Protein Family Alignment Annotation Tool svncode

PdbRibbonRenderer has been edited to allow the correct display of secondary structure ribbons.

BasicCanvas has been amended to reinstate navigation behaviours.

Paul Dana's 4th ATV chagnes

changes to ATV marked with // phdana atv4 ->

Also some misc Pfaat chagnes

Changes include:

* Print selected nodes in ATV
* Print renderring now same as ATVjframe rendering
* Set color of selected nodes
* Color button on ATVnodepanel
* Better unique color selection
* Scroll to first found node after search
* Fixed bug that caused crash in EditAnnotationsDialog
* Fixed bug that caused crash in editing residue annotations
* Column selection defaults the "selected columns" for printing

changed package name

Daniels changes.

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

*** empty log message ***

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