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[r25] by pauldana

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

 2004-06-04 16:54:21 Tree
[r24] by pauldana

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

 2004-06-01 00:18:20 Tree
[r23] by simonxi

merging Ethan's change into CVS

 2004-05-28 15:54:42 Tree
[r22] by colemanr

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
----------------------------------------------------------------------

 2004-05-21 14:59:20 Tree
[r21] by pauldana

20-May-2004

Added to CVS changes marked with:

// phdana printing ->

 2004-05-20 18:20:09 Tree
[r20] by pauldana

20-May-2003

Added changes marked with given comments to CVS:

// phdana version ->

 2004-05-20 18:17:34 Tree
[r19] by pauldana

20-May-2003

Added changes marked with given comments to CVS:

// phdana printing ->

 2004-05-20 18:01:39 Tree
[r18] by --none--

This commit was manufactured by cvs2svn to create tag 'version_1_0'.

 2004-05-11 21:32:25 Tree
[r17] by pauldana

phdana - testing write access

 2004-05-11 21:32:24 Tree
[r16] by simonxi

: ----------------------------------------------------------------------
Developer's guide. API documentation to be added soon.

 2003-05-02 13:45:29 Tree
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