITLE genes_In_Species;
+TAXA genes , species;
+ASSOCIATES
+ a1 a2 / A ,
+ b1 b2 / B ,
+ c1 c2 / C
+;
+END;
+=============================================
+
+
+Currently Mesquite reads and writes TaxaAssociation blocks in which a contained taxon is in more than one containing taxon (e.g. same haplotype in two populations) but its calculations cannot yet handle this situation.
+
+
+Questions:
+Do we allow a command which indicates the contained/containing polarity? e.g.
+ CONTAINED genes;
+One could imagine commands more for labelling, e.g.:
+ RELATIONSHIP host, parasite; [where order is that of blocks in TAXA command]
+
+Do we allow more than two taxa blocks to be associated simultaneously? e.g.
+
+BEGIN TaxaAssociation;
+TAXA genes , species, areas;
+ASSOCIATES
+ a1 a2 / A / Africa,
+ b1 b2 / B / Africa,
+ c1 c2 / C / South_America
+;
+END;
+
Added: trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/AssocEditor.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/AssocEditor.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/TaxonListAssoc.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/TaxonListAssoc/TaxonListAssoc.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/aAssocIntro/aAssocIntro.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/aAssocIntro/aAssocIntro.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/explanation.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/assoc/explanation.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/assoc/explanation.txt 2009-12-15 18:39:37 UTC (rev 383)
@@ -0,0 +1,2 @@
+Taxa Associations Package
+Manages and does some basic calculations and graphics for associations between blocks of taxa (e.g., genes sequenced as one set of taxa; their containing species or populations as a second set of taxa). Required for many of the Coalescence calculations.
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationHistory.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationSource.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationSource.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationsManager.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/AssociationsManager.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/lib/ReconstructAssociation.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/ReconstructAssociation.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/lib/SimpleTaxaList.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/SimpleTaxaList.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/lib/TaxaAssociation.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/TaxaAssociation.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/lib/TaxonWithTaxa.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/assoc/lib/TaxonWithTaxa.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/assoc/macros/setupAssocMacro
===================================================================
--- trunk/treebase-core/lib/mesquite/assoc/macros/setupAssocMacro (rev 0)
+++ trunk/treebase-core/lib/mesquite/assoc/macros/setupAssocMacro 2009-12-15 18:39:37 UTC (rev 383)
@@ -0,0 +1,38 @@
+telling mesquite.minimal.BasicFileCoordinator.BasicFileCoordinator 'Set up Associated Taxa block' 'Creates a block of taxa, creates an association between it and the previously existing block, and presents a way to build the associated block of taxa. Assumes the current file has a single block of taxa' 0;
+queryYesNo 'This macro assumes there is a single block of taxa available. It creates a second block and associates it with the first' 'Stop' 'Continue';
+Integer.answer *It;
+if *Integer.answer;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ String.existing *It;
+ newTaxa 1 'Associates';
+ tell It;
+ setTaxonName 0 'associate 1';
+ endTell;
+ endTell;
+
+ getEmployee #mesquite.assoc.ManageAssociations.ManageAssociations;
+ tell It;
+ makeAssociation 0 1;
+ endTell;
+
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ showTaxa 0 #mesquite.lists.TaxonList.TaxonList;
+ tell It;
+ getWindow;
+ tell It;
+ newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
+ newAssistant #mesquite.assoc.TaxonListAssoc.TaxonListAssoc;
+ tell It;
+ getEmployee #mesquite.assoc.StoredAssociations.StoredAssociations;
+ tell It;
+ setCurrentAssociation 0;
+ endTell;
+ endTell;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+ alert 'In the List of Taxa window is now a column labelled Associates. Select rows and then touch on this column heading to get a menu in which you can indicate what taxa in the other block are associated with the selected taxa. You can also create new taxa in that other block using the drop down menu. In this way you can complete the specification of what are the associated taxa';
+endIf;
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 18:38:54
|
Revision: 382
http://treebase.svn.sourceforge.net/treebase/?rev=382&view=rev
Author: rvos
Date: 2009-12-15 18:38:47 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/ancstates/
trunk/treebase-core/lib/mesquite/ancstates/AncestralStatesAll/
trunk/treebase-core/lib/mesquite/ancstates/AncestralStatesAll/AncestralStatesAll.class
trunk/treebase-core/lib/mesquite/ancstates/LabelStatesOnTree/
trunk/treebase-core/lib/mesquite/ancstates/LabelStatesOnTree/LabelStatesDecorator.class
trunk/treebase-core/lib/mesquite/ancstates/LabelStatesOnTree/LabelStatesOnTree.class
trunk/treebase-core/lib/mesquite/ancstates/RecAncestralStates/
trunk/treebase-core/lib/mesquite/ancstates/RecAncestralStates/RecAncestralStates.class
trunk/treebase-core/lib/mesquite/ancstates/ShadeStatesOnTree/
trunk/treebase-core/lib/mesquite/ancstates/ShadeStatesOnTree/ShadeStatesDecorator.class
trunk/treebase-core/lib/mesquite/ancstates/ShadeStatesOnTree/ShadeStatesOnTree.class
trunk/treebase-core/lib/mesquite/ancstates/TraceAllCharacters/
trunk/treebase-core/lib/mesquite/ancstates/TraceAllCharacters/TraceAllCharacters.class
trunk/treebase-core/lib/mesquite/ancstates/TraceAllCharacters/TraceAllOperator.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TCMPanel.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceCOTOperator.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceCharOverTrees.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceLegend.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceModule.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/SpecsPrintTextArea.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TCMPanel.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceCharacterHistory.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceCharacterOperator.class
trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceLegend.class
trunk/treebase-core/lib/mesquite/ancstates/UnambigChangesAtNodes/
trunk/treebase-core/lib/mesquite/ancstates/UnambigChangesAtNodes/UnambigChangesAtNodes.class
trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/
trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/aAncStatesIntro.class
trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/index.html
trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/splash.gif
trunk/treebase-core/lib/mesquite/ancstates/explanation.txt
Added: trunk/treebase-core/lib/mesquite/ancstates/AncestralStatesAll/AncestralStatesAll.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/AncestralStatesAll/AncestralStatesAll.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/LabelStatesOnTree/LabelStatesDecorator.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/LabelStatesOnTree/LabelStatesDecorator.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/LabelStatesOnTree/LabelStatesOnTree.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/LabelStatesOnTree/LabelStatesOnTree.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/RecAncestralStates/RecAncestralStates.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/RecAncestralStates/RecAncestralStates.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/ShadeStatesOnTree/ShadeStatesDecorator.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/ShadeStatesOnTree/ShadeStatesDecorator.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/ShadeStatesOnTree/ShadeStatesOnTree.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/ShadeStatesOnTree/ShadeStatesOnTree.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceAllCharacters/TraceAllCharacters.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceAllCharacters/TraceAllCharacters.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceAllCharacters/TraceAllOperator.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceAllCharacters/TraceAllOperator.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TCMPanel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TCMPanel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceCOTOperator.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceCOTOperator.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceCharOverTrees.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceCharOverTrees.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceLegend.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceLegend.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceModule.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceCharOverTrees/TraceModule.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/SpecsPrintTextArea.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/SpecsPrintTextArea.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TCMPanel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TCMPanel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceCharacterHistory.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceCharacterHistory.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceCharacterOperator.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceCharacterOperator.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceLegend.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/TraceCharacterHistory/TraceLegend.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/UnambigChangesAtNodes/UnambigChangesAtNodes.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/UnambigChangesAtNodes/UnambigChangesAtNodes.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/aAncStatesIntro.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/aAncStatesIntro.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/index.html
===================================================================
--- trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/index.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/index.html 2009-12-15 18:38:47 UTC (rev 382)
@@ -0,0 +1,124 @@
+<html>
+
+ <head>
+ <meta http-equiv="content-type" content="text/html;charset=iso-8859-1">
+ <meta name="generator" content="Adobe GoLive 4">
+ <title>Parsimony</title>
+ </head>
+
+ <body>
+ <h2>
+ <table border="4" cellpadding="0" cellspacing="2">
+ <tr>
+ <td><img height="64" width="164" src="splash.gif"></td>
+ <td>
+ <h2>Ancestral State Reconstruction Packages for Mesquite</h2>
+ </td>
+ </tr>
+ </table>
+ </h2>
+ <h4>Wayne Maddison & David Maddison</h4>
+
+<p>August 2005, version 1.06.</p>
+ <ul>
+ <li><a href="#overview">Overview</a>
+ <li><a href="#modules">Modules</a>
+ <li><a href="#examples">Examples</a>
+ </ul>
+ <h3><a name="overview"></a>Overview</h3>
+
+<p>See the <a href="../../../docs/mesquite/CharacterEvolution/AncestralStates.html">manual
+ page on ancestral states</a> for an introduction on how to use Mesquite to
+ reconstruct ancestral states.</p>
+<p>Mesquite's standard packages include several that provide calculations to
+ reconstruct ancestral states on a phylogenetic tree. These are the "<strong>ancstates</strong>"
+ package, which coordinates the reconstruction, the "<strong>parsimony</strong>" package, which
+ reconstructs using parsimony methods, and the "<strong>stochchar</strong>" package, which reconstructs
+ using likelihood methods.</p>
+<h3><a name="modules"></a>Modules</h3>
+ <p>Some of the modules available in these packages are:</p>
+ <ul>
+ <li><strong>Ancstates package: </strong>
+ <ul>
+ <li><b>Trace Character History</b> -- Displays on a tree the reconstructed
+ ancestral states at each of the nodes.
+ </li>
+ <li><b>Trace All Characters</b> -- Summarizes reconstructed ancestral
+ states for a series of characters at each of many nodes. </li>
+ <li><b>Trace Character Over Trees</b> -- Summarizes reconstructed ancestral
+ states for a character on each of many trees. </li>
+ </ul>
+ <li><strong>Parsimony package</strong></li>
+ <ul>
+ <li><strong>Parsimony Ancestral States</strong> -- Reconstructs the
+ history of ancestral states in the character
+ given a tree and a character distribution, so as to minimize amount of
+ character change. </li>
+ <li><strong>Parsimony Character Steps</strong> -- Calculates the parsimony
+ steps in a character given a tree. </li>
+ <li><strong>Treelength</strong> -- Calculates the treelength of a tree
+ for a character matrix. The treelength is the weighted sum of
+ parsimony steps over
+ characters. </li>
+ <li><strong>Parsimony Unordered</strong> --
+ Calculates the most parsimonious ancestral states at the nodes
+ of the tree assuming one
+ step per state change (this assumption is known as unordered or Fitch parsimony).
+ Also calculates the number of steps in a most parsimonious reconstruction. </li>
+ <li><strong>Parsimony Ordered</strong> - Calculates the most parsimonious
+ ancestral states at the nodes of the tree assuming states are
+ ordered (this assumption
+ is known as ordered, Farris or Wagner parsimony). Also calculates the number
+ of steps in a most parsimonious reconstruction. </li>
+ <li><strong>Parsimony Cost Matrix</strong> - Calculates the most parsimonious
+ ancestral states assuming state changes cost the number of steps
+ indicated
+ in the states X states matrix. Known as Stepmatrix or Cost Matrix parsimony. </li>
+ <li><strong>Stepmatrix Curator</strong> - Provides window to edit
+ stepmatrices. </li>
+ <li><b>Parsimony Linear</b> -- Calculates the most parsimonious
+ ancestral states at the nodes of the tree assuming a cost of <font size="4"><b>|x-y|</b></font><b> </b>on
+ a branch if the branch shows a change from state x to state y
+ (this assumption is known as linear, Farris, or Wagner parsimony).
+ Also
+ calculates the cost of a most parsimonious reconstruction. </li>
+ <li><b>Parsimony Squared</b> -- Calculates the most parsimonious
+ ancestral states at the nodes of the tree assuming a cost of <font size="4"><b>(x-y)<sup>2</sup></b></font> on
+ a branch if the branch shows a change from state x to state y
+ (this assumption is known as squared change or least-squares parsimony).
+ Also calculates the cost of a most parsimonious reconstruction. </li>
+ </ul>
+ <li><strong>Stochchar package</strong></li>
+ <ul>
+ <li><strong>Likelihood Ancestral States</strong><strong></strong> --
+ Reconstructs the history of ancestral states in the character
+ given a tree and a character distribution, so as to maximize
+ the probability of evolving the observed states. </li>
+ <li><strong>Likelihood in Character</strong> -- Calculates the likelihood
+ of a tree for a single character.</li>
+ <li><strong>Mk Model Curator</strong> -- Provides a window to edit
+ Mk1 models of evolution.</li>
+ <li><strong>AsymmMk Model Curator</strong> -- Provides a window to
+ edit AsymmMk models of evolution. </li>
+ <li><strong>Mk1 Rate</strong> -- Calculates the rate of character
+ change under an Mk1 model of evolution.</li>
+ <li><strong>Asymmetry LR</strong> -- Calculates the test statistic
+ for the likelihood ratio test comparing the asymmetrical and
+ one parameter models [2ln(Likelihood(AsymmMk.)/Likelihood(Mk1)],
+ on a tree for a given character . </li>
+ </ul>
+ </ul>
+
+ <h3><a name="examples"></a>Examples</h3>
+
+<p>See the examples files in Mesquite_Folder/examples/Ancestral_States.</p>
+ <h3>
+ <p>
+ <hr>
+ </p>
+ </h3>
+
+<p>© Wayne Maddison & David Maddison, 2002-2005
+</body>
+
+</html>
Added: trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/splash.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/ancstates/aAncStatesIntro/splash.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/ancstates/explanation.txt
===================================================================
--- trunk/treebase-core/lib/mesquite/ancstates/explanation.txt (rev 0)
+++ trunk/treebase-core/lib/mesquite/ancstates/explanation.txt 2009-12-15 18:38:47 UTC (rev 382)
@@ -0,0 +1,2 @@
+Ancestral States Package
+One of the core Mesquite packages. Coordinates reconstruction and display of ancestral states of characters on phylogenetic trees. Includes "Trace Character History". To function, requires other packages such as the parsimony or likelihood packages to perform the reconstruction.
\ No newline at end of file
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 18:38:00
|
Revision: 381
http://treebase.svn.sourceforge.net/treebase/?rev=381&view=rev
Author: rvos
Date: 2009-12-15 18:37:52 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/align/lib/
trunk/treebase-core/lib/mesquite/align/lib/AlignMatch.class
trunk/treebase-core/lib/mesquite/align/lib/AlignScoreForTaxonGen.class
trunk/treebase-core/lib/mesquite/align/lib/AlignTool.class
trunk/treebase-core/lib/mesquite/align/lib/AlignUtil.class
trunk/treebase-core/lib/mesquite/align/lib/AlignmentHelper.class
trunk/treebase-core/lib/mesquite/align/lib/AlignmentHelperLinearSpace.class
trunk/treebase-core/lib/mesquite/align/lib/AlignmentHelperQuadraticSpace.class
trunk/treebase-core/lib/mesquite/align/lib/BlockMover.class
trunk/treebase-core/lib/mesquite/align/lib/CellBlock.class
trunk/treebase-core/lib/mesquite/align/lib/ExternalSequenceAligner.class
trunk/treebase-core/lib/mesquite/align/lib/MultipleSequenceAligner.class
trunk/treebase-core/lib/mesquite/align/lib/PairwiseAligner.class
trunk/treebase-core/lib/mesquite/align/lib/TwoSequenceAligner.class
trunk/treebase-core/lib/mesquite/align/lib/TwoSequenceAlignerGaps.class
Added: trunk/treebase-core/lib/mesquite/align/lib/AlignMatch.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/AlignMatch.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/AlignScoreForTaxonGen.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/AlignScoreForTaxonGen.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/AlignTool.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/AlignTool.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/AlignUtil.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/AlignUtil.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/AlignmentHelper.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/AlignmentHelper.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/AlignmentHelperLinearSpace.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/AlignmentHelperLinearSpace.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/AlignmentHelperQuadraticSpace.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/AlignmentHelperQuadraticSpace.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/BlockMover.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/BlockMover.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/CellBlock.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/CellBlock.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/ExternalSequenceAligner.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/ExternalSequenceAligner.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/MultipleSequenceAligner.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/MultipleSequenceAligner.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/PairwiseAligner.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/PairwiseAligner.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/TwoSequenceAligner.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/TwoSequenceAligner.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/lib/TwoSequenceAlignerGaps.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/lib/TwoSequenceAlignerGaps.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 18:37:14
|
Revision: 380
http://treebase.svn.sourceforge.net/treebase/?rev=380&view=rev
Author: rvos
Date: 2009-12-15 18:37:06 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/align/MuscleAlign/
trunk/treebase-core/lib/mesquite/align/MuscleAlign/MuscleAlign.class
trunk/treebase-core/lib/mesquite/align/Notes/
trunk/treebase-core/lib/mesquite/align/Notes/Align Notes
trunk/treebase-core/lib/mesquite/align/Notes/align.nex
trunk/treebase-core/lib/mesquite/align/Notes/bugs/
trunk/treebase-core/lib/mesquite/align/Notes/bugs/bug.PairwiseAligner.nex
trunk/treebase-core/lib/mesquite/align/Notes/clustal Option List
trunk/treebase-core/lib/mesquite/align/Notes/coiLong.nex
trunk/treebase-core/lib/mesquite/align/Notes/prot.nex
trunk/treebase-core/lib/mesquite/align/RemoveAllGaps/
trunk/treebase-core/lib/mesquite/align/RemoveAllGaps/RemoveAllGaps.class
trunk/treebase-core/lib/mesquite/align/ShiftOtherToMatch/
trunk/treebase-core/lib/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.class
trunk/treebase-core/lib/mesquite/align/ShiftToMinimizeStops/
trunk/treebase-core/lib/mesquite/align/ShiftToMinimizeStops/ShiftToMinimizeStops.class
trunk/treebase-core/lib/mesquite/align/SidePusher/
trunk/treebase-core/lib/mesquite/align/SidePusher/SidePusher.class
trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab32.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab64.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab32.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab64.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft32.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft64.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight32.gif
trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight64.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover32.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover64.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/SimpleBlockMover.class
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock32.gif
trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock64.gif
trunk/treebase-core/lib/mesquite/align/ZapGaps/
trunk/treebase-core/lib/mesquite/align/ZapGaps/ZapGaps.class
trunk/treebase-core/lib/mesquite/align/ZapGapsRight/
trunk/treebase-core/lib/mesquite/align/ZapGapsRight/ZapGapsRight.class
Added: trunk/treebase-core/lib/mesquite/align/MuscleAlign/MuscleAlign.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/MuscleAlign/MuscleAlign.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/Notes/Align Notes
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/Align Notes (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/Align Notes 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,46 @@
+Align ToDo
+
+
+
+
+==============
+
+
+ - speed up getCost
+ - test code
+
+ Basic PairwiseAligner:
+ - have preprocess cost matrix for DNA data
+ - deal with terminal gaps with lower cost
+ - give it access to a user-supplied cost matrix
+ - GUI for costs
+ - preferences
+
+
+======
+Travis:
+ - pickCosts is no longer used to set the basic costs. That is now done by getDefaultCosts in AlignUtil
+
+ - I've changed the code so that it copes with amino acid data (it didn't before). e.g., alphabetLength
+ is now passed along; the substitution matrix produced by getDefaultCosts is now
+ of a size appropriate to the data
+
+ - Ambiguity codes are now dealt with. This requires different storage in the int[] A and int[]B.
+ The values in these arrays NO LONGER correspond to the A=0, C=1, G=2, T=3. Instead, the values
+ here are simply int representations of the lower 32 bits of the state set.
+ e.g., the following state sets will have the following integer values:
+ A = 1
+ C = 2
+ G = 4
+ T = 8
+ A or G = 5
+
+ This requires that when two values are compared, a method is now used to calculate the subsitution cost.
+ This function is AlignUtil.getCost(subs,a,b,alphabetLength), and it figures out the ambiguity cost.
+ We should make this faster for DNA data by having a pre-processed subs matrix that is
+ 16x16, but I just haven't managed to do that yet.
+
+ - I commented out your "score is" logging as it was taking too long!
+
+ - some of the modules I wrote (e.g., AlignMatch) now use PairwiseAligner rather than a module.
+
\ No newline at end of file
Added: trunk/treebase-core/lib/mesquite/align/Notes/align.nex
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/align.nex (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/align.nex 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,171 @@
+#NEXUS
+[written Tue May 02 21:58:45 MST 2006 by Mesquite version 1.06+ (build h57) at em/192.168.1.110]
+BEGIN AUTHORS;
+AUTHOR NAME = David_Maddison CODE = bembidion LASTSAVER;
+
+END;
+
+BEGIN TAXA;
+ TITLE Untitled_Taxa_Block;
+ DIMENSIONS NTAX=5;
+ TAXLABELS
+ taxon_1 taxon_2 taxon_3 taxon_4 taxon_5
+ ;
+ IDS bembidion10a77cd018680 bembidion10a77cd018681 bembidion10a77cd018682 bembidion10a77cd018683 bembidion10a77cd018684 ;
+ BLOCKID bembidion10a77cd01872;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE Untitled_Character_Matrix;
+ DIMENSIONS NCHAR=23;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ taxon_1 ---ACG{C,G}TT--GTTGAACCGGGG
+
+ taxon_2 ---ACGAGTTGAA----------
+
+ taxon_3 ACGTT---GTACAAC--------
+
+ taxon_4 ACGTTGGTACAAC----------
+
+ taxon_5 -----------------------
+
+
+;
+
+
+ IDS _ _ _ bembidion10a77cd33602801 bembidion10a77cd33602802 bembidion10a77cd33602803 bembidion10a77cd33602804 bembidion10a77cd33602805 bembidion10a77cd33602806 bembidion10a77cd33602807 bembidion10a77cd33602808 bembidion10a77cd33602809 bembidion10a77cd33602810 bembidion10a77cd33602811 bembidion10a77cd33602812 bembidion10a77cd33602813 bembidion10a77cd33602814 bembidion10a77cd33602815 bembidion10a77cd33602816 bembidion10a77cd33602817 bembidion10a77cd33602818 bembidion10a77cd33602819 bembidion10a77cd33602820 ;
+
+
+END;
+
+BEGIN CHARACTERS;
+ TITLE Untitled_Character_Matrix;
+ DIMENSIONS NCHAR=7;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ taxon_1 C------
+
+ taxon_2 C------
+
+ taxon_3 -------
+
+ taxon_4 -------
+
+ taxon_5 -------
+
+
+;
+
+
+ IDS bembidion10a77d5a58420 bembidion10a77d5a58421 bembidion10a77d5a58422 bembidion10a77d5a58423 bembidion10a77d5a58424 bembidion10a77d5a58425 bembidion10a77d5a58426 ;
+
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = universal: 1 - 23;
+CODESET * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = universal: 1 - 7;
+
+
+END;
+
+BEGIN CHARCHANGEHISTORY;
+LINK CHARACTERS = Untitled_Character_Matrix;
+LINK CHARACTERS = Untitled_Character_Matrix;
+
+END;
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = unord: 1 - 23;
+TYPESET * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = unord: 1 - 7;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = 'Jukes-Cantor': 1 - 7;
+ProbModelSet * UNTITLED (CHARACTERS = Untitled_Character_Matrix) = 'Jukes-Cantor': 1 - 7;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 5103472236502170046 bembidion10a77cd01872;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 949177808083695603;
+ checksum 0 3286705137;
+ setID 1 3564779954115045874;
+ checksum 1 1310667400;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #949177808083695603 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setSize 835 323;
+ setLocation 153 412;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ setTool mesquite.align.AlignToDropped.AlignToDropped.alignToDropped;
+ endTell;
+ setActive;
+ setTool mesquite.align.AlignToDropped.AlignToDropped.alignToDropped;
+ colorCells #mesquite.charMatrices.ColorByState.ColorByState;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames off;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
+ tell It;
+ gapCosts 8 3;
+ endTell;
+ endTell;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/mesquite/align/Notes/bugs/bug.PairwiseAligner.nex
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/bugs/bug.PairwiseAligner.nex (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/bugs/bug.PairwiseAligner.nex 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,171 @@
+#NEXUS
+[written Sat Oct 13 09:50:16 MST 2007 by Mesquite version 2.0+ (build j07) at dhcp-96875d2a.cals.arizona.edu/150.135.93.42 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=10;
+ TAXLABELS
+ Bemb_transversale_ID_2184 Bemb_transversale_NS_2158 Bemb_transversale_NS_2160 Bemb_transversale_UT_2183 Bemb_transversale_WY_2097 Bemb_transversale_ID_2164 Bemb_transversale_MT_2185 Bemb_transversale_UT_2251 Bemb_cf.transversale_CA_2321 Bemb_cf.transversale_CA_2318
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE Untitled_Character_Matrix;
+ DIMENSIONS NCHAR=73;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ Bemb_transversale_ID_2184 ctgaagcccgtggtcggaaacggctactgggcaatgtagtgtttgggagagcccgtctaacccgagtactgtt
+
+ Bemb_transversale_NS_2158 cccgtggtcggaaacggctactgggcaatgtagtgtttgggaGAGCccgtctaacccgagtactgtt------
+
+ Bemb_transversale_NS_2160 ctgaagcccgtggtcggaaAcggctactgggcaatgtagtgtttgggagagcccgtctaacccgagtactgtt
+
+ Bemb_transversale_UT_2183 ctgaagcccgtggtcggaaAcggctactgggcMatgtagtgtttgggagagcccgtctaacccgagtactgtt
+
+ Bemb_transversale_WY_2097 ctgaagcccgtggtcggaaacggctactgggcaatgtagtgtttgggagagcccgtctaacccgagtactgtt
+
+ Bemb_transversale_ID_2164 gcccgtctaacccgagtactgttagcgtgtccaagtccttcttgAAGGGGGCcactcg---------------
+
+ Bemb_transversale_MT_2185 gcccgtctaacccgagtactgttagcgtgtccaagtccttcttgaaGGGgGCcactcg---------------
+
+ Bemb_transversale_UT_2251 gcccgtctaacccgagtactgttagcgtgtccaagtccttcttgaaGGGGGCcactcg---------------
+
+ Bemb_cf.transversale_CA_2321 gCccgtctaacCCgagtattgttagcgtgtccaagtccttcttgAAGGGGGCcactcg---------------
+
+ Bemb_cf.transversale_CA_2318 GCccgtctaacCCgagtattgttagcGtgtccaagtcctTCTTGAAGGGGGCcactcg---------------
+
+
+;
+
+
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 73;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 73;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 73;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 1931082895948101767;
+ tell It;
+ setSelected 6 - 10;
+ setDefaultOrder 14 18 19 20 22 13 17 21 8 5;
+ attachments ;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 8552805928968270532;
+ checksum 0 3695288835 null;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #8552805928968270532 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1513 387;
+ setLocation 5 81;
+ setFont Arial;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ endTell;
+ setActive;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.ColorByState.ColorByState;
+ setBackground White;
+ toggleShowNames on;
+ toggleShowTaxonNames on;
+ toggleTight off;
+ toggleShowChanges off;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames off;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
+ tell It;
+ gapCosts 8 3 2 2;
+ subCosts 10 5 10 10 10 5 5 10 10 10 5 10;
+ endTell;
+ getEmployee #mesquite.chromaseq.ColorQuality.ColorQuality;
+ tell It;
+ toggleAmbiguities on;
+ toggleMarks on;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.TextWindowMaker.TextWindowMaker;
+ tell It;
+ setText 'Pairwise aligner bug:^n^n - drop taxa 6 through 10 on 5. ^n^nNote the way the dragged sequences on the right are not aligned.';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1041 290;
+ setLocation 76 636;
+ setFont Arial;
+ setFontSize 10;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/mesquite/align/Notes/clustal Option List
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/clustal Option List (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/clustal Option List 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,71 @@
+clustalw option list:-
+ -help
+ -check
+ -options
+ -align
+ -newtree=filename
+ -usetree=filename
+ -newtree1=filename
+ -usetree1=filename
+ -newtree2=filename
+ -usetree2=filename
+ -bootstrap
+ -tree
+ -quicktree
+ -convert
+ -interactive
+ -batch
+ -infile=filename
+ -profile1=filename
+ -profile2=filename
+ -type=protein OR dna
+ -profile
+ -sequences
+ -matrix=filename
+ -dnamatrix=filename
+ -negative
+ -noweights
+ -gapopen=f
+ -gapext=f
+ -endgaps
+ -nopgap
+ -nohgap
+ -novgap
+ -hgapresidues=string
+ -maxdiv=n
+ -gapdist=n
+ -pwmatrix=filename
+ -pwdnamatrix=filename
+ -pwgapopen=f
+ -pwgapext=f
+ -ktuple=n
+ -window=n
+ -pairgap=n
+ -topdiags=n
+ -score=percent OR absolute
+ -transweight=f
+ -seed=n
+ -kimura
+ -tossgaps
+ -bootlabels=node OR branch
+ -debug=n
+ -output=gcg OR gde OR pir OR phylip OR nexus OR fasta
+ -outputtree=nj OR phylip OR dist OR nexus
+ -outfile=filename
+ -outorder=input OR aligned
+ -case=lower OR upper
+ -seqnos=off OR on
+ -seqno_range=off OR on
+ -range=string
+ -nosecstr1
+ -nosecstr2
+ -secstrout=structure OR mask OR both OR none
+ -helixgap=n
+ -strandgap=n
+ -loopgap=n
+ -terminalgap=n
+ -helixendin=n
+ -helixendout=n
+ -strandendin=n
+ -strandendout=n
+Peziza:~ david$
Added: trunk/treebase-core/lib/mesquite/align/Notes/coiLong.nex
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/coiLong.nex (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/coiLong.nex 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,200 @@
+#NEXUS
+[written Sat May 06 13:12:01 MST 2006 by Mesquite version 1.06+ (build h57) at Fume-Hood-Computer.local/169.254.176.45]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=5;
+ TAXLABELS
+ Bemb_rothfelsi_NC_1951 Bemb_antiquum_MO_1963 Bemb_rothfelsi_MO_1962 Bemb_rothfelsi_MO_1961 Bemb_rothfelsi_MO_1960
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "coiPseudoRootFull.nex"';
+ DIMENSIONS NCHAR=1533;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ Bemb_rothfelsi_NC_1951 ----------------------------------------ttttggagcatgatcgggaataGtaggtActtctctaagAataCTAATTCGAGCAGAATTAGGAAACCCTGGCTCATTaatcggaGATGATCAAATTTATAATGTTATTGTAACTGCTCATGCTTTTGTAATAATTTTTTTTATAGTAATGCCAATTTTAATTGGAGGATTTGGAAATTGATTAGTTCCATTAATATTAGGAGCACCTGATATAGCCTTTCCtCGAATAAATAAtaTAAGATTCTGATTACTCCCTCCTTCATTAACTTTACTATTAATAAGTTCTATAGTAGAAAGAGGAGCTGGCACAGGTTGAACAGTGTATCCTCCACTAtcatCTTCAATTGCTCACAGAGGAGCATCCGTAGATCTAGCAATTTTTAGATTACATTTGGCAGGGGTATCTTCAATTTTAGGAGCTGTAAATTTTATTACTACAATTATTAATATACGATCTGTAGGAATAACATTTGATCGAATACCTTTATTTGTATGATCAGTAGGAATTACTGCATTATTATTACTCTTATCATTACCTGTTTTAGCTGGAGCTATTACAATATTACTAACTGATCGAAATTTAAATACTTCCTTTTTCGACCCGGCAGGAGGAGGTGATCCAATTTTATACCAACATTTATTTTGATTTTTTGGCCATCCtgaagtgtacattttgattttaccaggatttggtatAATTTCccataTTAtTaGTCaagaaAgTGGAAAAAAGGAAACATTTGGATCTTTAGGAATAATTTATGCTATATTAGCTATTGGTTTATTAGGATTTGtggtatgagCTCACCATATATTTACTGTAGGAATAGATGTTGATACTCGAGCCTATTTTACATCAGCAACAATAATTATTGCTGtgcCAACTGGAATTAAAATTTTTTCATGATTAGCCACATTACATGGAACACAattATCTTAtagacCATCATTATTATGAGCTTTAGGATTTGTATTTTTATTTACTGTAGGAGGATTAACAGGAGTAGTTTTAGCAAATTCATCAATTGATATTGTATTACATGATACATATTATGTAGTTGCTCATTTTCATTATGTATTATCTATAGGAGCAGTATTTGCAATTATAGCTGGATTTATTCAATGATTTCCTTTGTTtacTGGATTAATAATAAACAATAATTTATTAAAAATTCAATTTATTGTTATATTTATTGGAGTAAATAtaACATTTTTTcctCAACATTTCCTAGGATTAAGAGGAatgcctcgACGATATtcagacTATCCAGATGCATATACTTCATGAAATGTAATTTCATCAATTGGATCAACAATTTCATTTATTGGAGTTTTATTATTCATTTACATTATTTGAGAAAGTTTTATTTCacaacGATTAGTTTTATtTtCtaatcAAATATCAACttctattGAATGATTACAAAaccatCcacCCgctgaacatagttactctgaactacctat--------------------------
+
+ Bemb_antiquum_MO_1963 ----------------ggatattggaactttatattttatttttggagcatgatcaggaATAGTAGGAACTTCTTTAAGAATACTAATTCGAGCAGAATTAGGAAATCCGGGCTCATTAATTGGAGACGATCAAATTTATAATGTTATTGTAACTGCTCATGCTTTTGTAATAATTTTTTTTATAGTAATACCAATTTTAATTGGAGGATTTGGAAATTGATTAGTCCCATTAATATTAGGAGCACCAGATATAGCTTTCCCACGAATAAATAATATAAGATTTTGATTACTTCCTCCTTCATTAACTTTATTATTAATAAGCTCTATGGTAGAAAGAGGGGCTGGTACAGGCTGAACAGTATACCCACCCCTATCCTCTTCAATTGCCCATAGAGGGGCATCCGTAGACCTAGCAATTTTTAGATTACATTTAGCAGGGGTATCTTCAATTTTAGGAGCTGTAAATTTTATTACTACAATTATTAATATACGATCTATAGGAATAACATTTGATCGAATACCTTTATTTGTATGATCTGTTGGAATTACTGCATTATTATTACTTTTATCTTTACCTGTCTTAGCTGGAGCTATTACAATATTATTAACTGATCGAAATTTAAATACTTCTTTTTTCGACCCGGCAGGAGGGGGTGACCCAATTTTATACCAACATTTATTTTGATTTTTTGGTCATCCTGAAGTATATATTTTAATTTTACCTGGATTTGGTATAATTTCCCATATTATTAGCCAAGAAAGTGGAAAAAAAGAAACATTTGGATCTTTAGGAATAATTTATGCCATATTAGCTATTGGTCTATTAGGATTTGTAGTATGAGCCCACCATATGTTTACTGTAGGAATAGATGTTGATACTCGAGCTTATTTTACATCAGCTACAATAATTATTGCTGTTCCAACCGGAATTAAAATTTTTTCATGATTAGCTACATTACATGGAACACAATTATCTTATAGACCTTCATTATTATGAGCTTTAGGATTTGTATTTTTATTTACTGTAGGAGGACTAACAGGAGTAATCTTAGCAAACTCATCAATTGATATTGTATTACATGATACATATTATGTAGTTGCTCATTTTCATTATGTATTATCAATAGGAGCAGTGTTTGCAATTATAGCTGGATTTATCCAATGATTCCCGTTATTTACAGGATTAATAATAAATAATAATTTATTAAAAATTCAATTTATTATTATGTTTATTGGAGTAAATATAACATTTTTTCCTCAACATTTTTTAGGATTAAGAGGAATACCTCGACGATATTCAGACTACCCAGATGCATATACCTCATGAAATATTATTTCATCAATTGGATCAACAATTTCATTTATTGGAGTTTTATTATTTATTTATATTATTTGAGAAAGTTTTATTTCACAACGATTAATTTTATTTTCTAATCAAATACCAACTTCTATCGAATGACTACAAAATCATCCACCGGCTGAACatagttactctgaactacctata-------------------------
+
+ Bemb_rothfelsi_MO_1962 -------------------------------------------------------------------------------------------------------------cTGGCTCaTTAATTtgAgat{C,T}atcAAATTTATAATGTTATTGTaacTgctcaTGCTTTTGTAAtactTTTTtta{A,T}a{A,G}tAA{A,T}gCcaa{C,T}t{A,T}ta{A,G}ttgGagGattggGAAattgttTaGTTCc{A,C}tTAatgtaagGagc{A,C}cc{C,T}g{A,C}tATAGCctt{C,T}cctCGAATAAATAA{C,T}aTAAGattCTGATTAct{C,G}cctCCTTCATTAACTTTACTATTAATAAGTTc{C,T}{A,C}tagtaGAAAGa{G,T}gagc{C,T}ggcac{A,C}{C,G}{C,G}tTGAACAgt{A,G}taCCCTCCACTa{A,T}ga{A,C}c{C,T}tCAATTGCTCACAGAGGAGCATc{C,T}gTAGATCTAGCAATTTt{A,T}aGAT{A,T}ACATTTG{C,G}CAGGGGTat{C,G}TTCAATTTTAGGAGCTGTAAATTTTATta{C,T}taCAATTATTAATATACGATCTGTAGGAATAACATTTGATcg{A,G}aT{A,C}CC{C,T}TTATTTGTATGatc{A,T}gTAGGAATTAC{C,T}GCATTATTATT{A,G}CTCTTaTCATTACCTGTTTTAGCTGGAGCTATTACAATATta{A,T}aAaccgaTCGAAATTTAAATAct{C,T}c{C,T}tTTTTCgacCcAGCAg{A,G}agg{A,G}ggtGATCCAATTTTAta{C,T}caaCaTTTATTTTGATTTTTTGGCCATCCTGAagta{G,T}acattt{A,T}aattTtacc{A,C}gaa{A,T}ttggTATAA{A,T}TTCcc{A,C}{A,T}atta{A,T}tagtcaa{A,G}caagtggaAAAAAGGAAAC{A,C}Tt{C,T}gGATCTTt{C,G}gGAATAATt{A,T}aTGCTATATTAGCTATTGGTTTATTAGGATTTgt{A,G}gaaTgggCTCACCa{C,T}ATATTTACTGTAGga{A,C}taGAt{A,G}TTGATACTCGAGCCTATTTTACATCAGCAACAATAATTATTGCTGT{C,G}CCAACTGGAATTAAAATTTTTTCATGATTAGCCACATTACATGGAACACAATTATCTTATACACCATCATta{A,T}taTGAGct{A,T}{A,T}agGATTTGTATTTTTATTTACTGTAGGAggacTAACAGGAGTAGTTTTAGCAAATTCATCAATTGATAT{A,T}GTATTACACGATACAtGTTATGTAGTTG{C,G}TCATTTTCATTATGTATTATCTATAGGAGC{A,C}GTATt{G,T}gCAa{C,T}taaAGCTGGATTTATTCAATGATt{C,T}cCTTTATTTGCTGG{A,G}TTAATAATAAACAA{A,T}AATTTATTAAAAA{C,T}TCAATTt{A,T}tTGTTATATTTATt{G,T}gagTAAATATGACATTTTTt{C,T}{C,T}t{C,T}aACATTTCCTAGGATTAag{A,G}gGAATTcct{C,T}gacgatATtta{A,G}actatccAgATGCATATACTTCATGAAATGTAATTTcaTCAattgGATCAACAATTt{C,T}attTATtggag{G,T}tTta{A,T}tattta{A,T}tTATattattTgagaaagttttatttcaa{A,G}acgattagttttaattt{C,T}t{A,T}a{C,T}caaat--------------------------------------------------------------------------------------------
+
+ Bemb_rothfelsi_MO_1961 ------------------------------------------------------------------------------------------------------------CctggctcaTTAAtttgAgat{C,T}atcAAATTTATAatgttATtgtaacTGCTCATGCTTTtgtaata{A,C}tttTTtta{A,T}a{A,G}tAa{A,T}gccaa{A,C}tt{C,T}{A,T}{A,G}tt{G,T}Ga{A,G}g{A,G}ttgggaaa{A,T}t{G,T}{G,T}ttag{C,T}Tcc{A,C}ttaa{A,T}g{G,T}aa{A,G}{G,T}agcacc{C,T}g{A,C}{C,T}aT{A,T}GCctttc{C,G}{G,T}cGAa{G,T}aAAtaa{C,T}ataag{A,T}tt{C,T}tGATTAct{C,G}c{C,G}{G,T}cc{G,T}TCATTA{A,G}{C,G}TTTACtatTAA{A,T}AA{G,T}Tt{C,T}{C,T}atagtagAAaga{G,T}gagc{C,T}g{C,G}cac{A,C}{C,G}{C,G}{C,T}TGAACAgt{A,G}t{A,G}CCCTCCa{C,T}T{A,C}t{C,G}a{C,T}c{C,T}tCAATTGCTCACAGAGgagc{A,T}t{C,T}{C,T}gtAGATCTAGCAA{G,T}TTt{A,T}aGATTACATTTG{C,G}CAGGGGTat{C,G}TTCAATTTTAGGAGCT{C,G}TAAATTTTATTa{A,C}taC{A,C}ATTATTAATATACGATCTGTAGGAATAACATT{G,T}GATcg{A,G}aTACCTT{C,T}ATTTGTA{C,T}GATCAGTAGGAA{A,T}TAC{C,T}GC{A,C}TtaTTATTACTCTTATCATTACCTGTTTTAGCTGGAGCTATTACAATATTa{A,T}aAaccgatCGAAA{C,T}TTAAATACtTcctttTTCGAcCcAGCAggaggaggtGATCCAATTTTAta{C,T}caacatttATTTTGATTTTTTGGCCATCCTGAAgtatac{A,C}ttttaattTtaccag{A,G}{A,G}tttgg{G,T}a{A,T}aA{A,T}TTCcc{A,C}tatta{A,T}ta{A,G}tcaagcaag{G,T}ggaAAAAaggaAACatt{C,T}ggaTCTTt{C,T}ggAATAATt{A,T}aTGCTATATTAGCTATTGGTTTATTAGGATTTgtagaaTg{A,G}gCTCACCa{C,T}ATATTTACTGTAGg{A,G}{A,C}taGAt{A,G}tTGATACTCGAGCCTATTTTACATCAGCAACAATAATTATTGCTGt{C,G}CCAACTGGAATTAAAATTTTTTCATGATTAGCCACATTACATGGAACACAA{C,T}TATCTTATACACCATCATta{A,T}{A,T}aTGAGct{A,T}{A,T}agGATTTGTATTTTTATTTACTGTAGGAGGA{C,T}TAACAGGAGTAGTTTTAGCAAATTCATCAATTGATATTGTATTACACGATACAtGTTATGTAGTTGCTCATTTTCATTATGTATTATCTaTAGGAGCAGTatt{G,T}gcaa{C,T}ta{A,T}aG{C,G}TGGATTTATTCAATGatt{C,T}{C,T}ctTTATTTG{C,G}TGGATTAATAATAAACAATAATTTATTAAAAA{C,T}tcaAttt{A,T}ttgTTATATTTatt{G,T}gagTAAATATGACATTTTTt{C,T}{C,T}tcAACATTTCCTAGGATTAAG{A,G}GGAATTcct{C,T}gacgAtATtta{A,G}actatccAgATGCATATACTTCATGAAATGTAATTTCATcaattgGATCAAcAATTt{C,T}atttattggagttTTattatt{C,T}attTATattatttgagaaagttttatttca{A,C}{A,G}acgattagttttaattt{C,T}taa{C,T}caaat--------------------------------------------------------------------------------------------
+
+ Bemb_rothfelsi_MO_1960 -------------------------------------------------------------------------------------------------------------CTggctcaTTAAtTtGAgat{C,T}atcAAATTTAtAatgttattgtaacTGCTCATGCTTTTGTAAtactTTTTtta{A,T}a{A,G}taa{A,T}g{C,G}c{A,C}a{A,C}tt{C,T}a{A,G}ttgga{A,G}ga{A,T}tggGAAattg{G,T}tta{A,G}tt{C,T}c{A,C}ttaa{A,T}g{G,T}aa{A,G}g{A,G}{A,G}c{A,C}cc{C,T}ga{A,T}a{A,T}{A,T}gcc{C,T}t{C,T}cc{C,T}c{C,G}aataaaTaac{A,C}taa{A,G}{A,G}{A,T}t{C,T}{C,T}ga{A,T}tac{C,T}tcc{C,T}cc{C,T}tc{A,C}ttaactttac{C,T}a{A,T}taa{A,T}aa{A,G}ttc{C,T}atggaa{A,G}aaa{A,G}a{A,T}ga{A,G}c{C,T}gg{C,G}{A,C}c{C,G}{A,G}gttgaa{A,C}a{A,G}tatAccc{C,T}cca{A,C}ta{A,T}ga{A,C}c{C,T}t{C,T}aattg{C,G}{C,T}ca{A,C}a{A,G}a{A,G}ga{A,G}c{A,C}t{C,T}{C,T}g{G,T}a{A,G}a{A,T}{C,T}{C,T}agc{A,C}aTttt{A,T}a{A,G}a{A,T}ta{A,C}{A,C}tttgg{C,G}a{A,G}ggg{G,T}{A,T}tatt{C,T}{A,C}{A,T}tttta{A,G}{A,G}a{A,G}c{C,T}g{G,T}aAATTTTATtattac{A,C}attATTAAta{A,T}acGATC{C,T}G{G,T}aGGAATAA{A,C}{A,C}tttgatc{C,G}ga{A,T}acc{C,T}ttaTTTg{G,T}A{C,T}G{A,G}{A,T}ttg{G,T}aggaattac{C,T}gc{A,C}{G,T}tattatt{A,G}ctc{A,T}{C,T}atc{A,C}{C,T}{C,T}{A,G}CCT{C,G}TTTTAGCTG{C,G}AGc{A,T}ATTAcaat{A,T}Tta{A,T}aaaccgatCGAAATTTAAATACttc{C,G}tt{A,T}ttcGACCCagcag{A,G}agg{A,G}ggTGATCCAATTTTAta{C,T}caacatTTATT{G,T}TGATTTTTTGGCCATCC{C,T}Gaa{C,G}tatacattt{A,T}aattTtaccaga{A,G}tttggtataa{A,T}ttccc{A,C}tatta{A,T}tagtc{A,C}agcaag{G,T}gg{A,G}AAAAAGgAAACatt{C,T}ggaTCttt{A,C}ggaATAATTAATGCTATATTAGCTATTGGTTTATTAGGATTTgtagaaTgggCTCACCa{C,T}ATATTTACTGTAGga{A,C}tagAt{A,G}TTGATACTCGAGCCTATTTTACATCAGCAACAATAATTATTGCTGT{C,G}CCAACTGGAATTAAAATTTTTTCATGATTAGCCACATTACATGGAACACAATTATCTTATACACCATCATta{A,T}taTGAGct{A,T}{A,T}agGATTTGTATTTTTATTTACTGTAGGAGGACTAACAGGAGTAGTTTTAGCAAATTCATCAATTGATATTGTATTAc{A,C}cGATACAtGTTATGTAGTTGCTCATTTTCATTATGTATTATCTaTAGGAGCAGTATt{G,T}gCAa{C,T}taaaGCTGGATTTATTCAATGattccctTTATTTG{C,G}TGG{A,G}TTAATAAT{A,T}AAC{A,C}A{A,T}AATTTATTAAAAA{C,T}tCAAttt{A,T}ttgTTATATTTatt{G,T}gagTAAATATGACATTTTTt{C,T}{C,T}tcAACATTTCCTAGGATTAAG{A,G}GGAATTcct{C,T}gacGATATtta{A,G}actATCCAGATGCATATACTTCATGAAATGTAATTTCATCAattgGATCAACAATtt{C,T}atttattgg{A,G}g{G,T}tTTa{A,T}tatttattTATattattTgagaaagtttTAtttca{A,C}{A,G}acgattagttttaattt{C,T}taa{C,T}caatatc{A,C}actttcatcg{A,C}atgattacaaaatcatccacccgctga---------------------------------------------------
+
+
+;
+
+
+
+END;
+
+BEGIN CODONS;
+CODONPOSSET * UNTITLED = 1: 3 6 9 12 15 18 21 24 27 30 33 36 39 42 45 48 51 54 57 60 63 66 69 72 75 78 81 84 87 90 93 96 99 102 105 108 111 114 117 120 123 126 129 132 135 138 141 144 147 150 153 156 159 162 165 168 171 174 177 180 183 186 189 192 195 198 201 204 207 210 213 216 219 222 225 228 231 234 237 240 243 246 249 252 255 258 261 264 267 270 273 276 279 282 285 288 291 294 297 300 303 306 309 312 315 318 321 324 327 330 333 336 339 342 345 348 351 354 357 360 363 366 369 372 375 378 381 384 387 390 393 396 399 402 405 408 411 414 417 420 423 426 429 432 435 438 441 444 447 450 453 456 459 462 465 468 471 474 477 480 483 486 489 492 495 498 501 504 507 510 513 516 519 522 525 528 531 534 537 540 543 546 549 552 555 558 561 564 567 570 573 576 579 582 585 588 591 594 597 600 603 606 609 612 615 618 621 624 627 630 633 636 639 642 645 648 651 654 657 660 663 666 669 672 675 678 681 684 687 690 693 696 699 702 705 708 711 714 717 720 723 726 729 732 735 738 741 744 747 750 753 756 759 762 765 768 771 774 777 780 783 786 789 792 795 798 801 804 807 810 813 816 819 822 825 828 831 834 837 840 843 846 849 852 855 858 861 864 867 870 873 876 879 882 885 888 891 894 897 900 903 906 909 912 915 918 921 924 927 930 933 936 939 942 945 948 951 954 957 960 963 966 969 972 975 978 981 984 987 990 993 996 999 1002 1005 1008 1011 1014 1017 1020 1023 1026 1029 1032 1035 1038 1041 1044 1047 1050 1053 1056 1059 1062 1065 1068 1071 1074 1077 1080 1083 1086 1089 1092 1095 1098 1101 1104 1107 1110 1113 1116 1119 1122 1125 1128 1131 1134 1137 1140 1143 1146 1149 1152 1155 1158 1161 1164 1167 1170 1173 1176 1179 1182 1185 1188 1191 1194 1197 1200 1203 1206 1209 1212 1215 1218 1221 1224 1227 1230 1233 1236 1239 1242 1245 1248 1251 1254 1257 1260 1263 1266 1269 1272 1275 1278 1281 1284 1287 1290 1293 1296 1299 1302 1305 1308 1311 1314 1317 1320 1323 1326 1329 1332 1335 1338 1341 1344 1347 1350 1353 1356 1359 1362 1365 1368 1371 1374 1377 1380 1383 1386 1389 1392 1395 1398 1401 1404 1407 1410 1413 1416 1419 1422 1425 1428 1431 1434 1437 1440 1443 1446 1449 1452 1455 1458 1461 1464 1467 1470 1473 1476 1479 1482 1485 1488 1491 1494 1497 1500 1503 1506 1509 1512 1515 1518 1521 1524 1527 1530 1533, 2: 1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70 73 76 79 82 85 88 91 94 97 100 103 106 109 112 115 118 121 124 127 130 133 136 139 142 145 148 151 154 157 160 163 166 169 172 175 178 181 184 187 190 193 196 199 202 205 208 211 214 217 220 223 226 229 232 235 238 241 244 247 250 253 256 259 262 265 268 271 274 277 280 283 286 289 292 295 298 301 304 307 310 313 316 319 322 325 328 331 334 337 340 343 346 349 352 355 358 361 364 367 370 373 376 379 382 385 388 391 394 397 400 403 406 409 412 415 418 421 424 427 430 433 436 439 442 445 448 451 454 457 460 463 466 469 472 475 478 481 484 487 490 493 496 499 502 505 508 511 514 517 520 523 526 529 532 535 538 541 544 547 550 553 556 559 562 565 568 571 574 577 580 583 586 589 592 595 598 601 604 607 610 613 616 619 622 625 628 631 634 637 640 643 646 649 652 655 658 661 664 667 670 673 676 679 682 685 688 691 694 697 700 703 706 709 712 715 718 721 724 727 730 733 736 739 742 745 748 751 754 757 760 763 766 769 772 775 778 781 784 787 790 793 796 799 802 805 808 811 814 817 820 823 826 829 832 835 838 841 844 847 850 853 856 859 862 865 868 871 874 877 880 883 886 889 892 895 898 901 904 907 910 913 916 919 922 925 928 931 934 937 940 943 946 949 952 955 958 961 964 967 970 973 976 979 982 985 988 991 994 997 1000 1003 1006 1009 1012 1015 1018 1021 1024 1027 1030 1033 1036 1039 1042 1045 1048 1051 1054 1057 1060 1063 1066 1069 1072 1075 1078 1081 1084 1087 1090 1093 1096 1099 1102 1105 1108 1111 1114 1117 1120 1123 1126 1129 1132 1135 1138 1141 1144 1147 1150 1153 1156 1159 1162 1165 1168 1171 1174 1177 1180 1183 1186 1189 1192 1195 1198 1201 1204 1207 1210 1213 1216 1219 1222 1225 1228 1231 1234 1237 1240 1243 1246 1249 1252 1255 1258 1261 1264 1267 1270 1273 1276 1279 1282 1285 1288 1291 1294 1297 1300 1303 1306 1309 1312 1315 1318 1321 1324 1327 1330 1333 1336 1339 1342 1345 1348 1351 1354 1357 1360 1363 1366 1369 1372 1375 1378 1381 1384 1387 1390 1393 1396 1399 1402 1405 1408 1411 1414 1417 1420 1423 1426 1429 1432 1435 1438 1441 1444 1447 1450 1453 1456 1459 1462 1465 1468 1471 1474 1477 1480 1483 1486 1489 1492 1495 1498 1501 1504 1507 1510 1513 1516 1519 1522 1525 1528 1531, 3: 2 5 8 11 14 17 20 23 26 29 32 35 38 41 44 47 50 53 56 59 62 65 68 71 74 77 80 83 86 89 92 95 98 101 104 107 110 113 116 119 122 125 128 131 134 137 140 143 146 149 152 155 158 161 164 167 170 173 176 179 182 185 188 191 194 197 200 203 206 209 212 215 218 221 224 227 230 233 236 239 242 245 248 251 254 257 260 263 266 269 272 275 278 281 284 287 290 293 296 299 302 305 308 311 314 317 320 323 326 329 332 335 338 341 344 347 350 353 356 359 362 365 368 371 374 377 380 383 386 389 392 395 398 401 404 407 410 413 416 419 422 425 428 431 434 437 440 443 446 449 452 455 458 461 464 467 470 473 476 479 482 485 488 491 494 497 500 503 506 509 512 515 518 521 524 527 530 533 536 539 542 545 548 551 554 557 560 563 566 569 572 575 578 581 584 587 590 593 596 599 602 605 608 611 614 617 620 623 626 629 632 635 638 641 644 647 650 653 656 659 662 665 668 671 674 677 680 683 686 689 692 695 698 701 704 707 710 713 716 719 722 725 728 731 734 737 740 743 746 749 752 755 758 761 764 767 770 773 776 779 782 785 788 791 794 797 800 803 806 809 812 815 818 821 824 827 830 833 836 839 842 845 848 851 854 857 860 863 866 869 872 875 878 881 884 887 890 893 896 899 902 905 908 911 914 917 920 923 926 929 932 935 938 941 944 947 950 953 956 959 962 965 968 971 974 977 980 983 986 989 992 995 998 1001 1004 1007 1010 1013 1016 1019 1022 1025 1028 1031 1034 1037 1040 1043 1046 1049 1052 1055 1058 1061 1064 1067 1070 1073 1076 1079 1082 1085 1088 1091 1094 1097 1100 1103 1106 1109 1112 1115 1118 1121 1124 1127 1130 1133 1136 1139 1142 1145 1148 1151 1154 1157 1160 1163 1166 1169 1172 1175 1178 1181 1184 1187 1190 1193 1196 1199 1202 1205 1208 1211 1214 1217 1220 1223 1226 1229 1232 1235 1238 1241 1244 1247 1250 1253 1256 1259 1262 1265 1268 1271 1274 1277 1280 1283 1286 1289 1292 1295 1298 1301 1304 1307 1310 1313 1316 1319 1322 1325 1328 1331 1334 1337 1340 1343 1346 1349 1352 1355 1358 1361 1364 1367 1370 1373 1376 1379 1382 1385 1388 1391 1394 1397 1400 1403 1406 1409 1412 1415 1418 1421 1424 1427 1430 1433 1436 1439 1442 1445 1448 1451 1454 1457 1460 1463 1466 1469 1472 1475 1478 1481 1484 1487 1490 1493 1496 1499 1502 1505 1508 1511 1514 1517 1520 1523 1526 1529 1532;
+CODONPOSSET CodonPositions = 1: 3 6 9 12 15 18 21 24 27 30 33 36 39 42 45 48 51 54 57 60 63 66 69 72 75 78 81 84 87 90 93 96 99 102 105 108 111 114 117 120 123 126 129 132 135 138 141 144 147 150 153 156 159 162 165 168 171 174 177 180 183 186 189 192 195 198 201 204 207 210 213 216 219 222 225 228 231 234 237 240 243 246 249 252 255 258 261 264 267 270 273 276 279 282 285 288 291 294 297 300 303 306 309 312 315 318 321 324 327 330 333 336 339 342 345 348 351 354 357 360 363 366 369 372 375 378 381 384 387 390 393 396 399 402 405 408 411 414 417 420 423 426 429 432 435 438 441 444 447 450 453 456 459 462 465 468 471 474 477 480 483 486 489 492 495 498 501 504 507 510 513 516 519 522 525 528 531 534 537 540 543 546 549 552 555 558 561 564 567 570 573 576 579 582 585 588 591 594 597 600 603 606 609 612 615 618 621 624 627 630 633 636 639 642 645 648 651 654 657 660 663 666 669 672 675 678 681 684 687 690 693 696 699 702 705 708 711 714 717 720 723 726 729 732 735 738 741 744 747 750 753 756 759 762 765 768 771 774 777 780 783 786 789 792 795 798 801 804 807 810 813 816 819 822 825 828 831 834 837 840 843 846 849 852 855 858 861 864 867 870 873 876 879 882 885 888 891 894 897 900 903 906 909 912 915 918 921 924 927 930 933 936 939 942 945 948 951 954 957 960 963 966 969 972 975 978 981 984 987 990 993 996 999 1002 1005 1008 1011 1014 1017 1020 1023 1026 1029 1032 1035 1038 1041 1044 1047 1050 1053 1056 1059 1062 1065 1068 1071 1074 1077 1080 1083 1086 1089 1092 1095 1098 1101 1104 1107 1110 1113 1116 1119 1122 1125 1128 1131 1134 1137 1140 1143 1146 1149 1152 1155 1158 1161 1164 1167 1170 1173 1176 1179 1182 1185 1188 1191 1194 1197 1200 1203 1206 1209 1212 1215 1218 1221 1224 1227 1230 1233 1236 1239 1242 1245 1248 1251 1254 1257 1260 1263 1266 1269 1272 1275 1278 1281 1284 1287 1290 1293 1296 1299 1302 1305 1308 1311 1314 1317 1320 1323 1326 1329 1332 1335 1338 1341 1344 1347 1350 1353 1356 1359 1362 1365 1368 1371 1374 1377 1380 1383 1386 1389 1392 1395 1398 1401 1404 1407 1410 1413 1416 1419 1422 1425 1428 1431 1434 1437 1440 1443 1446 1449 1452 1455 1458 1461 1464 1467 1470 1473 1476 1479 1482 1485 1488 1491 1494 1497 1500 1503 1506 1509 1512 1515 1518 1521 1524 1527 1530 1533, 2: 1 4 7 10 13 16 19 22 25 28 31 34 37 40 43 46 49 52 55 58 61 64 67 70 73 76 79 82 85 88 91 94 97 100 103 106 109 112 115 118 121 124 127 130 133 136 139 142 145 148 151 154 157 160 163 166 169 172 175 178 181 184 187 190 193 196 199 202 205 208 211 214 217 220 223 226 229 232 235 238 241 244 247 250 253 256 259 262 265 268 271 274 277 280 283 286 289 292 295 298 301 304 307 310 313 316 319 322 325 328 331 334 337 340 343 346 349 352 355 358 361 364 367 370 373 376 379 382 385 388 391 394 397 400 403 406 409 412 415 418 421 424 427 430 433 436 439 442 445 448 451 454 457 460 463 466 469 472 475 478 481 484 487 490 493 496 499 502 505 508 511 514 517 520 523 526 529 532 535 538 541 544 547 550 553 556 559 562 565 568 571 574 577 580 583 586 589 592 595 598 601 604 607 610 613 616 619 622 625 628 631 634 637 640 643 646 649 652 655 658 661 664 667 670 673 676 679 682 685 688 691 694 697 700 703 706 709 712 715 718 721 724 727 730 733 736 739 742 745 748 751 754 757 760 763 766 769 772 775 778 781 784 787 790 793 796 799 802 805 808 811 814 817 820 823 826 829 832 835 838 841 844 847 850 853 856 859 862 865 868 871 874 877 880 883 886 889 892 895 898 901 904 907 910 913 916 919 922 925 928 931 934 937 940 943 946 949 952 955 958 961 964 967 970 973 976 979 982 985 988 991 994 997 1000 1003 1006 1009 1012 1015 1018 1021 1024 1027 1030 1033 1036 1039 1042 1045 1048 1051 1054 1057 1060 1063 1066 1069 1072 1075 1078 1081 1084 1087 1090 1093 1096 1099 1102 1105 1108 1111 1114 1117 1120 1123 1126 1129 1132 1135 1138 1141 1144 1147 1150 1153 1156 1159 1162 1165 1168 1171 1174 1177 1180 1183 1186 1189 1192 1195 1198 1201 1204 1207 1210 1213 1216 1219 1222 1225 1228 1231 1234 1237 1240 1243 1246 1249 1252 1255 1258 1261 1264 1267 1270 1273 1276 1279 1282 1285 1288 1291 1294 1297 1300 1303 1306 1309 1312 1315 1318 1321 1324 1327 1330 1333 1336 1339 1342 1345 1348 1351 1354 1357 1360 1363 1366 1369 1372 1375 1378 1381 1384 1387 1390 1393 1396 1399 1402 1405 1408 1411 1414 1417 1420 1423 1426 1429 1432 1435 1438 1441 1444 1447 1450 1453 1456 1459 1462 1465 1468 1471 1474 1477 1480 1483 1486 1489 1492 1495 1498 1501 1504 1507 1510 1513 1516 1519 1522 1525 1528 1531, 3: 2 5 8 11 14 17 20 23 26 29 32 35 38 41 44 47 50 53 56 59 62 65 68 71 74 77 80 83 86 89 92 95 98 101 104 107 110 113 116 119 122 125 128 131 134 137 140 143 146 149 152 155 158 161 164 167 170 173 176 179 182 185 188 191 194 197 200 203 206 209 212 215 218 221 224 227 230 233 236 239 242 245 248 251 254 257 260 263 266 269 272 275 278 281 284 287 290 293 296 299 302 305 308 311 314 317 320 323 326 329 332 335 338 341 344 347 350 353 356 359 362 365 368 371 374 377 380 383 386 389 392 395 398 401 404 407 410 413 416 419 422 425 428 431 434 437 440 443 446 449 452 455 458 461 464 467 470 473 476 479 482 485 488 491 494 497 500 503 506 509 512 515 518 521 524 527 530 533 536 539 542 545 548 551 554 557 560 563 566 569 572 575 578 581 584 587 590 593 596 599 602 605 608 611 614 617 620 623 626 629 632 635 638 641 644 647 650 653 656 659 662 665 668 671 674 677 680 683 686 689 692 695 698 701 704 707 710 713 716 719 722 725 728 731 734 737 740 743 746 749 752 755 758 761 764 767 770 773 776 779 782 785 788 791 794 797 800 803 806 809 812 815 818 821 824 827 830 833 836 839 842 845 848 851 854 857 860 863 866 869 872 875 878 881 884 887 890 893 896 899 902 905 908 911 914 917 920 923 926 929 932 935 938 941 944 947 950 953 956 959 962 965 968 971 974 977 980 983 986 989 992 995 998 1001 1004 1007 1010 1013 1016 1019 1022 1025 1028 1031 1034 1037 1040 1043 1046 1049 1052 1055 1058 1061 1064 1067 1070 1073 1076 1079 1082 1085 1088 1091 1094 1097 1100 1103 1106 1109 1112 1115 1118 1121 1124 1127 1130 1133 1136 1139 1142 1145 1148 1151 1154 1157 1160 1163 1166 1169 1172 1175 1178 1181 1184 1187 1190 1193 1196 1199 1202 1205 1208 1211 1214 1217 1220 1223 1226 1229 1232 1235 1238 1241 1244 1247 1250 1253 1256 1259 1262 1265 1268 1271 1274 1277 1280 1283 1286 1289 1292 1295 1298 1301 1304 1307 1310 1313 1316 1319 1322 1325 1328 1331 1334 1337 1340 1343 1346 1349 1352 1355 1358 1361 1364 1367 1370 1373 1376 1379 1382 1385 1388 1391 1394 1397 1400 1403 1406 1409 1412 1415 1418 1421 1424 1427 1430 1433 1436 1439 1442 1445 1448 1451 1454 1457 1460 1463 1466 1469 1472 1475 1478 1481 1484 1487 1490 1493 1496 1499 1502 1505 1508 1511 1514 1517 1520 1523 1526 1529 1532;
+
+CODESET * UNTITLED = universal: 1 - 1533;
+
+
+END;
+
+BEGIN paup;
+ outgroup Bemb_californicum_CA_1451 Bemb_concolor_NS_1470;
+
+END;
+BEGIN ASSUMPTIONS;
+ OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 1533;
+
+ EXSET * UNTITLED = 1 - 50 1479 - 1533;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 1533;
+END;
+
+BEGIN MacClade;
+ Version 4.0 87;
+ LastModified -1071261665;
+ FileSettings editor '0' '0' '1' '1';
+ Singles 000;
+ Editor 00011001110111100100010111 '4' '8' Geneva '9' '216' '1' all;
+ EditorPosition '70' '118' '643' '999';
+ TreeWindowPosition '46' '6' '809' '1230';
+ ListWindow Characters closed Geneva '9' '70' '45' '129' '406' 000;
+ ListWindow Taxa closed Geneva '9' '50' '10' '276' '490' 100000000;
+ ListWindow Trees closed Geneva '9' '50' '10' '276' '490';
+ ListWindow TypeSets closed Geneva '9' '50' '10' '276' '490';
+ ListWindow WtSets closed Geneva '9' '50' '10' '276' '490';
+ ListWindow ExSets closed Geneva '9' '50' '10' '276' '490';
+ ListWindow CharSets closed Geneva '9' '50' '10' '276' '490';
+ ListWindow TaxSets closed Geneva '9' '50' '10' '276' '490';
+ ListWindow CharPartitions closed Geneva '9' '50' '10' '276' '490';
+ ListWindow CharPartNames closed Geneva '9' '50' '10' '276' '490';
+ ListWindow WtSets closed Geneva '9' '50' '10' '276' '490';
+ ChartWindowPosition '52' '30' '772' '1220';
+ StateNamesSymbols closed Geneva '9' '10' '50' '30' '148' '220';
+ WindowOrder Data;
+ OtherSymbols & / 00 ? -;
+ Correlation '0' '0' '1000' '0' '0' 10011010;
+ Salmo 00000001;
+ EditorFile '4';
+ ExportHTML _ MOSS '100' 110000;
+ PrettyPrint 10;
+ EditorToolsPosition '720' '44' '115' '165';
+ TreeWindowProgram 10;
+ TreeWindow 0000;
+ Continuous '0' '3' 1;
+ Calculations 0000001;
+ SummaryMode '0' '0' 0;
+ Charts Geneva '9' ( normal ) 0010;
+ NexusOptions '0' '0' '50' 001011011;
+ TipLabel '1';
+ TreeFont Geneva '9' ( normal );
+ TreeShape 1.0 1.0 0100;
+ TraceLabels 0101;
+ ChartColors '0' '0' '65535' '9' '0' 1;
+ ChartBiggestSpot 1;
+ ChartPercent 10;
+ ChartBarWidth '10' 1;
+ ChartVerticalAxis 10101;
+ ChartMinMax '0';
+ TraceAllChangesDisplay '1' 1;
+ BarsOnBranchesDisplay '0' '0' '60000' '10000' '10000' '10000' '10000' '60000' '65000' '65000' '65000' '6' '1' 0000101;
+ ContinuousBranchLabels 0;
+ AllStatesBranchLabels 1;
+ IndexNotation '2' 1;
+ PrintTree 10.00 '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' '2' Geneva '9' ( normal ) Geneva '10' ( normal ) Geneva '9' ( normal ) Geneva '9' ( normal ) Geneva '9' ( bold ) Geneva '9' ( normal ) Geneva '9' ( normal ) '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '0' '1' '1' '1' '1' '0' '0' '-39' '4' '-40' '0' '1' '2' '1' '8' '0' '0' '0' '2' 1000111000000000000100000111000;
+ MatchChar 00 .;
+ EntryInterpretation 01;
+ ColorOptions 00;
+ TreeTools '0' '5' '4' '0' '10' '4' '0' 00100111111101110;
+ EditorTools '0' '0' '0' '1000' '0' '0' '6' '3' '0' 100010101110001;
+ PairAlign '2' '2' '3' '2' '1' '1' '2' '1' '3' 1010;
+ BothTools '1';
+
+END;
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6370606309008394174;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 6733066121074379816;
+ checksum 0 2978122628;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #6733066121074379816 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setSize 1484 556;
+ setLocation 60 22;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ setTool mesquite.align.AlignToDropped.AlignToDropped.alignToDropped;
+ endTell;
+ setActive;
+ setTool mesquite.align.AlignToDropped.AlignToDropped.alignToDropped;
+ colorCells #mesquite.charMatrices.ColorByState.ColorByState;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges off;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames off;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
+ tell It;
+ gapCosts 8 3;
+ endTell;
+ endTell;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/mesquite/align/Notes/prot.nex
===================================================================
--- trunk/treebase-core/lib/mesquite/align/Notes/prot.nex (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/Notes/prot.nex 2009-12-15 18:37:06 UTC (rev 380)
@@ -0,0 +1,153 @@
+#NEXUS
+[written Sun Apr 30 12:16:37 MST 2006 by Mesquite version 1.06+ (build h57) at david-maddisons-computer.local/192.168.0.4]
+
+BEGIN TAXA;
+ TITLE Untitled_Taxa_Block;
+ DIMENSIONS NTAX=3;
+ TAXLABELS
+ taxon_1 taxon_2 taxon_3
+ ;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE Untitled_Character_Matrix;
+ DIMENSIONS NCHAR=15;
+ FORMAT DATATYPE = Protein GAP = - MISSING = ?;
+ MATRIX
+ taxon_1 AGVLTT--GGVL---
+
+ taxon_2 HGEQPGVLTTGGMNI
+
+ taxon_3 MFGATACCTCEQRDM
+
+
+;
+
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 15;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 15;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 15;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 5649887706477911529;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 5596208106298272285;
+ checksum 0 3074286207;
+ endTell;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ showTaxa #5649887706477911529 #mesquite.lists.TaxonList.TaxonList;
+ tell It;
+ setTaxa #5649887706477911529;
+ getWindow;
+ tell It;
+ newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder;
+ newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
+ setSize 360 400;
+ setLocation 60 22;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #5596208106298272285 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setSize 699 286;
+ setLocation 113 176;
+ setFont SanSerif;
+ setFontSize 10;
+ onInfoBar;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
+ endTell;
+ setActive;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.ibeam;
+ colorCells #mesquite.charMatrices.ColorByState.ColorByState;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWithCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ getEmployee #mesquite.align.AlignToDropped.AlignToDropped;
+ tell It;
+ gapCosts 8 3;
+ endTell;
+ endTell;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/mesquite/align/RemoveAllGaps/RemoveAllGaps.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/RemoveAllGaps/RemoveAllGaps.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/ShiftOtherToMatch/ShiftOtherToMatch.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ShiftToMinimizeStops/ShiftToMinimizeStops.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/ShiftToMinimizeStops/ShiftToMinimizeStops.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/SidePusher.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/SidePusher.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab32.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab32.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab64.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/leftGrab64.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab32.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab32.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab64.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/rightGrab64.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft32.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft32.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft64.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockLeft64.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight32.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight32.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight64.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SidePusher/splitBlockRight64.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover32.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover32.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover64.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/BlockMover64.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/SimpleBlockMover.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/SimpleBlockMover.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock32.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock32.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock64.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/SimpleBlockMover/splitBlock64.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ZapGaps/ZapGaps.class
===================================================================
(Binary files differ)
Property cha...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-15 18:35:51
|
Revision: 379
http://treebase.svn.sourceforge.net/treebase/?rev=379&view=rev
Author: rvos
Date: 2009-12-15 18:35:41 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/mesquite/
trunk/treebase-core/lib/mesquite/align/
trunk/treebase-core/lib/mesquite/align/AlignDNAToProtein/
trunk/treebase-core/lib/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.class
trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxon/
trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxon/AlignScoreForTaxon.class
trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxonRC/
trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxonRC/AlignScoreForTaxonRC.class
trunk/treebase-core/lib/mesquite/align/AlignSequences/
trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignSequences.class
trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignThread.class
trunk/treebase-core/lib/mesquite/align/AlignToDropped/
trunk/treebase-core/lib/mesquite/align/AlignToDropped/AlignToDropped.class
trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped.gif
trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped32.gif
trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped64.gif
trunk/treebase-core/lib/mesquite/align/ClustalAlign/
trunk/treebase-core/lib/mesquite/align/ClustalAlign/ClustalAlign.class
trunk/treebase-core/lib/mesquite/align/ColorForAlignment/
trunk/treebase-core/lib/mesquite/align/ColorForAlignment/ColorForAlignment.class
trunk/treebase-core/lib/mesquite/align/ColorMisaligned/
trunk/treebase-core/lib/mesquite/align/ColorMisaligned/ColorMisaligned.class
trunk/treebase-core/lib/mesquite/align/aAlignIntro/
trunk/treebase-core/lib/mesquite/align/aAlignIntro/Templates/
trunk/treebase-core/lib/mesquite/align/aAlignIntro/Templates/standard.dwt
trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/
trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/2col_leftNav.css.mno
trunk/treebase-core/lib/mesquite/align/aAlignIntro/aAlignIntro.class
trunk/treebase-core/lib/mesquite/align/aAlignIntro/acknowledgements.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/additions.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/automated.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/citation.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/colorMisaligned.jpg
trunk/treebase-core/lib/mesquite/align/aAlignIntro/faq.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/future.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/BlockMover.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/alignToDropped.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/email.jpg
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/leftGrab.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/mesquiteIcon.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/rightGrab.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/splashAlign.psd
trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/splashAlign2.psd
trunk/treebase-core/lib/mesquite/align/aAlignIntro/index.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/manualAlignment.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/overview.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/sourceCode.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/splash.gif
trunk/treebase-core/lib/mesquite/align/aAlignIntro/statistics.html
trunk/treebase-core/lib/mesquite/align/aAlignIntro/styles/
trunk/treebase-core/lib/mesquite/align/aAlignIntro/styles/mesquitePackage.css
trunk/treebase-core/lib/mesquite/align/aAlignIntro/visualization.html
Added: trunk/treebase-core/lib/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignDNAToProtein/AlignDNAToProtein.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxon/AlignScoreForTaxon.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxon/AlignScoreForTaxon.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxonRC/AlignScoreForTaxonRC.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignScoreForTaxonRC/AlignScoreForTaxonRC.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignSequences.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignSequences.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignThread.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignSequences/AlignThread.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignToDropped/AlignToDropped.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignToDropped/AlignToDropped.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped32.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped32.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped64.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/AlignToDropped/alignToDropped64.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ClustalAlign/ClustalAlign.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/ClustalAlign/ClustalAlign.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ColorForAlignment/ColorForAlignment.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/ColorForAlignment/ColorForAlignment.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/ColorMisaligned/ColorMisaligned.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/ColorMisaligned/ColorMisaligned.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/Templates/standard.dwt
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/Templates/standard.dwt (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/Templates/standard.dwt 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,58 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- TemplateBeginEditable name="doctitle" -->
+<title>Untitled Document</title>
+<!-- TemplateEndEditable -->
+<link rel="stylesheet" href="../styles/mesquitePackage.css" type="text/css">
+<!-- TemplateBeginEditable name="head" --><!-- TemplateEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="../splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- TemplateBeginEditable name="subtitle" -->subtitle<!-- TemplateEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- TemplateBeginEditable name="content" -->content<!-- TemplateEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="../index.html">Home</a></li>
+ <li><a href="../manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="../automated.html">Automated Alignment</a></li>
+ <li><a href="../visualization.html">Visualization Features</a></li>
+ <li><a href="../statistics.html">Statistics</a></li>
+ <li><a href="../citation.html">Citation</a></li>
+ <li><a href="../faq.html">FAQs</a></li>
+ <li><a href="../future.html">Future Directions</a></li>
+ <li><a href="../acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="../sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="../images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+</html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/2col_leftNav.css.mno
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/2col_leftNav.css.mno (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/2col_leftNav.css.mno 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,4 @@
+<?xml version="1.0" encoding="utf-8" ?>
+<info>
+ <infoitem key="mm_new_doc_type" value="exclude" />
+</info>
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/_notes/2col_leftNav.css.mno
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/aAlignIntro.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/aAlignIntro.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/acknowledgements.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/acknowledgements.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/acknowledgements.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,60 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Acknowledgements</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Acknowledgements<!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p>We can't really think of anyone to thank at the moment. </p>
+ <!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/additions.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/additions.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/additions.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,52 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+<html>
+<head>
+<title>Untitled Document</title>
+<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
+</head>
+
+<body>
+<h3>Coloring Cells for Alignment</h3>
+<p>Manual alignment can be made easier by appropriate choice of a method to color
+ cells. You can set the method to color cells using the Matrix>Color cells
+ submenu. Three useful methods are:</p>
+<ul>
+ <li><strong>Character State</strong> — This colors cells according to
+ nucleotide. This is the default coloring, but in case it has been turned off,
+ you can turn it back on by going to Matrix>Color Cells>Character State.</li>
+ <li><strong>Aligning Colors</strong> — This colors pyrimidines by similar
+ colors, and likewise purines</li>
+ <li><strong>Highlight Apparently Slightly Misaligned</strong> — This highlights
+ subsequences that appear better shifted one or two sites left or right:<br>
+ <img src="colorMisaligned.jpg" width="249" height="252"> <br>
+ It bases its calculations on the dominant nucleotides in the columns, and
+ hence is useful only in a matrix that is mostly well aligned. Shifts more
+ distant than one or two sites are not considered. Do not consider this a definitive
+ indication that the cells should move; its purpose is only to help you find
+ possible issues, but the decision as to whether to shift or not is still up
+ to you. The highlight does not specify which direction the subsequences might
+ be best shifted; to learn this, hold the cursor over the sites in question.</li>
+</ul>
+<h3>Selecting Hint</h3>
+<p>To select from one cell to the end of the sequence, select the cell and then
+ hit Shift-Alt-Arrow key (or, on OS X, Shift-Option-Arrow key), where the arrow
+ key is either the right or left arrow key.</p>
+<h3>Preparing the Matrix</h3>
+<p>Several options under Matrix>Alter/Transform may be useful to modify the
+ matrix in preparation for alignment. Some of these options are under "Other
+ Choices...".</p>
+<ul>
+ <li>Collapse Gaps to Left</li>
+ <li>Collapse Gaps to Right</li>
+ <li>Trim Terminal Gaps Character</li>
+ <li>Gaps to Missing </li>
+ <li>Missing to Gaps</li>
+ <li>Terminal Gaps to ?</li>
+ <li>Terminal ? to Gaps</li>
+ <li>Reverse Complement</li>
+ <li>Reverse</li>
+ <li>Nucleotide Complement</li>
+</ul>
+<p> </p>
+</body>
+</html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/automated.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/automated.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/automated.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,110 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Automated Alignment Tools</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Automated Alignment <!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <h3><img src="images/alignToDropped.gif" alt="Pairwise Aligner" width="16" height="16">Pairwise Alignment tool </h3>
+ <p>This tool allows one to drop one or a selected set of sequences onto a reference sequence; the sequences dropped will then be aligned to the reference sequence, preserving whatever gaps are present in the reference sequence. In the process, if gaps need to be inserted into the reference sequence, then they will be also inserted into other, non-selected sequences. </p>
+ <p>The dropdown menu for this tool allows you to change the gap opening cost (default
+ 8) the gap extension cost (default 3) within bases of a sequences, as well
+ as the equivalent costs at the ends of the sequence (default 2 and 2, respectively). </p>
+ <p>The default substitution costs
+ are:</p>
+ <ul>
+ <li>for DNA and RNA data, 5 for a transition and 10 for a transversion</li>
+ <li>for protein data, 5 for each substitution.</li>
+ </ul>
+ <p>These costs can be changed using the Substitution Costs dialog box available from the tool's dropdown menu.</p>
+
+
+ <h3>Aligning nucleotide sequences to match an amino acid alignment </h3>
+ <p>This feature allows one to take a matrix of nucleotides, and an existing alignment of their translated amino acids, and have the nucleotides realigned to match the amino acid alignment.
+ To do this, you will need to have in the same Mesquite file both the nucleotide matrix and the protein matrix. For example, you could do the following: </p>
+ <ul>
+ <li>Assign codon positions and genetic code to a nucleotide matrix (see the main Mesquite manual for details).</li>
+ <li>Adjust each sequence so that its reading frame is correct, by using the <a href="manualAlignment.html#shiftMinStops">Shift To Minimize Stops</a> feature.</li>
+ <li>Trim any incomplete codons from the ends of the sequences by selecting the
+ entire matrix and choosing <font size="-1"><u>Matrix>Alter/Transform>Other
+ Choices</u></font>... and selecting
+ Trim Terminal Incomplete Codons. "Terminal Incomplete Codons" are nucleotides
+ that are only part of a codon. For example, if one sequence starts at a third
+ position, then that third position nucleotide represents only one-third of a
+ codon, and it will be trimmed. Once this is done, only complete codons will
+ be left in the sequence </li>
+ <li>Translate the DNA matrix to amino acids by choosing <font size="-1"><u>Characters>Make New Matrix From>Translate
+ DNA To Protein</u></font>. You will now have the protein matrix in your file.</li>
+
+ <li>Align the protein matrix. You could use, for example, the Clustal Align
+ feature described below. If instead you export the matrix (e.g., using
+ the <u><font size="-1">File>Export</font></u> options), align the proteins in a separate program, you
+ will then need to choose <u><font size="-1">File>Include</font></u> file to include the output of the
+ alignment program into your file.</li>
+ <li>Finally, go to your DNA matrix, and choose <font size="-1"><u>Matrix>Alter/Transform>Align
+ DNA to Protein</u></font>. </li>
+ </ul>
+
+ <h3>ClustalW Align </h3>
+ <p>This feature allows one to select a single block of sequences, and then have ClustalW align them. To do this, select the block, then choose Matrix>Align Multiple Sequences>Clustal Align... </p>
+ <p>You will be presented first with a query as to whether you want to do the ClustalW alignment on a separate thread, or on the same thread. Mesquite can do multiple things at once, because it can have one thing running on one computational "thread", and another thing happening on a separate thread. There is a main thread of the program that is the thread the user deals with directly, and that allows you to give commands to Mesquite (via menus, etc.). If this main thread is busy with a calculation, then you will not be able to ask for new things to happen in Mesquite until the calculation is done. By choosing "Separate" in the query that appears, you are asking Mesquite to create a thread separate from the main thread, thus enabling you to do things in Mesquite while the Clustal alignment is proceeding. However, if you do this, you must remember not to edit the matrix or close the window showing the matrix; if you do, Mesquite will be very unhappy. The safest thing to do is choose "No" to that query. </p>
+ <p>Once you make that choice, you will see a dialog box in which you must enter the directory location of ClustalW; if you use the Browse button in the dialog box you can choose ClustalW and have the location filled in automatically. If you wish, you can also alter the options of clustalw. If you then press OK, Mesquite will send that section of the matrix to ClustalW and ask for it to be aligned; it will then harvest the results and reincorporate that piece into the matrix.</p>
+ <p>The version of ClustalW that is to be used by Mesquite <em>must</em> be a version of ClustalW that is executable from the command line of your operating system. </p>
+ <p> </p>
+
+ <h3>Muscle Align </h3>
+ <p>This tool is just like the ClustalW Align feature described above, except that it works for Robert C. Edgar's <a href="http://www.drive5.com/muscle/">MUSCLE</a> program. </p>
+ <p> </p>
+
+<!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/citation.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/citation.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/citation.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,64 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Untitled Document</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Citation<!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p><font face="Trebuchet MS">Align should be cited as:</font></p>
+ <p><font face="Trebuchet MS"><br />
+ Maddison, D.R., T.J. Wheeler, and W.P. Maddison. 2006. Align: a Mesquite
+ package for aligning sequence data. Version 1.0.<em> http://mesquiteproject.org</em></font></p>
+ <p> </p>
+ <!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/colorMisaligned.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/colorMisaligned.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/faq.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/faq.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/faq.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,65 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Frequently Asked Questions</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Frequently Asked Questions <!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p> </p>
+ <p>Q: Can I change the substitution costs used by the pairwise aligner tools? </p>
+ <p>A: Yes. You can now do this using the Substitution Costs menu item that
+ is available in the dropdown menu that appears if you touch down on the Pairwise
+ Aligner tool in the tool palette.</p>
+ <p> </p>
+<!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/future.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/future.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/future.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,68 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Future Directions</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Future Directions <!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p>In the future, we plan to:</p>
+ <ul>
+ <li>allow more control by the user over the alignment parameters used by the pairwise aligner</li>
+ <li>add various graphical features for aiding with alignment of ribosomal DNA</li>
+ <li>add more manual alignment tools, including a tools that lets one manipulate multiple sequences at once <br>
+ </li>
+ <li>add more features derived from the pairwise aligner calculations. </li>
+ </ul>
+ <h3> </h3>
+ <!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/BlockMover.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/BlockMover.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/alignToDropped.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/alignToDropped.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/email.jpg
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/email.jpg
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/leftGrab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/leftGrab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/mesquiteIcon.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/mesquiteIcon.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/rightGrab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/rightGrab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/splashAlign.psd
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/splashAlign.psd
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/splashAlign2.psd
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/images/splashAlign2.psd
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/index.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/index.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/index.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Mesquite: Chromaseq</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" -->
+<style type="text/css">
+<!--
+.style1 {
+ color: #009999;
+ font-weight: bold;
+}
+-->
+</style>
+<!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" --><!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <h2><font face="Trebuchet MS">Align: a Mesquite
+ package for aligning sequence data </font></h2>
+ <p>The Align package provides some basic tools involving alignment of sequence data. The Align package contains:</p>
+ <ul>
+ <li>Tools for <a href="manualAlignment.html">manual alignment</a>
+ <ul>
+ <li>a Move Blocks tool</li>
+ <li>a Push Sequence tool</li>
+ <li>commands to remove gaps <em>en masse</em> </li>
+ </ul>
+ </li>
+ <li>Tools for <a href="automated.html">automated alignment </a>
+ <ul>
+ <li>a Pairwise Aligner tool</li>
+ <li>the ability to have a nucleotide matrix realigned to match an amino acid alignment</li>
+ <li>the ability to send a block of the matrix to ClustalW or MUSCLE to align </li>
+ </ul>
+ </li>
+ <li>Various <a href="statistics.html">statistics</a> about taxa based about alignments
+ <ul>
+ <li>the alignment score of a taxon against a reference taxon</li>
+ <li>the ratio of the alignment score of a taxon and its reverse complement against a reference taxon; this allows one to quickly detect sequences that are reverse complements of others.</li>
+ </ul>
+ </li>
+ </ul>
+<!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/manualAlignment.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/manualAlignment.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/manualAlignment.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Manual Alignment Tools</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Manual Alignment <!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <h2>Moving bases by hand </h2>
+ <p>There are two tools available for moving bases by hand. One is the Move Blocks tool (<img src="images/BlockMover.gif" alt="Block Mover" width="16" height="16">), the other is the Push Sequence tool (<img src="images/rightGrab.gif" alt="Push Sequence" width="16" height="16">). </p>
+ <p>Both of these tools have a "Live update analyses, etc." option in their popup menus. If this is chosen, then all calculations (e.g., charts, character tracings, etc.) that depend upon these data will be redone <em>as you use</em> these tools. (Recalculations will be done once you let go of the mouse button, in any event.) If some of these calculations take a while, this can dramatically slow down use of these tools. </p>
+ <p>There are some <a href="visualization.html">visualization features</a> in Mesquite that can aid in manual
+ alignment.</p>
+ <h3><img src="images/BlockMover.gif" alt="Block Mover" width="16" height="16"> Move Blocks Tool </h3>
+ <p>This tool will move a contiguous block of a single sequence. If you move the tool between two bases it will let you split a block in two, inserting gaps. </p>
+ <p>If you wish, you can move more than a single, contiguous block by turning on "Move Selected Block" within the tool's popup menu, then using the tool to move selected bases and gaps. </p>
+ <h3><img src="images/rightGrab.gif" alt="Push Sequence" width="16" height="16"> Push Sequence Tool</h3>
+ <p>This tool pushes to the right the entire sequence to the right of the tool, or, if you have the Option key held down, it pushes to the left the entire sequence to the left of the tool. </p>
+ <h2>Shifting sequences </h2>
+ <p>Select a portion of a single sequence. If you then choose Matrix>Alter/Transform>Shift Other to Match..., then you will be presented with a dialog box that lets you choose a range of taxa, as well as a percentage. By default the range of taxa is the remaining taxa in the matrix. The default percentage is 75%. </p>
+ <p>If you press OK, Mesquite will look at each of the taxa within the range, and see if it can find a portion of each that is at least as similar as the percentage indicated to the selected portion (no gaps allowed). For each taxon that it can find such a match, it will shift those sequence such that the matched regions are lined up with the selected region. </p>
+ <p>Note that this is not an alignment algorithm; it simply shifts the sequences, maintaining whatever gaps are there or not in the sequences to be shifted. </p>
+ <p><a name="shiftMinStops"></a> You can also choose Matrix>Alter/Transform>Shift To Minimize Stop
+ Codons to shifts each <br>
+sequence 0, 1, or 2 bases so as to minimize the number of stop codons. The amount
+each sequence will be shifted will vary from sequence to sequence. This feature
+requires that codon
+positions be designated.</p>
+ <h2>Removal of Gaps</h2>
+ <h3>Remove All-Gap Characters </h3>
+ <p>Choosing this from Matrix>Alter/Transform>Remove All-Gap Characters will remove all sites in the matrix that consist entirely of gaps. </p>
+ <h3>Collapse Gaps </h3>
+ <p>With a block of the matrix selected, choosing Matrix>Alter/Transform>Collapse Gaps will remove all gaps in the selected block, with the bases or amino acids pushed as far to the left as possible. </p>
+<h2>Selecting Hint</h2>
+<p>To select from one cell to the end of the sequence, select the cell and then
+ hit Shift-Alt-Arrow key (or, on OS X, Shift-Option-Arrow key), where the arrow
+ key is either the right or left arrow key.</p>
+<h2>Preparing the Matrix</h2>
+<p>Several options under Matrix>Alter/Transform may be useful to modify the
+ matrix in preparation for alignment. Some of these options are under "Other
+ Choices...".</p>
+<ul>
+ <li>Collapse Gaps to Left</li>
+ <li>Collapse Gaps to Right</li>
+ <li>Trim Terminal Gaps Character</li>
+ <li>Gaps to Missing </li>
+ <li>Missing to Gaps</li>
+ <li>Terminal Gaps to ?</li>
+ <li>Terminal ? to Gaps</li>
+ <li>Reverse Complement</li>
+ <li>Reverse</li>
+ <li>Nucleotide Complement</li>
+</ul>
+<!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/overview.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/overview.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/overview.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,81 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Chromaseq Overview</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Overview<!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p>The Align package contains:</p>
+ <ul>
+ <li>Tools for <a href="manualAlignment.html">manual alignment</a>
+ <ul>
+ <li>a Move Blocks tool</li>
+ <li>a Push Sequence tool</li>
+ <li>commands to remove gaps <em>en masse</em> </li>
+ </ul>
+ </li>
+ <li>Tools for <a href="automated.html">automated alignment </a>
+ <ul>
+ <li>a Pairwise Aligner tool</li>
+ <li>the ability to send a block of the matrix to ClustalW to align </li>
+ </ul>
+ </li>
+ <li>Various <a href="statistics.html">statistics</a> about taxa based about alignments
+ <ul>
+ <li>the alignment score of a taxon against a reference taxon</li>
+ <li>the ratio of the alignment score of a taxon and its reverse complement against a reference taxon; this allows one to quickly detect sequences that are reverse complements of others. </li>
+ </ul>
+ </li>
+ </ul>
+ <!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/sourceCode.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/sourceCode.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/sourceCode.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,60 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Source Code</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Source Code<!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p><font face="Trebuchet MS">The source code for Align is distributed as part of the standard <a href="http://mesquiteproject.org/mesquite/download/source.html">source distribution</a> of Mesquite. </font></p>
+ <!-- InstanceEndEditable --></div>
+<!--end content -->
+<div id="navBar">
+ <div id="sectionLinks">
+ <ul>
+ <li><a href="index.html">Home</a></li>
+ <li><a href="manualAlignment.html">Manual Alignment</a></li>
+ <li><a href="automated.html">Automated Alignment</a></li>
+ <li><a href="visualization.html">Visualization Features</a></li>
+ <li><a href="statistics.html">Statistics</a></li>
+ <li><a href="citation.html">Citation</a></li>
+ <li><a href="faq.html">FAQs</a></li>
+ <li><a href="future.html">Future Directions</a></li>
+ <li><a href="acknowledgements.html">Acknowledgements</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><a href="sourceCode.html">Source Code</a></li>
+ <li style="margin-top: 20px;"></li>
+ <li><protectedURL>a href="../../../docs/mesquite/manual.html"</protectedURL>Mesquite Manual</a></li>
+ </ul>
+ <p> </p>
+ <ul><li> <a href="http://mesquiteproject.org" style="border: 0px;"><img src="images/mesquiteIcon.gif" alt="Mesquite Home" width="32" height="32"> Mesquite Home</a> </li>
+ </ul>
+ </div>
+</div>
+</div>
+<div id="navBarExtension"> </div>
+<!--end navbar -->
+<div id="siteInfo"> Copyright © 2007 <a href="http://david.bembidion.org">David
+R. Maddison, </a><a href="http://traviswheeler.com/">Travis J. Wheeler</a>, and <a href="http://salticidae.org/wpm/home.html">Wayne
+P. Maddison</a></div>
+<br>
+</body>
+<!-- InstanceEnd --></html>
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/splash.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/mesquite/align/aAlignIntro/splash.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/mesquite/align/aAlignIntro/statistics.html
===================================================================
--- trunk/treebase-core/lib/mesquite/align/aAlignIntro/statistics.html (rev 0)
+++ trunk/treebase-core/lib/mesquite/align/aAlignIntro/statistics.html 2009-12-15 18:35:41 UTC (rev 379)
@@ -0,0 +1,63 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+"http://www.w3.org/TR/html4/loose.dtd">
+<html><!-- InstanceBegin template="/Templates/standard.dwt" codeOutsideHTMLIsLocked="false" -->
+<head>
+<meta http-equiv="Content-Type" content="text/html; charset=">
+<!-- InstanceBeginEditable name="doctitle" -->
+<title>Alignment Statistics</title>
+<!-- InstanceEndEditable -->
+<link rel="stylesheet" href="styles/mesquitePackage.css" type="text/css">
+<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable -->
+</head>
+
+
+<body>
+<div id="masthead">
+ <div id="banner"><img src="splash.gif" width="164" height="64"></div>
+ <div id="mainTitle"><font id="packageName"><b>Align</b></font><font id="version"><br>
+ Version 1.11<br>
+ 20 November 2007</font><BR>
+ David R. Maddison, Travis J. Wheeler, and Wayne P. Maddison </div>
+ <div id="subtitle"><!-- InstanceBeginEditable name="subtitle" -->Statistics<!-- InstanceEndEditable --></div>
+
+</div>
+<div>
+<!-- end masthead -->
+<div id="content"><!-- InstanceBeginEditable name="content" -->
+ <p>Align provides two statistics that can be calculate for each taxon in a matrix.
+ </p>
+ <p>The first, the <strong>Alignment Score</strong>, is simply the "cost" of the alignment between that taxon and a reference sequence, using Mesquite's defau...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-15 18:16:38
|
Revision: 378
http://treebase.svn.sourceforge.net/treebase/?rev=378&view=rev
Author: rvos
Date: 2009-12-15 18:16:21 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/examples/Diversification/
trunk/treebase-core/lib/examples/Diversification/00-introduction.nex
trunk/treebase-core/lib/examples/Diversification/01-lineagesThroughTime.nex
trunk/treebase-core/lib/examples/Diversification/02-speciationExtinctionRates.nex
trunk/treebase-core/lib/examples/Diversification/03-sisterDiversification.nex
trunk/treebase-core/lib/examples/Diversification/04-BiSSEViewer.nex
trunk/treebase-core/lib/examples/Diversification/05-BiSSENetViewer.nex
trunk/treebase-core/lib/examples/Diversification/06-BiSSEtrees.nex
trunk/treebase-core/lib/examples/Diversification/07-contTreeSim.nex
trunk/treebase-core/lib/examples/Diversification/08-binaryTreeSim.nex
trunk/treebase-core/lib/examples/Introduction.nex
trunk/treebase-core/lib/examples/Molecular/
trunk/treebase-core/lib/examples/Molecular/00-introduction.nex
trunk/treebase-core/lib/examples/Molecular/01-gcContentChart.nex
trunk/treebase-core/lib/examples/Molecular/02-gcContentMatrix.nex
trunk/treebase-core/lib/examples/Molecular/03-gcContentBirdsEye.nex
trunk/treebase-core/lib/examples/Molecular/03a-cytochromeB.nex
trunk/treebase-core/lib/examples/Molecular/04-gcContentTaxa.nex
trunk/treebase-core/lib/examples/Molecular/05-gcContentTaxaExons.nex
trunk/treebase-core/lib/examples/Molecular/06-cytochromeB.nex
trunk/treebase-core/lib/examples/Molecular/07-cytochromeBHydro.nex
trunk/treebase-core/lib/examples/Molecular/08-cytochromeBlinked.nex
trunk/treebase-core/lib/examples/Molecular/09-cytochromeBscatter.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/
trunk/treebase-core/lib/examples/Multivariate_Continuous/00-introduction.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/01-wingsPlot.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/02-wingsPCA.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/03-wingsCVA.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/04-anoles.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/05-anoles.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/06-anoles.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/07-anoles.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/08-anoles.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/09-pcaSim.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/10-pcaLiveSim.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/11-cvaLiveSim.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/12-epca.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/13-epca.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/14-epca.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/15-epca.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/16-epcaLiveSim.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/17-landmarks.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/18-landmarks.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/19-landmarks.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/20-landmarks.nex
trunk/treebase-core/lib/examples/Multivariate_Continuous/epca/
trunk/treebase-core/lib/examples/Multivariate_Continuous/epca/Image1.gif
trunk/treebase-core/lib/examples/Multivariate_Continuous/epca/Image2.gif
trunk/treebase-core/lib/examples/Multivariate_Continuous/fish/
trunk/treebase-core/lib/examples/Multivariate_Continuous/fish/blue.gif
trunk/treebase-core/lib/examples/Multivariate_Continuous/fish/one.gif
trunk/treebase-core/lib/examples/Multivariate_Continuous/fish/red.gif
trunk/treebase-core/lib/examples/Multivariate_Continuous/fish/two.gif
trunk/treebase-core/lib/examples/Other_Examples/
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/01.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/02.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/03.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/04.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/05.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/06.concatenatingMatrices.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/07.mergedMatrix.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreDifferent/otherGeneMatrix.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreTheSame/
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreTheSame/01.concatenatingMatricesSimple.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreTheSame/02.concatenatingMatricesSimple.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreTheSame/03.concatenatingMatricesSimple.nex
trunk/treebase-core/lib/examples/Other_Examples/ConcatenatingMatrices/TaxonNamesAreTheSame/otherGeneMatrix.nex
Added: trunk/treebase-core/lib/examples/Diversification/00-introduction.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/00-introduction.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/00-introduction.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,33 @@
+#NEXUS
+[written Thu Sep 20 14:35:29 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium.local/192.168.0.3 (David Maddison)]
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '01-lineagesThroughTime.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 429 288;
+ setLocation 7 29;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'Phylogeny can be used to explore species diversification, speciation and extinction. Here are some example files of relevant Mesquite features.^n^nTo go from one file to another, hit the "Next" button';
+ setTitle Species_Diversification;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addFileLink Return_to_main_Introduction '../Introduction.nex';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Diversification/01-lineagesThroughTime.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/01-lineagesThroughTime.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/01-lineagesThroughTime.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,329 @@
+#NEXUS
+[written Thu Sep 20 16:42:25 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ taxon_1 taxon_2 taxon_3 taxon_4 taxon_5 taxon_6 taxon_7 taxon_8 taxon_9 taxon_10 taxon_11 taxon_12 taxon_13 taxon_14 taxon_15 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32
+ ;
+ IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
+ BLOCKID WM1148f47d2081;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "01-lineagesThroughTime.nex"';
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ taxon_1 0
+ taxon_2 1
+ taxon_3 0
+ taxon_4 0
+ taxon_5 0
+ taxon_6 1
+ taxon_7 0
+ taxon_8 1
+ taxon_9 1
+ taxon_10 1
+ taxon_11 1
+ taxon_12 1
+ taxon_13 1
+ taxon_14 1
+ taxon_15 1
+ taxon_16 1
+ taxon_17 1
+ taxon_18 0
+ taxon_19 1
+ taxon_20 0
+ taxon_21 0
+ taxon_22 0
+ taxon_23 1
+ taxon_24 1
+ taxon_25 1
+ taxon_26 1
+ taxon_27 1
+ taxon_28 1
+ taxon_29 1
+ taxon_30 1
+ taxon_31 1
+ taxon_32 0
+
+;
+ IDS WM1148f4828fe0 ;
+ BLOCKID WM114911738c20;
+
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1;
+
+
+END;
+
+BEGIN TREES;
+ Title 'Trees from "01-lineagesThroughTime.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 taxon_1,
+ 2 taxon_2,
+ 3 taxon_3,
+ 4 taxon_4,
+ 5 taxon_5,
+ 6 taxon_6,
+ 7 taxon_7,
+ 8 taxon_8,
+ 9 taxon_9,
+ 10 taxon_10,
+ 11 taxon_11,
+ 12 taxon_12,
+ 13 taxon_13,
+ 14 taxon_14,
+ 15 taxon_15,
+ 16 taxon_16,
+ 17 taxon_17,
+ 18 taxon_18,
+ 19 taxon_19,
+ 20 taxon_20,
+ 21 taxon_21,
+ 22 taxon_22,
+ 23 taxon_23,
+ 24 taxon_24,
+ 25 taxon_25,
+ 26 taxon_26,
+ 27 taxon_27,
+ 28 taxon_28,
+ 29 taxon_29,
+ 30 taxon_30,
+ 31 taxon_31,
+ 32 taxon_32;
+ TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6732219986260810463 WM1148f47d2081;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 444104661901299517 WM114911738c20;
+ checksum 0 909469476 WM114911738c20;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 786.1187814845004.4817563795317733133;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 833 341;
+ setLocation 386 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.SelectTaxaInClade.SelectTaxaToolExtra.SelectTaxa;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 2;
+ orientRight;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFontSize 9;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newWindowAssistant #mesquite.diverse.LineagesThroughTime.LineagesThroughTime;
+ tell It;
+ makeWindow;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 682 344;
+ setLocation 500 510;
+ setFont SanSerif;
+ setFontSize 10;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.charts.Histogram.Histogram;
+ tell It;
+ showAverageToggle on;
+ setCumulativeMode 0;
+ showAsBarChartToggle off;
+ showRawToggle off;
+ setNumberIntervals 20;
+ setIntervalSize 1.0;
+ setMovingWindowSize 5.0 1.0;
+ setMode 0;
+ endTell;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #444104661901299517 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 833 341;
+ setLocation 386 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ hideWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '02-speciationExtinctionRates.nex';
+ setPrevFileName '00-introduction.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 375 333;
+ setLocation 1 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'Availabe in the Analysis menu of the Tree Window is Lineages Through Time, which plots the logarithm of the number of lineages in a tree through time. With a pure birth process, one expects the plot to be a straight line.';
+ setTitle Lineages_Through_Time;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Diversification/02-speciationExtinctionRates.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/02-speciationExtinctionRates.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/02-speciationExtinctionRates.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,315 @@
+#NEXUS
+[written Thu Sep 20 16:42:34 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ taxon_1 taxon_2 taxon_3 taxon_4 taxon_5 taxon_6 taxon_7 taxon_8 taxon_9 taxon_10 taxon_11 taxon_12 taxon_13 taxon_14 taxon_15 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32
+ ;
+ IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
+ BLOCKID WM1148f47d2081;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "02-speciationExtinctionRates.nex"';
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ taxon_1 0
+ taxon_2 1
+ taxon_3 0
+ taxon_4 0
+ taxon_5 0
+ taxon_6 1
+ taxon_7 0
+ taxon_8 1
+ taxon_9 1
+ taxon_10 1
+ taxon_11 1
+ taxon_12 1
+ taxon_13 1
+ taxon_14 1
+ taxon_15 1
+ taxon_16 1
+ taxon_17 1
+ taxon_18 0
+ taxon_19 1
+ taxon_20 0
+ taxon_21 0
+ taxon_22 0
+ taxon_23 1
+ taxon_24 1
+ taxon_25 1
+ taxon_26 1
+ taxon_27 1
+ taxon_28 1
+ taxon_29 1
+ taxon_30 1
+ taxon_31 1
+ taxon_32 0
+
+;
+ IDS WM1148f4828fe0 ;
+ BLOCKID WM114910e80a10;
+
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1;
+
+
+END;
+
+BEGIN TREES;
+ Title 'Trees from "02-speciationExtinctionRates.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 taxon_1,
+ 2 taxon_2,
+ 3 taxon_3,
+ 4 taxon_4,
+ 5 taxon_5,
+ 6 taxon_6,
+ 7 taxon_7,
+ 8 taxon_8,
+ 9 taxon_9,
+ 10 taxon_10,
+ 11 taxon_11,
+ 12 taxon_12,
+ 13 taxon_13,
+ 14 taxon_14,
+ 15 taxon_15,
+ 16 taxon_16,
+ 17 taxon_17,
+ 18 taxon_18,
+ 19 taxon_19,
+ 20 taxon_20,
+ 21 taxon_21,
+ 22 taxon_22,
+ 23 taxon_23,
+ 24 taxon_24,
+ 25 taxon_25,
+ 26 taxon_26,
+ 27 taxon_27,
+ 28 taxon_28,
+ 29 taxon_29,
+ 30 taxon_30,
+ 31 taxon_31,
+ 32 taxon_32;
+ TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6732219986260810463 WM1148f47d2081;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 444104661901299517 WM114910e80a10;
+ checksum 0 909469476 WM114910e80a10;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 786.1187814845004.4817563795317733133;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1019 626;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.SelectTaxaInClade.SelectTaxaToolExtra.SelectTaxa;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 8;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newWindowAssistant #mesquite.diverse.CharIndepDivViewer.CharIndepDivViewer;
+ tell It;
+ setCalculator #mesquite.diverse.SpecExtincLikelihood.SpecExtincLikelihood;
+ tell It;
+ getIntegTask #mesquite.diverse.SpecExtincMLCalculator.SpecExtincMLCalculator;
+ tell It;
+ setUnderflowCheckFreq -1;
+ setStepCount 1000.0;
+ conditionOnSurvival off;
+ endTell;
+ setS ?;
+ setE ?;
+ endTell;
+ doCounts;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #444104661901299517 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1019 626;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ hideWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '03-sisterDiversification.nex';
+ setPrevFileName '01-lineagesThroughTime.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 623 267;
+ setLocation 33 631;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'A likelihood analysis can give estimates of speciation and extinction rates. Here a method reduced from Maddison, Midford & Otto''s BiSSE method is used to calculate likelihoods for a simple birth/death model, where lambda = birth = speciation rate, and mu = death = extinction rate.^n^nThis calculation is available as Diversification (Char. Indep.) in the Analysis menu of the Tree Window.';
+ setTitle Speciation_and_Extinction_Rates;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Diversification/03-sisterDiversification.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/03-sisterDiversification.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/03-sisterDiversification.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,346 @@
+#NEXUS
+[written Thu Sep 20 16:44:06 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ taxon_1 taxon_2 taxon_3 taxon_4 taxon_5 taxon_6 taxon_7 taxon_8 taxon_9 taxon_10 taxon_11 taxon_12 taxon_13 taxon_14 taxon_15 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32
+ ;
+ IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
+ BLOCKID WM1148f47d2081;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "03-sisterDiversification.nex"';
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ taxon_1 0
+ taxon_2 1
+ taxon_3 0
+ taxon_4 0
+ taxon_5 0
+ taxon_6 1
+ taxon_7 0
+ taxon_8 1
+ taxon_9 1
+ taxon_10 1
+ taxon_11 1
+ taxon_12 1
+ taxon_13 1
+ taxon_14 1
+ taxon_15 1
+ taxon_16 1
+ taxon_17 1
+ taxon_18 0
+ taxon_19 1
+ taxon_20 0
+ taxon_21 0
+ taxon_22 0
+ taxon_23 1
+ taxon_24 1
+ taxon_25 1
+ taxon_26 1
+ taxon_27 1
+ taxon_28 1
+ taxon_29 1
+ taxon_30 1
+ taxon_31 1
+ taxon_32 0
+
+;
+ IDS WM1148f4828fe0 ;
+ BLOCKID WM1149106b2f00;
+
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1;
+
+
+END;
+
+BEGIN TREES;
+ Title 'Trees from "03-sisterDiversification.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 taxon_1,
+ 2 taxon_2,
+ 3 taxon_3,
+ 4 taxon_4,
+ 5 taxon_5,
+ 6 taxon_6,
+ 7 taxon_7,
+ 8 taxon_8,
+ 9 taxon_9,
+ 10 taxon_10,
+ 11 taxon_11,
+ 12 taxon_12,
+ 13 taxon_13,
+ 14 taxon_14,
+ 15 taxon_15,
+ 16 taxon_16,
+ 17 taxon_17,
+ 18 taxon_18,
+ 19 taxon_19,
+ 20 taxon_20,
+ 21 taxon_21,
+ 22 taxon_22,
+ 23 taxon_23,
+ 24 taxon_24,
+ 25 taxon_25,
+ 26 taxon_26,
+ 27 taxon_27,
+ 28 taxon_28,
+ 29 taxon_29,
+ 30 taxon_30,
+ 31 taxon_31,
+ 32 taxon_32;
+ TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6732219986260810463 WM1148f47d2081;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 444104661901299517 WM1149106b2f00;
+ checksum 0 909469476 WM1149106b2f00;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 786.1187814845004.4817563795317733133;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1141 555;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 8;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #444104661901299517;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX -162;
+ setInitialOffsetY -163;
+ setLegendWidth 142;
+ setLegendHeight 161;
+ resume ;
+ endTell;
+ newWindowAssistant #mesquite.diverse.CharAssocDivViewer.CharAssocDivViewer;
+ tell It;
+ getCharSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #444104661901299517;
+ endTell;
+ endTell;
+ setCalculator #mesquite.diverse.SisterDiversification.SisterDiversification;
+ setCharacter -1;
+ doCounts;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #444104661901299517 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1141 555;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ hideWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '04-BiSSEViewer.nex';
+ setPrevFileName '02-speciationExtinctionRates.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 522 211;
+ setLocation 28 594;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'This and the following two example files answer the question: are rates of diversification (speciation and extinction) associated with the state of a binary character?^n^nThis analysis, available by chosing Character-Associated Diversification from the Analysis menu of the Tree window, uses the simple sign test analysis for independent sister clade pairs in the style of Mitter, Farrell and Wiegmann 1988. The analysis automatically finds sister clade pairs that contrast in the character state of the binary character. Each clade must be completely uniform in state. The number of pairs favoring state 1 (i.e. the clade with state 1 is larger) and favoring state 0 are counted and used as the basis for the sign test.';
+ setTitle Sister_Clade_comparison;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Diversification/04-BiSSEViewer.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/04-BiSSEViewer.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/04-BiSSEViewer.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,361 @@
+#NEXUS
+[written Thu Sep 20 16:44:18 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ taxon_1 taxon_2 taxon_3 taxon_4 taxon_5 taxon_6 taxon_7 taxon_8 taxon_9 taxon_10 taxon_11 taxon_12 taxon_13 taxon_14 taxon_15 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32
+ ;
+ IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
+ BLOCKID WM1148f47d2081;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "04-BiSSEViewer.nex"';
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ taxon_1 0
+ taxon_2 1
+ taxon_3 0
+ taxon_4 0
+ taxon_5 0
+ taxon_6 1
+ taxon_7 0
+ taxon_8 1
+ taxon_9 1
+ taxon_10 1
+ taxon_11 1
+ taxon_12 1
+ taxon_13 1
+ taxon_14 1
+ taxon_15 1
+ taxon_16 1
+ taxon_17 1
+ taxon_18 0
+ taxon_19 1
+ taxon_20 0
+ taxon_21 0
+ taxon_22 0
+ taxon_23 1
+ taxon_24 1
+ taxon_25 1
+ taxon_26 1
+ taxon_27 1
+ taxon_28 1
+ taxon_29 1
+ taxon_30 1
+ taxon_31 1
+ taxon_32 0
+
+;
+ IDS WM1148f4828fe0 ;
+ BLOCKID WM11490f84ae00;
+
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1;
+
+
+END;
+
+BEGIN TREES;
+ Title 'Trees from "04-BiSSEViewer.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 taxon_1,
+ 2 taxon_2,
+ 3 taxon_3,
+ 4 taxon_4,
+ 5 taxon_5,
+ 6 taxon_6,
+ 7 taxon_7,
+ 8 taxon_8,
+ 9 taxon_9,
+ 10 taxon_10,
+ 11 taxon_11,
+ 12 taxon_12,
+ 13 taxon_13,
+ 14 taxon_14,
+ 15 taxon_15,
+ 16 taxon_16,
+ 17 taxon_17,
+ 18 taxon_18,
+ 19 taxon_19,
+ 20 taxon_20,
+ 21 taxon_21,
+ 22 taxon_22,
+ 23 taxon_23,
+ 24 taxon_24,
+ 25 taxon_25,
+ 26 taxon_26,
+ 27 taxon_27,
+ 28 taxon_28,
+ 29 taxon_29,
+ 30 taxon_30,
+ 31 taxon_31,
+ 32 taxon_32;
+ TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6732219986260810463 WM1148f47d2081;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 444104661901299517 WM11490f84ae00;
+ checksum 0 909469476 WM11490f84ae00;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 786.1187814845004.4817563795317733133;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1141 555;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 8;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #444104661901299517;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX -162;
+ setInitialOffsetY -163;
+ setLegendWidth 142;
+ setLegendHeight 161;
+ resume ;
+ endTell;
+ newWindowAssistant #mesquite.diverse.CharAssocDivViewer.CharAssocDivViewer;
+ tell It;
+ getCharSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #444104661901299517;
+ endTell;
+ endTell;
+ setCalculator #mesquite.diverse.BiSSELikelihood.BiSSELikelihood;
+ tell It;
+ suspend ;
+ setParameters ? ? ? ? =2 ? ? =4;
+ setReportMode Likelihood;
+ getIntegTask #mesquite.diverse.BiSSELikelihoodCalculator.BiSSELikelihoodCalculator;
+ tell It;
+ suspend ;
+ setUnderflowCheckFreq 2;
+ setStepCount 1000.0;
+ setIterations 2;
+ conditionOnSurvival off;
+ resume ;
+ endTell;
+ resume ;
+ endTell;
+ setCharacter -1;
+ doCounts;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #444104661901299517 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1141 555;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ hideWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '05-BiSSENetViewer.nex';
+ setPrevFileName '03-sisterDiversification.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 531 336;
+ setLocation 28 594;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'Here the BiSSE likelihood calculations are done. When you have a tree and a binary character (here stored in a matrix), you can select Character-Associated Diversification from the Analysis menu of the Tree window, and indicate you want BiSSE Speciation/Extinction likelihood to be calculated. The BiSSE method is described by Maddison, Midford and Otto 2007.^n^nIn the panel are shown the estimated values of the speciation (lambda) and extinction (mu) rates for states 0 and 1, and the transition rates between states 0 and 1 (q''s). In the Parameters dialog box (in the Diversification(Ch) menu) you can set and constrain parameters. Here, mu1 is constrainted equal to mu0 and q10 is constrained equal to q01.^n^nTo do a likelihood ratio test, change the parameters to an alternative set of constaints, and compare the likelihood. ^n^nA chi-square approximation appears reasonable for significance of the likelihood ratio, but you can also generate a null distribution of log likelihood differences using simulations. The manual outlines the procedure.';
+ setTitle BiSSE_Diversification;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Diversification/05-BiSSENetViewer.nex
===================================================================
--- trunk/treebase-core/lib/examples/Diversification/05-BiSSENetViewer.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Diversification/05-BiSSENetViewer.nex 2009-12-15 18:16:21 UTC (rev 378)
@@ -0,0 +1,358 @@
+#NEXUS
+[written Thu Sep 20 16:44:38 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=32;
+ TAXLABELS
+ taxon_1 taxon_2 taxon_3 taxon_4 taxon_5 taxon_6 taxon_7 taxon_8 taxon_9 taxon_10 taxon_11 taxon_12 taxon_13 taxon_14 taxon_15 taxon_16 taxon_17 taxon_18 taxon_19 taxon_20 taxon_21 taxon_22 taxon_23 taxon_24 taxon_25 taxon_26 taxon_27 taxon_28 taxon_29 taxon_30 taxon_31 taxon_32
+ ;
+ IDS WM1148f47d2061 WM1148f47d2072 WM1148f47d2073 WM1148f47d2074 WM1148f47d2075 WM1148f47d2076 WM1148f47d2077 WM1148f47d2078 WM1148f47d2079 WM1148f47d20710 WM1148f47d20711 WM1148f47d20712 WM1148f47d20713 WM1148f47d20714 WM1148f47d20715 WM1148f47d20716 WM1148f47d20717 WM1148f47d20718 WM1148f47d20719 WM1148f47d20720 WM1148f47d20721 WM1148f47d20722 WM1148f47d20723 WM1148f47d20724 WM1148f47d20725 WM1148f47d20726 WM1148f47d20727 WM1148f47d20728 WM1148f47d20729 WM1148f47d20830 WM1148f47d20831 WM1148f47d20832 ;
+ BLOCKID WM1148f47d2081;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "05-BiSSENetViewer.nex"';
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ taxon_1 0
+ taxon_2 1
+ taxon_3 0
+ taxon_4 0
+ taxon_5 0
+ taxon_6 1
+ taxon_7 0
+ taxon_8 1
+ taxon_9 1
+ taxon_10 1
+ taxon_11 1
+ taxon_12 1
+ taxon_13 1
+ taxon_14 1
+ taxon_15 1
+ taxon_16 1
+ taxon_17 1
+ taxon_18 0
+ taxon_19 1
+ taxon_20 0
+ taxon_21 0
+ taxon_22 0
+ taxon_23 1
+ taxon_24 1
+ taxon_25 1
+ taxon_26 1
+ taxon_27 1
+ taxon_28 1
+ taxon_29 1
+ taxon_30 1
+ taxon_31 1
+ taxon_32 0
+
+;
+ IDS WM1148f4828fe0 ;
+ BLOCKID WM11493c252d50;
+
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1;
+
+
+END;
+
+BEGIN TREES;
+ Title 'Trees from "05-BiSSENetViewer.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 taxon_1,
+ 2 taxon_2,
+ 3 taxon_3,
+ 4 taxon_4,
+ 5 taxon_5,
+ 6 taxon_6,
+ 7 taxon_7,
+ 8 taxon_8,
+ 9 taxon_9,
+ 10 taxon_10,
+ 11 taxon_11,
+ 12 taxon_12,
+ 13 taxon_13,
+ 14 taxon_14,
+ 15 taxon_15,
+ 16 taxon_16,
+ 17 taxon_17,
+ 18 taxon_18,
+ 19 taxon_19,
+ 20 taxon_20,
+ 21 taxon_21,
+ 22 taxon_22,
+ 23 taxon_23,
+ 24 taxon_24,
+ 25 taxon_25,
+ 26 taxon_26,
+ 27 taxon_27,
+ 28 taxon_28,
+ 29 taxon_29,
+ 30 taxon_30,
+ 31 taxon_31,
+ 32 taxon_32;
+ TREE Tree = (((((7:5.187000000000067,22:5.186999999999937):2.4919999999998366,(2:5.19600000000007,((31:2.6009999999998246,14:2.6009999999998246):2.269999999999861,26:4.870999999999961):0.32500000000000023):2.4829999999999215):0.6730000000000005,((((6:0.8290000000000006,9:0.8290000000000006):0.3140000000000002,16:1.142999999999985):2.6749999999998164,(((15:0.20300000000000015,12:0.20300000000000015):0.2490000000000002,8:0.45200000000000035):1.360999999999961,32:1.8129999999999111):2.00499999999989):3.5429999999998403,((23:0.8660000000000007,(17:0.0010,24:0.0010):0.8650000000000007):1.0020000000000004,(18:1.059999999999994,4:1.059999999999994):0.8080000000000006):5.4930000000000865):0.9910000000000008):2.2739999999998606,((((10:0.21500000000000016,29:0.21500000000000016):1.1809999999999807,21:1.395999999999957):6.895000000000504,27:8.291000000000466):2.2449999999998638,((11:0.5600000000000004,19:0.5600000000000004):7.632000000000883,3:8.192000000000526):2.343999999999853):0.09000000000000007):2.389999999999848,((5:3.7479999999996982,(20:0.03300000000000002,1:0.03300000000000002):3.714999999999702):5.209999999999916,((28:0.5840000000000004,13:0.5840000000000004):7.191000000000736,(25:1.5889999999999358,30:1.5889999999999358):6.185999999999934):1.1829999999999805):4.0579999999997804):0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6732219986260810463 WM1148f47d2081;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 444104661901299517 WM11493c252d50;
+ checksum 0 909469476 WM11493c252d50;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6732219986260810463 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 786.1187814845004.4817563795317733133;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 1141 555;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.BasicTreeWindowMaker.BasicTreeWindow.arrow;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 8;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #444104661901299517;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX -162;
+ setInitialOffsetY -163;
+ setLegendWidth 142;
+ setLegendHeight 161;
+ ...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-15 18:14:58
|
Revision: 377
http://treebase.svn.sourceforge.net/treebase/?rev=377&view=rev
Author: rvos
Date: 2009-12-15 18:14:51 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/examples/Correlation/
trunk/treebase-core/lib/examples/Correlation/00-introduction.nex
trunk/treebase-core/lib/examples/Correlation/00a-FelsensteinsContrasts.nex
trunk/treebase-core/lib/examples/Correlation/00b-pagel94Hominids.nex
trunk/treebase-core/lib/examples/Correlation/00c-pairwiseIntro.nex
trunk/treebase-core/lib/examples/Correlation/01-pairwise.nex
trunk/treebase-core/lib/examples/Correlation/02-pairwiseFig2(1).nex
trunk/treebase-core/lib/examples/Correlation/03-pairwiseFig2(2).nex
trunk/treebase-core/lib/examples/Correlation/04-pairwiseFig2(3).nex
trunk/treebase-core/lib/examples/Correlation/05-pairwiseFig3-6(1).nex
trunk/treebase-core/lib/examples/Correlation/06-pairwiseFig3-6(2).nex
trunk/treebase-core/lib/examples/Correlation/07-pairwiseFig3-6(3).nex
Added: trunk/treebase-core/lib/examples/Correlation/00-introduction.nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/00-introduction.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/00-introduction.nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,33 @@
+#NEXUS
+[written Mon Sep 03 09:22:06 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '00a-FelsensteinsContrasts.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 429 288;
+ setLocation 5 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'Phylogenetic tests of whether two characters have correlated evolution can be done in three ways using Mesquite:^n^n(1) Two continuous characters: Felsenstein''s independent contrasts^n^n(2) Two categorical two-state characters: Pagel''s 1994 method.^n^n(3) Two categorical or one categorical and one continuous character: pairwise comparisons.^n^nHere are example files for these various methods^n^nTo go from one file to another, hit the "Next" button';
+ setTitle Character_Correlation;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addFileLink Return_to_main_Introduction '../Introduction.nex';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/00a-FelsensteinsContrasts.nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/00a-FelsensteinsContrasts.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/00a-FelsensteinsContrasts.nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,373 @@
+#NEXUS
+[written Mon Sep 03 09:22:19 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=49;
+ TAXLABELS
+ Tm Ur Um Nn pl Mp Ml Cp Ct Lp Ca Uc Vf Hh Cc Aj Pp Pt Pq Tb Cs Db Eh Ec Eb Lg Cd Gc Sc Bb To Gg Gt Ac Mk Oa Oc He Am Cu Dl Ab Aa cq Dd Al Rt Ov Oh
+ ;
+ BLOCKID WM114cc2658fc35;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = CONTINUOUS;
+ MATRIX
+ Tm 2.423245874 2.062957834
+ Ur 2.400192489 1.918030337
+ Um 1.970346876 1.754348336
+ Nn 0.6434526765 0.0211892991
+ pl 0.84509804 0.0569048513
+ Mp 0.3979400087 0.3979400087
+ Ml 1.064457989 -0.060480747
+ Cp 1.547774705 2.307067951
+ Ct 1.123851641 1.653212514
+ Lp 1.301029996 2.204119983
+ Ca 0.9444826722 0.9590413923
+ Uc 0.5682017241 0.0413926852
+ Vf 0.6812412374 0.587710965
+ Hh 1.428134794 2.184123354
+ Cc 1.716003344 1.397940009
+ Aj 1.769377326 1.7930916
+ Pp 1.719331287 1.365487985
+ Pt 2.206825876 1.84260924
+ Pq 2.192567453 2.372912003
+ Tb 2.397940009 0.3010299957
+ Cs 3.301029996 0.8228216453
+ Db 3.079181246 1.193124598
+ Eh 2.301029996 1.544068044
+ Ec 2.544068044 1.352182518
+ Eb 2.371067862 2.217483944
+ Lg 1.977723605 -0.301029996
+ Cd 2.740362689 2.0
+ Gc 3.031408464 1.927370363
+ Sc 2.792391689 2.139879086
+ Bb 2.937016107 2.123851641
+ To 2.7084209 1.942008053
+ Gg 1.795880017 1.301029996
+ Gt 1.311753861 0.7242758696
+ Ac 1.574031268 0.8129133566
+ Mk 0.6989700043 -1.36653154
+ Oa 2.054995862 1.356981401
+ Oc 1.929418926 1.15624619
+ He 2.355068206 1.903089987
+ Am 1.726319612 0.5797835966
+ Cu 2.334453751 1.875061263
+ Dl 2.113943352 0.3424226808
+ Ab 2.133538908 0.6989700043
+ Aa 1.698970004 1.0
+ cq 2.477121255 1.111598525
+ Dd 1.740362689 0.1139433523
+ Al 2.584331224 1.206825876
+ Rt 2.0 1.477121255
+ Ov 1.755874856 0.2922560714
+ Oh 1.86923172 0.45484486
+
+;
+ BLOCKID WM114cc26593f0;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 Tm,
+ 2 Ur,
+ 3 Um,
+ 4 Nn,
+ 5 pl,
+ 6 Mp,
+ 7 Ml,
+ 8 Cp,
+ 9 Ct,
+ 10 Lp,
+ 11 Ca,
+ 12 Uc,
+ 13 Vf,
+ 14 Hh,
+ 15 Cc,
+ 16 Aj,
+ 17 Pp,
+ 18 Pt,
+ 19 Pq,
+ 20 Tb,
+ 21 Cs,
+ 22 Db,
+ 23 Eh,
+ 24 Ec,
+ 25 Eb,
+ 26 Lg,
+ 27 Cd,
+ 28 Gc,
+ 29 Sc,
+ 30 Bb,
+ 31 To,
+ 32 Gg,
+ 33 Gt,
+ 34 Ac,
+ 35 Mk,
+ 36 Oa,
+ 37 Oc,
+ 38 He,
+ 39 Am,
+ 40 Cu,
+ 41 Dl,
+ 42 Ab,
+ 43 Aa,
+ 44 cq,
+ 45 Dd,
+ 46 Al,
+ 47 Rt,
+ 48 Ov,
+ 49 Oh;
+ TREE Untitled_Tree = ((((((1:2000000.0,2:2000000.0)n95:3000000.0,3:5000000.0)n31:3.9E7,((4:5000000.0,5:5000000.0)n92:2.6E7,(6:2.0E7,7:2.0E7)n07:1.1E7)n93:1.3E7)n06:8000000.0,(((((8:2500000.0,9:2500000.0)n34:500000.0,10:3000000.0)n32:3000000.0,11:6000000.0)n28:3000000.0,12:9000000.0)n22:500000.0,13:9500000.0)n21:4.25E7)n05:6000000.0,((14:5000000.0,15:5000000.0)n18:2.1E7,(16:9000000.0,(17:2500000.0,(18:2000000.0,19:2000000.0)n36:500000.0)n35:6500000.0)n23:1.7E7)n10:3.2E7)n03:1.2E7,(((20:5.0E7,(21:1.3E7,22:1.3E7)n16:3.7E7)n99:6000000.0,(23:7000000.0,(24:6000000.0,25:6000000.0)n29:1000000.0)n26:4.9E7)n04:1.0E7,((26:1.75E7,27:1.75E7)n77:2.55E7,(28:2.05E7,((((29:1.0E7,30:1.0E7)n98:9000000.0,31:1.9E7)n24:500000.0,((((32:2500000.0,33:2500000.0)n27:4500000.0,34:7000000.0)n90:4000000.0,35:1.1E7)n19:5000000.0,((36:4000000.0,37:4000000.0)n97:1.15E7,(38:9000000.0,(39:6500000.0,(40:5500000.0,(41:3500000.0,42:3500000.0)n33:2000000.0)n30:1000000.0)n20:2500000.0)n91:6500000.0)n14:500000.0)n13:3500000.0)n12:500000.0,(43:1.95E7,((44:4000000.0,45:4000000.0)n96:7000000.0,(46:5500000.0,(47:5000000.0,(48:1000000.0,49:1000000.0)n39:4000000.0)n38:500000.0)n37:5500000.0)n17:8500000.0)n11:500000.0)n09:500000.0)n08:2.25E7)n88:2.3E7)n02:4000000.0)n01:0.0;
+
+END;
+
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = Squared: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = Brownian_default: 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 7933746709840163491 WM114cc2658fc35;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 4190772235764235829 WM114cc26593f0;
+ checksum 0 2240152432 WM114cc26593f0;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #7933746709840163491 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 404.985450020823.5565377021587689415;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 570 329;
+ setLocation 5 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.SquareTree.SquareTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 2;
+ orientRight;
+ toggleCorners off;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newWindowAssistant #mesquite.trees.MirrorTreeWindowMaker.MirrorTreeWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 30;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 543 446;
+ setLocation 614 29;
+ setFont SanSerif;
+ setFontSize 10;
+ newAssistantLeft #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #4190772235764235829;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared;
+ tell It;
+ toggleWeight on;
+ endTell;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend off;
+ toggleGray off;
+ toggleWeights on;
+ resume ;
+ endTell;
+ newAssistantRight #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #4190772235764235829;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ getEmployee #mesquite.parsimony.ParsimonySquared.ParsimonySquared;
+ tell It;
+ toggleWeight on;
+ endTell;
+ endTell;
+ endTell;
+ setCharacter 2;
+ setMapping 1;
+ toggleShowLegend off;
+ toggleGray off;
+ toggleWeights on;
+ resume ;
+ endTell;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientLeft;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels off;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '00b-pagel94Hominids.nex';
+ setPrevFileName '00-introduction.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 570 379;
+ setLocation 5 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'This example file shows the distribution of two continuous characters on a tree. To test whether there is a significant association, Felsenstein''s Independent Contrasts can be used. ^n^nCalculation of Felsenstein''s independent contrasts is not part of the basic version of Mesquite, but rather is available in the PDAP package of modules for Mesquite. It is available at http://mesquiteproject.org/pdap_mesquite (see link below). ^n^nTo learn more about Felsenstein''s contrast calculations, download PDAP and explore its example files.';
+ setTitle 'Felsenstein''s independent contrasts';
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addWebLink Mesquite_PDAP_website 'http://mesquiteproject.org/pdap_mesquite';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/00b-pagel94Hominids.nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/00b-pagel94Hominids.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/00b-pagel94Hominids.nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,319 @@
+#NEXUS
+[written Mon Sep 03 09:16:16 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ Homo_sapiens Pan_troglodytes Pan_paniscus Gorilla_gorilla Pongo_pygmaeus Hylobates_syndactylus Hylobates_sp. Colobus_guereza Colobus_badius
+ ;
+ IDS 010a627b503f49 010a627b503f50 010a627b503f51 010a627b503f52 010a627b503f53 010a627b504054 010a627b504055 010a627b504056 010a627fb2ef57 ;
+ BLOCKID 010a627b503c3;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 advertisement / absent present, 2 mating_system / one_male 'multi-male' ;
+ MATRIX
+ Homo_sapiens 00
+ Pan_troglodytes 11
+ Pan_paniscus 11
+ Gorilla_gorilla 00
+ Pongo_pygmaeus 10
+ Hylobates_syndactylus 00
+ Hylobates_sp. 00
+ Colobus_guereza 00
+ Colobus_badius 11
+
+;
+ IDS 010a627b503f4 010a627b503f5 ;
+ BLOCKID WM114cc27480d0;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 Homo_sapiens,
+ 2 Pan_troglodytes,
+ 3 Pan_paniscus,
+ 4 Gorilla_gorilla,
+ 5 Pongo_pygmaeus,
+ 6 Hylobates_syndactylus,
+ 7 Hylobates_sp.,
+ 8 Colobus_guereza,
+ 9 Colobus_badius;
+ TREE page_16_example = ((8:2.0,9:2.0):56.0,((5:22.0,(4:20.0,(1:29.0,(2:9.0,3:5.0):15.0):11.0):10.0):18.0,(6:3.0,7:2.0):28.0):10.0):1.0;
+
+END;
+
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 878585605735200005 010a627b503c3;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 7359026449824636807 WM114cc27480d0;
+ checksum 0 1601284411 WM114cc27480d0;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #878585605735200005 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 1199.1144113549683.1862327035904205997;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 688 483;
+ setLocation 488 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ setTool mesquite.trees.BranchLengthsAdjust.AdjustToolExtra.adjustor;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.SquareTree.SquareTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale off;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 6;
+ orientRight;
+ toggleCorners off;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFontSize 14;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize on;
+ toggleTextOnTree off;
+ newWindowAssistant #mesquite.trees.MirrorTreeWindowMaker.MirrorTreeWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 30;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 476 392;
+ setLocation 12 409;
+ setFont SanSerif;
+ setFontSize 10;
+ newAssistantLeft #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #7359026449824636807;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend off;
+ toggleGray off;
+ toggleWeights on;
+ resume ;
+ endTell;
+ newAssistantRight #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #7359026449824636807;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 2;
+ setMapping 1;
+ toggleShowLegend off;
+ toggleGray off;
+ toggleWeights on;
+ resume ;
+ endTell;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.SquareTree.SquareTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle on;
+ branchLengthsToggle off;
+ toggleScale off;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 10;
+ orientLeft;
+ toggleCorners off;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFontSize 12;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ showWindow;
+ endTell;
+ newWindowAssistant #mesquite.correl.CorrelationViewer.CorrelationViewer;
+ tell It;
+ getCharSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #7359026449824636807;
+ endTell;
+ endTell;
+ setCorrelationCalculator #mesquite.correl.Pagel94.Pagel94;
+ tell It;
+ setSeed 1188836136528;
+ setSimCount 100;
+ togglePresentPValue off;
+ setNumIterations 10;
+ endTell;
+ setX -1;
+ setY 0;
+ doCounts;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '00c-pairwiseIntro.nex';
+ setPrevFileName '00a-FelsensteinsContrasts.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 454 246;
+ setLocation 10 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'Pagel''s 1994 method uses likelihood ratio tests to determine if two categorical characters are correlated. Mesquite requires the two characters to be binary (0,1) characters. To turn on an analysis, choose Pagel 94 Analysis from the Analysis menu of the Tree Window.^n^nThis is an example from Pagel''s Discrete manual. Two characters appear to be associated as shown in the Mirror tree window above. At right is the analysis. To estimate the significance value, select Present P value in the Pagel94 menu of the tree window at right. ^n^nBelow is a link to the section in manual describing the method.';
+ setTitle 'Pagel''s method';
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addWebLink Page_in_manual 'docs/mesquite/CharacterEvolution/ProcessCharEvol.html#pagel94';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/00c-pairwiseIntro.nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/00c-pairwiseIntro.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/00c-pairwiseIntro.nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,34 @@
+#NEXUS
+[written Mon Sep 03 09:16:57 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '01-pairwise.nex';
+ setPrevFileName '00b-pagel94Hominids.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 429 310;
+ setLocation 318 26;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'The following examples concern pairwise tests of character association^n^nThey illustrate the methods described in: ^n^nMaddison, W.P. 2000. Testing character correlation using pairwise comparisons on a phylogeny. Journal of Theoretical Biology. 202: 195-204.^n^nThis paper describes methods to choose pairs of taxa for comparative method calculations (tests of character association). The corresponding Mesquite modules automatically find phylogenetically separate pairs of taxa according to specific criteria. ^n^nThe example files begin with a fairly complex example, then proceed through the examples of the figures of the paper cited above.^n';
+ setTitle Pairwise_comparison_examples;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ setEditorsVisible;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/01-pairwise.nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/01-pairwise.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/01-pairwise.nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,409 @@
+#NEXUS
+[written Mon Sep 03 09:17:33 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=24;
+ TAXLABELS
+ species_0 species_1 species_2 species_3 species_4 species_5 species_6 species_7 species_8 species_9 species_10 species_11 species_12 species_13 species_14 species_15 species_16 species_17 species_18 species_19 species_20 species_21 species_22 species_23
+ ;
+ BLOCKID WM114cc2916be37;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE habitat;
+ DIMENSIONS NCHAR=1;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 habitat / aquatic terrestrial ;
+ MATRIX
+ species_0 0
+ species_1 1
+ species_2 0
+ species_3 0
+ species_4 1
+ species_5 1
+ species_6 0
+ species_7 0
+ species_8 1
+ species_9 1
+ species_10 0
+ species_11 0
+ species_12 0
+ species_13 0
+ species_14 0
+ species_15 1
+ species_16 1
+ species_17 1
+ species_18 0
+ species_19 0
+ species_20 1
+ species_21 0
+ species_22 0
+ species_23 0
+
+;
+ BLOCKID WM114cc2916ef0;
+
+
+END;
+BEGIN CHARACTERS;
+ TITLE physiology;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = CONTINUOUS;
+CHARSTATELABELS
+ 1 metabolic_rate,
+ 2 sprint_speed ;
+ MATRIX
+ species_0 1.219 11.3
+ species_1 3.56 17.98
+ species_2 0.98 15.16
+ species_3 2.341 19.53
+ species_4 1.998 23.07
+ species_5 2.951 20.78
+ species_6 0.5681 20.44
+ species_7 1.153 17.82
+ species_8 2.713 22.37
+ species_9 5.673 20.12
+ species_10 0.112 13.0
+ species_11 0.6743 15.91
+ species_12 0.9881 16.19
+ species_13 1.231 20.35
+ species_14 1.987 20.32
+ species_15 1.7 18.87
+ species_16 2.987 22.82
+ species_17 3.209 29.87
+ species_18 0.456 19.53
+ species_19 0.9868 16.07
+ species_20 1.233 24.62
+ species_21 0.871 21.01
+ species_22 0.3451 12.83
+ species_23 0.795 13.99
+
+;
+ BLOCKID WM114cc2917030;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 species_0,
+ 2 species_1,
+ 3 species_2,
+ 4 species_3,
+ 5 species_4,
+ 6 species_5,
+ 7 species_6,
+ 8 species_7,
+ 9 species_8,
+ 10 species_9,
+ 11 species_10,
+ 12 species_11,
+ 13 species_12,
+ 14 species_13,
+ 15 species_14,
+ 16 species_15,
+ 17 species_16,
+ 18 species_17,
+ 19 species_18,
+ 20 species_19,
+ 21 species_20,
+ 22 species_21,
+ 23 species_22,
+ 24 species_23;
+ TREE mtDNA_phylogeny = (((((1,16),((9,17),14)),(((6,20),(((8,24),(15,(18,21))),(10,((11,22),12)))),(7,(2,19)))),4),((3,(13,23)),5));
+
+END;
+
+
+BEGIN CODONS;
+CODESET * UNTITLED (CHARACTERS = habitat) = universal: 1;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED (CHARACTERS = habitat) = unord: 1;
+TYPESET Current_Parsimony_Models (CHARACTERS = habitat) = unord: 1;
+TYPESET * UNTITLED (CHARACTERS = physiology) = Linear: 1 - 2;
+TYPESET Current_Parsimony_Models (CHARACTERS = physiology) = Linear: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED (CHARACTERS = habitat) = 'Mk1 (est.)': 1;
+ProbModelSet * UNTITLED (CHARACTERS = physiology) = Brownian_default: 1 - 2;
+ProbModelSet Current_Probability_Models (CHARACTERS = physiology) = Brownian_default: 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 5616496406151607698 WM114cc2916be37;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 5359875599842773608 WM114cc2916ef0;
+ checksum 0 2437689620 WM114cc2916ef0;
+ setID 1 1344182101150933612 WM114cc2917030;
+ checksum 1 573191175 WM114cc2917030;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #5616496406151607698 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 865.967565541874.2516291620293279705;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 584 546;
+ setLocation 559 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientRight;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.pairwise.PairwiseComparison.PairwiseComparison;
+ tell It;
+ requireCalculate;
+ showStates off;
+ setPairSelector #mesquite.pairwise.PairsOneChar.PairsOneChar;
+ tell It;
+ setLimit 5;
+ endTell;
+ getCharacterSourceA #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #5359875599842773608;
+ endTell;
+ endTell;
+ getCharacterSourceB #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #1344182101150933612;
+ endTell;
+ endTell;
+ setCharacterA 1;
+ setCharacterB 1;
+ setPairing 1;
+ setInitialOffsetX 3;
+ setInitialOffsetY -494;
+ calculate;
+ endTell;
+ newWindowAssistant #mesquite.trees.MirrorTreeWindowMaker.MirrorTreeWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 562 470;
+ setLocation 6 336;
+ setFont SanSerif;
+ setFontSize 10;
+ newAssistantLeft #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #5359875599842773608;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX 20;
+ setInitialOffsetY -161;
+ setLegendWidth 142;
+ setLegendHeight 161;
+ resume ;
+ endTell;
+ newAssistantRight #mesquite.ancstates.TraceCharacterHistory.TraceCharacterHistory;
+ tell It;
+ suspend ;
+ setDisplayMode #mesquite.ancstates.ShadeStatesOnTree.ShadeStatesOnTree;
+ tell It;
+ toggleLabels off;
+ toggleGray off;
+ endTell;
+ setHistorySource #mesquite.ancstates.RecAncestralStates.RecAncestralStates;
+ tell It;
+ getCharacterSource #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #1344182101150933612;
+ endTell;
+ endTell;
+ setMethod #mesquite.parsimony.ParsAncestralStates.ParsAncestralStates;
+ tell It;
+ setModelSource #mesquite.parsimony.CurrentParsModels.CurrentParsModels;
+ endTell;
+ endTell;
+ setCharacter 1;
+ setMapping 1;
+ toggleShowLegend on;
+ toggleGray off;
+ toggleWeights on;
+ setInitialOffsetX -162;
+ setInitialOffsetY -305;
+ setLegendWidth 142;
+ setLegendHeight 305;
+ resume ;
+ endTell;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientLeft;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '02-pairwiseFig2(1).nex';
+ setPrevFileName '00-introduction.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 475 188;
+ setLocation 5 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'This file shows the use of pairwise comparisons to test association between characters on a phylogeny. At right are two data matrices, categorical and continuous. The first character of each is compared in the mirror tree window. Above left is an analysis of pairwise comparisons automatically chosen by the algorithm of W. Maddison (2000). There are 3696 pairings of terminal taxa with 7 pairs contrasting the independent (categorical) variable. The first pairing (#1) is shown: all 7 of its pairs have the dependent variable greater in the terrestrial species, significant with p=0.0078. However, among all 3696 pairings, some are not significant (worst p is 0.2265).';
+ setTitle Pairwise_comparison;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/02-pairwiseFig2(1).nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/02-pairwiseFig2(1).nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/02-pairwiseFig2(1).nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,299 @@
+#NEXUS
+[written Mon Sep 03 09:17:53 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=20;
+ TAXLABELS
+ A B C D E F G H I J K L M N O P Q R S T
+ ;
+ BLOCKID WM114cc29a60438;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ A 00
+ B 11
+ C 00
+ D 00
+ E 11
+ F 11
+ G 01
+ H 00
+ I 00
+ J 00
+ K 11
+ L 11
+ M 00
+ N 00
+ O 11
+ P 11
+ Q 10
+ R 00
+ S 00
+ T 00
+
+;
+ BLOCKID WM114cc29a6140;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 A,
+ 2 B,
+ 3 C,
+ 4 D,
+ 5 E,
+ 6 F,
+ 7 G,
+ 8 H,
+ 9 I,
+ 10 J,
+ 11 K,
+ 12 L,
+ 13 M,
+ 14 N,
+ 15 O,
+ 16 P,
+ 17 Q,
+ 18 R,
+ 19 S,
+ 20 T;
+ TREE UNTITLED = ((9,14),((15,11),(18,(((7,(20,19)),12),(((1,(10,((16,17),6))),(13,8)),(((4,5),2),3))))));
+
+END;
+
+
+BEGIN MACCLADE;
+Version 3.05;
+LastModified - 1306936660;
+Singles 0100& / 0;
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 3196237234391053769 WM114cc29a60438;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 2832606891834185499 WM114cc29a6140;
+ checksum 0 4257668035 WM114cc29a6140;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #3196237234391053769 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 2369.970632536606.3126887053844580137;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 859 497;
+ setLocation 398 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.pairwise.PairwiseComparison.PairwiseComparison;
+ tell It;
+ requireCalculate;
+ showStates on;
+ setPairSelector #mesquite.pairwise.PairsNoChars.PairsNoChars;
+ getCharacterSourceA #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #2832606891834185499;
+ endTell;
+ endTell;
+ getCharacterSourceB #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #2832606891834185499;
+ endTell;
+ endTell;
+ setCharacterA 1;
+ setCharacterB 2;
+ setPairing 1;
+ setInitialOffsetX -200;
+ setInitialOffsetY -340;
+ calculate;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #2832606891834185499 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 386 277;
+ setLocation 6 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '03-pairwiseFig2(2).nex';
+ setPrevFileName '01-pairwise.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 386 317;
+ setLocation 6 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'For figure 2 of Maddison, W.P. 2000. Testing character correlation using pairwise comparisons on a phylogeny. Journal of Theoretical Biology. 202: 195-204.^n^nThis shows choice of pairs without regard to states of characters. The grey boxes over the terminal taxa show in bold what is designated the Independent variable, and below that the dependent variable.';
+ setTitle Pairwise;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/03-pairwiseFig2(2).nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/03-pairwiseFig2(2).nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/03-pairwiseFig2(2).nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,302 @@
+#NEXUS
+[written Mon Sep 03 09:18:09 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=20;
+ TAXLABELS
+ A B C D E F G H I J K L M N O P Q R S T
+ ;
+ BLOCKID WM114cc29f73d39;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ A 00
+ B 11
+ C 00
+ D 00
+ E 11
+ F 11
+ G 01
+ H 00
+ I 00
+ J 00
+ K 11
+ L 11
+ M 00
+ N 00
+ O 11
+ P 11
+ Q 10
+ R 00
+ S 00
+ T 00
+
+;
+ BLOCKID WM114cc29f77a0;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 A,
+ 2 B,
+ 3 C,
+ 4 D,
+ 5 E,
+ 6 F,
+ 7 G,
+ 8 H,
+ 9 I,
+ 10 J,
+ 11 K,
+ 12 L,
+ 13 M,
+ 14 N,
+ 15 O,
+ 16 P,
+ 17 Q,
+ 18 R,
+ 19 S,
+ 20 T;
+ TREE UNTITLED = ((9,14),((15,11),(18,(((7,(20,19)),12),(((1,(10,((16,17),6))),(13,8)),(((4,5),2),3))))));
+
+END;
+
+
+BEGIN MACCLADE;
+Version 3.05;
+LastModified - 1306936660;
+Singles 0100& / 0;
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6595404229671493286 WM114cc29f73d39;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 8234977281528109195 WM114cc29f77a0;
+ checksum 0 4257668035 WM114cc29f77a0;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6595404229671493286 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 2440.970632551984.9050636877436007407;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 854 499;
+ setLocation 370 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.pairwise.PairwiseComparison.PairwiseComparison;
+ tell It;
+ requireCalculate;
+ showStates on;
+ setPairSelector #mesquite.pairwise.PairsOneChar.PairsOneChar;
+ tell It;
+ setLimit 5;
+ endTell;
+ getCharacterSourceA #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #8234977281528109195;
+ endTell;
+ endTell;
+ getCharacterSourceB #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #8234977281528109195;
+ endTell;
+ endTell;
+ setCharacterA 1;
+ setCharacterB 2;
+ setPairing 1;
+ setInitialOffsetX -200;
+ setInitialOffsetY -340;
+ calculate;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #8234977281528109195 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 337 221;
+ setLocation 6 26;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '04-pairwiseFig2(3).nex';
+ setPrevFileName '02-pairwiseFig2(1).nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 337 261;
+ setLocation 6 26;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'For figure 2 of Maddison, W.P. 2000. Testing character correlation using pairwise comparisons on a phylogeny. Journal of Theoretical Biology. 202: 195-204.^n^nThis shows choice of pairs to contrast the states of character 1.';
+ setTitle Pairwise;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Correlation/04-pairwiseFig2(3).nex
===================================================================
--- trunk/treebase-core/lib/examples/Correlation/04-pairwiseFig2(3).nex (rev 0)
+++ trunk/treebase-core/lib/examples/Correlation/04-pairwiseFig2(3).nex 2009-12-15 18:14:51 UTC (rev 377)
@@ -0,0 +1,302 @@
+#NEXUS
+[written Mon Sep 03 09:18:51 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=20;
+ TAXLABELS
+ A B C D E F G H I J K L M N O P Q R S T
+ ;
+ BLOCKID WM114cc2a351040;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ MATRIX
+ A 00
+ B 11
+ C 00
+ D 00
+ E 11
+ F 11
+ G 01
+ H 00
+ I 00
+ J 00
+ K 11
+ L 11
+ M 00
+ N 00
+ O 11
+ P 11
+ Q 10
+ R 00
+ S 00
+ T 00
+
+;
+ BLOCKID WM114cc2a35620;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 A,
+ 2 B,
+ 3 C,
+ 4 D,
+ 5 E,
+ 6 F,
+ 7 G,
+ 8 H,
+ 9 I,
+ 10 J,
+ 11 K,
+ 12 L,
+ 13 M,
+ 14 N,
+ 15 O,
+ 16 P,
+ 17 Q,
+ 18 R,
+ 19 S,
+ 20 T;
+ TREE UNTITLED = ((9,14),((15,11),(18,(((7,(20,19)),12),(((1,(10,((16,17),6))),(13,8)),(((4,5),2),3))))));
+
+END;
+
+
+BEGIN MACCLADE;
+Version 3.05;
+LastModified - 1306936660;
+Singles 0100& / 0;
+
+END;
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 5715784789562340009 WM114cc2a351040;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 5834500797987800771 WM114cc2a35620;
+ checksum 0 4257668035 WM114cc2a35620;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #5715784789562340009 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 2511.970632567011.3284971206291078;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 807 457;
+ setLocation 396 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.pairwise.PairwiseComparison.PairwiseComparison;
+ tell It;
+ requireCalculate;
+ showStates on;
+ setPairSelector #mesquite.pairwise.PairsTwoChars.PairsTwoChars;
+ tell It;
+ setLimit 5;
+ endTell;
+ getCharacterSourceA #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #5834500797987800771;
+ endTell;
+ endTell;
+ getCharacterSourceB #mesquite.charMatrices.CharSrcCoordObed.CharSrcCoordObed;
+ tell It;
+ setCharacterSource #mesquite.charMatrices.StoredCharacters.StoredCharacters;
+ tell It;
+ setDataSet #5834500797987800771;
+ endTell;
+ endTell;
+ setCharacterA 1;
+ setCharacterB 2;
+ setPairing 1;
+ setInitialOffsetX -200;
+ setInitialOffsetY -340;
+ calculate;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTr...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-15 18:14:34
|
Revision: 376
http://treebase.svn.sourceforge.net/treebase/?rev=376&view=rev
Author: rvos
Date: 2009-12-15 18:14:26 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Added Paths:
-----------
trunk/treebase-core/lib/examples/Coalescence/
trunk/treebase-core/lib/examples/Coalescence/00-introduction.nex
trunk/treebase-core/lib/examples/Coalescence/01-coalescence.nex
trunk/treebase-core/lib/examples/Coalescence/02-coalescence2.nex
trunk/treebase-core/lib/examples/Coalescence/03-coalescenceDepth.nex
trunk/treebase-core/lib/examples/Coalescence/04-associations.nex
trunk/treebase-core/lib/examples/Coalescence/05-twoPopulations.nex
trunk/treebase-core/lib/examples/Coalescence/06-twoPopulations2.nex
trunk/treebase-core/lib/examples/Coalescence/08-fluctuating.nex
trunk/treebase-core/lib/examples/Coalescence/09-genesInSpecies.nex
trunk/treebase-core/lib/examples/Coalescence/10-speciesTreeSearch.nex
trunk/treebase-core/lib/examples/Coalescence/11-geneInSpecies2.nex
trunk/treebase-core/lib/examples/Coalescence/outOfAfrica/
trunk/treebase-core/lib/examples/Coalescence/outOfAfrica/01-outOfAfrica.nex
trunk/treebase-core/lib/examples/Coalescence/outOfAfrica/02-outOfAfrica.nex
trunk/treebase-core/lib/examples/Coalescence/outOfAfrica/03-outOfAfrica.nex
trunk/treebase-core/lib/examples/Coalescence/outOfAfrica/04-outOfAfrica.nex
trunk/treebase-core/lib/examples/Coalescence/tutorial/
trunk/treebase-core/lib/examples/Coalescence/tutorial/01-associationsHow1.nex
trunk/treebase-core/lib/examples/Coalescence/tutorial/02-associationsHow2.nex
trunk/treebase-core/lib/examples/Coalescence/tutorial/02b-associationsHow2.nex
trunk/treebase-core/lib/examples/Coalescence/tutorial/03-associationsHow3.nex
trunk/treebase-core/lib/examples/Coalescence/tutorial/04-associationsHow4.nex
Added: trunk/treebase-core/lib/examples/Coalescence/00-introduction.nex
===================================================================
--- trunk/treebase-core/lib/examples/Coalescence/00-introduction.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Coalescence/00-introduction.nex 2009-12-15 18:14:26 UTC (rev 376)
@@ -0,0 +1,40 @@
+#NEXUS
+[written Mon Sep 03 09:21:05 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+BEGIN NOTES;
+
+ TEXT FILE TEXT = 'Example files for coalescence calculations^n^nThe files linked to this one illustrate some of the coalescence calculations that can be done by the package of coalescence modules of the Mesquite system. To learn more about this package, use the Coalescence Package menu item of the Help menu, or touch on the banner in the Mesquite Startup window. (It should take you to your web browser, perhaps after asking you to locate the browser.)^n^nTo go from one file to another, hit the "Go" button in the green window.';
+
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '01-coalescence.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 415 316;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 14;
+ setActive;
+ setExplanation 'Example files for coalescence calculations^n^nThe files linked to this one illustrate some of the coalescence calculations that can be done by the package of coalescence modules of the Mesquite system. To learn more about this package, go to the population genetics section of the manual using the button below, or use the Coalescence Package menu item of the Help menu, or touch on the banner in the Mesquite Startup window. (It should take you to your web browser, perhaps after asking you to locate the browser.)^n^nTo go from one file to another, hit the "Next" button.';
+ setTitle Coalescence_examples;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addWebLink Manual 'mesquite:docs/mesquite/popGen/popGen.html';
+ addFileLink Return_to_main_Introduction '../Introduction.nex';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Coalescence/00-introduction.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Coalescence/01-coalescence.nex
===================================================================
--- trunk/treebase-core/lib/examples/Coalescence/01-coalescence.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Coalescence/01-coalescence.nex 2009-12-15 18:14:26 UTC (rev 376)
@@ -0,0 +1,195 @@
+#NEXUS
+[written Mon Sep 03 09:21:19 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ g1 g2 g3 g4 g5 g6 g7 g8 g9
+ ;
+ BLOCKID WM1148c10e06e14;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=19;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ g1 AACATCTGGGAACCGTGCG
+
+ g2 C?CGTCTGAGACCCGTCCG
+
+ g3 AAGATACGGGTACCGTCCG
+
+ g4 AACATACGGGAAGCGTCCG
+
+ g5 AAGGTACGGGAACCGTCCG
+
+ g6 AAAGTACGGGACCCGTGCG
+
+ g7 AACGTACGGGAACCGTGCG
+
+ g8 AAAGCACGGGAACCGTGCG
+
+ g9 AACGCACGAGAACCGTGCG
+
+
+;
+
+
+ BLOCKID WM1148c10e0900;
+
+
+END;
+
+BEGIN NOTES;
+
+ TEXT FILE TEXT = 'This file shows a tree window with gene trees simulated by coalescence within a population. Scroll through trees to see other simulated gene trees. The organisms simulated are haploids. The effective population size is by default 10000. To change this, choose Set Ne from the Tree menu.^n^nTo go to next example file: click the button in the "Go To File" window.^n^nTo duplicate this file: Select "New" from the File menu, and indicate the name of the set of taxa (genes) and the number of taxa (gene copies). In the list window that will be shown, you may rename the taxa. Then, select the set of taxa from the "Tree Window" submenu of the Taxa&Trees menu to show a tree window. Initially, default trees will be shown. Go to the Tree menu of the tree window, and select "Coalescent trees" from "Simulated Trees" submenu of the the "Tree source" submenu of the "Tree" menu.^n^nTo make it pretty, choose "Curvogram" from the "Tree form" submenu of the Tree menu, then choose "Show Branch Lengths" from the Tree menu. To make it so all trees are displayed on the same scale, choose Fixed Scaling and indicate a number about 2-4 times the effective population size. ^n';
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 19;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 19;
+TYPESET Current_Parsimony_Models = unord: 1 - 19;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 19;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 1469954533384391314 WM1148c10e06e14;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 4636206365576148138 WM1148c10e0900;
+ checksum 0 1947097330 WM1148c10e0900;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #1469954533384391314 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.SimulateTree.SimulateTree;
+ tell It;
+ setTreeSimulator #mesquite.coalesce.CoalescentTrees.CoalescentTrees;
+ tell It;
+ getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
+ tell It;
+ setEffective 10000;
+ toggleExponential on;
+ endTell;
+ endTell;
+ setSeed 983242417684;
+ endTell;
+ setAssignedID 302.971276427933.7117688824995678366;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 459 407;
+ setLocation 490 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ setFixedScaling 30000.0;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 4;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '02-coalescence2.nex';
+ setPrevFileName '00-introduction.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 459 415;
+ setLocation 10 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'This file shows a tree window with gene trees simulated by coalescence within a population. Scroll through trees to see other simulated gene trees. The organisms simulated are haploids. The effective population size is by default 10000. To change this, choose Set Ne from the Coalescent Simulation submenu of the Tree menu.^n^nTo duplicate this file: Select "New" from the File menu, and indicate the name of the set of taxa (genes) and the number of taxa (gene copies). In the list window that will be shown, you may rename the taxa. Then, select the set of taxa from the "Tree Window" submenu of the Taxa&Trees menu to show a tree window. Initially, default trees will be shown. Go to the Tree menu of the tree window, and select "Coalescent trees" from "Simulated Trees" submenu of the the "Tree Source" submenu of the "Tree" menu.^n^nTo make it pretty, choose "Curvogram" from the "Tree Form" submenu of the Drawing menu, then choose "Branches Proportional to Lengths" from the Drawing menu. To make it so all trees are displayed on the same scale, choose Fixed Scaling and indicate a number about 2-4 times the effective population size. ^n';
+ setTitle Simulated_gene_trees;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Coalescence/01-coalescence.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Coalescence/02-coalescence2.nex
===================================================================
--- trunk/treebase-core/lib/examples/Coalescence/02-coalescence2.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Coalescence/02-coalescence2.nex 2009-12-15 18:14:26 UTC (rev 376)
@@ -0,0 +1,181 @@
+#NEXUS
+[written Mon Sep 10 21:53:06 EDT 2007 by Mesquite version 2.0BETA3 (build i57) at Thrandina.local/10.71.1.127 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ g1 g2 g3 g4 g5 g6 g7 g8 g9
+ ;
+ BLOCKID WM1148c1835ae15;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=19;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ g1 AACATCTGGGAACCGTGCG
+
+ g2 C?CGTCTGAGACCCGTCCG
+
+ g3 AAGATACGGGTACCGTCCG
+
+ g4 AACATACGGGAAGCGTCCG
+
+ g5 AAGGTACGGGAACCGTCCG
+
+ g6 AAAGTACGGGACCCGTGCG
+
+ g7 AACGTACGGGAACCGTGCG
+
+ g8 AAAGCACGGGAACCGTGCG
+
+ g9 AACGCACGAGAACCGTGCG
+
+
+;
+
+
+ BLOCKID WM1148c1835cf0;
+
+
+END;
+
+BEGIN NOTES;
+
+ TEXT FILE TEXT = 'At left is a "Multi Tree Window" to show a series of gene trees simulated by coalescence within a population. You can scroll down to see other such simulated trees. Note that the root tends to be between 1000 and 2000 generations deep.^n^nThe effective population size is 1000 (haploid), and can be changed using the "Set Ne.." menu item in the Multi-Tree menu of the Trees window.';
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 19;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 19;
+TYPESET Current_Parsimony_Models = unord: 1 - 19;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 19;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 4451700786596653131 WM1148c1835ae15;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 4972659033594616137 WM1148c1835cf0;
+ checksum 0 1947097330 WM1148c1835cf0;
+ endTell;
+ newAssistant #mesquite.trees.MultiTreeWindowMaker.MultiTreeWindowMaker;
+ tell It;
+ setTaxa #4451700786596653131;
+ setNumColumns 4;
+ setNumRows 4;
+ getTreeSource #mesquite.trees.DefiniteTreeSource.DefiniteTreeSource;
+ tell It;
+ setTreeSource #mesquite.trees.SimulateTree.SimulateTree;
+ tell It;
+ setTreeSimulator #mesquite.coalesce.CoalescentTrees.CoalescentTrees;
+ tell It;
+ getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
+ tell It;
+ setEffective 1000;
+ toggleExponential on;
+ endTell;
+ endTell;
+ setSeed 1189475568974;
+ endTell;
+ assignNumTrees 100;
+ endTell;
+ makeWindow;
+ toggleLegendBotRight off;
+ setNamesVisible on;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 626 641;
+ setLocation 456 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ setFixedScaling 2500.0;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 3;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ showWindow;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '03-coalescenceDepth.nex';
+ setPrevFileName '01-coalescence.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 420 268;
+ setLocation 13 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'At left is a "Multi Tree Window" to show a series of gene trees simulated by coalescence within a population. You can scroll down to see other such simulated trees. Note that the root tends to be between 1000 and 2000 generations deep.^n^nThe effective population size is 1000 (haploid), and can be changed using the "Set Ne.." menu item in the Coalescent SImulation submenu of the Multi-Tree menu of the Trees window.';
+ setTitle Gene_trees;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Coalescence/02-coalescence2.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Coalescence/03-coalescenceDepth.nex
===================================================================
--- trunk/treebase-core/lib/examples/Coalescence/03-coalescenceDepth.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Coalescence/03-coalescenceDepth.nex 2009-12-15 18:14:26 UTC (rev 376)
@@ -0,0 +1,161 @@
+#NEXUS
+[written Tue Aug 21 23:00:45 PDT 2007 by Mesquite version 2.0BETA3 (build i50) at Thrandina.local/10.0.1.2 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ g1 g2 g3 g4 g5 g6 g7 g8 g9
+ ;
+ BLOCKID WM1148c2865d916;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=19;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ g1 AACATCTGGGAACCGTGCG
+
+ g2 C?CGTCTGAGACCCGTCCG
+
+ g3 AAGATACGGGTACCGTCCG
+
+ g4 AACATACGGGAAGCGTCCG
+
+ g5 AAGGTACGGGAACCGTCCG
+
+ g6 AAAGTACGGGACCCGTGCG
+
+ g7 AACGTACGGGAACCGTGCG
+
+ g8 AAAGCACGGGAACCGTGCG
+
+ g9 AACGCACGAGAACCGTGCG
+
+
+;
+
+
+ BLOCKID WM1148c2865eb0;
+
+
+END;
+
+BEGIN NOTES;
+
+ TEXT FILE TEXT = 'This file contains a small set of taxa representing gene copies within a population. The chart shows the depth to the last coalescence in a sample of 100 gene trees simulated by coalescence. ^n^nTo change the number of trees sampled, go to the chart window and select "Number of Trees" from the Chart menu. The effective population size (haploid) is 1000; change this by choosing "Set Ne" from the Chart window..^n^nTo duplicate this file: Select "New" from the file menu. Once the file is established, choose "Tree Values" from the Charts menu. Indicate "Tree Depth" as the value, then "Simulate Trees" as the tree source, "Coalescent trees" as the simulator. Then, choose "Fixed Number of Groups" under "Grouping on X" and set number to 50.^n';
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 19;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+ TYPESET * UNTITLED = unord: 1 - 19;
+TYPESET Current_Parsimony_Models = unord: 1 - 19;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Jukes-Cantor': 1 - 19;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 2914423799126459326 WM1148c2865d916;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 5851865005210875165 WM1148c2865eb0;
+ checksum 0 1947097330;
+ endTell;
+ newAssistant #mesquite.charts.TreeValuesChart.TreeValuesChart;
+ tell It;
+ suspendCalculations;
+ setTaxa #2914423799126459326;
+ setTreeSource #mesquite.trees.SimulateTree.SimulateTree;
+ tell It;
+ setTreeSimulator #mesquite.coalesce.CoalescentTrees.CoalescentTrees;
+ tell It;
+ getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
+ tell It;
+ setEffective 1000;
+ toggleExponential on;
+ endTell;
+ endTell;
+ setSeed 983242234061;
+ endTell;
+ setCalculator #mesquite.coalesce.TreeDepth.TreeDepth;
+ getCharter #mesquite.charts.ItemValuesChart.ItemValuesChart;
+ tell It;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 443 426;
+ setLocation 472 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ itemsByValues;
+ setChartType #mesquite.charts.Histogram.Histogram;
+ tell It;
+ showAverageToggle on;
+ setCumulativeMode 0;
+ showAsBarChartToggle on;
+ showRawToggle off;
+ setNumberIntervals 50;
+ setIntervalSize 1.0;
+ setMovingWindowSize 5.0 1.0;
+ setMode 4;
+ endTell;
+ toggleColorItems off;
+ setNumberItems 100;
+ endTell;
+ enableCalculations;
+ endTell;
+ setChartVisible;
+ doCounts;
+ resumeCalculations;
+ showWindow;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '04-associations.nex';
+ setPrevFileName '02-coalescence2.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 443 434;
+ setLocation 2 23;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'This file contains a small set of taxa representing gene copies within a population. The chart shows the depth to the last coalescence in a sample of 100 gene trees simulated by coalescence. ^n^nTo change the number of trees sampled, go to the chart window and select "Number of Trees" from the Chart menu. The effective population size (haploid) is 1000; change this by choosing "Set Ne" from the Coalescent Simulation submenu of the Chart menu of the Chart window.^n^nTo duplicate this file: Select "New" from the file menu. Once the file is established, choose Analysis>New Bar & Line Chart for>Tree Values. In the dialog box that appears, check Show Secondary Choices, then select Tree Depth as the value, then "Simulate Trees" as the tree source, "Coalescent trees" as the simulator, and set the effective population size to 1000. Once the histogram appears, choose "Fixed Number of Groups" in the "Grouping on X" submenu from the Chart menu, and set number to 50.^n';
+ setTitle Gene_tree_depths;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Coalescence/03-coalescenceDepth.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Coalescence/04-associations.nex
===================================================================
--- trunk/treebase-core/lib/examples/Coalescence/04-associations.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Coalescence/04-associations.nex 2009-12-15 18:14:26 UTC (rev 376)
@@ -0,0 +1,398 @@
+#NEXUS
+[written Tue Aug 21 23:04:42 PDT 2007 by Mesquite version 2.0BETA3 (build i50) at Thrandina.local/10.0.1.2 (Wayne Maddison)]
+
+BEGIN TAXA;
+ TITLE Species;
+ DIMENSIONS NTAX=3;
+ TAXLABELS
+ speciesA speciesB speciesC
+ ;
+ BLOCKID WM1148c28a29d17;
+
+END;
+
+
+
+BEGIN TAXA;
+ TITLE Genes;
+ DIMENSIONS NTAX=5;
+ TAXLABELS
+ geneA1 geneA2 geneB geneC1 geneC2
+ ;
+ BLOCKID WM1148c28a2ae18;
+
+END;
+
+
+BEGIN TaxaAssociation;
+TITLE how_genes_fit_into_species;
+TAXA Species , Genes;
+ASSOCIATES
+
+ speciesA / geneA1 geneA2 ,
+ speciesB / geneB ,
+ speciesC / geneC1 geneC2
+
+;
+
+END;
+
+
+BEGIN TREES;
+ LINK Taxa = Species;
+ TRANSLATE
+ 1 speciesA,
+ 2 speciesB,
+ 3 speciesC;
+ TREE Species_tree = ((1,2),3);
+
+END;
+
+
+BEGIN TREES;
+ LINK Taxa = Genes;
+ TRANSLATE
+ 1 geneA1,
+ 2 geneA2,
+ 3 geneB,
+ 4 geneC1,
+ 5 geneC2;
+ TREE concordant = (((1,2),3),(4,5));
+ TREE discordant = ((1,2),((4,3),5));
+ TREE unresolved = ((1,2),4,3,5);
+
+END;
+
+
+BEGIN NOTES;
+
+ TEXT FILE TEXT = 'The ability to handle more than one set of taxa in a file, and to associate the taxa between the sets, allows analysis of gene trees within species trees. This file has a set of taxa of three species, and a second set of taxa for five genes (see tree windows at left). Above is a species tree drawn using the "Contained Associates" tree drawer, showing a gene tree within the species tree. Scroll through trees in the gene tree window at left to see that there are three stored trees, one concordant with the species tree, one discordant, and one poorly resolved.^n^nTo see each of these trees within the species trees, scroll through them in the "Contained Tree" legend. The gene tree is reconstructed within the species tree so as to minimized the depth of coalescences. The "Cost" indicated in the legend is the number of failures to coalesce within a species lineage (the number of "extra" gene lineages of W. Maddison 1997, Syst. Biol. 46:523). The red lines shown for the unresolved gene tree are lineages that were resolved out of a polytomy (assuming the gene tree polytomy represents lack of resolution).^n^nTo see how to duplicate this file, check out the tutorial files by clicking on the Blue "Go To File" window. ';
+
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 6147812854687186808 WM1148c28a29d17;
+ setID 1 6651160229924971687 WM1148c28a2ae18;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #6147812854687186808 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTaxa #6147812854687186808;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 558.964495543348.6195579460590305404;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 556 317;
+ setLocation 612 502;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker;
+ tell It;
+ getNote;
+ tell It;
+ setBounds 4 32 100 22;
+ setFont SanSerif;
+ setFontSize 14;
+ setOffsetX 4;
+ setOffsetY 32;
+ setNote Species_Tree;
+ setOffsetX 4;
+ setOffsetY 32;
+ endTell;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ makeTreeWindow #6651160229924971687 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTaxa #6651160229924971687;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 577.964495543796.3141002713096155948;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 556 317;
+ setLocation 5 445;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker;
+ tell It;
+ getNote;
+ tell It;
+ setBounds 4 34 100 22;
+ setFont SanSerif;
+ setFontSize 14;
+ setOffsetX 4;
+ setOffsetY 34;
+ setNote Gene_Tree;
+ setOffsetX 4;
+ setOffsetY 34;
+ endTell;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ makeTreeWindow #6147812854687186808 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTaxa #6147812854687186808;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 596.964495544767.2058576892485762804;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 608 391;
+ setLocation 590 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.assoc.ContainedAssociates.ContainedAssociates;
+ tell It;
+ suppress ;
+ getAssociationSource #mesquite.assoc.StoredAssociations.StoredAssociations;
+ tell It;
+ setCurrentAssociation 0;
+ endTell;
+ getReconstructor #mesquite.coalesce.RecCoalescenceHistory.RecCoalescenceHistory;
+ tell It;
+ toggleUnrooted off;
+ toggleResolve on;
+ toggleUseLengths on;
+ endTell;
+ setEdgeWidth 64;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTaxa #6651160229924971687;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setContained 1;
+ toggleScale on;
+ setInitialOffsetX -406;
+ setInitialOffsetY -160;
+ desuppress ;
+ getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ namesAngle ?;
+ endTell;
+ endTell;
+ setBackground White;
+ setBranchColor Blue;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '05-twoPopulations.nex';
+ setPrevFileName '03-coalescenceDepth.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 556 325;
+ setLocation 8 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'The ability to handle more than one set of taxa in a file, and to associate the taxa between the sets, allows analysis of gene trees within species trees. This file has a set of taxa of three species, and a second set of taxa for five genes (see tree windows at left). At right is a species tree drawn using the "Contained Associates" tree drawer, showing a gene tree within the species tree. Scroll through trees in the gene tree window below to see that there are three stored trees, one concordant with the species tree, one discordant, and one poorly resolved.^n^nTo see each of these trees within the species trees, scroll through them in the "Contained Tree" legend. The gene tree is reconstructed within the species tree so as to minimize the depth of coalescences. The "Cost" indicated in the legend is the number of failures to coalesce within a species lineage (the number of "extra" gene lineages of W. Maddison 1997, Syst. Biol. 46:523). The red lines shown for the unresolved gene tree are lineages that were resolved out of a polytomy (assuming the gene tree polytomy represents lack of resolution).^n^nTo see how to duplicate this file, check out the tutorial files by clicking on the "Go" button, below. ';
+ setTitle Associations_between_taxa;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addFileLink 'Tutorial: How to duplicate this file' 'tutorial/01-associationsHow1.nex';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Coalescence/04-associations.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Coalescence/05-twoPopulations.nex
===================================================================
--- trunk/treebase-core/lib/examples/Coalescence/05-twoPopulations.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Coalescence/05-twoPopulations.nex 2009-12-15 18:14:26 UTC (rev 376)
@@ -0,0 +1,353 @@
+#NEXUS
+[written Tue Aug 21 23:05:35 PDT 2007 by Mesquite version 2.0BETA3 (build i50) at Thrandina.local/10.0.1.2 (Wayne Maddison)]
+
+BEGIN TAXA;
+ TITLE Populations;
+ DIMENSIONS NTAX=2;
+ TAXLABELS
+ East West
+ ;
+ BLOCKID WM1148c2c4a0319;
+
+END;
+
+
+
+BEGIN TAXA;
+ TITLE genes_sampled;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ East1 East2 East3 East4 West1 West2 West3 West4 West5
+ ;
+ BLOCKID WM1148c2c4a1820;
+
+END;
+
+
+BEGIN LABELS;
+TAXAGROUPLABEL Eastern_samples COLOR = (RGB 0.20392157 1.0 0.42745098) ;
+TAXAGROUPLABEL Western_Samples COLOR = (RGB 1.0 0.81568627 0.20392157) ;
+
+
+END;
+
+BEGIN SETS;
+TAXPARTITION * UNTITLED (TAXA = genes_sampled) = Eastern_samples : 1 - 4, Western_Samples : 5 - 9;
+
+END;
+
+BEGIN TREES;
+ LINK Taxa = Populations;
+ TRANSLATE
+ 1 East,
+ 2 West;
+ TREE tree = (1:10.0,2:10.0):100.0;
+ TREE tree = (1:50.0,2:50.0):100.0;
+ TREE tree = (1:100.0,2:100.0):100.0;
+ TREE tree = (1:200.0,2:200.0):100.0;
+
+END;
+
+
+BEGIN TaxaAssociation;
+TITLE location;
+TAXA Populations , genes_sampled;
+ASSOCIATES
+
+ East / East1 East2 East3 East4 ,
+ West / West1 West2 West3 West4 West5
+
+;
+
+END;
+
+
+BEGIN NOTES;
+
+ TEXT FILE TEXT = 'Coalescence simulations can be blended with associations between containing and contained trees by simulating gene trees within a species tree. In this file, the species tree is actually a population tree, and there are only two populations.^n^nThere are two sets of taxa, one representing populations (East and West) and the other representing genes sampled from those populations. At left is a population tree within which is simulated a gene tree by coalescence. The time since the populations split was 50 generations; the effective population size is 100 (you can change time divergence as described below; change Ne using the menu item in the Contained menu of the tree window). Scroll through simulated gene trees by hitting the arrows under "Contained Tree" in the legend.^n^nThe degree to which the gene tree is expected to show a clean separation of genes sampled in the West from those sampled in the East depends on the time since separation of the populations. To increase the time since separation of the populations, change the branch lengths of the species tree. Do this in one of two ways: (1) use the ruler tool (to change both branches at once, select both branches using the branch select tool, holding down the shift key as you are selecting the second branch to accumulate the selection. Then, once both branches are selected, apply the ruler tool to one of them), or (2) select "Set all branch lengths" from the "Branch lengths" submenu of the Tree menu of the tree window.^n^nNote that the longer are the branch lengths, the more completely the genes in each population have coalesced before they reach the ancestral populations. You can see this clearly in the tree window showing a gene tree by itself. Because there is a TaxaPartition stored in the data file that indicates the West samples are to be colored tan and the East samples to be colored green, their names in the gene tree window are colored accordingly. This gene tree is simulated, and as you change the lengths of the branches of the population tree, you may see a change in the degree of mixing of the East and West samples in the gene tree.^n^nTo go to the next example, hit the button in the "Go To File" window at left.^n^nTo duplicate this file, create a file with two sets of taxa and an association block indicating how they are linked. Ask to show a tree window for the populations. Select "Contained Associates" for the tree form, selecting Simulate Tree and Contained Coalescence for the tree source. Ask to show branch lengths.';
+
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 2717996828273828747 WM1148c2c4a0319;
+ setID 1 2319072353600653909 WM1148c2c4a1820;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #2717996828273828747 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTaxa #2717996828273828747;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 1442.971300502392.3825508766828255405;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 536 458;
+ setLocation 572 32;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.assoc.ContainedAssociates.ContainedAssociates;
+ tell It;
+ suppress ;
+ getAssociationSource #mesquite.assoc.StoredAssociations.StoredAssociations;
+ tell It;
+ setCurrentAssociation 0;
+ endTell;
+ getReconstructor #mesquite.coalesce.RecCoalescenceHistory.RecCoalescenceHistory;
+ tell It;
+ toggleUnrooted off;
+ toggleResolve on;
+ toggleUseLengths on;
+ endTell;
+ setEdgeWidth 64;
+ setTreeSource #mesquite.trees.SimulateTree.SimulateTree;
+ tell It;
+ setTreeSimulator #mesquite.coalesce.ContainedCoalescence.ContainedCoalescence;
+ tell It;
+ getAssociationTask #mesquite.assoc.StoredAssociations.StoredAssociations;
+ tell It;
+ setCurrentAssociation 0;
+ endTell;
+ getTreeSource #mesquite.trees.TreeOfContext.TreeOfContext;
+ tell It;
+ setContextID 1442.971300502392.3825508766828255405;
+ endTell;
+ setSimulator #mesquite.coalesce.ContainedCoalescSim.ContainedCoalescSim;
+ tell It;
+ getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
+ tell It;
+ setEffective 100;
+ toggleExponential on;
+ endTell;
+ endTell;
+ forgetAssociation ;
+ endTell;
+ setSeed 984411246198;
+ endTell;
+ setContained 1;
+ toggleScale on;
+ setInitialOffsetX -424;
+ setInitialOffsetY -177;
+ desuppress ;
+ getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ namesAngle ?;
+ endTell;
+ endTell;
+ setBackground White;
+ setBranchColor Blue;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition on;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ setTree '(1:50.0,2:50.0):100.0;';
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker;
+ tell It;
+ getNote;
+ tell It;
+ setBounds 328 221 123 86;
+ setFont Serif;
+ setFontSize 18;
+ setOffsetX 328;
+ setOffsetY 221;
+ setNote Population_tree_with_contained_gene_tree;
+ setOffsetX 328;
+ setOffsetY 221;
+ endTell;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ makeTreeWindow #2319072353600653909 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.SimulateTree.SimulateTree;
+ tell It;
+ setTreeSimulator #mesquite.coalesce.ContainedCoalescence.ContainedCoalescence;
+ tell It;
+ getAssociationTask #mesquite.assoc.StoredAssociations.StoredAssociations;
+ tell It;
+ setCurrentAssociation 0;
+ endTell;
+ getTreeSource #mesquite.trees.TreeOfContext.TreeOfContext;
+ tell It;
+ setContextID 1442.971300502392.3825508766828255405;
+ endTell;
+ setSimulator #mesquite.coalesce.ContainedCoalescSim.ContainedCoalescSim;
+ tell It;
+ getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
+ tell It;
+ setEffective 100;
+ toggleExponential on;
+ endTell;
+ endTell;
+ forgetAssociation ;
+ endTell;
+ setSeed 984411246666;
+ endTell;
+ setAssignedID 1471.971300503030.3721084600339604932;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 518 301;
+ setLocation 587 584;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.ArcTree.ArcTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 4;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition off;
+ toggleShadePartition on;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ newAssistant #mesquite.trees.TreeNotesMaker.TreeNotesMaker;
+ tell It;
+ getNote;
+ tell It;
+ setBounds 23 4 100 24;
+ setFont Serif;
+ setFontSize 18;
+ setOffsetX 23;
+ setOffsetY 4;
+ setNote Gene_tree;
+ setOffsetX 23;
+ setOffsetY 4;
+ endTell;
+ endTell;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '06-twoPopulations2.nex';
+ setPrevFileName '04-associations.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 531 631;
+ setLocation 5 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'Coalescence simulations can be blended with associations between containing and contained trees by simulating gene trees within a species tree. In this file, the species tree is actually a population tree, and there are only two populations.^n^nThere are two sets of taxa, one representing populations (East and West) and the other representing genes sampled from those populations. At right, above, is a population tree within which is simulated a gene tree by coalescence. The time since the populations split was 50 generations; the effective population size is 100 (you can change time divergence as described below; change Ne using the menu item in the Coalescent Simulation submenu of the Contained menu of the tree window). Scroll through simulated gene trees by hitting the arrows under "Contained Tree" in the legend.^n^nThe degree to which the gene tree is expected to show a clean separation of genes sampled in the West from those sampled in the East depends on the time since separation of the populations. To increase the time since separation of the populations, change the branch lengths of the species tree. Do this in one of two ways: (1) use the ruler tool (to change both branches at once, select both branches using the branch select tool, holding down the shift key as you are selecting the second branch to accumulate the selection. Then, once both branches are selected, apply the ruler tool to one of them), or (2) select "Set all branch lengths" from the "Branch lengths" submenu of the Tree menu of the tree window.^n^nNote that the longer are the branch lengths, the more completely the genes in each population have coalesced before they reach the ancestral populations. You can see this clearly in the tree window, below, showing a gene tree by itself. Because the taxa are partitioned into two groups, and set so that the West samples are to be colored tan and the East samples to be colored green, their names in the gene tree window are colored accordingly. This gene tree is simulated, and as you change the lengths of the branches of the population tree, you may see a change in the degree of mixing of the East and West samples in the gene tree.^n^nTo duplicate this file, create a file with two sets of taxa and an association block indicating how they are linked. Ask to show a tree window for the populations. Select "Contained Associates" for the tree form, selecting Simulate Tree and Contained Coalescence within Current Tree for the tree source. Ask to show branch lengths.';
+ setTitle Diverging_populations;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Coalescence/05-twoPopulations.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Coalescence/06-twoPopulations2.nex
===================================================================
--- trunk/treebase-core/lib/examples/Coalescence/06-twoPopulations2.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Coalescence/06-twoPopulations2.nex 2009-12-15 18:14:26 UTC (rev 376)
@@ -0,0 +1,300 @@
+#NEXUS
+[written Wed Aug 22 09:07:26 PDT 2007 by Mesquite version 2.0BETA3 (build i50) at Thrandina.local/10.0.1.2 (Wayne Maddison)]
+
+BEGIN TAXA;
+ TITLE Populations;
+ DIMENSIONS NTAX=2;
+ TAXLABELS
+ East West
+ ;
+ BLOCKID WM1148e5376f035;
+
+END;
+
+
+
+BEGIN TAXA;
+ TITLE genes_sampled;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ East1 East2 East3 East4 West1 West2 West3 West4 West5
+ ;
+ BLOCKID WM1148e5376fa36;
+
+END;
+
+
+BEGIN LABELS;
+TAXAGROUPLABEL Eastern_samples COLOR = (RGB 0.20392157 1.0 0.42745098) ;
+TAXAGROUPLABEL Western_Samples COLOR = (RGB 1.0 0.81568627 0.20392157) ;
+
+
+END;
+
+BEGIN SETS;
+TAXPARTITION * UNTITLED (TAXA = genes_sampled) = Eastern_samples : 1 - 4, Western_Samples : 5 - 9;
+
+END;
+
+BEGIN TREES;
+ LINK Taxa = Populations;
+ TRANSLATE
+ 1 East,
+ 2 West;
+ TREE tree = (1:10.0,2:10.0):100.0;
+ TREE tree = (1:50.0,2:50.0):100.0;
+ TREE tree = (1:100.0,2:100.0):100.0;
+ TREE tree = (1:200.0,2:200.0):100.0;
+
+END;
+
+
+BEGIN TaxaAssociation;
+TITLE location;
+TAXA Populations , genes_sampled;
+ASSOCIATES
+
+ East / East1 East2 East3 East4 ,
+ West / West1 West2 West3 West4 West5
+
+;
+
+END;
+
+
+BEGIN NOTES;
+
+ TEXT FILE TEXT = 'The degree to which the gene tree is expected to show a clean separation of genes sampled in the West from those sampled in the East depends on the time since separation of the populations. Slatkin and Maddison (1989) suggested using as a statistic the number of parsimony steps in a character for the genes whose states represent the source population of the genes (i.e., location sampled). The time since separation can be estimated by measuring "s" on a reconstructed gene tree, and comparing it to the expected s values for gene trees that have undergone neutral coalescence in populations with varying times since separation. (This assumes there has not been ongoing gene flow and that the two populations have maintained similar population sizes.). ^n^nAt left is a chart of the s value for a sample of 100 gene trees simulated within the population tree by coalescence. An "s" value of 1 would mean that at least one of the population''s sampled genes were monophyletic on the gene tree. When the populations have been split for 0.5 generations times the effective population size (Ne = 100), as shown initially here, the most common s is 2.^n^nBy changing the branch lengths in the population tree, you can affect the value of s in the chart. To change the branch lengths, go to the the "Set all branch lengths" item in the Branch Lengths submenu of the Tree menu of the tree window.^n^nTo duplicate the chart at left, select Value for Trees from the Charts window, indicate s of Slatkin and Maddison as the value to be calculated, the tree source to be Simulate Tree, and the simulator to be Contained Coalescence.';
+
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 7114850956850836156 WM1148e5376f035;
+ setID 1 4791169349505029750 WM1148e5376fa36;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #7114850956850836156 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTaxa #7114850956850836156;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 1533.971300618301.6347497454875668222;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 467 413;
+ setLocation 565 29;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.assoc.ContainedAssociates.ContainedAssociates;
+ tell It;
+ suppress ;
+ getAssociationSource #mesquite.assoc.StoredAssociations.StoredAssociations;
+ tell It;
+ setCurrentAssociation 0;
+ endTell;
+ getReconstructor #mesquite.coalesce.RecCoalescenceHistory.RecCoalescenceHistory;
+ tell It;
+ toggleUnrooted off;
+ toggleResolve on;
+ toggleUseLengths on;
+ endTell;
+ setEdgeWidth 64;
+ setTreeSource #mesquite.trees.SimulateTree.SimulateTree;
+ tell It;
+ setTreeSimulator #mesquite.coalesce.ContainedCoalescence.ContainedCoalescence;
+ tell It;
+ getAssociationTask #mesquite.assoc.StoredAssociations.StoredAssociations;
+ tell It;
+ setCurrentAssociation 0;
+ endTell;
+ getTreeSource #mesquite.trees.TreeOfContext.TreeOfContext;
+ tell It;
+ setContextID 1533.971300618301.6347497454875668222;
+ endTell;
+ setSimulator #mesquite.coalesce.ContainedCoalescSim.ContainedCoalescSim;
+ tell It;
+ getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
+ tell It;
+ setEffective 100;
+ toggleExponential on;
+ endTell;
+ endTell;
+ forgetAssociation ;
+ endTell;
+ setSeed 984411288026;
+ endTell;
+ setContained 1;
+ toggleScale on;
+ setInitialOffsetX -142;
+ setInitialOffsetY -160;
+ desuppress ;
+ getEmployee #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle on;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter on;
+ toggleEven on;
+ namesAngle ?;
+ endTell;
+ endTell;
+ setBackground White;
+ setBranchColor Blue;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setFont SanSerif;
+ setFontSize 10;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 2;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.charts.TreeValuesChart.TreeValuesChart;
+ tell It;
+ suspendCalculations;
+ setTaxa #4791169349505029750;
+ setTreeSource #mesquite.trees.SimulateTree.SimulateTree;
+ tell It;
+ setTreeSimulator #mesquite.coalesce.ContainedCoalescence.ContainedCoalescence;
+ tell It;
+ getAssociationTask #mesquite.assoc.StoredAssociations.StoredAssociations;
+ tell It;
+ setCurrentAssociation 0;
+ endTell;
+ getTreeSource #mesquite.trees.TreeOfContext.TreeOfContext;
+ tell It;
+ setContextID 1533.971300618301.6347497454875668222;
+ endTell;
+ setSimulator #mesquite.coalesce.ContainedCoalescSim.ContainedCoalescSim;
+ tell It;
+ getEmployee #mesquite.coalesce.NeutralCoalescence.NeutralCoalescence;
+ tell It;
+ setEffective 100;
+ toggleExponential on;
+ endTell;
+ endTell;
+ forgetAssociation ;
+ endTell;
+ setSeed 984411288443;
+ endTell;
+ setCalculator #mesquite.coalesce.SlatkinMaddisonS.SlatkinMaddisonS;
+ tell It;
+ getEmployee #mesquite.assoc.StoredAssociations.StoredAssociations;
+ tell It;
+ setCurrentAssociation 0;
+ endTell;
+ endTell;
+ getCharter #mesquite.charts.ItemValuesChart.ItemValuesChart;
+ tell It;
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 513 323;
+ setLocation 10 515;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ itemsByValues;
+ setChartType #mesquite.charts.Histogram.Histogram;
+ tell It;
+ showAverageToggle on;
+ setCumulativeMode 0;
+ showAsBarChartToggle on;
+ showRawToggle off;
+ setNumberIntervals 20;
+ setIntervalSize 1.0;
+ setMovingWindowSize 5.0 1.0;
+ setMode 0;
+ endTell;
+ toggleColorItems off;
+ setNumberItems 100;
+ endTell;
+ enableCalculations;
+ endTell;
+ setChartVisible;
+ doCounts;
+ resumeCalculations;
+ showWindow;
+ endTell;
+ newAssistan...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-15 18:13:40
|
Revision: 375
http://treebase.svn.sourceforge.net/treebase/?rev=375&view=rev
Author: rvos
Date: 2009-12-15 18:13:33 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/examples/Character_Simulations/
trunk/treebase-core/lib/examples/Character_Simulations/00-introduction.nex
trunk/treebase-core/lib/examples/Character_Simulations/01-modelTree.nex
trunk/treebase-core/lib/examples/Character_Simulations/02-gammaTest.nex
trunk/treebase-core/lib/examples/Character_Simulations/03-TestingTreeStructure.nex
trunk/treebase-core/lib/examples/Character_Simulations/templates/
trunk/treebase-core/lib/examples/Character_Simulations/templates/GIGTRTest.template
trunk/treebase-core/lib/examples/Character_Simulations/templates/GTRTest.template
trunk/treebase-core/lib/examples/Character_Simulations/templates/GammaInvarTest.template
trunk/treebase-core/lib/examples/Character_Simulations/templates/GammaTest.template
trunk/treebase-core/lib/examples/Character_Simulations/templates/TiTvTest.template
Added: trunk/treebase-core/lib/examples/Character_Simulations/00-introduction.nex
===================================================================
--- trunk/treebase-core/lib/examples/Character_Simulations/00-introduction.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Character_Simulations/00-introduction.nex 2009-12-15 18:13:33 UTC (rev 375)
@@ -0,0 +1,40 @@
+#NEXUS
+[written Mon Sep 03 09:21:31 PDT 2007 by Mesquite version 2.0BETA3 (build i55) at Thrandina.local/127.0.0.1 (Wayne Maddison)]
+BEGIN NOTES;
+
+ TEXT FILE TEXT = 'Example files for coalescence calculations^n^nThe files linked to this one illustrate some of the coalescence calculations that can be done by the package of coalescence modules of the Mesquite system. To learn more about this package, use the Coalescence Package menu item of the Help menu, or touch on the banner in the Mesquite Startup window. (It should take you to your web browser, perhaps after asking you to locate the browser.)^n^nTo go from one file to another, hit the "Go" button in the green window.';
+
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '01-modelTree.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 533 261;
+ setLocation 2 22;
+ setFont SanSerif;
+ setFontSize 14;
+ setActive;
+ setExplanation 'Example files for character simulations and hypothesis testing.^n^nTo go from one file to another, hit the "Next" button.';
+ setTitle Character_Simulations;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addWebLink Manual 'mesquite:docs/mesquite/AncestralStates/AncestralStates.html';
+ addFileLink Return_to_main_Introduction '../Introduction.nex';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Character_Simulations/00-introduction.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Character_Simulations/01-modelTree.nex
===================================================================
--- trunk/treebase-core/lib/examples/Character_Simulations/01-modelTree.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Character_Simulations/01-modelTree.nex 2009-12-15 18:13:33 UTC (rev 375)
@@ -0,0 +1,516 @@
+#NEXUS
+[written Thu Sep 20 14:31:40 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium.local/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=49;
+ TAXLABELS
+ Omus Oxycheila Clinidium Omoglymmius Trachypachus Systolosoma Metrius Pachyteles Scaphinotus Nebria Loricera Elaphrus Antarctonomus Omophron Pasimachus Clivinini Dyschirius Creobius Bembidion Psydrus Mecyclothorax Agonum Chlaenius Haliplus_laminatus Haliplus_ruficollis Copelatus Cybister Hydroporus Laccophilus Neoporus Gyrinus Spanglerogyrus Hygrobius Hydrocanthus Noterus Suphis Bruchela Tenebrio Helochares Dynastes Cyphon Clambus Hydroscapha Torridincola Distocupes Sialis Anisochrysa Oliarces Phaeostigma
+ ;
+ BLOCKID WM114cbd0cfc02;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "01-modelTree.nex"';
+ DIMENSIONS NCHAR=2543;
+ FORMAT DATATYPE = DNA GAP = - MISSING = ?;
+ MATRIX
+ Omus TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CCAAAA--TTAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC-----ACATATACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCTAACCGGAGACGGAAGGAGTGCTTTTATTAGATCAAAACCAAT-TGTGGC-----GTCC--C--GGGCTCCATATGATTCTGTACCTTTGCGTA--CG--TTCATGT-GTCCTGG-TGTGCGTTCACACAT-ATTACTGGTGAATCTGAATAACTT---GCTGATCGCATGGTC-TCGTACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTTTCGATGGTAGGATCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCTTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACAAGGAGCAACTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAGTAGCGTATATTAAAGTTGTTGCGGTTAAGAAGCTCGTAGTTGAATTTGTGTCTCGCGCTGTCGGTTCATCGCCTGCGTGCGGTGTT-AACTGGCACGCC--GCGGGACGTCTTG-CCGGAAGG--------AC-CGGTATGTGTTTGCTTCG--------TGT-CGTTCTTGATGTCCATGTTACTCTAATGTCCATAATTTTATGATTTGTTGTTGTGGTATATTTATATTTTAAACGGTATATTATATATTACACACATTTC---------------TTAT-TATG----------------------GGTTCA-----------TATTGTCATGGC-------------------------------------------TCC---------------------------------ATCAT--GC-TTCGG--------------CCGGCT----------TA---GTGCGT------------------ACGT-AGTCC--GACT----TT--A-ATCCTGTCTAGGTGCTCTTAACTGAGTGTCGTGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTTAAAGCAGGC----TAT-T-GTT---GCCTGAATACAGT-GTGCATGGAATAATGAAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAAT-TA-CGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGACCGTCGCAAGACGAACTTAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACTATAAACGATGCCAACTAGCGATCGGCCGACGTTCCT-CCGATGACTCGGTCGGCAGCT-TCCGGGAAACCAAAGTCTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCTTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCGGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAGCGAGACTCTAGCCTGCTAACTAGACGTACATACTCGATTT-----TCGAGAGCCCGGTATTCCGAGGGT-CGT--TCCTGCT--ACTT---CTG--G----------CCGTTGT-T-------------CGTGCA-TGTC------CT---GTGCG-------TACATA
+TGTG---C-GGT-------------ACGTGTTATGCACTTTGTGTATTACCTCCGTGCCGTCATTTGTT----TCGTA--CT-TG---CTCGT-------GTCGG-CAACGATA--CT--GGTTGTTT--GTGGGCGATCTTTACTACCGGCGTACACATA-AATCTTCTTAGAGGGACAGGCGGCTTCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCATGTC-CTCCCTGGCCGAGAGGTCCGGGTAATCCGGTGAAACTCCTTCGTGCTAGGGATTGGGGCTTGCAATTATTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCCGACCGGTACTC--CGAC-G----ACGTTTC-GAC------------------------------------------
+
+ Oxycheila TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAA---CTTAA---TGAAAGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTAC------AAAGTTACATGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCGTACCGGAGACGGAATGAGTGCTTTTATTAGATCAAAACCAAT-TGTGGC-----ATCC--CTAAGGCTCCATATGATTCTGTGTCTTTGCACA--CG--TTCATAT-GTCCTGGGTGTATGTTCATATTTTTTTATTGGTGAATCTGAATAACTT---GCTGATCGCATGGTC-TTGTACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTTTCGATGGTAGGATCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCTTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACAAGGAGCAACTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAGTAGCGTATATTAAAGTTGTTGCGGTTAAGAAGCTCGTAGTTGAATTTGTGTCTTGCTCTGTCGGTTCATCGCTGAC-TGCGGTGTTTAACTGGCATGGT--GCGAGACGTCTTG-CCGGAAGG--------GCATGGTATATGTTTTATTTG--------TGT-AAAATATAAT-------------------------------------------------------ATATACACTGGTAATTAATATTATATAGTTAATAG---------------CTATATTTA----------------------TATTTTAT---------TATTGGTTGTTT-------------------------------------------TAT---------------------------------ATTAT--AT-TGCGC--------------CAGATAA---------TA---ACGTGT------------------ACGT-AGTCC--GACT----TTATA-ATCCTGTCGAGGTGCTCTTAACTGAGTGTCGTCG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTTAAAGCAGGC----TAA-T-GTT---GCCTGAATATAGT-GTGCATGGAATAATGAAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCTGATC-AAACGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGACCGTCGCAAGACGAACTTAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACTATAAACGATGCCAGCTAGCGATCGGCCGAAGTTCCT-CCGATGACTCGGTCGGCAGCT-TTCGGGAAACCAAAGCCTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCTTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCAGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAGCGAGACTCTAGCCTGCTAAATAGACGTATAAACTCGATTTAACGATCGGGAGTCCGGTATTTCGAGGGT-TGT---CCTTCG--GCAA---CTG--G----------CCATTAT-T-------------TGTTCG-CTAC------TT---GTAT--------TTTACA
+TTTG---A-TGT-------------ATATAATACTTGTTAT-TGTATATATTTGG-------ATGTGTT----TTA----CT-TG---TTTGC-------GTCGAATAATGTAA--CT--AGTTGTTT--GTTGGCAATCTTTACTACCGGCGTATATTTG-TATCTTCTTAGAGGGACAGGCGGCTTCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAACGTGTC-TTCCCTGTTCGAGAGAACCGGGTAATCCGTTGAAACTCCTTCGTGCTAGGGATTGGGGCTTGCAATTATTCCCCATAAACGAGGAATTCCCAGTAAGCGTGAGTCATAAGCTCGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCGGACCGG--TACT-CGGCCG----ATGTTTC-GACG-----------------------------------------
+
+ Clinidium TCGTCTCAAAGATTAGGCCACGCATGTCTAAGTACAGCTTTCTATGTA-ATAAAGTGAAACCGCGAAAGGCTCATTAAATCAGTCATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCTGACCGGAAACGGGAGGAGTGCTTTTATTAGAACAAAACTGAT-CG---------GTGTTTCGTCTATTT------------------TATAGG--CG--TGC-----ATCGCAAGT---------GA-----AC--TGGTGAATCTGAATAACTTT-TGCTGATCGCATAGTCATAGCACTAGCGACAAATCTTTCAAATGTCTGCCCTATCAACTGTCGATGGTAAGATCTGCGCTTACCATGGTGATAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACTTCTAAGGAAGGCAGCAGGCGCGCAAATTACCCAATCCCGGCTCGGGGAGGTAGTGACGAAAAATAACGACACGGGACTCATCCGAGGCCCCGTGATCGGAATGAGTACACTTTAAATAATTTAACGAGGAACTATCGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCGATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATCTGTGTTCCGCGCTGTCGGTTCGCCGTTC----GCGGCGAT-CACCGGCACGTTC-GCGGAACGTCTTGGCCGGTGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCTTGGTGCTCTTTATTGAGTGTCTCGTCTT-TTCACCGGCACATTTTACTTTGAACAAATTAGAGTGCTTAAAGCAGGCAGCGTAACGCATTG--GCCTGTATAATGT-GTGCATGGAATAATGGAACAGGACCTCGGTTCTATGTTTCGTTGGTTTTGGAGAG--CACGAGGTAATGATTAACAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACTTAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAACGAAAGTCAGAGGATCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGAAGTTCTTATTTATGACTCGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCGGACACTGAAAGGATTGACAGATTGATAGCTCTTTCTCGATACAGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAGCGAGACTCTATCCTGCTAAATAGACGTTTA--------TCAAAAACCGG--------TATCACGAAGGCTTGTTGGCCCTTGTCGGTGTCATTGAGATG------------CACAACAC----------TTTTCAATGCTGATTACTAATATTACGGAC---GAATGCT
+TGTTGATTTCCT--------------CACGGGGTTGAT------------------------AAGTGTTCGGCTCGTATGAGGTGGTTAGTACTTGGAATGCTGGGGTCCCTCAGTGCCCACTTGTT---GGTCACGGTTTTTACTACCGGCGTACAATTG-AATCTTCTTAGAGGGACAGGCGGCTTCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCTGGGCCGCACGCGCGCTACACTGAAGGAATCAACGTGTG-CTCCCTGGCTGAGAGGCCCGGGTAATCCGTTGAACCTCCTTCGTGCTAGGGATCGGGGATTGCAATTATTCCCCGTGAACGAGGAATTCCTAGTAAACGTCTGTCATAAGCGGGCGTTGAATACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTGGTGAGGTCTTCGGACCGG--CACG-TGGC-A----ATGTTTC-GGCATTGCTGGCGG-CGCTGTAAAGATGACCGAACCTGATTATTT
+
+ Omoglymmius -----------------CCATGCATGTCTAAGTACAGCTTTCTATGTAACAAAAGTGAACCCGCGAAAGGCTCATTAAATCAGTCATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCTGACAGGAGACTGAAGGAGTGCTTTTATTAGATCAAAACTGAT-CGGTGTGTTTTACGGC-CGGACGTTTTA----------------CGTACG--TG--TCCGTAG-GCCACCG-----------CAAGT--GAACTGGTGAATCTGAATAACTT-ATGCTGATCGCATGGTC-ACGTACCGGCGACGCATCTTTCAAATGTCTGCCCTATCAACTGTCGATGGTAGGATCTGCGCCTACCATGGTGATAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCAATCCCAGATCGGGGAGGTAGTGACGAAAAATAACGACACGGGACTCATCCGAGGCCCCGTGATCGGAATGAGTACACTTTAAATAATTTAACGAGGAACTATCGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCGATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATCTGTGTTTCGCGCTGTCGGTTCGCCGTTC----GCGGCGAT-CACCGGCACGTTC-GCGAAACGTCTTGGCCGATGG-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------GTCTTGGTGCTCTTTATTGAGTGTCTCGACTTGTTCATCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTTAAAGCAGGCAGCGTAACGCATTG--GCCTATATAATGT-GTGCATGGAATAATGAAACAGGACCTCGGTTCTATGTTTCGTTGGTTTTGGAGAG--CACGAGGTAATGATTAACAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACTTAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAACGAAAGTCAGAGGATCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGAAGTTCCT-CCGATGACTCGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCGGACACTGAAAGGATTGACAGATTGATAGCTCTTTCTCGATACAGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAGCGAGACTCTATCCTGCTAACTAGACGTTTA--------TTAAA-ACCGG--------TATCACGAAGGCTCGTTGGCCCTTGTTGGTGTCATTTTGGTGTACAATTCTTTTTGGGGGCTA--------ATTTTCAATATGA-----CTTGACTGTGT-----TCCTATT
+TATAGGGCATGGCTT----------GTATGAGATT---------------------------ATTAGTTTTC-TTGAA----ATGCT-TGCGT--------CCCAA-------GGTGCCCACTTGTT---GGTCACGGTTTTTACTACCGGCGTACAATTT-AATCTTCTTAGAGGGACAGGCGGCTTCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTCCTGGGCCGCACGCGCGCTACACTGAAGGAATCAACGTGTG-CTCCCTGGCTGAGAGGCCCGGGTAATCCGTTGAACCTCCTTCGTGCTAGGGATCGGGGATTGCAATTATTCCCCGTGAACGAGGAATTCCTAGTAAACGTCTGTCATAAGCGGGCGTTGAATACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTGGTGAGGTCTTCGGACCGG--CACG-TGGC-A----ATGTTTC-GACATTCCTGGG---------------------------------
+
+ Trachypachus TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CCAAA---TTAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGTTCCAACCGGAGACGGAAGGAATGCTTTTATTAGATCAAAACCAAT-CG---------GCGG--CGGTCGCTT-------------------GCGAT--CG--TTC-----GCCGGCA-----------CA-------CTTGGTGACTCTGAATAACTTTATGCTGATCGCACGGTC-TTGCACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACGAGGATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATCTGTGTCCCGTGCTGTCGGTTCACCGCCC----GCGGTGTTAAACTGGCACGTTC-ACGGGACGTCCTG-CCGGTGGAT-----------------TGGTTAT------------TGCTT-----------------------------------------------------------------TATGCTATTGTTTTCTGTTTCAT---GC---------------------TCGCATGTGTATG--------------TACGTGTTAAA---------GCGTAATATATTAT------------------------------------------------------------------------------GTGTGTTGTATGTAT--------------TCAGTTAGTG-----------ATACATTTTGC-------------AGTACCATCC--GACT----TTTAA--TCCTGTCGCGGTGCTCTTAATTGAGTGTCGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----TAA-A-ATTT-CGCCTGAATATTGT-GTGCATGGAATAATGGAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAA--CCCCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAAATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGACGTTCCT-CCGATGACTCGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCAGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTAGCCTGCTAACTAGGCGTAC--------TTTA----CCGG--------TATCTCGAAGGCTCAC--AGCTCCC---TTA---TCGGTG--------------TGTGC-------------TGCACGTTATTG------TCATTCTTG---------CATT
+TCGGTGTTAAGTT-------------------------------------------------ATGTACTTTA-GCGTG---TTTG---TACATT-------TCCG-----------TTTGTGGAGTT------TGTGGTTTTTACTACCGGCGTACAATTG-AATCTTCTTAGAGGGACAGGCGGCTCCTAGCCGCATGAGATTGAGCAATAACAGGTCTGTAATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTC-TTCCCTGGCCGAACGGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTAGGGATTGGGGCTTGCAATTGTTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCAGACCGG--TACG-CGAT-G----ACGTTTC-GACGT----------------------------------------
+
+ Systolosoma TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CCACA---TTAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCCGACCGGAGACGGAAGGAGTGCTTTTATTAGATCAAAACCAAT-CG---------GTGG--CGTTGCTTTA----------------CGGCTT---CG--TTC-----ACCGGCA-----------CA-----TT--TGGTGACTCTGAATAACTTTATGCTGATCGTACGGTC-TTGCACCGACGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATCTGTGTCCCGTGCTGTCGGTTCACCGCCC----GCGGTGTTAAACTGGCACGTCTCACGGGACGTCCTG-CCGGTGGACGTTGTTATCGTGCTGTTTCGGCTGCATATGCTTGCATGCATGCGCGCCCTAC-C-------------------------------------A--------TATCAGTGCTGTATGATGACTCTTGAG----------------------------TAACATGTGCG--------------------CATTTGGTG--------TGTAGGGGTCGTCG-----------------------------------------TGTGTATG---------------------------TGTGGTGTGTGTGTGC--------------TGTGCA---------------GTGTGG-------------------TGCACGTCC--GACTT---TTGAA-ATCCTGTCGCGGTGCTCTTAATTGAGTGTCGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTTAAAGCAGGC----TAA-A-ATTT-CGCCTGAATACTGT-GTGCATGGAATAATAGAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAA--CCCCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAAATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGTCGACGTTCCT-CCGATGACTCGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCGGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTAGCCTGCTAACTAGGCGTTA--------CTTA----CCGG--------TATCTCGAAGGCTCGC--TGCTCCCTTGCTTAG-CTGCCGTT-------TGTGTTGTGTA-CGC-------GCGCACATTATCTC----GCAG-GTATG-------CCCGTG
+TCCGCACGGTA--------------GTGTAC-C------------------------------TGTGCGGGT-GTGTGTGTTGTG---TGCGTGGCCGGCGGTGGTGT-----G--CTTGTGGAGTT------TGCGGTTTTTACTACCGGCGTACAATTG-AATCTTCTTAGAGGGACAGGCGGCTCCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTC-TTCCCTGGCCGAACGGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTAGGGATTGGGGCTTGCAATTGTTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGAATGAATGATTTAGTGAGGTCTTCGGACCGG--TACG-CGAT-G----ACATTTCGTGTGTGATCGATGT-CGCGGGGAAGATGAACAAACTTGATCATTT
+
+ Metrius TTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACAAA---CTTTTTA-TAAAAGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATGGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACTGAGCTCCAACCGGTGACGGAAGGAGTGCTTTTATTAGATCAAAACCAATACGGCG------GCGA--CTATTGTTT--TA-------------TTACTTT--AG--TTCGTAC-GTCGCAA----------ATA------T--TGGTGACTCTGAGTAACTT-ATGCTGATCGTACGGTC-TAGTACCGACGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGATCTGCGCCTACCATGGTTGTAACGGGTAACGGG-AATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCACGCAAATTACCCACTCCCAGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACGAGGATCTATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATCCCAGCTCCAATAGTGTTTATTAAAGTTGTTGCGGTTAAAAAGCTCGTGGTTGAATTTGTGTCCCGTGCTGTCGGAACACTGCCC----GCAGTGTTTAACTGGCATGTTTCACGGGACGTCCTG-CCGGTGGATGCGTCATACTTTATACGTGTACTTACCA--------TACACATAATTTACCATTTGGTGATAATAACATTGCAATTAAAACATTTCATATTATGTTGCGGGCACGACTCTTTATTAAAATTAATCATATTATGGCCCCCCAT--------TAAAATTATTGGTGCACGATTT--------TATCGTTGTTTATCAATATTTTATATGGTCATAAT-------------------------------------------TGATTAAAAAGATGTTCGTTGTTTATCGCTCATTATGTTATGTGCTTTTGTTTTCTTAT------CCGGTTTATTATGTTTAA---ATGTATGGGGTCCGTATATTTGTTATGC-CATCC--AGACT---CATAA-ATCCTGTCGCGGTGCTCTTAATCGAGTGTCGAGG----CAGGCCGGCACATTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----CAA-A-ATTA-TGCCTGAATACAATTATGCA-GGAATAATGGAATAGGGCCTCGGTCCTAT--TTTGTTGGTTTTTGGA---CAATGAGGTAATGATTAATAGGGACAAGATGGGGGCATTCGTATTCCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACTAAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAGCGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGAAGTTCCT-CCGATGACTCGGCGGGCAGCTATACGGGAAACCCAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCAGACACTGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCAGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTAATTCCGATAACGAACGA-ACTCTAACCTGCTAACTAGGCGTA---------TTTAA---CCGG--------TATCCTGAAGGCTCGT--GTTCACC--GCATTAACTGGTGATCGGTAC-CCCATTGT-GT-TCTACATCACACATATA-TGTGAGG---TT---GTATG-------GGCATC
+TATG---A-TGTTTCGTCTTAATTGACGTTCTTATAGTTGTACCGCTACCTATTCAAACACATTATGTT----GTTTG--TT-AG---TTCACT----GGGTTCTTGTCCGTGA--TCTGGGCGGTCT--GTTCACGGTTTTTACTACCGGCGTACACATA-AATCTTCTTAGAGGGACTGGCGGCATCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTAATTCCTTGGCCGAAAGGTCCGGGTAAACCGTTGAATCTCCTTCGTGCTAGGGATTGGGGATTGCAATTATTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTTGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTCCGGACCGG--CACC-CGGC-G----GTGTTTC-GATATCGCCGATGCGTGCTGGGAAGTTGACCAAACTTGGTCATTT
+
+ Pachyteles TTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACAAA---CTTTTTA-TAAAAGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATGGTACC-----ACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACTGAGCTCTAACCGGTGACGGAAGGAGTGCTTTTATTAGATCAAAACCAATACGACG------GCAT--TATTTATTTTTAATAA------------ATTAA--TG--TAC-----GTCGTTT-T---------TA------T--TGATGAATCTGAGTAACTT-ATGCAGATCGTATGGTC-TAGTACCGACGACGCATCTTTCAAATGTCTGACTTATCAACTGTCGATGGTAGGATCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCACGCAAATTACCCACTCCCAGAACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACGAGGATCTATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGTTTAAAAAGCTCGTAGTTGAAATTGTGTCCCGTGCTGTCGGTACACCGCCC----GCGGTGTTTAACTGGCATGTTTCACGGGACGTCCTG-CCGGTGGGTGCGTCGTACAATTTACGTGTACTTACCATACAACATTGTCCATATGATAAATACATTGTATTTAAAAACGTTCATTTATAAATATGTTGACGGTGCACGTTATTTATATAATATTTAAATAAATATATTATGGTTCCCCAATATATTAAATAAATTTACTGGTGCACGATATATATATTATATATTTATTATATACATATATATATCGTTTTGTTATCAGTAAAAATATATTGGTCATAATAAATAAAAATTTATTTATAATATATAATAAATAACGTTGTTTTTATCGCTCATATTTTATGTTCGTACATTGTTTAAATTTATCGGTCAATGTAAATTAAAATGTTTGGAAGTCCGTAAATTTGTTTACGC-CATCC--AGACT---CATAA-ATCCTGTCGCGGTGCTCTTAATCGAGTGTCGAGG----CAGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----AAA-A-ATTA-TGCCTGAATACATTTATGCATGGAATAATGGAATAGGACCTCGGTTCTAT--TTTGTTGGTTTTTTTGAA-CAATGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACTAAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAGCGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGTCGAAGTTCCT-CCGATGACTCGACGGGCAGCTATACGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAATCTCACCAGGCCCAGACACTGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCAGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTAGCCTGCTAACTAGGCGTA---------CTTAA---CCGG--------TATCTAGAAGGCTCGT--GTTCACC--GCATTAACTGGTGATCAATAAATTTCTTATATA-TACCAACACTATGTTAA-TATGGGG---TT---GTTTGTGGTAACTATATT
+TTCA---T-TACTAGTTGATGTTTAATATAGTTTTCTGCTTTCAATCTAATTTGTAAACATATTTCATT----GTTGT--TT-TG---TGTATATATAAGGGTTTGTTTTGTGA--TCTGGGCGGTCT--GTTCACGGTTTTTACTACCGGCGTACACATA-TATCTTCTTAGAGGGACTGGCGGCATCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTATTTCCTTGGCCGAAAGGTCCGGGTAAACCGTTGAAACTCCTTCGTGCTAGGGATTGGGGATTGCAATTATTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTTGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTCCGGACTGG--CACC-CGAC-G----GTATTAC-GATATCGCCGATGTGTGCTGGGAAGTTGACCAAACTTGGTCATTT
+
+ Scaphinotus TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CCAAAA--ATAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCCGACCGGAGACGGGAGGAGTGCTTTTATTAGATCAAAACCAAT-CG---------GTGG--C--GGGTTC-------------GCGTTCGCG----CG--TTCA--C-GTCCACCGT---------CAA-----TAATGGTGACTCTGAATAACTTTATGCTGATCGCACGGTC-TCGCACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACAAGGATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATTTGTGTCCCGCGCTGTCGGTTCACCGCCC----GCGGTGTTTAACTGGCACGATC-GCGGGACGTCCTG-CCGGTGGA-------------------------------------TGTTTGT----------------------------------------------------------------GTGTGGCTGGGTTC----------------------------------TCATGTGTGTG--------------------TGTTGT-----------TACAGTGCCTTCG------------------------------------------TGGT--------------------------------GTTGT---TTCGCGCACCGTGT-------GGGGCTC--------------GCATGTCA----------------CCGCACATCC--GACT----CAAAA-ATCCTGTCGCGGTGCTCTTAATTGAGTGTCGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTTAAAGCAGGC----TAA-A-ATTT-TGCCTGAATATTGT-GTGCATGGAATAATGAAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAAC-CACCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATTGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAAATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGTCGATGTTCCT-CCGATGACTCGACGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCGGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTGGCCTGCTAACTAGGCGTAA--------CTTA----CCGG--------TATCTTGAAGGCTTGC--GTCTCTC--GTTCT--CTGT------------CCGTGAG---------------TGTGTG-TGTGCG----TT---GGGTGT------GGCGTT
+TGGG---TGTAC--------------CGTGCGTTTTGGCGTTTGGTCACA-----------CTCTCGTTCAT-TCGCG--TA-TA---TACATTACTACGGGCAA--------G--GC--GGGAGTT------CGTGGTTTTTACTACCGGCGTACAATTG-TATCTTCTTAGAGGGACAGGCGGCTCCTAGCCGCACGAGAATGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTC-CTCCCTGGCCGAACGGCCCGGGTAACCCGCTGAAACTCCTTCGTGCTAGGGATTGGGGCTTGCAATTGTTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGCGTTGAATACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTTGGACTGG--CACG-CGGC-A----GCGTTTC-CACATTGCCGATGT-CGCCGGGAAGATGACCAAACTTGATCATTT
+
+ Nebria TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CCAAA---ATAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACA----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACACGCAAACAGAGCTCCGACCAGAGATGGAAGGAGTGCTTTTATTAGATCAAAACCAAT-CG---------GCGGG-CAGGCACTGC-----------------TGTC----TG--TTC-----GTCGCCC-----------TA-------TTTGGTGACTCTGAATAACTTTATGCTGATCGTACGGTC-TTGCACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACAAGGACCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATCTGTGTCCCGTGCTGTCGGTTCACCGCCC----GCGGTGCT-AACTGGCACGTCTCACGGGACGTCCTG-CCGGTGGA---------------------------------------------------------------------------------------------------------------AGACCA-A-------------------------------------TCGCTCA-----------------------GTATTGTC----------TGGGGTCTGTGCGT---------------------------------------------------------------------------GCATAACGCGCGTACAGAATTCC--------CGGGT----------------GCTCGG-------------------TGATCCTTCC-GACTT---TTTTAAATCCTGTCGCGGTGCTCTTAATTGAGTGTCGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----TAA-A-ATTT-CGCCTGAATACTAT-GTGCATGGAATAATGGAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAA--CCCCGAGGTAATGATTAATAGGGACG-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAAATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGTCGATGTTCCT-CCGATGACTCGACGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACAAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAACCTCACCAGGCCCGGACACCGGAAGGATTGACAGATTGATAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGTCGTTCTTAGTTGGTAGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTAGCCTGCTAAATAGGCGTAC--------TCTA----CCGG--------TATCTCGAAGGCTCAC--ATCTTCCGTACTAA--CCGTA-----------CGTCTGT---------------TCGTCGGTGTTTC---------AATCG--------GTGTT
+CATA-------------------------------------------------------------CACTGTGCGAGCATTTTGCGGC-TTCGT--------GCGG-----------GC-GGAATGTT-------GTGGTTTTTACTACCGGCGTACATTTT-AATCTTCTTAGAGGGACAAACGGCTTATAGCCGTATGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTC-TTCCCTGGCCGAATGGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTAGGGATTGGGGATTGCAATTATTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAACTCGTGTTGATTAAGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCGGACTGG--TACT-CGGCCG----GGGTTTC-GACAT----------------------------------------
+
+ Loricera TTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACAAG---CTAAA---ATAAAGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGACCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCCAACCGGAGACGGAAGGAGTGCTTTTATTAGATCAAAACCAAT-CG---------GTAGA-C--GGGTCCGTTACGG-----CG-----GTCTC--CG--TTT-----ATCGTACAC---------CA-------AATGGTGACTCTGAATAACTTT-TGCTGATCGCACGGTC-TCGCACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGATCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCAGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACAAGGACCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGTTTAAAAAGCTCGTAGTTGAATCTGTGTGTCGCACTGTCGGTTCACCGCCC----GCGGTGTC-AACTGGCACGTT--GCGAGACGTCCTG-CCGGTGGA------------------------------------------------------------------------------------------------------------------------------------------------------------CTGTAGGTA----------------------TATCAT-----------TTCGGTG-------------------------------------------------------------------------------------------GTATGC----------------CAAG-----------------GTCCG-------------------------GTTT--TTTGT---TAAAA-ATCCTGTCCTGGTGCTCTTGATTGAGTGTCTCGG----CAGGCTGGCACGTTT-ACTTTGAACAAATTAAAGTGCTCAAAGCAGGC----GAA-A-ATTA-TGCTTAAATAGTGT-GTGCATGGAATAATATAATAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAACATTCCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACTAAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAACGAAAGTCAGAGGCTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGTCGACGTTCCT-CCGATGACTCGACGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACTGGAAACCTCACCAGGCCCAGACACCGAAAGGATTGACAGATTGAGAGCTCTTTCTTGATACGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGATTGATTTGTCTGCTTAATTGCGATAACGAACGAGACTCTAGCCTATTAAATAGACGTTA--------CTTA----CCGG--------TATCTCGAAGGT-CGT--GGCTACC--GCTTCATTCGTCA----------CGGGCAT---------------TTTTCA-TACAA------C---GTACAA------CTTGT-
+TGTG---CCTGT---------------ATGA--------------------------------TGTGTT----CTG-------TG---TGCGT--------TATGTT----------C--GGTGGTT------CATGGTTTTTACTACCGGCGTACATATG-AATCTTCTTAGAGGGACAGGCGACTTCTAGTCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACAATGAAGGAATCAGCGTGTC-TTCCCTGGCCGAGAGGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTTGGGATTGGGGCTTGCAATTGTTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATTATTTAGTGAGGTCTTCAGACTGG--CACC-CGGT-G----GCGTTTCTAACA-----------------------------------------
+
+ Elaphrus TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CCAAA---TTAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC----CACATTTACATGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAACTCCAACCGGAGACGGAAGGAGTGCTTTTATTAGATCAAAGCCAAT-CG--GC-----GTC---T--GGGTTC-------------------GCC----CG--TTC-----GCCGCCC-T---------CA------T--TGGTGACTCTGAATAACTTTTGGCTGATCGCACGGTC-TTGCACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGAACACTTTAAATCCTTTAACAATTAACAATTGGAGGGTAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATCTGTGTCCCGCGCTGTCGGTTCACCGCCC----GCGGTGTT-AACTGGCATGTCTTGCGGGACGTCCTG-CCGGTGGA---------------------------CG--------CGT-CGT--------------------------------------------------------------A-------CG-----------------------------------------TAC--GTG----------------------TATTCA-----------TTC-GTC----T-------------------------------------------TGA---------------------------------ACGGT--GT-TGCAC--------------GTGGC----------------GTGCG----------------------C-CGTCC--GACT----TACGA-ATCCTGTCGCGGTGCTCTTAATTGAGTGTCGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----TAA-A-ATTT-CGCCTGAATACTGT-GTGCATGGAATAATAGAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAAC-CC-CGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAAATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGAAGTTCCT-CCGATGACTCGACGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAATCTTACCAGGCCCGGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGGTTTGTCTGGTTTATTCCGTTAACGAACGAGACTCTAGCCTGTTAACTAGGCGTTACT-------TA-----CCGG--------TATCTCGAAGGCTCGC--GTCTGCC--G-TA---CTGCAG----------C-GTCGT----------------GTGCA-CGTA-------T---GTGTG-------TCCGTT
+ACGG---C-GGT-------------GCATGT------------GCGT------------------TGTT----ACTGG--CG-TG---CGCGG-------G----------------C--GGGAGTT------CGCGGTTTTTACTACCGGCGTACAATTG-AATCTTCTTAGAGGGACAGGCGGCTTTTAGCCGCACGAGATTGAGCAATAACAGGTCTGTAATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTC-CTCCCTGGCCGAACGGTCCGGGTAACCCGCTGAAACTCCTTCGTGCTAGGGATTGGGGCTTGCAATTCTTCCCCATGAACGAGGAATTCCCAGTAAGCGTGAGTCATTAACTCACGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCGGACTGG--TACG-CGAT-G----GTGTTTC-GACAC----------------------------------------
+
+ Antarctonomus TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAA---CTAAA---ATAAAGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCCAACCGGAGACGGAAGGAGTGCTTTTATTAGATCAAAACCAAT-CG---------GCGGCGGGTTCGTTTCGG---------------CGTTCTC-CG--TTC-----GTCGCAC-----------TG-------TTTGGTGACTCTGAATAACTTTATGCTGATCGCACGGTC-GAGCACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACGAGGACCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATCTGTGTCTCGCACTGTTGGTTCACCGCCC----GCGGTGTTTAACTGGCACGTT--GCGAGACGTCCTG-CCGGTGGA------------------TCGTGTCATGG-----GCATGCTCGCG-------------------------------------------------------------AGCTGTAATTGCA-------------------------------------TTCTCCGTACA--------------------CATTCGT---------GTGTTGCGGT-----------------------------------------------------------------------------------TTATGTGTATGCACG-------------CACGTTGT-------------GTATGTTCC---------------ATGCACATCC--GACG----TTAGAAATCCTGTCGCGGTGCTCTTAATTGAGTGTCGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----TAA-A-ATTT-TGCCTGAATATTGT-GTGCATGGAATAATGGAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAA--CCCCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAAATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGACGTTCCT-CCGATGACTCGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCAGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTAGCCTGCTAACTAGGCGTAA--------CTTA----CCGG--------TATCTCGAAGGCTCGT--GTCTTTCGTCTTTCGGCTGCG-----------TATTCGTGCAACG---------TACACGCCGTCTC---------GTACG----------GTT
+TGTG-----------------------------------------------------------CCTGTT-----CA--------G---TACGTT------GTCCG---------------GGGCGTTA--GTTCACGGTTTTTACTACCGGCGTACATATG-AATCTTCTTAGAGGGACAGGCGGCTTCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTC-TTCCCTGGCCGAACGGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTAGGGATTGGGGCTTGCAATTGTTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCGGACCGG--CACG-CGGC-G----GCGTTTC-GACATCGCCGATGT-CGCTGGGAAGATGACCAAACGTGATCATTT
+
+ Omophron TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CCAAA---TTAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCTGACTGGAGACGGAAAGAGTGCTTTTATTAGATCAAAACCAAT-CG---------GCGT--C--GGGTTCCGT--------TTACGCGGGCT----CG--TTC-----GTCGCCC-----------TA------T-TTGGTGACTCTGAATAACTTTTGGCTGATCGCACGGTC-TTGCACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACAAGGACCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTATTTGAATCTGTGTCCCGCGCTGTCGGTTCACCGCCC----GCGGTGTTTAACTGGCACGTCTCGCGGGACGTCCTG-CCGGTGGGTGCGTTGTTCGTTCTATATGTACACTTTATTATGTTATATGTGATTTCCAA---------------------------------------TTGAT-----------ACTTACAATAATGTTACCTATT----------------------------TTATATATA----------------------TATTTATTA-GTATATATTTAGTGTTTTCAT-----------------------------------------TGGTTTGGGG---------------T----------ATTGTTGGTGCATGTATATACAT--T--TTAAAT----------------GTGTCTTTAGTTCTGA--------ATAC-CACCC--GACT----TACGA-ATCCTGTCGCGGTGCTCTTAACCGAGTGTCGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----TAA-A-ATTT-CGCCTGAATATTGT-GTGCATGGAATAATGGAAAAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAAC-CCCCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAAATGTTTTCATTAATCAAGAACGAAAGTCAGAGGCTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGTCGACGTTCCT-CCGATGACTCGACGGGCAGCT-TCCGGGAAACCAAAGTTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAATCTCACTAGGTCCGGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGATTGGTTTGTCTGGTTAATTCCGATAACGAACGAGATTCTAGCCTGCTAACTAGGCGTT----------CT-----CCGG--------TATCTAGAAGGCTCGC--GGCTCTC--GTTA---ACGTGAA----------CATTGTGTT-CA--AATACGAAGTGTA-TGTTGTG---TT---CTATAGGTCTTGCTTGTT
+TATGAAATGTGTAATGGTAGCAATACTATTGCATATGATTATCAAGTGTAGGTCTATA---TATCCACTGCA-TTAGT--TT-TG---GCCAT-------GTTTA---C----G--GTACGAGTGTT------CGCGGTTTTTACTACCGGCGTACAATTA-AATCTTCTTAGAGGGACAGGTGGCGCTTAGCCGCACGAGATTGAGCAATAACAGGTCTGTAATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTC-CTCCCTGGCCGAATGGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTAGGGATTGGGGCTTGCAATTATTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGCGTTGATTAAGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCGGACTGG--TACG-CGGTGG----AATTTTTCGATT-----------------------------------------
+
+ Pasimachus TTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACATA---CTATA---ATAAAGTAAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCATTAGATCGTACCACTATAAGTTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAATTCTGACCGGAGACGGGAGGAATGCTTTTATTAGATCAAAACTAAT-CG---------ATGT--CG-GAATTTT-T-----------------TTTC--CG--TTT-----ATCGTAAAT-----TTTTTA------TG-TGGTGAATCTGAATAACTTT-TGCTGATCGCATGGTC-TTGTACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGATCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCACGCAAATTACCCACTCCCAGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACGAGGACCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAGAAGCTCGTAGTTTGATTTGTGTCTCACGCTGTTGGTCCACTGCCC----GCAGTGTT-AACTGATATGAC--GTGAGACGTCTAG-CCGGTGAA---------------------------------------TTCA-----------------------------------------------------------------ACAAGGTTGCAGTTTTT-CA----------------------------TTTTCTATA----------------------TATTTAA---------ATA-AATTTT----------------------------------------------TA----------------------------------ATGATA-ACTTGTAA--------------ACGGTTGA-------------ATTCAAC----------------------TTTAT--GTTTA---TAAAG-ATCCTGTCACAGTGCTCTTGACCGAGTGTTTTGC----CAGGCCGGCCCATTT-ACTTTGAACAAATTAGAGTGCTTAAAGCAGGC----AAA-A-ATTTACGCCTGAATAATAT-GTGCATGGAATAATAGAATAGGACCTCGATTCTAT--TTTGTTGGTTTTGAGAA--TTAAGAGGTAATGATTAATAGGGACA-GATGGGGGCATTTGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACAGACTTAAGCGAAAGCATTTGCCAAATATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGAAGTTACT-ACCACGACTCGGCGGGTAGCT-TTCGGGAAACCAAAGCCTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAATTTACCAGGCCCAGACACTGGAAGGATTGACAGATTGATAGCTCTTTCTTGATTCAGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTAGCCTACTAAATAGACGTACGA-T----TTT-----CCGG--------TATCTTGAAGGCGCAC--TTCATTC--GGTTTA-CCAT-ATGTTTTTGGTGTATTGTTCT-TGGGGAAAC--TCTTCA-CATTTT----TT---CAATGGAC--ACTTTATC
+ATCAATTCACTTTA-------------ATTTGTTTTGGTGTTATTGTTGTTTCTATTGTTAAATGAGTTGTT-GTGAAACCT-TG---ACCGGT----GTATCCAATTCATTGG--TC--GAATGTA----TGTGTTGTTTTTACTACCGGCGTACATTAA-ATTCTTCTTAGAGGGACAGGCGGCTTCTAGCCGCATGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACAATGAAGGACTCAACGTGTC-CTCCCTGACCGAATGGTCCGGGTAACCCGTTGAAACTCCTTCGTGATTGGGATTGGGGATTGCAATTTTTCCCCATGAACGAGGAATTCCAAGTAAACGCGAGTCATAAGCTTGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCAGACTGG--TACCACGGC-G----ATGCGTC-AAAAC----------------------------------------
+
+ Clivinini TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CCAAA---TTAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCCGACCGGAGACGGAAGGAGTGCTTTTATTAGATCAAAACTAAT-CG---------GCGA--CGGTGACTCTTTTTAA-----GGGTTTTAT-----CG--TTC-----GTCGTTC-T--------ATA------T---GGTGACTCTGAATAACTTTATGCTGATCGCACGGTC-TCGTACCGGCGACATATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACGAGGACCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATTTGTGTCCCACGCTGTCGGTTCACCGCCC----GCGGTGTT-AACTGGCACGTTTCGTGGGACGTCCTG-CCGGT-GA--------A--TGTTAGCGTTTCTTCATT--------TGC-CGC--------------------------------------------------------------ATGCTTACCCATATTTTAT-------------CAC---------------TTAA--TTG----------------------CGGTGAA----------TATGGGGGTGTG-------------------------------------------TTG---------------------------------GTTATTTGT-TGTA---------------TTGGC-----------------TACAT------------------TCGA-CTTGT--AATA----TA-GA-CTCCTGTCACGGTGCTCTTAACTGAGTGTCGAGG----CAGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----TAA-A-ATTTACGCCTGAATATTGT-GTGCATGGAATAATGGAACAGGACCTTGGTTCTAT--TTTGTTGGTTTTCGGAAC-CC-CAAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGACGTTCCT-CCGATGACTCGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGAAAACCTCACCAGGCCCGGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTAGCCTATTAACTAGGCGTTACA--C---TTT-----CCGG--------TATCTCGAAGG--------CCCACA--TCAT---TCG---------------GTTAG-C-------------CTTTCG-CGT--------T---GTACG-------CATGTC
+AGGG---T-TAC-------------GCATGTTTC-----------------------------TCTGCT----GCG-------TG---CGCGT-------GTTTG--------G--TC--GGATGTT----TGTGCGGTTTTTACTACCGGCGTACAATTA-ATTCTTCTTAGAGGGACAGGCGGCTTCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAACGTGTT-TTCCCTGGCCGAATAGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTAGGGATTGGGGATTGCAATTATTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGTGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATGTAGTGAGGTCTTCAGACTGG--TACG-CGGC-G----GTATTTT-CGGAT----------------------------------------
+
+ Dyschirius TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CCAAA---TTAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCTGACCGGAGACGGAAAGAGTGCTTTTATTAGATCAAAACCAAT-CG---------GCGG--CGGTGTTTC------------------GGC-AT--CG--TTT-----GTCGTCC-----------TA-------TTTGGTGACTCTGAATAACTTTATGCTGATCGCATGGTC-TCGTACCGGCGATGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACGAGGATCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATCTGTGTCCCACGCTGTCGGTTCACCGCCC----GCGGTGTT-AACTGGCACGTTTCGTGGGACGTCCTG-CCGGTGGA-------------------------------------------------------------------------------------------------------------TGGGGTTGCG-----TATG-----------------------------TAT-TATG----------------------TGTTC------------TATTGTTATTTA-------------------------------------------TAAC--------------------------------ATAGT---TTCATG---------------TATGC----------------ATGCGT---------------------CCCATCC--GACTTTTATAAGA-TTCCTGTCACGGTGCTCTTAATTGAGTGTCGAGA----TAGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----TAA-A-TTTAACGCCTGAATATTGT-GTGCATGGAATAATAGAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAA--CCCCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGACGTTCCT-CCGATGACTCGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCGGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTAGCCTGCTAAATAGGCGTAAC-------TTT-----CCGG--------TATCTCGAAGGCTCAC--ATCTTTC--GGTATG-CCG-----------------TGT----------------ATGCG-TGTCGC----TTGA-ACACA-------TTCATC
+TTCG-------------------G---GTGG---------------------------------ATGATGG--GCA-----T-CG---GCCGTAT------GCCGG----------TC--GGAAGTT----TGTGTGGTTTTTACTACCGGCGTACAATTA-ATTCTTCTTAGAGGGACAGGCGGCTTTCAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAACGTGTC-TTCCCTGGCCGAATGGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTAGGGATTGGGGCTTGCAATTGTTCCCCATGAACGAGGAATTCCCAGTAAGTGCGAGTCATAAGCTCGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCGGACTGG--TACG-CGGCGG----TAGTTTCGATTATTGCCGATGT-AGCTGGGAAGATGACCAAAGTTGAT-----
+
+ Creobius TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CTAAA---CTAAAGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATTGTACCACA-AAAATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTTTAACCAGAGATGGAAAAAGTGCTTTTATTTGAACAAAACCAAT-CG---------GTGA--C--GTGTTTC----------------CAGTTTAC-TGGTTTCACATAATCACTG----------AAA-----TTTATGATGAGTCTGAATAACTTTTTGCTGATCGCATGGTC-TTGCACCGGCGACGTATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGATTTGCGCCTACCATGGTTGTTACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCATTCCCAGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACAAGGACCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATTTGTGTCTCGTGCTGTTGGTTCACCGCCC----GCGGTGTT-AACTAGCATGTTC-ACGGGACGTCCTG-CCGGTGGG--------------T----------------------TGTTGGAGCTTTACA-----------------------------------------------------TCATTTCTACCATATAATACA-A-----------------------------TAAAAATAG---------------------TATTATT----------TTTAATAATTACT------------------------------------------------------------------------------ATTTTTCATATGTGTGTG-----------AGGGTGTTCTGT----------TGCACAATCC-------------GTTACTGCTTATAACACAACAGTAAAATCCTGTCGCGGTGCTCTTAATTGAGTGTCGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAAAGTGCTCAAAGCAGGC----TAA-A-ATTT-TGCCTGAATATTGT-CTGCATGGAATAATGGAAGAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAA--CACCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGACGTTCCT-CCGATGACTCGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCAGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAATGATTTGTCTGCTTAATTGCGATAACGAACGAGACTCTAGCCTGCTAACTAGGCGTTA--------CTTA----CCGG--------TATCTCGAAGGCTCGC--GGCTCTTT-GTTATA-ACGTGG----------C---CGTGC-----------------CAGTGTTAGGTATTC---ATATACAAAATTCTTGTA
+ATTG-----------------------------------------------------------CGTATTG---GTGCCTTCCATTGAACACGT-------AACCACG---------GTGCAAGAGTT------TGCGGTTTTTACTACCGGCGTACATATA-TATCTTCTTAGAGGGACAGGCGTCTTCCAGACGCACGAGATTGAGCAATAACAGGTCTGTAATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAACGTGTC-CTCCCTGGCCGAAAGGTCCGGGTAACCCGTTGAACCTCCTTCGTGCTAGGGATTGGGGCTTGCAATTGTTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGCGCTGATTAAGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCGGACCGG--CACA-CGAT-G----GTGTCTTCGATACCATTGATGC-CGCTGGGAAGATGACCGAAC----------
+
+ Bembidion TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAG---CCAAA---TTAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCCGACCGGAGACGGGAGGAGTGCTTTTATTAGATCAAAACCAAT-CG---------GCGTC-AGTACGTTTCG---G------------CGTTAC--TG--TTC-----GTCGCAC-T-----------------TTTTGGTGACTCTGAATAACTTTTGGCTGATCGCACGGTC-TTGCACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTATAACAAGGACCAATTAGAGGGCAAGTCTGGTGCCAGCCGCCGCGGTAACTCCAGCTCTAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATCTGTGTTCTGCGCTGTCGGTTCACCGCCC----GCGGTGTT-AACTGGCACGTCTCGCAGAACGTCCTG-CCGGTGGA-------------------------------------TGTGTGTCCTT-----------------------------------------------------------TGTCTACTTGC------CCA-----------------------------TTATGCGTG----------------------TGCAAC-----------TTCGGTTGTTAC-------------------------------------------TGT---------------------------------ATAGT--GCGTGTA---------------AGGGTCAA-------------ATGTGT-------------------CAC-CATCC--GACT----CAATA-ATCCTGTCGCGGTGCTCTTAACTGAGTGTCGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----TAA-A-ATTT-TGCCTGAATACTGT-GTGCATGGAATAATGGAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAA--CCCCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAAATGTTTTCATTAATCAAGAACGAAAGTCAGAGGCTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGACGTTCCT-CCGATGACTCGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGACACCTTACCAGGCCCGGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGTGCGAATTGTCTGGTTAATTCCGATAACGAACGAGACTCTAGCCTGCTAAATAGGCGTTA---------TTA----CCGG--------TATCCTGAAGGC-CGT--GGCTCTC--GTTTT--CTG----------------TCGT--------------ACTTTCGCTGTGG------C---GTATCA-------TCGTT
+TAGG-----CG----------------GTG---------------------------------TGCGTC----GCACG------G---GGTAT-------GTTCA--------G---TGCGGGAGTT------CACGGTTTTTACTACCGGCGTACATATA-ATTCTTCTTAGAGGGACAGGCGGCTTCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTAATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTT-TTCCCTGGCCGAGTGGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTAGGGATTGGGGCTTGCAATTTTTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGCGTTGATTAAGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCGGACTGG--TACG-CGGC-G----GCATTTT-GATGT----------------------------------------
+
+ Psydrus TTGTCTCAAAGATTAAGCCATGCATGTCTCAGTACAAA---CCAAA---TTAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACC----CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCCGACCGGAGACGGAAGGAGTGCTTTTATTAGATCAAAACCAAT-CG---------GCGG--CG-GTGTCTT-----------------TGCGATGCCG--TTC-----GTCGCAT-----------TG------T-TTGGTGACTCTGAATAACTTTTGGCTGATCGCACGGTC-TTGCACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGTTCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTGATCGGAATGAGTACACTTTAAATCCTTTAACAAGGACCCATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAACTTGTGTCCCGCGCTGTCGGTTCACAGCCC----GCTGTGTT-AACTGGCACGTCTCGCGGGACGTCCTG-CCGGTGGA-------------------------------------------------------------------------------------------------------------------------------------------------------------TGTGTTT-----------------------TGTT-------------CATAGTGT-----------------------------------------------------------------------------------GTCGTTTAACTATG---------------CTCAT-----------------TATGTTCA-----------------AACTATCC--TACA-----ACGA-ATCCTGTCGCGGTGCTCTTAATTGAGTGTCTCGG----TGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----TAA-A-ATTT-CGCCTGAATACTGT-GTGCATGGAATAATGGAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAA--CTTCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACAGAAGCGAAAGCATTTGCCAAAAATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGACGTTCCT-CCGATGACTCGGCGGGCAGCT-TTCGGAAAACCAAAGCATTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAAATTTACCAGGTCCAGACACCGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCGGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGTGATTTGTCTGGTTAATTCCGATAACGAACGAGATACTAACCTGCTAACTAGGCGTTA--------CTTA----CCGG--------TATCTCGAAGGCTCGCGGGTCTC----GTAA---CTGGCA-----------TATCGTTCC------------TCTACA-CGTT------------TTTGA-------TCGCT
+TCTG------------------------------------------------------------TGGTCATCTGCGTGCATGTCG----GTATT------GTTGG-----------CC--GAGATTT------CGCGGTTTTTACTACCGGCGTACAATTG-AATCTTCTTAGAGGGACAGGCGGCTTCTAGCCGCACGAGATTGTGCAATAACAGGTCTGTAATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAAGGAATCAACGTGTC-CTCCCTGGCCGAATGGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTAGGGATTGGGGCTTGCAATTTTTCCCCATGAACGAGGAATTCCCAGTAAGCGCGAGTCATAAGCTCGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCGGACTGA--TACA-CGGCTC----GTGTTTC-GACATGGCCGGAGA-CTTTGGGAAGATGACCAAACTTGATCATTT
+
+ Mecyclothorax TTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACAAG---CCAAA---TTAAGGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACCA---CACATTTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCTGACCAGAGATGGGAGGAGTGCTTTTATTAGATCAAAACCAAA-CGGCA------GCAGT-CATTACTTTCGGGTG-----------TGGCT-G--TG--TTT-----GTCGATTTT--------ATG-------ATTGGTGACTCTGAATAACTTTATGCTGATCGCATGGTC-TTGTACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAAGATCTGCGCTTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACAAGGACCAATTGGAGGGCCAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAGTTGAATCTGTGTCCCGTGCTGTCGGTTCACTGCTCG---TCAGTGAT-CACTGGCATGTTC-ACGGGACGTCCTG-CCGGTGGA----------------TGTGTGTGTTTGATACAAGAGTCTCTATT-------------------------------------------------------------ATGTCTAGCTATATTACACACT----------------------------TTTTGCATGCGCC--------------TCTTTCTTCCTTAACCGGGGTTAAAGGCAGTGCAT-----------------------------------------TAA---------------------------------GTTCAGTGTGTATGGGCGGTAG-------TAGGTAAG----------A-CGTGTATTCA-----A---------TCAC-CGTCC--TAGT----AATAT-ATCCTGTCGCAGTGCTCTTAATTGAGTGTTGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----T---C-ATTTATGCCTGAATATTGT-GTGCATGGAATAATGGAACAGGACCTCGGTTCTAT--TTTGTTGGTTTTCGGAATAATCCGAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCAACGTTAGAGGTGAAATTCTTGGATCGTTGCAAGACGGACTAAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCGACGTTCCT-CCGATGACTCGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCAGACACTGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCAGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGAAGCGATTTGTCTGGTTAATTCCGATAACGAACGAGACTCTAGCCTGCTAACTAGGCGTAA---------CCAAATACCGG--------TATCTTGAAGGC-------TCCGAC--ACTTGTTCCGTGA----------TGTTCATTC-------------TGTGCG-CATTACT---TTTG-GTTCGTAGTTGAATCGTT
+ACTA---TTTGT-------------ACTTGTGCAAATGTGTGCGG------------------TTTGCT----GCGGG---T-CG---GGTGT-------GTTGTATGGGTGGC--TCTGGAATGATG--TTGTTGGGTTTTTACTACCGGCGTATATATACAATCTTCTTAGAGGGACAGGCGGCTTCTAGCCGCACGAGATTGAGCAATAACAGGTCTGTGATGCCCTTAGATGTTTTGGGCCGCACGCGCGCTACACTGAAGGAATCAGCGTGTC-TTCCCTGGCCGAAAGGTCCGGGTAACCCGCTGAACCTCCTTCGTGCTAGGGATTGGGGCTTGCAATTATTCCCCATGAACGAGGAATTCCCAGTAAGCGTGAGTCATAAGCTCGCGTTGATTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTACTACCGATTGAATGATTTAGTGAGGTCTTCAGACTGG--TACT-CGGT-G----ATGTTTCGTACATTACCGAAGTACGCTAGGAAGATGACCAAACTTGATTAAT-
+
+ Agonum TTGTCTCAAAGATTAAGCCATGCATGTCTAAGTACAAA---CTATA---TTAAAGTGAAACCGCGAAAGGCTCATTAAATCAGTTATGGTTCCTTAGATCGTACCACA--ACAATTACTTGGATAACTGTGGTAATTCTAGAGCTAATACATGCAAACAGAGCTCTGACCGGAAACGGAAGGAGTGCTTTTATTAGATCAAAACCAAT-CG--GC-----ATCGG-TAACATTTCGGT--G-----------TTATC----CG--TTT-----GTCGCTC-------AATATA---------TGGTGAATCTGAATAACTTTATGCTGATCGCATGGTC-TTGCACCGGCGACGCATCTTTCAAATGTCTGCCTTATCAACTGTCGATGGTAGGATCTGCGCCTACCATGGTTGTAACGGGTAACGGGGAATCAGGGTTCGATTCCGGAGAGGGAGCCTGAGAAACGGCTACCACATCCAAGGAAGGCAGCAGGCGCGCAAATTACCCACTCCCGGCACGGGGAGGTAGTGACGAAAAATAACGATACGGGACTCATCCGAGGCCCCGTAATCGGAATGAGTACACTTTAAATCCTTTAACAAGGACCAATTGGAGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTAAAGTTGTTGCGGTTAAAAAGCTCGTAATTGAATTTGTGTCTCGCACTGTCGGTTCACCGCCC----GCGGTGTT-AACTGGCATGTTT-GCGAGACGTCCTG-CCGGTGGA---------TG---------------------------GTACGC--------------------------------------------------------------------AATGGA--------------------------------------TTTT--ATG----------------------TGCTATA----------CATTATCCCTAC--------------------------------------------GG---------------------------------ATTTT-CGTATACAT--------------GTAAT-----------------TTTCT-------------------TGCTCATCC--GACTT---TATAA-ATCCTGTCGCGGTGCTCTTAATTGAGTGTCGAGG----CGGGCCGGCACGTTT-ACTTTGAACAAATTAGAGTGCTCAAAGCAGGC----T---A-ATTAATGCCTGAATAAT-TAGTGCATGGAATAATAGAACAGGACCTTGGTTCTAT--TTTGTTGGTTTTCGGAA--CCCCAAGGTAATGATTAATAGGGACA-GATGGGGGCATTCGTATTGCGACGTTAGAGGTGAAATTCTTGGATCGTCGCAAGACGGACTAAAGCGAAAGCATTTGCCAAAGATGTTTTCATTAATCAAGAACGAAAGTCAGAGGTTCGAAGGCGATCAGATACCGCCCTAGTTCTGACCATAAACGATGCCAGCTAGCGATCCGCCAAAGTTCCT-CCGATGACTTGGCGGGCAGCT-TCCGGGAAACCAAAGCTTTTGGGTTCCGGGGGAAGTATGGTTGCAAAGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGAAACCTCACCAGGCCCAGACACTGGAAGGATTGACAGATTGAGAGCTCTTTCTTGATTCAGTGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACTCTAGCCTACTAAATAGACGTTACA------CTTA----CCAG--------TATCTCGAAGGCTCAC--ATCTTCT--ATTACTTTTA----------------TTGC----------------TTGTACTGCT------------TATGGGG--GTTGCATT
+TCGG-----TGT---------------ATAT--C-----------------...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-15 18:13:08
|
Revision: 374
http://treebase.svn.sourceforge.net/treebase/?rev=374&view=rev
Author: rvos
Date: 2009-12-15 18:12:58 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/examples/Basic_Examples/
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/01-basics.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/02-standardMenus.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/03-characterMatrices.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/04-treeWindow.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/04a-windowTabs.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/05-windowModes.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/06-helpMenu.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/07-moreHelp.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/08-logFile.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/09-windowFonts.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/10-scripting.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/11-newFile.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/12-fileFormats.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/13-blockOfTaxa.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/13-matrix.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/13-trees.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/14-included.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/15-annotations.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/16-webLinks.nex
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/fubonidiaGizmoid.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/fubonidiaKnobble.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/fubonidiaZibinator.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/quidnubiaGizmoid.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/quidnubiaKnobble.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/quidnubiaZibinator.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/snorolopaGizmoid.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/snorolopaKnobble.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/snorolopaZibinator.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/zorabynyxGizmoid.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/zorabynyxKnobble.gif
trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/fubonidianImages/zorabynyxZibinator.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/
trunk/treebase-core/lib/examples/Basic_Examples/characters/01-characters.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/02-newMatrix.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/03-newMatrix.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/04-characterLists.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/05-dataEditing.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/06-fill.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/07-dataEditing.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/08-addDelete.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/09-copyPaste.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/10-names.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/11-viewingStyles.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/11a-annotations.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/12-continuous.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/13-continuousItems.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/14-partitions.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/15-selecting.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/16-charSources.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/17-charSources.nex
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/fubonidiaGizmoid.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/fubonidiaKnobble.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/fubonidiaZibinator.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/quidnubiaGizmoid.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/quidnubiaKnobble.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/quidnubiaZibinator.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/snorolopaGizmoid.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/snorolopaKnobble.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/snorolopaZibinator.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/zorabynyxGizmoid.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/zorabynyxKnobble.gif
trunk/treebase-core/lib/examples/Basic_Examples/characters/fubonidianImages/zorabynyxZibinator.gif
trunk/treebase-core/lib/examples/Basic_Examples/charts/
trunk/treebase-core/lib/examples/Basic_Examples/charts/01-charts.nex
trunk/treebase-core/lib/examples/Basic_Examples/charts/02-histogram.nex
trunk/treebase-core/lib/examples/Basic_Examples/charts/03-scattergram.nex
trunk/treebase-core/lib/examples/Basic_Examples/charts/04-scattergram.nex
trunk/treebase-core/lib/examples/Basic_Examples/continuous/
trunk/treebase-core/lib/examples/Basic_Examples/continuous/01-editContinuous.nex
trunk/treebase-core/lib/examples/Basic_Examples/continuous/03-trace.nex
trunk/treebase-core/lib/examples/Basic_Examples/continuous/04-branchLengths.nex
trunk/treebase-core/lib/examples/Basic_Examples/continuous/05-treeSearch.nex
trunk/treebase-core/lib/examples/Basic_Examples/continuous/06-sim.nex
trunk/treebase-core/lib/examples/Basic_Examples/continuous/07-mirrorTree.nex
trunk/treebase-core/lib/examples/Basic_Examples/continuous/08-plotTree.nex
trunk/treebase-core/lib/examples/Basic_Examples/continuous/09-plotTreeSim.nex
trunk/treebase-core/lib/examples/Basic_Examples/introduction.nex
trunk/treebase-core/lib/examples/Basic_Examples/taxa/
trunk/treebase-core/lib/examples/Basic_Examples/taxa/01-taxa.nex
trunk/treebase-core/lib/examples/Basic_Examples/taxa/02-addingDeleting.nex
trunk/treebase-core/lib/examples/Basic_Examples/taxa/03-partitions.nex
trunk/treebase-core/lib/examples/Basic_Examples/taxa/04-partitions.nex
trunk/treebase-core/lib/examples/Basic_Examples/taxa/05-selecting.nex
trunk/treebase-core/lib/examples/Basic_Examples/taxa/06-selecting.nex
trunk/treebase-core/lib/examples/Basic_Examples/taxa/07-selecting.nex
trunk/treebase-core/lib/examples/Basic_Examples/taxa/08-multipleBlocks.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/01-editingTrees.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/02-editingTrees.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/03-editingTrees.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/04-branchLengths.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/05-branchColorNames.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/06-branchSelection.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/07-storedTrees.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/08-listOfTrees.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/09-treeBlocks.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/10-externalTrees.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/10-treeFile.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/11-treeSources.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/12-treeSources.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_manipulation/13-instability.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/01-treeWindow.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/02-treeForm.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/03-drawingSize.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/04-moreTreeForms.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/05-moreTreeForms.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/06-printingTrees.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/07-dependentWindow.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/08-mirrorTree.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/09-multiTrees.nex
trunk/treebase-core/lib/examples/Basic_Examples/tree_viewing/10-multiTrees.nex
Added: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/01-basics.nex
===================================================================
--- trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/01-basics.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/01-basics.nex 2009-12-15 18:12:58 UTC (rev 374)
@@ -0,0 +1,112 @@
+#NEXUS
+[written Mon Aug 20 22:10:59 PDT 2007 by Mesquite version 2.0BETA3 (build i50) at Thrandina.local/10.0.1.4 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ Aus Fubonidia Ibbinidibe Snorolopa Quidnubia Suinon Zorabynyx Huichoros Jotinupa
+ ;
+ BLOCKID WM114861883b02;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 number_of_eyes / one two, 2 tail_color / blue red ;
+ MATRIX
+ Aus 11
+ Fubonidia 11
+ Ibbinidibe 11
+ Snorolopa 1(0,1)
+ Quidnubia 00
+ Suinon 00
+ Zorabynyx 00
+ Huichoros 00
+ Jotinupa 00
+
+;
+ BLOCKID WM114861883d90;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 Aus,
+ 2 Fubonidia,
+ 3 Ibbinidibe,
+ 4 Snorolopa,
+ 5 Quidnubia,
+ 6 Suinon,
+ 7 Zorabynyx,
+ 8 Huichoros,
+ 9 Jotinupa;
+ TREE First_Tree = ((((1,5),4),((7,6),2)),((9,8),3));
+ TREE Second_Tree = ((((9,((4,1),2)),6),3),((8,7),5));
+ TREE Third_Tree = ((8,((2,6),1)),((((3,9),7),4),5));
+ TREE Polytomous = ((1,5),(7,6,2),4,((9,8),3));
+ TREE Partial_tree = (((9,(1,2)),(8,7)),(3,5));
+
+END;
+
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 8476784597994698209 WM114861883b02;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 974864624972105434 WM114861883d90;
+ checksum 0 4129971366;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '02-standardMenus.nex';
+ setPrevFileName '../introduction.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 528 432;
+ setLocation 420 31;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'Mesquite has a few standard windows, such as the startup window, and the main Mesquite window (showing the Mesquite log, Project and Files, and Search results). ^n^nThe Mesquite Log window shows you a log of what commands have been given, and it may display errors. Also, you can use it to give commands if you have that mode selected in its Defaults submenu of the File menu.^n^nThe Projects and Files window shows the files that are currently open, and some of their major components. For instance, there is currently one file open, named "01-basics.nex" (to which this note belongs). Included in the file are one block of taxa, a character matrix, and a tree block. To see this, touch on the Projects & Files tab of the main Mesquite window.^n^nMesquite automatically groups files into projects. When you have only one file open, you can consider a "project" to be equivalent to that open file. The idea of a project becomes useful if you link several files together. If you link several files together so that their information can be combined in analyses, Mesquite considers all the linked files to belong to a single "project". A subsequent example file will discuss linking and including files.^n^nThe Projects and Files window is a useful place to manage the contents of files. If you touch on the labels (e.g., for taxa, matrices, etc.) in the window, a menu will drop down that will allow you to do various things to the object touched. For example, touching on "Taxa: Fubonidians" yields a drop-down menu that will display the list of taxa, or allow you to rename or delete the taxa block, etc. Also, as you pass the cursor over the labels, the explanation area in the window gives useful information about the objects.^n^nHit the Next button in to go to the next example file.';
+ setTitle 'Windows, Log, and Projects';
+ toggleFileNames off;
+ setPrevButtonName Return;
+ setNextButtonName Next;
+ addFileLink 'Extra example: linking' '13-blockOfTaxa.nex';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/01-basics.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/02-standardMenus.nex
===================================================================
--- trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/02-standardMenus.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/02-standardMenus.nex 2009-12-15 18:12:58 UTC (rev 374)
@@ -0,0 +1,112 @@
+#NEXUS
+[written Mon Aug 20 20:33:30 PDT 2007 by Mesquite version 2.0BETA3 (build i50) at Thrandina.local/10.0.1.6 (Wayne Maddison)]
+
+BEGIN TAXA;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ Aus Fubonidia Ibbinidibe Snorolopa Quidnubia Suinon Zorabynyx Huichoros Jotinupa
+ ;
+ BLOCKID WM1148618b2783;
+
+END;
+
+
+BEGIN CHARACTERS;
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 number_of_eyes / one two, 2 tail_color / blue red ;
+ MATRIX
+ Aus 11
+ Fubonidia 11
+ Ibbinidibe 11
+ Snorolopa 1(0,1)
+ Quidnubia 00
+ Suinon 00
+ Zorabynyx 00
+ Huichoros 00
+ Jotinupa 00
+
+;
+ BLOCKID WM1148618b2900;
+
+
+END;
+BEGIN TREES;
+ TRANSLATE
+ 1 Aus,
+ 2 Fubonidia,
+ 3 Ibbinidibe,
+ 4 Snorolopa,
+ 5 Quidnubia,
+ 6 Suinon,
+ 7 Zorabynyx,
+ 8 Huichoros,
+ 9 Jotinupa;
+ TREE First_Tree = ((((1,5),4),((7,6),2)),((9,8),3));
+ TREE Second_Tree = ((((9,((4,1),2)),6),3),((8,7),5));
+ TREE Third_Tree = ((8,((2,6),1)),((((3,9),7),4),5));
+ TREE Polytomous = ((1,5),(7,6,2),4,((9,8),3));
+ TREE Partial_tree = (((9,(1,2)),(8,7)),(3,5));
+
+END;
+
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 8476784597994698209 WM1148618b2783;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 974864624972105434 WM1148618b2900;
+ checksum 0 4129971366;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '03-characterMatrices.nex';
+ setPrevFileName '01-basics.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 462 368;
+ setLocation 418 30;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'Mesquite has several standard menus:^n^nFile - Making new files, open, saving, printing, and closing files, quitting.^n^nEdit - Copying, pasting, undoing, and some other basic features for editing.^n^nCharacters - Managing characters, character matrices, and associated information like assumptions about characters.^n^nTaxa&Trees - Managing trees and taxa, showing tree windows.^n^nAnalysis - Displaying charts for trees, taxa and characters, tracing characters, creating batch files for automated analyses, and doing various other analyes.^n^nWindows - Controlling the current window, displaying and managing other windows.^n^nHelp - Links to documentation.^n^nThe menus that are available at any one time depend upon which window is frontmost. If you cannot find a menu item to do something you wish to do to the contents of a window, click on the window to make sure it is frontmost, and its menus will appear.^n^nTo learn more about Mesquite''s menus, use the button below.';
+ setTitle Standard_menus;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addWebLink Menu_documentation 'mesquite:docs/mesquite/menus.html';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/02-standardMenus.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/03-characterMatrices.nex
===================================================================
--- trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/03-characterMatrices.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/03-characterMatrices.nex 2009-12-15 18:12:58 UTC (rev 374)
@@ -0,0 +1,185 @@
+#NEXUS
+[written Thu Nov 22 19:48:16 PST 2007 by Mesquite version 2.0+ (build j18a) at Thrandina.local/10.0.1.3 (Wayne Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ Aus Fubonidia Ibbinidibe Snorolopa Quidnubia Suinon Zorabynyx Huichoros Jotinupa
+ ;
+ BLOCKID WM114861935156;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "03-characterMatrices.nex"';
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 number_of_eyes / one two, 2 tail_color / blue red ;
+ MATRIX
+ Aus 11
+ Fubonidia 11
+ Ibbinidibe 11
+ Snorolopa 1(0,1)
+ Quidnubia 00
+ Suinon 00
+ Zorabynyx 00
+ Huichoros 00
+ Jotinupa 00
+
+;
+ BLOCKID WM114861935490;
+
+
+END;
+BEGIN TREES;
+ Title 'Trees from "03-characterMatrices.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 Aus,
+ 2 Fubonidia,
+ 3 Ibbinidibe,
+ 4 Snorolopa,
+ 5 Quidnubia,
+ 6 Suinon,
+ 7 Zorabynyx,
+ 8 Huichoros,
+ 9 Jotinupa;
+ TREE First_Tree = ((((1,5),4),((7,6),2)),((9,8),3));
+ TREE Second_Tree = ((((9,((4,1),2)),6),3),((8,7),5));
+ TREE Third_Tree = ((8,((2,6),1)),((((3,9),7),4),5));
+ TREE Polytomous = ((1,5),(7,6,2),4,((9,8),3));
+ TREE Partial_tree = (((9,(1,2)),(8,7)),(3,5));
+
+END;
+
+
+BEGIN NOTES;
+
+ TEXT TAXA = Untitled_Block_of_Taxa TAXON = 5 TEXT = Lives_deep_in_dark_caves;
+
+ TEXT TAXON = 4 CHARACTER = 2 TEXT = 'Some individuals are blue, others are red. Why, no one knows.';
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 8476784597994698209 WM114861935156;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 974864624972105434 WM114861935490;
+ checksum 0 4129971366 WM114861935490;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #974864624972105434 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 52;
+ setAnnotationSize 52;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 677 223;
+ setLocation 460 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleShowTaxonNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '04-treeWindow.nex';
+ setPrevFileName '02-standardMenus.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 441 418;
+ setLocation 6 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'This file shows the spreadsheet editor for character matrices. At its left side is a tool palette with a selection tool (the arrow), an editing tool (the I-beam), and others. When you select a tool by touching its button, its explanation shows up in the explanation area at the bottom of the window.^n^nThe matrix editing window has a "Matrix" menu which controls many of its functions. In it you can control appearance and operate utilities that alter the data. You can also add and delete taxa and characters.^n^nWhen you touch a cell in the matrix that begins or ends with *, you may see an annotation (footnote) for that cell in the annotation area near the bottom of the window (the white area just above the yellowish explanation area). To edit an annotation, select the cell, and then go down to the annotation area and type in it.^n^nTo see more details on the data editor, touch the button in below. Otherwise, use the Next button to go to the next example.';
+ setTitle Character_matrix_editor;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addFileLink More_details_on_characters '../characters/01-characters.nex';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/03-characterMatrices.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/04-treeWindow.nex
===================================================================
--- trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/04-treeWindow.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/04-treeWindow.nex 2009-12-15 18:12:58 UTC (rev 374)
@@ -0,0 +1,209 @@
+#NEXUS
+[written Thu Sep 20 14:03:46 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium.local/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ Aus Fubonidia Ibbinidibe Snorolopa Quidnubia Suinon Zorabynyx Huichoros Jotinupa
+ ;
+ BLOCKID WM11486199fff7;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "04-treeWindow.nex"';
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 number_of_eyes / one two, 2 tail_color / blue red ;
+ MATRIX
+ Aus 11
+ Fubonidia 11
+ Ibbinidibe 11
+ Snorolopa 1(0,1)
+ Quidnubia 00
+ Suinon 00
+ Zorabynyx 00
+ Huichoros 00
+ Jotinupa 00
+
+;
+ BLOCKID WM1148619a00b0;
+
+
+END;
+BEGIN TREES;
+ Title 'Trees from "04-treeWindow.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 Aus,
+ 2 Fubonidia,
+ 3 Ibbinidibe,
+ 4 Snorolopa,
+ 5 Quidnubia,
+ 6 Suinon,
+ 7 Zorabynyx,
+ 8 Huichoros,
+ 9 Jotinupa;
+ TREE First_Tree = ((((1,5),4),((7,6),2)),((9,8),3));
+ TREE Second_Tree = ((((9,((4,1),2)),6),3),((8,7),5));
+ TREE Third_Tree = ((8,((2,6),1)),((((3,9),7),4),5));
+ TREE Polytomous = ((1,5),(7,6,2),4,((9,8),3));
+ TREE Partial_tree = (((9,(1,2)),(8,7)),(3,5));
+
+END;
+
+
+BEGIN NOTES;
+
+ TEXT TAXA = Untitled_Block_of_Taxa TAXON = 5 TEXT = Lives_deep_in_dark_caves;
+
+ TEXT TAXON = 4 CHARACTER = 2 TEXT = 'Some individuals are blue, others are red. Why, no one knows.';
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 8476784597994698209 WM11486199fff7;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 974864624972105434 WM1148619a00b0;
+ checksum 0 4129971366 WM1148619a00b0;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #8476784597994698209 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 908.983934835544.585850784873249678;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 52;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 560 306;
+ setLocation 500 34;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '04a-windowTabs.nex';
+ setPrevFileName '03-characterMatrices.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 480 375;
+ setLocation 8 27;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'This file shows the tree window in which trees can be viewed and edited. At left is a tool palette, whose tools can be used for manipulating the tree. There is also a control with blue arrows to scroll from one tree to another from the current source of trees. ^n^nThe Tree Window has a Tree menu in which you can control the trees appearance, and choose the source of trees. There is also an Analysis menu from which you can initiate analyses with the tree.^n^nThe tree window also has an annotation and explanation area at the bottom for communicating with the user.^n^nFor more information about viewing and editing trees, follow the "Go" button below beside "Viewing trees". For more information about manipulating trees, follow the "Go" button beside "Manipulating trees". Otherwise, go to the next example via the Next button.';
+ setTitle Tree_window;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ addFileLink Viewing_trees '../tree_viewing/01-treeWindow.nex';
+ addFileLink Manipulating_trees '../tree_manipulation/01-editingTrees.nex';
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/04-treeWindow.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/04a-windowTabs.nex
===================================================================
--- trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/04a-windowTabs.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/04a-windowTabs.nex 2009-12-15 18:12:58 UTC (rev 374)
@@ -0,0 +1,296 @@
+#NEXUS
+[written Thu Nov 22 19:49:10 PST 2007 by Mesquite version 2.0+ (build j18a) at Thrandina.local/10.0.1.3 (Wayne Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ Aus Fubonidia Ibbinidibe Snorolopa Quidnubia Suinon Zorabynyx Huichoros Jotinupa
+ ;
+ BLOCKID WM11486199fff7;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "04a-windowTabs.nex"';
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 number_of_eyes / one two, 2 tail_color / blue red ;
+ MATRIX
+ Aus 11
+ Fubonidia 11
+ Ibbinidibe 11
+ Snorolopa 1(0,1)
+ Quidnubia 00
+ Suinon 00
+ Zorabynyx 00
+ Huichoros 00
+ Jotinupa 00
+
+;
+ BLOCKID WM1148619a00b0;
+
+
+END;
+BEGIN TREES;
+ Title 'Trees from "04a-windowTabs.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 Aus,
+ 2 Fubonidia,
+ 3 Ibbinidibe,
+ 4 Snorolopa,
+ 5 Quidnubia,
+ 6 Suinon,
+ 7 Zorabynyx,
+ 8 Huichoros,
+ 9 Jotinupa;
+ TREE First_Tree = ((((1,5),4),((7,6),2)),((9,8),3));
+ TREE Second_Tree = ((((9,((4,1),2)),6),3),((8,7),5));
+ TREE Third_Tree = ((8,((2,6),1)),((((3,9),7),4),5));
+ TREE Polytomous = ((1,5),(7,6,2),4,((9,8),3));
+ TREE Partial_tree = (((9,(1,2)),(8,7)),(3,5));
+
+END;
+
+
+BEGIN NOTES;
+
+ TEXT TAXA = Untitled_Block_of_Taxa TAXON = 5 TEXT = Lives_deep_in_dark_caves;
+
+ TEXT TAXON = 4 CHARACTER = 2 TEXT = 'Some individuals are blue, others are red. Why, no one knows.';
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 8476784597994698209 WM11486199fff7;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 974864624972105434 WM1148619a00b0;
+ checksum 0 4129971366 WM1148619a00b0;
+ endTell;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ showTaxa #8476784597994698209 #mesquite.lists.TaxonList.TaxonList;
+ tell It;
+ setTaxa #8476784597994698209;
+ getWindow;
+ tell It;
+ newAssistant #mesquite.lists.DefaultTaxaOrder.DefaultTaxaOrder;
+ newAssistant #mesquite.lists.TaxonListCurrPartition.TaxonListCurrPartition;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 647 380;
+ setLocation 500 34;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.lists.TaxonListAnnotPanel.TaxonListAnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #8476784597994698209 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 908.983934835544.585850784873249678;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 52;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 647 358;
+ setLocation 500 34;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ getEmployee #mesquite.charMatrices.BasicDataWindowCoord.BasicDataWindowCoord;
+ tell It;
+ showDataWindow #974864624972105434 #mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindowMaker;
+ tell It;
+ getWindow;
+ tell It;
+ setExplanationSize 30;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 647 380;
+ setLocation 500 34;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setTool mesquite.charMatrices.BasicDataWindowMaker.BasicDataWindow.arrow;
+ colorCells #mesquite.charMatrices.NoColor.NoColor;
+ setBackground White;
+ toggleShowNames on;
+ toggleShowTaxonNames on;
+ toggleTight off;
+ toggleShowChanges on;
+ toggleSeparateLines off;
+ toggleShowStates on;
+ toggleAutoWCharNames on;
+ toggleShowDefaultCharNames off;
+ toggleConstrainCW on;
+ setColumnWidth 16;
+ toggleBirdsEye off;
+ toggleColorsPanel off;
+ birdsEyeWidth 2;
+ toggleLinkedScrolling on;
+ toggleScrollLinkedTables off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.categ.StateNamesStrip.StateNamesStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.AnnotPanel.AnnotPanel;
+ tell It;
+ togglePanel off;
+ endTell;
+ getEmployee #mesquite.charMatrices.CharReferenceStrip.CharReferenceStrip;
+ tell It;
+ showStrip off;
+ endTell;
+ getEmployee #mesquite.charMatrices.ColorCells.ColorCells;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.charMatrices.QuickKeySelector.QuickKeySelector;
+ tell It;
+ autotabOff;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '05-windowModes.nex';
+ setPrevFileName '04-treeWindow.nex';
+ getWindow;
+ tell It;
+ popOut;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 480 353;
+ setLocation 8 27;
+ setFont SanSerif;
+ setFontSize 10;
+ setExplanation 'This file shows how Mesquite''s functional windows are grouped as tabs within a single window of your operating system. At right is a window showing a list of taxa (the List of Taxa window). If you touch on the tabs along the top of the window, you can see a Tree Window, and a Character Matrix Editor. ^n^nThis system of tabs represents a change from version 1 of Mesquite. You can pop out a window to be independent by touching on the little circled arrow in the tab for the window; after it''s independent you can pop it back in by touching the arrow at top left of the indepedent window.^n^nYou can revert to the old style of all independent windows if you deselect Open Windows as Tabs in the Defaults submenu of the File menu.';
+ setTitle Window_Tabs;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ setEditorsVisible;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Added: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/05-windowModes.nex
===================================================================
--- trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/05-windowModes.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/05-windowModes.nex 2009-12-15 18:12:58 UTC (rev 374)
@@ -0,0 +1,453 @@
+#NEXUS
+[written Thu Sep 20 14:09:04 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium.local/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ Aus Fubonidia Ibbinidibe Snorolopa Quidnubia Suinon Zorabynyx Huichoros Jotinupa
+ ;
+ BLOCKID WM114861a64c410;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "05-windowModes.nex"';
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 number_of_eyes / one two, 2 tail_color / blue red ;
+ MATRIX
+ Aus 11
+ Fubonidia 11
+ Ibbinidibe 11
+ Snorolopa 1(0,1)
+ Quidnubia 00
+ Suinon 00
+ Zorabynyx 00
+ Huichoros 00
+ Jotinupa 00
+
+;
+ BLOCKID WM114861a64f80;
+
+
+END;
+BEGIN TREES;
+ Title 'Trees from "05-windowModes.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 Aus,
+ 2 Fubonidia,
+ 3 Ibbinidibe,
+ 4 Snorolopa,
+ 5 Quidnubia,
+ 6 Suinon,
+ 7 Zorabynyx,
+ 8 Huichoros,
+ 9 Jotinupa;
+ TREE First_Tree = ((((1,5),4),((7,6),2)),((9,8),3));
+ TREE Second_Tree = ((((9,((4,1),2)),6),3),((8,7),5));
+ TREE Third_Tree = ((8,((2,6),1)),((((3,9),7),4),5));
+ TREE Polytomous = ((1,5),(7,6,2),4,((9,8),3));
+ TREE Partial_tree = (((9,(1,2)),(8,7)),(3,5));
+
+END;
+
+
+BEGIN NOTES;
+
+ TEXT TAXA = Untitled_Block_of_Taxa TAXON = 5 TEXT = Lives_deep_in_dark_caves;
+
+ TEXT TAXON = 4 CHARACTER = 2 TEXT = 'Some individuals are blue, others are red. Why, no one knows.';
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 8476784597994698209 WM114861a64c410;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 974864624972105434 WM114861a64f80;
+ checksum 0 4129971366 WM114861a64f80;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #8476784597994698209 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 908.983934835544.585850784873249678;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 537 282;
+ setLocation 533 24;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ makeTreeWindow #8476784597994698209 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 886.1053111291939.6488771259174774010;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 492 395;
+ setLocation 9 403;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ showPage 1;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ makeTreeWindow #8476784597994698209 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 908.1053111292798.248682516746150818;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 20;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 487 225;
+ setLocation 529 400;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ showPage 2;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ makeTreeWindow #8476784597994698209 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 930.1053111293428.7666447681000981525;
+ getTreeWindow;
+ tell It;
+ popOut;
+ setExplanationSize 52;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 485 265;
+ setLocation 706 505;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ showPage 3;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ endTell;
+ showWindow;
+ getEmployee #mesquite.trees.ColorBranches.ColorBranches;
+ tell It;
+ setColor Red;
+ removeColor off;
+ endTell;
+ getEmployee #mesquite.ornamental.BranchNotes.BranchNotes;
+ tell It;
+ setAlwaysOn off;
+ endTell;
+ getEmployee #mesquite.ornamental.ColorTreeByPartition.ColorTreeByPartition;
+ tell It;
+ colorByPartition off;
+ endTell;
+ endTell;
+ endTell;
+ newAssistant #mesquite.basic.ExamplesNavigator.ExamplesNavigator;
+ tell It;
+ setNextFileName '06-helpMenu.nex';
+ setPrevFileName '04a-windowTabs.nex';
+ getWindow;
+ tell It;
+ setExplanationSize 0;
+ setAnnotationSize 0;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 520 303;
+ setLocation 4 22;
+ setFont SanSerif;
+ setFontSize 10;
+ setActive;
+ setExplanation 'Most windows have several modes for viewing, controlled by the information bar at the top. The information bar has five tabs, "Graphics", "Text", "Parameters", "Modules" and "Citations". If the information bar does not appear at the top of a window, it may be turned on using the "Show Information Bar" menu item in the Windows menu.^n^nThe four windows shown here are all tree windows, being show in each of four different modes. The "Graphics" mode is the standard mode in which you''re likely to work. The "Text" mode gives an alternative, text-based view of the window. The "Parameters" mode shows important parameter settings of the various modules participating in the window. This can be useful to see what are the parameters values or assumptions for an analysis. The "Modules" mode shows the hierarchy of Mesquite modules involved in making the window. If you pass the cursor over the names of the modules, information about each module will appear in the explanation area at the bottom of the window. Touching on the name of the module also gives information. The "Citations" mode shows citations of any modules involved in the calculations that consider themselves citable in the sense of producing substantive results.';
+ setTitle Window_modes;
+ toggleFileNames off;
+ setPrevButtonName Previous;
+ setNextButtonName Next;
+ endTell;
+ showWindow;
+ endTell;
+ endTell;
+end;
+
+
Property changes on: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/05-windowModes.nex
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/06-helpMenu.nex
===================================================================
--- trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/06-helpMenu.nex (rev 0)
+++ trunk/treebase-core/lib/examples/Basic_Examples/basic_operation/06-helpMenu.nex 2009-12-15 18:12:58 UTC (rev 374)
@@ -0,0 +1,208 @@
+#NEXUS
+[written Thu Sep 20 14:09:20 MST 2007 by Mesquite version 2.0BETA4 (build i64) at Odontium.local/192.168.0.3 (David Maddison)]
+
+BEGIN TAXA;
+ TITLE Untitled_Block_of_Taxa;
+ DIMENSIONS NTAX=9;
+ TAXLABELS
+ Aus Fubonidia Ibbinidibe Snorolopa Quidnubia Suinon Zorabynyx Huichoros Jotinupa
+ ;
+ BLOCKID WM114861b8cfd11;
+
+END;
+
+
+BEGIN CHARACTERS;
+ TITLE 'Matrix in file "06-helpMenu.nex"';
+ DIMENSIONS NCHAR=2;
+ FORMAT DATATYPE = STANDARD GAP = - MISSING = ? SYMBOLS = " 0 1";
+ CHARSTATELABELS
+ 1 number_of_eyes / one two, 2 tail_color / blue red ;
+ MATRIX
+ Aus 11
+ Fubonidia 11
+ Ibbinidibe 11
+ Snorolopa 1(0,1)
+ Quidnubia 00
+ Suinon 00
+ Zorabynyx 00
+ Huichoros 00
+ Jotinupa 00
+
+;
+ BLOCKID WM114861b8d080;
+
+
+END;
+BEGIN TREES;
+ Title 'Trees from "06-helpMenu.nex"';
+ LINK Taxa = Untitled_Block_of_Taxa;
+ TRANSLATE
+ 1 Aus,
+ 2 Fubonidia,
+ 3 Ibbinidibe,
+ 4 Snorolopa,
+ 5 Quidnubia,
+ 6 Suinon,
+ 7 Zorabynyx,
+ 8 Huichoros,
+ 9 Jotinupa;
+ TREE First_Tree = ((((1,5),4),((7,6),2)),((9,8),3));
+ TREE Second_Tree = ((((9,((4,1),2)),6),3),((8,7),5));
+ TREE Third_Tree = ((8,((2,6),1)),((((3,9),7),4),5));
+ TREE Polytomous = ((1,5),(7,6,2),4,((9,8),3));
+ TREE Partial_tree = (((9,(1,2)),(8,7)),(3,5));
+
+END;
+
+
+BEGIN NOTES;
+
+ TEXT TAXA = Untitled_Block_of_Taxa TAXON = 5 TEXT = Lives_deep_in_dark_caves;
+
+ TEXT TAXON = 4 CHARACTER = 2 TEXT = 'Some individuals are blue, others are red. Why, no one knows.';
+
+END;
+
+BEGIN CODONS;
+CODESET * UNTITLED = universal: 1 - 2;
+
+
+END;
+
+BEGIN ASSUMPTIONS;
+OPTIONS DEFTYPE = unord PolyTcount = MINSTEPS;
+ TYPESET * UNTITLED = unord: 1 - 2;
+TYPESET Current_Parsimony_Models = unord: 1 - 2;
+
+END;
+
+BEGIN MESQUITECHARMODELS;
+ ProbModelSet * UNTITLED = 'Mk1 (est.)': 1 - 2;
+END;
+
+Begin MESQUITE;
+ MESQUITESCRIPTVERSION 2;
+ TITLE AUTO;
+ tell ProjectCoordinator;
+ getEmployee #mesquite.minimal.ManageTaxa.ManageTaxa;
+ tell It;
+ setID 0 8476784597994698209 WM114861b8cfd11;
+ endTell;
+ getEmployee #mesquite.charMatrices.ManageCharacters.ManageCharacters;
+ tell It;
+ setID 0 974864624972105434 WM114861b8d080;
+ checksum 0 4129971366 WM114861b8d080;
+ endTell;
+ getEmployee #mesquite.trees.BasicTreeWindowCoord.BasicTreeWindowCoord;
+ tell It;
+ makeTreeWindow #8476784597994698209 #mesquite.trees.BasicTreeWindowMaker.BasicTreeWindowMaker;
+ tell It;
+ setTreeSource #mesquite.trees.StoredTrees.StoredTrees;
+ tell It;
+ setTreeBlock 1;
+ toggleUseWeights off;
+ endTell;
+ setAssignedID 908.983934835544.585850784873249678;
+ getTreeWindow;
+ tell It;
+ setExplanationSize 52;
+ setAnnotationSize 20;
+ setFontIncAnnot 0;
+ setFontIncExp 0;
+ setSize 589 413;
+ setLocation 475 22;
+ setFont SanSerif;
+ setFontSize 10;
+ getToolPalette;
+ tell It;
+ endTell;
+ setActive;
+ getTreeDrawCoordinator #mesquite.trees.BasicTreeDrawCoordinator.BasicTreeDrawCoordinator;
+ tell It;
+ suppress;
+ setTreeDrawer #mesquite.trees.DiagonalDrawTree.DiagonalDrawTree;
+ tell It;
+ setNodeLocs #mesquite.trees.NodeLocsStandard.NodeLocsStandard;
+ tell It;
+ stretchToggle off;
+ branchLengthsToggle off;
+ toggleScale on;
+ toggleBroadScale off;
+ toggleCenter off;
+ toggleEven off;
+ namesAngle ?;
+ endTell;
+ setEdgeWidth 12;
+ orientUp;
+ endTell;
+ setBackground White;
+ setBranchColor Black;
+ showNodeNumbers off;
+ showBranchColors on;
+ labelBranchLengths off;
+ centerBrLenLabels on;
+ showBrLensUnspecified on;
+ showBrLenLabelsOnTerminals on;
+ setBrLenLabelColor 0 0 255;
+ setNumBrLenDecimals 6;
+ desuppress;
+ getEmployee #mesquite.trees.BasicDrawTaxonNames.BasicDrawTaxonNames;
+ tell It;
+ setColor Black;
+ toggleColorPartition on;
+ toggleShadePartition off;
+ toggleNodeLabels on;
+ toggleCenterNodeNames off;
+ toggleShowNames on;
+ endTell;
+ endTell;
+ setTreeNumber 1;
+ useSuggestedSize off;
+ toggleSizeToFit on;
+ toggleTextOnTree off;
+ endTell;
+ showWindow;
+...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-15 18:09:30
|
Revision: 372
http://treebase.svn.sourceforge.net/treebase/?rev=372&view=rev
Author: rvos
Date: 2009-12-15 18:09:22 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/headless/x/
trunk/treebase-core/lib/headless/x/swing/
trunk/treebase-core/lib/headless/x/swing/JComponent.class
trunk/treebase-core/lib/headless/x/swing/JEditorPane.class
trunk/treebase-core/lib/headless/x/swing/JFileChooser.class
trunk/treebase-core/lib/headless/x/swing/JScrollPane.class
trunk/treebase-core/lib/headless/x/swing/JViewport.class
trunk/treebase-core/lib/headless/x/swing/event/
trunk/treebase-core/lib/headless/x/swing/event/HyperlinkEvent$EventType.class
trunk/treebase-core/lib/headless/x/swing/event/HyperlinkEvent.class
trunk/treebase-core/lib/headless/x/swing/event/HyperlinkListener.class
trunk/treebase-core/lib/headless/x/swing/text/
trunk/treebase-core/lib/headless/x/swing/text/Document.class
trunk/treebase-core/lib/headless/x/swing/text/JTextComponent.class
trunk/treebase-core/lib/headless/x/swing/text/html/
trunk/treebase-core/lib/headless/x/swing/text/html/HTMLDocument.class
trunk/treebase-core/lib/headless/x/swing/text/html/HTMLFrameHyperlinkEvent.class
Added: trunk/treebase-core/lib/headless/x/swing/JComponent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/JComponent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/JEditorPane.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/JEditorPane.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/JFileChooser.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/JFileChooser.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/JScrollPane.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/JScrollPane.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/JViewport.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/JViewport.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/event/HyperlinkEvent$EventType.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/event/HyperlinkEvent$EventType.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/event/HyperlinkEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/event/HyperlinkEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/event/HyperlinkListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/event/HyperlinkListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/text/Document.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/text/Document.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/text/JTextComponent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/text/JTextComponent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/text/html/HTMLDocument.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/text/html/HTMLDocument.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/x/swing/text/html/HTMLFrameHyperlinkEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/x/swing/text/html/HTMLFrameHyperlinkEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 18:08:51
|
Revision: 371
http://treebase.svn.sourceforge.net/treebase/?rev=371&view=rev
Author: rvos
Date: 2009-12-15 18:08:43 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/headless/iowagie/
trunk/treebase-core/lib/headless/iowagie/text/
trunk/treebase-core/lib/headless/iowagie/text/pdf/
trunk/treebase-core/lib/headless/iowagie/text/pdf/PdfContentByte.class
Added: trunk/treebase-core/lib/headless/iowagie/text/pdf/PdfContentByte.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/iowagie/text/pdf/PdfContentByte.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 18:07:19
|
Revision: 370
http://treebase.svn.sourceforge.net/treebase/?rev=370&view=rev
Author: rvos
Date: 2009-12-15 18:07:10 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/headless/
trunk/treebase-core/lib/headless/awt/
trunk/treebase-core/lib/headless/awt/AWTEvent.class
trunk/treebase-core/lib/headless/awt/Adjustable.class
trunk/treebase-core/lib/headless/awt/AlphaComposite.class
trunk/treebase-core/lib/headless/awt/BasicStroke.class
trunk/treebase-core/lib/headless/awt/BorderLayout.class
trunk/treebase-core/lib/headless/awt/Button.class
trunk/treebase-core/lib/headless/awt/CardLayout.class
trunk/treebase-core/lib/headless/awt/Checkbox.class
trunk/treebase-core/lib/headless/awt/CheckboxGroup.class
trunk/treebase-core/lib/headless/awt/CheckboxMenuItem.class
trunk/treebase-core/lib/headless/awt/Choice.class
trunk/treebase-core/lib/headless/awt/Color.class
trunk/treebase-core/lib/headless/awt/Component.class
trunk/treebase-core/lib/headless/awt/Composite.class
trunk/treebase-core/lib/headless/awt/Container.class
trunk/treebase-core/lib/headless/awt/Cursor.class
trunk/treebase-core/lib/headless/awt/Dialog.class
trunk/treebase-core/lib/headless/awt/Dimension.class
trunk/treebase-core/lib/headless/awt/FileDialog.class
trunk/treebase-core/lib/headless/awt/Font.class
trunk/treebase-core/lib/headless/awt/FontMetrics.class
trunk/treebase-core/lib/headless/awt/Frame.class
trunk/treebase-core/lib/headless/awt/Graphics.class
trunk/treebase-core/lib/headless/awt/Graphics2D.class
trunk/treebase-core/lib/headless/awt/GridBagConstraints.class
trunk/treebase-core/lib/headless/awt/GridBagLayout.class
trunk/treebase-core/lib/headless/awt/GridLayout.class
trunk/treebase-core/lib/headless/awt/HBoolean.class
trunk/treebase-core/lib/headless/awt/Image.class
trunk/treebase-core/lib/headless/awt/ImageObserver.class
trunk/treebase-core/lib/headless/awt/ImageProducer.class
trunk/treebase-core/lib/headless/awt/Insets.class
trunk/treebase-core/lib/headless/awt/ItemSelectable.class
trunk/treebase-core/lib/headless/awt/Label.class
trunk/treebase-core/lib/headless/awt/LayoutManager.class
trunk/treebase-core/lib/headless/awt/List.class
trunk/treebase-core/lib/headless/awt/MediaTracker.class
trunk/treebase-core/lib/headless/awt/Menu.class
trunk/treebase-core/lib/headless/awt/MenuBar.class
trunk/treebase-core/lib/headless/awt/MenuComponent.class
trunk/treebase-core/lib/headless/awt/MenuContainer.class
trunk/treebase-core/lib/headless/awt/MenuItem.class
trunk/treebase-core/lib/headless/awt/MenuShortcut.class
trunk/treebase-core/lib/headless/awt/Panel.class
trunk/treebase-core/lib/headless/awt/Point.class
trunk/treebase-core/lib/headless/awt/Polygon.class
trunk/treebase-core/lib/headless/awt/PopupMenu.class
trunk/treebase-core/lib/headless/awt/PrintGraphics.class
trunk/treebase-core/lib/headless/awt/PrintJob.class
trunk/treebase-core/lib/headless/awt/PrinterGraphics.class
trunk/treebase-core/lib/headless/awt/Rectangle.class
trunk/treebase-core/lib/headless/awt/ScrollPane.class
trunk/treebase-core/lib/headless/awt/Scrollbar.class
trunk/treebase-core/lib/headless/awt/Shape.class
trunk/treebase-core/lib/headless/awt/Stroke.class
trunk/treebase-core/lib/headless/awt/TextArea.class
trunk/treebase-core/lib/headless/awt/TextComponent.class
trunk/treebase-core/lib/headless/awt/TextField.class
trunk/treebase-core/lib/headless/awt/Toolkit.class
trunk/treebase-core/lib/headless/awt/Window.class
trunk/treebase-core/lib/headless/awt/datatransfer/
trunk/treebase-core/lib/headless/awt/datatransfer/Clipboard
trunk/treebase-core/lib/headless/awt/datatransfer/Clipboard.class
trunk/treebase-core/lib/headless/awt/datatransfer/ClipboardOwner.class
trunk/treebase-core/lib/headless/awt/datatransfer/DataFlavor.class
trunk/treebase-core/lib/headless/awt/datatransfer/StringSelection.class
trunk/treebase-core/lib/headless/awt/datatransfer/Transferable.class
trunk/treebase-core/lib/headless/awt/dnd/
trunk/treebase-core/lib/headless/awt/dnd/DnDConstants.class
trunk/treebase-core/lib/headless/awt/dnd/DropTarget.class
trunk/treebase-core/lib/headless/awt/dnd/DropTargetDragEvent.class
trunk/treebase-core/lib/headless/awt/dnd/DropTargetDropEvent.class
trunk/treebase-core/lib/headless/awt/dnd/DropTargetEvent.class
trunk/treebase-core/lib/headless/awt/dnd/DropTargetListener.class
trunk/treebase-core/lib/headless/awt/event/
trunk/treebase-core/lib/headless/awt/event/ActionEvent.class
trunk/treebase-core/lib/headless/awt/event/ActionListener.class
trunk/treebase-core/lib/headless/awt/event/AdjustmentEvent.class
trunk/treebase-core/lib/headless/awt/event/AdjustmentListener.class
trunk/treebase-core/lib/headless/awt/event/ComponentAdapter.class
trunk/treebase-core/lib/headless/awt/event/ComponentEvent.class
trunk/treebase-core/lib/headless/awt/event/ComponentListener.class
trunk/treebase-core/lib/headless/awt/event/EventListener.class
trunk/treebase-core/lib/headless/awt/event/FocusAdapter.class
trunk/treebase-core/lib/headless/awt/event/FocusEvent.class
trunk/treebase-core/lib/headless/awt/event/FocusListener.class
trunk/treebase-core/lib/headless/awt/event/InputEvent.class
trunk/treebase-core/lib/headless/awt/event/ItemEvent.class
trunk/treebase-core/lib/headless/awt/event/ItemListener.class
trunk/treebase-core/lib/headless/awt/event/KeyAdapter.class
trunk/treebase-core/lib/headless/awt/event/KeyEvent.class
trunk/treebase-core/lib/headless/awt/event/KeyListener.class
trunk/treebase-core/lib/headless/awt/event/MouseEvent.class
trunk/treebase-core/lib/headless/awt/event/MouseListener.class
trunk/treebase-core/lib/headless/awt/event/MouseMotionListener.class
trunk/treebase-core/lib/headless/awt/event/TextEvent.class
trunk/treebase-core/lib/headless/awt/event/TextListener.class
trunk/treebase-core/lib/headless/awt/event/WindowAdapter.class
trunk/treebase-core/lib/headless/awt/event/WindowAdaptor.class
trunk/treebase-core/lib/headless/awt/event/WindowEvent.class
trunk/treebase-core/lib/headless/awt/event/WindowListener.class
trunk/treebase-core/lib/headless/awt/geom/
trunk/treebase-core/lib/headless/awt/geom/AffineTransform.class
trunk/treebase-core/lib/headless/awt/geom/Arc2D$Double.class
trunk/treebase-core/lib/headless/awt/geom/Arc2D.class
trunk/treebase-core/lib/headless/awt/geom/Rectangle2D.class
trunk/treebase-core/lib/headless/awt/geom/RectangularShape.class
trunk/treebase-core/lib/headless/awt/image/
trunk/treebase-core/lib/headless/awt/image/BufferedImage.class
trunk/treebase-core/lib/headless/awt/image/MemoryImageSource.class
trunk/treebase-core/lib/headless/awt/image/PixelGrabber.class
trunk/treebase-core/lib/headless/awt/print/
trunk/treebase-core/lib/headless/awt/print/PageFormat.class
trunk/treebase-core/lib/headless/awt/print/Paper.class
trunk/treebase-core/lib/headless/awt/print/Printable.class
trunk/treebase-core/lib/headless/awt/print/PrinterException.class
trunk/treebase-core/lib/headless/awt/print/PrinterJob.class
Added: trunk/treebase-core/lib/headless/awt/AWTEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/AWTEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Adjustable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Adjustable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/AlphaComposite.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/AlphaComposite.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/BasicStroke.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/BasicStroke.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/BorderLayout.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/BorderLayout.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Button.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Button.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/CardLayout.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/CardLayout.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Checkbox.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Checkbox.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/CheckboxGroup.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/CheckboxGroup.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/CheckboxMenuItem.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/CheckboxMenuItem.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Choice.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Choice.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Color.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Color.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Component.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Component.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Composite.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Composite.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Container.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Container.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Cursor.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Cursor.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Dialog.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Dialog.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Dimension.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Dimension.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/FileDialog.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/FileDialog.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Font.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Font.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/FontMetrics.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/FontMetrics.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Frame.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Frame.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Graphics.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Graphics.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Graphics2D.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Graphics2D.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/GridBagConstraints.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/GridBagConstraints.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/GridBagLayout.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/GridBagLayout.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/GridLayout.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/GridLayout.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/HBoolean.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/HBoolean.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Image.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Image.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/ImageObserver.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/ImageObserver.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/ImageProducer.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/ImageProducer.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Insets.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Insets.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/ItemSelectable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/ItemSelectable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Label.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Label.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/LayoutManager.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/LayoutManager.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/List.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/List.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/MediaTracker.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/MediaTracker.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Menu.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Menu.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/MenuBar.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/MenuBar.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/MenuComponent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/MenuComponent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/MenuContainer.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/MenuContainer.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/MenuItem.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/MenuItem.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/MenuShortcut.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/MenuShortcut.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Panel.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Panel.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Point.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Point.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Polygon.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Polygon.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/PopupMenu.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/PopupMenu.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/PrintGraphics.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/PrintGraphics.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/PrintJob.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/PrintJob.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/PrinterGraphics.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/PrinterGraphics.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Rectangle.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Rectangle.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/ScrollPane.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/ScrollPane.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Scrollbar.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Scrollbar.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Shape.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Shape.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Stroke.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Stroke.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/TextArea.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/TextArea.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/TextComponent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/TextComponent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/TextField.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/TextField.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Toolkit.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Toolkit.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/Window.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/Window.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/datatransfer/Clipboard
===================================================================
--- trunk/treebase-core/lib/headless/awt/datatransfer/Clipboard (rev 0)
+++ trunk/treebase-core/lib/headless/awt/datatransfer/Clipboard 2009-12-15 18:07:10 UTC (rev 370)
@@ -0,0 +1,6 @@
+package /*pkg*/headless.awt.datatransfer
+
+ public class Clipboard {
+
+ }
+
\ No newline at end of file
Property changes on: trunk/treebase-core/lib/headless/awt/datatransfer/Clipboard
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/treebase-core/lib/headless/awt/datatransfer/Clipboard.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/datatransfer/Clipboard.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/datatransfer/ClipboardOwner.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/datatransfer/ClipboardOwner.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/datatransfer/DataFlavor.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/datatransfer/DataFlavor.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/datatransfer/StringSelection.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/datatransfer/StringSelection.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/datatransfer/Transferable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/datatransfer/Transferable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/dnd/DnDConstants.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/dnd/DnDConstants.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/dnd/DropTarget.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/dnd/DropTarget.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/dnd/DropTargetDragEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/dnd/DropTargetDragEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/dnd/DropTargetDropEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/dnd/DropTargetDropEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/dnd/DropTargetEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/dnd/DropTargetEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/dnd/DropTargetListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/dnd/DropTargetListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/ActionEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/ActionEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/ActionListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/ActionListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/AdjustmentEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/AdjustmentEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/AdjustmentListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/AdjustmentListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/ComponentAdapter.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/ComponentAdapter.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/ComponentEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/ComponentEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/ComponentListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/ComponentListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/EventListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/EventListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/FocusAdapter.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/FocusAdapter.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/FocusEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/FocusEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/FocusListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/FocusListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/InputEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/InputEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/ItemEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/ItemEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/ItemListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/ItemListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/KeyAdapter.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/KeyAdapter.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/KeyEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/KeyEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/KeyListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/KeyListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/MouseEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/MouseEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/MouseListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/MouseListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/MouseMotionListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/MouseMotionListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/TextEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/TextEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/TextListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/TextListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/WindowAdapter.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/WindowAdapter.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/WindowAdaptor.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/WindowAdaptor.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/WindowEvent.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/WindowEvent.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/event/WindowListener.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/event/WindowListener.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/geom/AffineTransform.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/geom/AffineTransform.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/geom/Arc2D$Double.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/geom/Arc2D$Double.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/geom/Arc2D.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/geom/Arc2D.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/geom/Rectangle2D.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/geom/Rectangle2D.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/geom/RectangularShape.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/geom/RectangularShape.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/image/BufferedImage.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/image/BufferedImage.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/image/MemoryImageSource.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/image/MemoryImageSource.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/image/PixelGrabber.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/image/PixelGrabber.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/print/PageFormat.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/print/PageFormat.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/print/Paper.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/print/Paper.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/print/Printable.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/print/Printable.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/print/PrinterException.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/print/PrinterException.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/headless/awt/print/PrinterJob.class
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/headless/awt/print/PrinterJob.class
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
|
From: <rv...@us...> - 2009-12-15 18:04:48
|
Revision: 369
http://treebase.svn.sourceforge.net/treebase/?rev=369&view=rev
Author: rvos
Date: 2009-12-15 18:04:40 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/images/32arrow.gif
trunk/treebase-core/lib/images/32bucket.gif
trunk/treebase-core/lib/images/32disabled.gif
trunk/treebase-core/lib/images/32dropper.gif
trunk/treebase-core/lib/images/32ibeam.gif
trunk/treebase-core/lib/images/32info.gif
trunk/treebase-core/lib/images/32notesTool.gif
trunk/treebase-core/lib/images/32pointer.gif
trunk/treebase-core/lib/images/32revSort.gif
trunk/treebase-core/lib/images/32sort.gif
trunk/treebase-core/lib/images/32wand.gif
trunk/treebase-core/lib/images/32zoomIn.gif
trunk/treebase-core/lib/images/32zoomOut.gif
trunk/treebase-core/lib/images/64arrow.gif
trunk/treebase-core/lib/images/64bucket.gif
trunk/treebase-core/lib/images/64disabled.gif
trunk/treebase-core/lib/images/64dropper.gif
trunk/treebase-core/lib/images/64ibeam.gif
trunk/treebase-core/lib/images/64info.gif
trunk/treebase-core/lib/images/64notesTool.gif
trunk/treebase-core/lib/images/64pointer.gif
trunk/treebase-core/lib/images/64revSort.gif
trunk/treebase-core/lib/images/64sort.gif
trunk/treebase-core/lib/images/64wand.gif
trunk/treebase-core/lib/images/64zoomIn.gif
trunk/treebase-core/lib/images/64zoomOut.gif
trunk/treebase-core/lib/images/add.gif
trunk/treebase-core/lib/images/addRemote.gif
trunk/treebase-core/lib/images/and.gif
trunk/treebase-core/lib/images/annot.gif
trunk/treebase-core/lib/images/ant_logo_large.gif
trunk/treebase-core/lib/images/arrow.gif
trunk/treebase-core/lib/images/back.gif
trunk/treebase-core/lib/images/backDim.gif
trunk/treebase-core/lib/images/banner.gif
trunk/treebase-core/lib/images/banner.psd.zip
trunk/treebase-core/lib/images/bannerBeta.gif
trunk/treebase-core/lib/images/blackPixel.gif
trunk/treebase-core/lib/images/blackPixel3.gif
trunk/treebase-core/lib/images/blank-off.gif
trunk/treebase-core/lib/images/blank-off22.gif
trunk/treebase-core/lib/images/blank-on.gif
trunk/treebase-core/lib/images/blank-on22.gif
trunk/treebase-core/lib/images/blue-ball-small.gif
trunk/treebase-core/lib/images/bucket.gif
trunk/treebase-core/lib/images/buttons.gif
trunk/treebase-core/lib/images/checkMark.gif
trunk/treebase-core/lib/images/closeTriangleUp.gif
trunk/treebase-core/lib/images/colorLegend.gif
trunk/treebase-core/lib/images/compactTransparent.gif
trunk/treebase-core/lib/images/construction.gif
trunk/treebase-core/lib/images/dataSearch.gif
trunk/treebase-core/lib/images/decompactTransparent.gif
trunk/treebase-core/lib/images/decrease.gif
trunk/treebase-core/lib/images/disabled.gif
trunk/treebase-core/lib/images/downarrow-blue.gif
trunk/treebase-core/lib/images/downarrow-green.gif
trunk/treebase-core/lib/images/downarrow-red.gif
trunk/treebase-core/lib/images/downarrow.gif
trunk/treebase-core/lib/images/downarrowDisabled.gif
trunk/treebase-core/lib/images/downarrowPressed.gif
trunk/treebase-core/lib/images/dropper.gif
trunk/treebase-core/lib/images/empty.gif
trunk/treebase-core/lib/images/enterHoriz.gif
trunk/treebase-core/lib/images/enterHorizDisabled.gif
trunk/treebase-core/lib/images/enterHorizPressed.gif
trunk/treebase-core/lib/images/enterVert.gif
trunk/treebase-core/lib/images/enterVertDisabled.gif
trunk/treebase-core/lib/images/enterVertPressed.gif
trunk/treebase-core/lib/images/equilstatestab.gif
trunk/treebase-core/lib/images/equilstatestabOff.gif
trunk/treebase-core/lib/images/explanationMinus.gif
trunk/treebase-core/lib/images/explanationMinusOff.gif
trunk/treebase-core/lib/images/explanationPlus.gif
trunk/treebase-core/lib/images/goaway.gif
trunk/treebase-core/lib/images/goawayTransparent.gif
trunk/treebase-core/lib/images/green-ball-small.gif
trunk/treebase-core/lib/images/help.gif
trunk/treebase-core/lib/images/helpPressed.gif
trunk/treebase-core/lib/images/how.gif
trunk/treebase-core/lib/images/ibeam.gif
trunk/treebase-core/lib/images/increase.gif
trunk/treebase-core/lib/images/info.gif
trunk/treebase-core/lib/images/infoBarBase.gif
trunk/treebase-core/lib/images/infoBarIcons.gif
trunk/treebase-core/lib/images/infoBarTriangle.gif
trunk/treebase-core/lib/images/leftarrow-blue.gif
trunk/treebase-core/lib/images/leftarrow-gray.gif
trunk/treebase-core/lib/images/leftarrow-green.gif
trunk/treebase-core/lib/images/leftarrow-red.gif
trunk/treebase-core/lib/images/leftarrow.gif
trunk/treebase-core/lib/images/leftarrowDisabled.gif
trunk/treebase-core/lib/images/leftarrowPressed.gif
trunk/treebase-core/lib/images/link.gif
trunk/treebase-core/lib/images/list.gif
trunk/treebase-core/lib/images/listC.gif
trunk/treebase-core/lib/images/listP.GIF
trunk/treebase-core/lib/images/listT.gif
trunk/treebase-core/lib/images/manual.gif
trunk/treebase-core/lib/images/manualPressed.gif
trunk/treebase-core/lib/images/matrix.gif
trunk/treebase-core/lib/images/menuDropArrow.gif
trunk/treebase-core/lib/images/menus.gif
trunk/treebase-core/lib/images/mesquite.gif
trunk/treebase-core/lib/images/mesquite.psd.zip
trunk/treebase-core/lib/images/mesquiteBeta.gif
trunk/treebase-core/lib/images/mesquiteIcon.gif
trunk/treebase-core/lib/images/mesquiteIcon128.gif
trunk/treebase-core/lib/images/mesquiteIcon16.gif
trunk/treebase-core/lib/images/mesquiteIcon48.gif
trunk/treebase-core/lib/images/mesquitePlain.gif
trunk/treebase-core/lib/images/mesquitesmall.gif
trunk/treebase-core/lib/images/new.gif
trunk/treebase-core/lib/images/notesTool.gif
trunk/treebase-core/lib/images/ok.gif
trunk/treebase-core/lib/images/or.gif
trunk/treebase-core/lib/images/pause.gif
trunk/treebase-core/lib/images/play.gif
trunk/treebase-core/lib/images/pointer.gif
trunk/treebase-core/lib/images/prerelease.gif
trunk/treebase-core/lib/images/ratematrixtab.gif
trunk/treebase-core/lib/images/ratematrixtabOff.gif
trunk/treebase-core/lib/images/release.gif
trunk/treebase-core/lib/images/replaceLeft.gif
trunk/treebase-core/lib/images/revSort.gif
trunk/treebase-core/lib/images/rightarrow-blue.gif
trunk/treebase-core/lib/images/rightarrow-green.gif
trunk/treebase-core/lib/images/rightarrow-red.gif
trunk/treebase-core/lib/images/rightarrow.gif
trunk/treebase-core/lib/images/rightarrowDisabled.gif
trunk/treebase-core/lib/images/rightarrowPressed.gif
trunk/treebase-core/lib/images/rootstatestab.gif
trunk/treebase-core/lib/images/rootstatestabOff.gif
trunk/treebase-core/lib/images/sitetositetab.gif
trunk/treebase-core/lib/images/sitetositetabOff.gif
trunk/treebase-core/lib/images/sliderHoriz.gif
trunk/treebase-core/lib/images/sliderVert.gif
trunk/treebase-core/lib/images/sort.gif
trunk/treebase-core/lib/images/spot.gif
trunk/treebase-core/lib/images/spotgreen.gif
trunk/treebase-core/lib/images/subtract.gif
trunk/treebase-core/lib/images/tabLeft.gif
trunk/treebase-core/lib/images/tabOff.gif
trunk/treebase-core/lib/images/tabOn.gif
trunk/treebase-core/lib/images/tabRight.gif
trunk/treebase-core/lib/images/taxon.gif
trunk/treebase-core/lib/images/trashcan.gif
trunk/treebase-core/lib/images/triangleDown.gif
trunk/treebase-core/lib/images/triangleDownOff.gif
trunk/treebase-core/lib/images/triangleDownOn.gif
trunk/treebase-core/lib/images/triangleRightOff.gif
trunk/treebase-core/lib/images/triangleRightOn.gif
trunk/treebase-core/lib/images/triangleUpOn.gif
trunk/treebase-core/lib/images/uparrow-blue.gif
trunk/treebase-core/lib/images/uparrow-green.gif
trunk/treebase-core/lib/images/uparrow-red.gif
trunk/treebase-core/lib/images/uparrow.gif
trunk/treebase-core/lib/images/uparrowDisabled.gif
trunk/treebase-core/lib/images/uparrowPressed.gif
trunk/treebase-core/lib/images/wand.gif
trunk/treebase-core/lib/images/zoomIn.gif
trunk/treebase-core/lib/images/zoomOut.gif
Added: trunk/treebase-core/lib/images/32arrow.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32arrow.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32bucket.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32bucket.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32disabled.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32disabled.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32dropper.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32dropper.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32ibeam.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32ibeam.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32info.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32info.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32notesTool.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32notesTool.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32pointer.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32pointer.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32revSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32revSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32sort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32sort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32wand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32wand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32zoomIn.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32zoomIn.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/32zoomOut.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/32zoomOut.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64arrow.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64arrow.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64bucket.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64bucket.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64disabled.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64disabled.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64dropper.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64dropper.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64ibeam.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64ibeam.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64info.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64info.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64notesTool.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64notesTool.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64pointer.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64pointer.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64revSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64revSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64sort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64sort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64wand.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64wand.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64zoomIn.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64zoomIn.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/64zoomOut.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/64zoomOut.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/add.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/add.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/addRemote.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/addRemote.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/and.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/and.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/annot.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/annot.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/ant_logo_large.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/ant_logo_large.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/arrow.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/arrow.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/back.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/back.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/backDim.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/backDim.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/banner.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/banner.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/banner.psd.zip
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/banner.psd.zip
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/bannerBeta.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/bannerBeta.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/blackPixel.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/blackPixel.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/blackPixel3.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/blackPixel3.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/blank-off.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/blank-off.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/blank-off22.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/blank-off22.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/blank-on.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/blank-on.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/blank-on22.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/blank-on22.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/blue-ball-small.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/blue-ball-small.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/bucket.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/bucket.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/buttons.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/buttons.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/checkMark.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/checkMark.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/closeTriangleUp.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/closeTriangleUp.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/colorLegend.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/colorLegend.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/compactTransparent.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/compactTransparent.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/construction.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/construction.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/dataSearch.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/dataSearch.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/decompactTransparent.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/decompactTransparent.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/decrease.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/decrease.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/disabled.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/disabled.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/downarrow-blue.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/downarrow-blue.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/downarrow-green.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/downarrow-green.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/downarrow-red.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/downarrow-red.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/downarrow.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/downarrow.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/downarrowDisabled.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/downarrowDisabled.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/downarrowPressed.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/downarrowPressed.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/dropper.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/dropper.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/empty.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/empty.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/enterHoriz.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/enterHoriz.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/enterHorizDisabled.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/enterHorizDisabled.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/enterHorizPressed.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/enterHorizPressed.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/enterVert.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/enterVert.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/enterVertDisabled.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/enterVertDisabled.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/enterVertPressed.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/enterVertPressed.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/equilstatestab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/equilstatestab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/equilstatestabOff.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/equilstatestabOff.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/explanationMinus.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/explanationMinus.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/explanationMinusOff.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/explanationMinusOff.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/explanationPlus.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/explanationPlus.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/goaway.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/goaway.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/goawayTransparent.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/goawayTransparent.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/green-ball-small.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/green-ball-small.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/help.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/help.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/helpPressed.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/helpPressed.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/how.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/how.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/ibeam.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/ibeam.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/increase.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/increase.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/info.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/info.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/infoBarBase.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/infoBarBase.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/infoBarIcons.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/infoBarIcons.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/infoBarTriangle.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/infoBarTriangle.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/leftarrow-blue.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/leftarrow-blue.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/leftarrow-gray.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/leftarrow-gray.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/leftarrow-green.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/leftarrow-green.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/leftarrow-red.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/leftarrow-red.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/leftarrow.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/leftarrow.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/leftarrowDisabled.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/leftarrowDisabled.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/leftarrowPressed.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/leftarrowPressed.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/link.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/link.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/list.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/list.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/listC.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/listC.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/listP.GIF
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/listP.GIF
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/listT.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/listT.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/manual.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/manual.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/manualPressed.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/manualPressed.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/matrix.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/matrix.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/menuDropArrow.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/menuDropArrow.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/menus.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/menus.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/mesquite.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/mesquite.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/mesquite.psd.zip
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/mesquite.psd.zip
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/mesquiteBeta.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/mesquiteBeta.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/mesquiteIcon.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/mesquiteIcon.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/mesquiteIcon128.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/mesquiteIcon128.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/mesquiteIcon16.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/mesquiteIcon16.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/mesquiteIcon48.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/mesquiteIcon48.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/mesquitePlain.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/mesquitePlain.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/mesquitesmall.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/mesquitesmall.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/new.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/new.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/notesTool.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/notesTool.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/ok.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/ok.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/or.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/or.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/pause.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/pause.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/play.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/play.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/pointer.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/pointer.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/prerelease.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/prerelease.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/ratematrixtab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/ratematrixtab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/ratematrixtabOff.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/ratematrixtabOff.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/release.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/release.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/replaceLeft.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/replaceLeft.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/revSort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/revSort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/rightarrow-blue.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/rightarrow-blue.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/rightarrow-green.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/rightarrow-green.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/rightarrow-red.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/rightarrow-red.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/rightarrow.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/rightarrow.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/rightarrowDisabled.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/rightarrowDisabled.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/rightarrowPressed.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/rightarrowPressed.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/rootstatestab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/rootstatestab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/rootstatestabOff.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/rootstatestabOff.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/sitetositetab.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/sitetositetab.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/sitetositetabOff.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/sitetositetabOff.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/sliderHoriz.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/sliderHoriz.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/sliderVert.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/sliderVert.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/sort.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/sort.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/spot.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/spot.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/spotgreen.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/spotgreen.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/subtract.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/subtract.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/tabLeft.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/tabLeft.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/tabOff.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/tabOff.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/tabOn.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/tabOn.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/tabRight.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/tabRight.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/taxon.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/taxon.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/trashcan.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/trashcan.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/triangleDown.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/triangleDown.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/triangleDownOff.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/triangleDownOff.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/triangleDownOn.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/triangleDownOn.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/triangleRightOff.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/triangleRightOff.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/triangleRightOn.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/triangleRightOn.gif
___________________________________________________________________
Added: svn:executable
+ *
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/triangleUpOn.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/triangleUpOn.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/uparrow-blue.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/uparrow-blue.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/uparrow-green.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/uparrow-green.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/uparrow-red.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/uparrow-red.gif
_____...
[truncated message content] |
|
From: <rv...@us...> - 2009-12-15 17:59:29
|
Revision: 368
http://treebase.svn.sourceforge.net/treebase/?rev=368&view=rev
Author: rvos
Date: 2009-12-15 17:59:22 +0000 (Tue, 15 Dec 2009)
Log Message:
-----------
Adding mesquite classes
Added Paths:
-----------
trunk/treebase-core/lib/images/functionIcons/
trunk/treebase-core/lib/images/functionIcons/charSource.gif
trunk/treebase-core/lib/images/functionIcons/characterNumber.gif
trunk/treebase-core/lib/images/functionIcons/chart.gif
trunk/treebase-core/lib/images/functionIcons/fileInterpret.gif
trunk/treebase-core/lib/images/functionIcons/matrixEditor.gif
trunk/treebase-core/lib/images/functionIcons/matrixEditorUtil.gif
trunk/treebase-core/lib/images/functionIcons/matrixNumber.gif
trunk/treebase-core/lib/images/functionIcons/matrixSource.gif
trunk/treebase-core/lib/images/functionIcons/simulate.gif
trunk/treebase-core/lib/images/functionIcons/treeCharNumber.gif
trunk/treebase-core/lib/images/functionIcons/treeNumber.gif
trunk/treebase-core/lib/images/functionIcons/treeSource.gif
trunk/treebase-core/lib/images/functionIcons/treeWindow.gif
trunk/treebase-core/lib/images/functionIcons/treeWindowUtil.gif
Added: trunk/treebase-core/lib/images/functionIcons/charSource.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/charSource.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/characterNumber.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/characterNumber.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/chart.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/chart.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/fileInterpret.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/fileInterpret.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/matrixEditor.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/matrixEditor.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/matrixEditorUtil.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/matrixEditorUtil.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/matrixNumber.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/matrixNumber.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/matrixSource.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/matrixSource.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/simulate.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/simulate.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/treeCharNumber.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/treeCharNumber.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/treeNumber.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/treeNumber.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/treeSource.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/treeSource.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/treeWindow.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/treeWindow.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
Added: trunk/treebase-core/lib/images/functionIcons/treeWindowUtil.gif
===================================================================
(Binary files differ)
Property changes on: trunk/treebase-core/lib/images/functionIcons/treeWindowUtil.gif
___________________________________________________________________
Added: svn:mime-type
+ application/octet-stream
This was sent by the SourceForge.net collaborative development platform, the world's largest Open Source development site.
|
1 message has been excluded from this view by a project administrator.
