Protein Family Alignment Annotation Tool svncode

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 ->

20-May-2003

Added changes marked with given comments to CVS:

// phdana version ->

20-May-2003

Added changes marked with given comments to CVS:

// phdana printing ->

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

phdana - testing write access

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

extracted all patternsets. this removes annoying warnings during build