dcaffrey committed [72adf9] on gitcode

new version for TreeLoader.java and associated subclasses

dcaffrey committed [889a1c] on gitcode

Created TreeLoader.java and its subclasses NhxLoader.java, NhLoader.java etc to provide a scaleable and reusable framework for file extensions. Importantly, the file extensions determine how a file is read and saved in a consistent manner. The code is now used by the gui and all relevant command line tools. All references to the code in the gui were tested and seem to work as expected. The mrbayes format was not tested but all other formats were tested. About 5 of the commandline tools that r...

dcaffrey committed [7dc3fc] on gitcode

reformat a tree based on the file extensions

dcaffrey committed [ae6e45] on gitcode

Add javadppc and comments

dcaffrey committed [cc3b3a] on gitcode

TreeFrame now calls TreeFrame.exit() when it is a stand alone application

dcaffrey committed [c5ea08] on gitcode

TreeFrame now calls TreeFrame.exit() when it is a stand alone application

dcaffrey committed [8dc72c] on gitcode

TreeFrame now calls TreeFrame.exit() when it is a stand alone application

dcaffrey committed [d48001] on gitcode

Treeviewer.java now prepends the current working directory to a treefile when the user doesn't include ./ in the file name. This fixes isse where Treeviewer.java could open a file name file.nh fromthe cwd

dcaffrey committed [1d65d2] on gitcode

Add comment to document the fact that ToolTipManager manages all tooltips and changes made to the sharedInstance will be applied to every tooltip in your application. This is a problem as ttm.setDismissDelay(30000) in AlignmentPanel.java means the Dismiss Delay is too short for SequenceAnnotation1Panel.java etc

dcaffrey committed [0904fb] on gitcode

Added the --verbose option so that we only report sequences in the cDNA file that are missing in the protein MSA when --verbose is specified

dcaffrey committed [5e99e6] on gitcode

Comment out a print statement

dcaffrey committed [336344] on gitcode

Comment out a print statement

dcaffrey committed [444648] on gitcode

replace some ternary operators with full if else statements

dcaffrey committed [6a43b9] on gitcode

1) Replace new Integer(i) with Integer.valueOf(i). 2) Occasionally add type arguments for variables(e.g. HashMaps) that the Integer was added to. I only did this when the variable was local/had a few (around 5) references

dcaffrey committed [7fd099] on gitcode

Improve java doc

dcaffrey committed [fac5da] on gitcode

Replace the word highlight with select/selected from comments, parameter names, and previosly commented-out methods. The concept of highlighting is a misnomer and has been eradicated

dcaffrey committed [273242] on gitcode

Version 3.025

dcaffrey committed [1a4ba5] on gitcode

New version and date to mark the previous commit that commented out the abstract method DisplayPropertiesListener.displayHighlightsChanged(DisplayProperties dp, Sequence[] seqs).

dcaffrey committed [2045a5] on gitcode

Commented out the abstract method DisplayPropertiesListener.displayHighlightsChanged(DisplayProperties dp, Sequence[] seqs). Likewise, I commented out the corresponding method in all classes that implement DisplayPropertiesListener

dcaffrey committed [49a384] on gitcode

add java doc

dcaffrey committed [8ed9cd] on gitcode

Clean up column selection code, add comment, and add theoretical support for the apple command (there seems to be a java bug that means it only works when shift is also pressed with the apple command

dcaffrey committed [bf425e] on gitcode

1) Comment out DisplayProperties.fireDisplayHighlightsChanged(Sequence[] seqs) and replace it with DisplayProperties.fireResidueSelectionChanged(Sequence[] seqs) 2) Rename DisplayProperties.fireDisplayHighlightsChanged(Sequence seq) to DisplayProperties.fireResidueSelectionChanged(Sequence seq)

dcaffrey committed [84a5ae] on gitcode

Clean up of code to prior to addressing DisplayPropertiesListener.displayHighlightsChanged

dcaffrey committed [99c585] on gitcode

Rename methods that contain seHighlights with SelectedResidues or ResidueSelected

dcaffrey committed [8933b3] on gitcode

Rename methods that contain seHighlights with SelectedResidues or ResidueSelected

dcaffrey committed [000cf7] on gitcode

Rename methods that contain seHighlights with SelectedResidues or ResidueSelected

dcaffrey committed [bdffa3] on gitcode

Rename methods that contain seHighlights with SelectedResidues or ResidueSelected

dcaffrey committed [e53e21] on gitcode

Delete unused classes

Protein Family Alignment Annotation Tool released /Pfaat-3.023.exe

dcaffrey committed [7426fe] on gitcode

new build version 3.023

dcaffrey committed [ff629d] on gitcode

Changes to javadoc

dcaffrey committed [0ab485] on gitcode

Rename DisplayPropertiesListener.displayPropertiesAnnViewChanged(DisplayProperties dp, Sequence seq, boolean show) to DisplayPropertiesListener.displayPropertiesLineAnnotationViewChanged(DisplayProperties dp, Sequence seq, boolean show)

dcaffrey committed [07857c] on gitcode

rename some methods to clarify their involvmennt in line annotations

dcaffrey committed [69323b] on gitcode

Prepend various abstract methods with DisplayProperties and add boilerplate java doc

dcaffrey committed [5a937f] on gitcode

Rename DisplayPropertiesListener.displaySeqSelectChanged() to DisplayPropertiesListener.displayPropertiesSequenceSelectionChanged()

dcaffrey committed [e4eafe] on gitcode

Rename DisplayPropertiesListener.displayHighlightsChanged(DisplayProperties dp, Sequence seq) to DisplayPropertiesListener.displayPropertiesResidueSelectionChanged(DisplayProperties dp, Sequence seq)

dcaffrey committed [ba5bef] on gitcode

1) The selection status bar is now aligned to the left which is consistent with the toolbar with dropboxes / comboboxes. 2) Removed/ commented out the statusBarSeqNameInfo as it was taken up valuable space and wasn't providing very useful info. 3) Shortened wording of tool bar text by removing Number of from varios labels and added tool tips for them instead. 4) Added the number of selected sequences to the selection status bar

dcaffrey committed [6a2e5a] on gitcode

new version

Protein Family Alignment Annotation Tool released /Pfaat-3.023.dmg

Protein Family Alignment Annotation Tool released /Pfaat-3.022.exe

Protein Family Alignment Annotation Tool released /Pfaat-3.022.dmg

dcaffrey committed [53f8cf] on gitcode

new build

dcaffrey committed [53b229] on gitcode

The filter and sort boxes now are set to a dark grey when the box is clicked, and reset to their default color when deselected

dcaffrey committed [53b229] on gitcode

The filter and sort boxes now are set to a dark grey when the box is clicked, and reset to their default color when deselected

dcaffrey committed [f7fe25] on gitcode

1) The status bar now shows the Number of selected residues and the Number of selected columns. 2) The statusBarInformation was extracted from various methods and an innner class within Pfaat.java and improved to support #1.

dcaffrey committed [62fe53] on gitcode

reflects changes in DisplayProperties.java

dcaffrey committed [4eb0d6] on gitcode

reflects changes in DisplayProperties.java

dcaffrey committed [4eb0d6] on gitcode

reflects changes in DisplayProperties.java

dcaffrey committed [9ec8d7] on gitcode

rename some fields that refer to highlights as selectedResidues

dcaffrey committed [a39cd2] on gitcode

1) RulerAnnotationComponent.java is renamed ColumnSelectionComponent.java .2) Related to #1, the inner class Alignment.RulerAnnotation is removed and so are all related methods and references through out. The concept of ruler annotation was essentially obsolete as there was no way to add or edit them. Instead, the RulerAnnotationComponent only real purpose was to support column selection as now reflected in the appropriately named ColumnSelectionComponent.java

dcaffrey committed [3e2833] on gitcode

1) Rename some methods to more explicit names. 2) Collapsed nodes and their labels are now colored pink when 1 or more of their collapsed children are selected.

dcaffrey committed [3e2833] on gitcode

1) Rename some methods to more explicit names. 2) Collapsed nodes and their labels are now colored pink when 1 or more of their collapsed children are selected.

dcaffrey committed [e4e72c] on gitcode

Small tweak to java doc

dcaffrey committed [c856e1] on gitcode

Tweak build instructions slightly. New date

dcaffrey committed [dac93f] on gitcode

Various changes associate with renaming of methods in other classes

dcaffrey committed [4612d3] on gitcode

Use Sequence.getName() instead of Sequence.getDisplayedName()

dcaffrey committed [21a12a] on gitcode

1) Added overriding public String getToolTipText(MouseEvent event) which provides the appropriate tool tip when mousing over sequence annotation panel 1. Specifically, it displays associated structure information when (and only when) it exists for a sequence. 2) Rename mouse_row_pos to indexForSeqAnn1Component, rename findRow(int x, int y) to getIndexForSeqAnn1Component(int x, int y), Rename getMouseRowPosition() to getIndexForSeqAnn1Component()

dcaffrey committed [625ac7] on gitcode

deleting as this is not references and appears to be an old version of SequenceAnn3Component.java

dcaffrey committed [a9bb78] on gitcode

Tweaked java doc

dcaffrey committed [822065] on gitcode

1. Remove tooltip code that was written yesterday as it was clobbering right click sequence funcitonality. 2. replace Sequence.getDisplayedName() with Sequence.getAnnotationValueDisplayedAt1stComponent() and comment out old code that was using old logic / rationalle to determin the displayed values for the component.

dcaffrey committed [430314] on gitcode

Modify java doc

dcaffrey committed [424bb0] on gitcode

Rename View -> Sort Sequences By -> Name to View -> Sort Sequences By -> Sequence Name

dcaffrey committed [2eb95b] on gitcode

getMouseRowPosition() renamed to getIndexForSeqAnn1Component()

dcaffrey committed [4fa614] on gitcode

Deprecate Sequence.getDisplayedName()

dcaffrey committed [54faac] on gitcode

replace Sequence.getDisplayedName() with Sequence.getName()

dcaffrey committed [ae1c5f] on gitcode

Fix code causing warnings

dcaffrey committed [7320ed] on gitcode

Tool tips are now set for each SequenceAnn1Component and include the pdb file and associated chain when it exists

dcaffrey committed [03a393] on gitcode

add java doc

dcaffrey committed [6aed13] on gitcode

The help now refers to importing Meme results as residue annotations

dcaffrey committed [320da6] on gitcode

Comment out various print statements

dcaffrey committed [623909] on gitcode

Add basic comment

dcaffrey committed [e66795] on gitcode

version 3.0.20

Protein Family Alignment Annotation Tool released /Pfaat-3.020.exe

dcaffrey committed [78220f] on gitcode

Various changes that reflect the chaning of Tree.getNode(String) to Tree.getNode(String,boolean)

dcaffrey committed [c1e026] on gitcode

Added warnings for situations where the leaves in the hyphy result file and/or the seq names in the aligment did not match

dcaffrey committed [67d4b9] on gitcode

1. Added boolean returnNullWhenNoNodesFound paramater to getNode(). 2. Added public boolean nodeExists(String nodeName).

dcaffrey committed [5a2222] on gitcode

Fix code causing warnings

dcaffrey committed [f26dde] on gitcode

Fix code causing warnings

dcaffrey committed [a0e8de] on gitcode

Now uses AlignmentFileUtil.openAlignment(File) and AlignmentFileUtil.saveAlignment(Alignment, File, File) instead of local methods

dcaffrey committed [845814] on gitcode

Reference to VneScore is replace with ref to the new name ResidueConservationScores

dcaffrey committed [47af9d] on gitcode

Added code to report end time

dcaffrey committed [d3ed81] on gitcode

FIx code that is causing warnings

dcaffrey committed [59a7ce] on gitcode

trivial changes

dcaffrey committed [ea72bf] on gitcode

Don't need this as ReformatAlignment does the same job

dcaffrey committed [99e781] on gitcode

Rename VneScore.java to ResidueConservationScores.java

dcaffrey committed [0262ac] on gitcode

Modified openAlignment() so it catches a FileNotFoundException.

dcaffrey committed [d9e3ad] on gitcode

Remove code causing warning

dcaffrey committed [317ec8] on gitcode

remove code causing warning

dcaffrey committed [9de34a] on gitcode

Change ReformatAlignment reference to ImportSequenceAnnotations

dcaffrey committed [40fcdf] on gitcode

Change ReformatAlignment reference to CopyResidueAnnotsWithInPfaat

dcaffrey committed [afd261] on gitcode

Rename ReformatAlignment reference to ClosestResiduesToReceptor

dcaffrey committed [0d9ed6] on gitcode

Fix code causing warnings

dcaffrey committed [3005c2] on gitcode

Fix code that causes warnings

dcaffrey committed [46a04b] on gitcode

Fix code causing warnings

dcaffrey committed [7ed1cb] on gitcode

Fix code causing warnings

dcaffrey committed [173858] on gitcode

Fix code that cause warnings

dcaffrey committed [b105c7] on gitcode

Delete as ReformatAlignment does the same thing

dcaffrey committed [f85f67] on gitcode

Rename Clustal2Pfaat to ReformatAlignment

dcaffrey committed [0ab7de] on gitcode

Improve the java doc

dcaffrey committed [359120] on gitcode

ResidueColorScheme() now handles situation where the file is null