Protein Family Alignment Annotation Tool svncode

Daniels changes.

Version = 1.0.007 - 16-June-2004 - happy bday Paul

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Paul Dana's changes for column annotation import and multiple residue selection

changes marked with // phdana ca ->
changes marked with // phdana rs ->

Changes include:

* Residue Annotation import
* "properties" on Edit Residue Annotation dialog
* Select multiple residues with SHIFT and CONTROL keys
* extend selections

Changes NOT included

* Save "properties" for residue annotations to .pfaam file

Paul Dana's third round of ATV changes, and small align bug fix.

All changes marked with // phdana atv3 ->

or // phdana small align ->

Changes include

* Selection color overrides all others
* PropertyList class in forrester.tree
* Color by property
* Filling out rest of "hide/show"
* Unrooted tree loading fix

* small align bug in Alignment view fixed.

added class com.neogenesis.util.NoDouble

changes marked with // phdana no double ->

This is a utility class I use to remove extraneous "double lines"
(extra carriage returns and/or line feeds) from source files before
I edit them.

Paul Dana's 2nd round of ATV changes

changes marked with: // phdana atv2 ->

(unless said changes were already in middle of existing //phdana atv ->)

Changes include:

Analysis > Import New Hampshire renamed to File > Open Rooted Tree
Box next to seq name now shows selection status
Search works for synonyms equivalently to seq name
# synonyms increased to 10 from 5
Clustering based on cut
Fixed cutting algorithm
ClusterID support for NHX read/write and import from file
Added Coloring modes to View: none, by rgb, by cluster id, by LogL
Hide flags supported on node properties dialog
Hide flags for all properties now implemented (not just name,branchlength)
Fixed misc bugs

Paul Dana's first round of changes to ATV

changes marked with // phdana atv ->

Changes include
Merging new ATV
Using ATVjframe rather than our own frame
Merging ATV selection code from PCAT
New Tags: synonyms, unlimited # of user defined annotations, color
New GUI for new tags
Import new tags from file
Load/Save new tags in NHX
Display of synonyms and Hide Flags
Menu for synonyms and Hide Flags (for name and branch lengths)
Scale bar
Interactive Verticle Bar for showing # of groups

merging Ethan's change into CVS

Added Files:
src/com/neogenesis/pfaat/pdb/PdbSelectNearManager.java
Does Ligand Proximity selection in Pdb Viewer

src/com/neogenesis/pfaat/pdb/PdbSolAccRenderer.java
Does Solvent Accessible Spheres view

Following files were modified in support of these changes:
----------------------------------------------------------------------
Modified Files:
src/com/neogenesis/pfaat/pdb/PdbFrame.java
src/com/neogenesis/pfaat/pdb/PdbLoader.java
src/com/neogenesis/pfaat/pdb/PdbSelectionModeManager.java
src/com/neogenesis/pfaat/pdb/PdbStructure.java
src/com/neogenesis/pfaat/pdb/PdbStructureModeManager.java
----------------------------------------------------------------------

20-May-2004

Added to CVS changes marked with:

// phdana printing ->