File Release Notes and Changelog
Release Name: 1.0.0
Notes: Release 1.0.0 (10 October, 2006) ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ This is the first release of atvEditor, an extended ATV (A Tree Viewer) that allows manual modifications on trees. The history of atvEditor can be dated back to September 2004, when TreeFam needed a tool that was capable of changing the topology of a phylogenetic tree. There were very few such softwares at that time, and therefore I decided to write one by myself. Two years ago, I had little experiences in molecular evolution and even little in using the softwares in this area. I was not qualified to write a brand-new one from scratch. As suggested by Lachlan, a colleague and also a friend of mine, I chose ATV-1.9.2 as the ground, extended it and improved it, which gave the birth of atvEditor. Although the atvEditor looks pretty like ATV version 1.9.2 (not the latest 3.0.5), it really improved the original one in many ways: * Editing functions: change the topologies of phylogenetic trees, delete clades, and bifurcate/multifurcate nodes. * Colorize species. * Add more TreeFam-specific NHX tags: ":G=" and ":Sd=". And do not report an error when an unknown tag is encountered. * Code enhancement: Greatly simplify NHX string output using recursion. Improve reading speed when an NHX string with many white spaces are fed as the input. * Talk with TreeFam CGI for tree curation. * Link to source database by clicking a leaf. Note: If you are looking for an even powerful Java application that can edit trees in an easier way and do a lot of inferences to help tree curation, you should go for tctool (tree curation tool), the masterpiece of Lachlan.
Changes: 2006-09-29 10:08 liheng * ATVapp.java, ATVjapplet.java, forester/atv/ATVappletFrame.java, forester/tree/Node.java: for internal tags 2005-06-27 09:23 liheng * Makefile: change name ATV to eATV 2005-06-27 09:20 liheng * Makefile, manifest.txt: add manifest file 2005-06-27 09:08 liheng * forester/: atv/ATVcontrol.java, atv/ATVcontrol_applet.java, atv/ATVgraphic.java, atv/ATVgraphic_applet.java, atv_awt/ATVcontrol.java, atv_awt/ATVcontrol_applet.java, atv_awt/ATVgraphic.java, atv_awt/ATVgraphic_applet.java, tree/Tree.java: - fix bugs when demoting an external node - reserve a clade 2005-04-10 15:15 liheng * forester/: atv/ATVgraphic.java, atv_awt/Message.java, tree/TreeHelper.java: improve tree parser; improve plotting; 2005-04-03 21:12 liheng * forester/atv_awt/ATVappletFrame.java: add autoflush after the tree is modified. 2005-03-31 20:55 liheng * forester/atv/ATVappletFrame.java: - reload the URL when the tree is modified. 2005-03-31 20:06 liheng * forester/atv/ATVmouseMotionListener.java: Added by Zhang Zhang 2005-01-26 05:06 liheng * treefam/TreeFamPanel.java: add missing "phigs" 2005-01-19 08:01 liheng * Makefile, treefam/TreeFamClient.java, treefam/TreeFamPanel.java: * revise Makefile * fix a bug in TreeFamPanel.java 2005-01-08 07:38 liheng * MCview/Atom.java, MCview/Bond.java, MCview/Matrix.java, MCview/PDBChain.java, MCview/PDBfile.java, MCview/Residue.java, MCview/Zsort.java, MCview/myAtom.java, MCview/rotApplet.java, MCview/rotAppletFrame.java, MCview/rotCanvas.java, MCview/rotFrame.java, forester/atv/ATVjframe.java, forester/atv_awt/Message.java, jalview/AlignApplet.java, jalview/AlignFrame.java, jalview/AlignFrameApplet.java, jalview/AlignSeq.java, jalview/AlignThread.java, jalview/Alignment.java, jalview/AlignmentPanel.java, jalview/AppletFilePopup.java, jalview/AppletPostscriptPopup.java, jalview/BLCFile.java, jalview/BackTranslate.java, jalview/BigPanel.java, jalview/BinaryNode.java, jalview/BinarySequence.java, jalview/Blosum62ColourScheme.java, jalview/BrowserFrame.java, jalview/BuriedColourScheme.java, jalview/ButtonAlignApplet.java, jalview/CGI.java, jalview/ClustalFile.java, jalview/ClustalwCGI.java, jalview/ClustalwPanel.java, jalview/ClustalwThread.java, jalview/ClustalxColourScheme.java, jalview/ColorSelect.java, jalview/ColourAdapter.java, jalview/ColourCanvas.java, jalview/ColourChooserFrame.java, jalview/ColourChooserPanel.java, jalview/ColourPanel.java, jalview/ColourProperties.java, jalview/ColourScheme.java, jalview/ColourTable.java, jalview/CommandThread.java, jalview/ConsThread.java, jalview/Consensus.java, jalview/ConsensusColour.java, jalview/Conservation.java, jalview/ConservationColourScheme.java, jalview/DrawableAlignment.java, jalview/DrawableSequence.java, jalview/EstAlign.java, jalview/FastaFile.java, jalview/FeatureColourScheme.java, jalview/FeatureFrame.java, jalview/FileParse.java, jalview/FilePopup.java, jalview/FileProperties.java, jalview/Format.java, jalview/FormatAdapter.java, jalview/FormatProperties.java, jalview/GroupPopup.java, jalview/HelixColourScheme.java, jalview/HelpFile.java, jalview/HydrophobicColourScheme.java, jalview/IdCanvas.java, jalview/IdPanel.java, jalview/IncrementPopup.java, jalview/InputPopup.java, jalview/Java1.java, jalview/JnetCGI.java, jalview/JnetFile.java, jalview/ListProperties.java, jalview/MSFfile.java, jalview/MSPFile.java, jalview/MSPSequence.java, jalview/Mail.java, jalview/MailApplet.java, jalview/MailPopup.java, jalview/MailProperties.java, jalview/MailTextPopup.java, jalview/Matrix.java, jalview/MessageBox.java, jalview/NJTree.java, jalview/Output.java, jalview/OutputFilePopup.java, jalview/OutputGenerator.java, jalview/OutputPopup.java, jalview/PCA.java, jalview/PCAFrame.java, jalview/PCAPanel.java, jalview/PCAThread.java, jalview/PDBPopup.java, jalview/PIDColourScheme.java, jalview/PIRFile.java, jalview/PairAlignFrame.java, jalview/PairAlignThread.java, jalview/PercentIdentityPopup.java, jalview/PfamFile.java, jalview/Popup.java, jalview/PostalCGI.java, jalview/PostalColourScheme.java, jalview/PostalFile.java, jalview/Postscript.java, jalview/PostscriptFilePopup.java, jalview/PostscriptPopup.java, jalview/PostscriptProperties.java, jalview/ProgressFrame.java, jalview/ProgressPanel.java, jalview/QuickSort.java, jalview/RedundancyPopup.java, jalview/ResidueColourScheme.java, jalview/ResidueProperties.java, jalview/RotatableCanvas.java, jalview/RotatableMatrix.java, jalview/RunnableProcess.java, jalview/ScaleCanvas.java, jalview/ScalePanel.java, jalview/ScoreColourScheme.java, jalview/ScorePanel.java, jalview/ScoreSequence.java, jalview/SecondaryColourScheme.java, jalview/SendFileApplet.java, jalview/SendFileCGI.java, jalview/SeqCanvas.java, jalview/SeqPanel.java, jalview/Sequence.java, jalview/SequenceFeature.java, jalview/SequenceFeatureThread.java, jalview/SequenceGroup.java, jalview/SequenceNode.java, jalview/SequencePoint.java, jalview/SequenceProperties.java, jalview/SimpleBrowser.java, jalview/StrandColourScheme.java, jalview/SwissprotFile.java, jalview/TaylorColourScheme.java, jalview/TextAreaPrintStream.java, jalview/TextFrame.java, jalview/ThresholdPanel.java, jalview/TreeFile.java, jalview/TreeFrame.java, jalview/TreePanel.java, jalview/TreeScore.java, jalview/TreeThread.java, jalview/TurnColourScheme.java, jalview/URLPopup.java, jalview/UserColourScheme.java, jalview/ZappoColourScheme.java, jalview/pog.java, treefam/TFtextFrame.java, treefam/TreeFamClient.java, treefam/TreeFamFrame.java, treefam/TreeFamPanel.java: - better interface - jalview added - auto-fetch added - and more... 2004-12-01 07:26 liheng * manifest.txt: MANIFEST file 2004-12-01 07:26 liheng * Makefile: nothing important 2004-12-01 05:10 liheng * forester/: atv/ATVjframe.java, tree/TreeHelper.java: split openURL() to several methods 2004-12-01 05:08 liheng * treefam/: TFtextFrame.java, TreeFamClient.java, TreeFamPanel.java: - use httpclient to connect with TreeFam - a raw version is available 2004-12-01 00:50 liheng * Makefile, forester/atv/ATVjframe.java, treefam/TreeFamClient.java, treefam/TreeFamFrame.java, treefam/TreeFamPanel.java: - make runnable JAR - prepare to add treefam connection 2004-11-30 05:05 liheng * ATVjapplet.java, forester/atv/ATVgraphic.java, forester/atv/ATVjframe.java, forester/atv_awt/ATVappletWjsFrame.java: - add PostScript output by Zhang Zhang - remove tailing ^M in some files 2004-11-04 00:12 liheng * ATVapplet.java, forester/atv_awt/ATVappletFrame.java, forester/atv_awt/ATVcontrol.java: add TreeFam menu to applet 2004-11-03 22:04 liheng * ATVjapplet.java, forester/atv/ATVappletFrame.java, forester/atv/ATVcontrol.java, forester/atv/ATVcontrol_applet.java, forester/atv/ATVgraphic.java, forester/tree/Tree.java: talk with TreeFam CGI 2004-10-31 10:29 liheng * forester/: atv/ATVcontrol_applet.java, atv/ATVgraphic.java, atv/ATVgraphic_applet.java, atv_awt/ATVappletFrame.java, atv_awt/ATVcontrol.java, atv_awt/ATVcontrol_applet.java, atv_awt/ATVgraphic.java, atv_awt/ATVgraphic_applet.java: add multifurcate/delete to atv_awt. I am afraid that ATVjapplet.jar does not work under damned IE. 2004-10-29 21:53 liheng * forester/atv/ATVgraphic_applet.java: a bug 2004-10-29 21:49 liheng * forester/: atv/ATVcontrol.java, atv/ATVcontrol_applet.java, atv/ATVgraphic.java, atv/ATVgraphic_applet.java, tree/Node.java, tree/Tree.java: - add de-multifurcate when right-click a node - add deleteNode() 2004-10-29 19:58 liheng * forester/: atv/ATVcontrol.java, atv/ATVcontrol_applet.java, atv/ATVgraphic.java, atv/ATVgraphic_applet.java, tree/Node.java, tree/Tree.java: add multifurcation 2004-10-29 19:40 liheng * Makefile, forester/atv/ATVcontrol.java, forester/atv/ATVcontrol_applet.java, forester/atv/ATVgraphic.java, forester/atv/ATVgraphic_applet.java: merge promote/demote radio; but Japplet has not been tested. 2004-10-29 19:30 liheng * forester/: atv/ATVappletFrame.java, atv/ATVjframe.java, tree/Node.java, tree/Tree.java: permit multifurcation in output 2004-10-24 12:25 liheng * Makefile, forester/atv/ATVappletFrame.java, forester/atv/ATVcontrol_applet.java, forester/atv/ATVgraphic.java, forester/atv/ATVgraphic_applet.java, forester/atv_awt/ATVgraphic.java, forester/atv_awt/ATVgraphic_applet.java, forester/tree/Tree.java: - add multi-line NHX output - Japplet works 2004-10-18 20:36 liheng * ClustalTree.java: a good applet for tree viewing 2004-10-18 19:30 liheng * forester/: atv_awt/ATVgraphic_applet.java, tree/Node.java: fix an output bug; add links to more species 2004-10-17 13:15 liheng * forester/: atv/ATVcontrol.java, atv/ATVgraphic.java, atv_awt/ATVcontrol.java, atv_awt/ATVcontrol_applet.java, atv_awt/ATVgraphic.java, atv_awt/ATVgraphic_applet.java, tree/Node.java: - extend NHX format. add ":G=" and ":Sd=", representing GeneName and isSeed respectively. - improve web search by looking up gene name 2004-10-14 23:40 liheng * forester/: atv/ATVgraphic.java, atv_awt/ATVcontrol.java, atv_awt/ATVcontrol_applet.java, atv_awt/ATVgraphic.java, atv_awt/ATVgraphic_applet.java: add species color in both ATVapp and ATVapplet; improve web search in applet 2004-10-11 20:59 liheng * forester/: atv/ATVcontrol.java, atv/ATVgraphic.java, atv/ATVjframe.java, atv_awt/ATVcontrol_applet.java, atv_awt/ATVgraphic.java: change default radio; add Sanger to 'About' menu. 2004-10-11 20:29 liheng * ATVapp.java, ATVapplet.java, ATVjapplet.java, Makefile, species.nhx, forester/atv/ATVappletFrame.java, forester/atv/ATVcontrol.java, forester/atv/ATVcontrol_applet.java, forester/atv/ATVgraphic.java, forester/atv/ATVgraphic_applet.java, forester/atv/ATVjframe.java, forester/atv/ATVmouseListener.java, forester/atv/ATVnodeFrame.java, forester/atv/ATVnodePanel.java, forester/atv/ATVpanel.java, forester/atv/ATVpanel_applet.java, forester/atv/ATVprinter.java, forester/atv/ATVtextframe.java, forester/atv/DoubleDocument.java, forester/atv/IntegerDocument.java, forester/atv_awt/ATVappletFrame.java, forester/atv_awt/ATVappletWjs.java, forester/atv_awt/ATVappletWjsFrame.java, forester/atv_awt/ATVcontrol.java, forester/atv_awt/ATVcontrol_applet.java, forester/atv_awt/ATVframe.java, forester/atv_awt/ATVgraphic.java, forester/atv_awt/ATVgraphic_applet.java, forester/atv_awt/ATVmouseListener.java, forester/atv_awt/ATVnodeFrame.java, forester/atv_awt/ATVnodePanel.java, forester/atv_awt/ATVpanel.java, forester/atv_awt/ATVpanel_applet.java, forester/atv_awt/Message.java, forester/atv_awt/OutputFileRemotePopup.java, forester/atv_awt/PopupProtected.java, forester/datastructures/BasketDataStructure.java, forester/tools/DistanceCalculator.java, forester/tools/DoRIO.java, forester/tools/Int.java, forester/tools/NameAndValues.java, forester/tools/OE.java, forester/tools/RIO.java, forester/tools/SDI.java, forester/tools/SDIdirectory.java, forester/tools/SDIse.java, forester/tools/SDIunrooted.java, forester/tools/printAllSpecies.java, forester/tools/printSameOrder.java, forester/tools/testNHX.java, forester/tools/transfersBranchLenghts.java, forester/tree/Branch.java, forester/tree/Iterator.java, forester/tree/Node.java, forester/tree/PostorderTreeIterator.java, forester/tree/PreorderTreeIterator.java, forester/tree/StackItem.java, forester/tree/Tree.java, forester/tree/TreeHelper.java: atvEditor, check out from treeFam repository
