Protein Family Alignment Annotation Tool svncode

Fixed bug where deleted seq remain highlighed in ATV window
Added SPECIES and SYNONYM1-10 as "standard" seq. annotations
Created NodeChangeListener and synchronized species and synoyms across PFAAT and open ATV windows
Fixed crash bug in loading some pesky PDB files

Paul Dana's changes for deleting columns and sorting by group

changes marked by // phdana del columns
and by // phdana sort3

fixed various bugs

* show all column bug
* import residue misalingment bug

small changes

* print sort boxes option
* set groups from visible cluster functionality
* load from FASTA in file menu
* change PDB viewer mouse behaviour
* changed Sort by Percent Idenity to TWO
* sort by percent ident of consensus (existing)
* sort by percetn ident of seq (new)

adding sample file from Daniel

Paul's fixes for PDB renumbering and Column Sort features

Changes marked with

// phdana pdb renumber ->
// phdana sort ->

Respectively

Lots of changes...too numerous to mention them all but main ones:

Column Hiding bug fixed
Edit Annotations dialog now shows
* seq annotations
* all informatoin for residue annotations
Select residues by annotation bug fixed
Fixed bug to scroll to given residue when residue selected (from column hiding)
Fixed bug to scroll to given seq when residue selected (from seq hiding)
Fix for Arrow keys but when hidden columns or hidden sequences
Structure browser now shows the author's residue #s in selection panel
Misc menu renaming
Checked in sample files for Seq and Residue annotation
Checked in sample .fa file

Lots of changes...too numerous to mention them all but main ones:

Column Hiding bug fixed
Edit Annotations dialog now shows
* seq annotations
* all informatoin for residue annotations
Select residues by annotation bug fixed
Fixed bug to scroll to given residue when residue selected (from column hiding)
Fixed bug to scroll to given seq when residue selected (from seq hiding)
Fix for Arrow keys but when hidden columns or hidden sequences
Structure browser now shows the author's residue #s in selection panel
Misc menu renaming
Checked in sample files for Seq and Residue annotation
Checked in sample .fa file

Paul's mixed bag of changes including:

* Column filtering
* Load/Save in .pfaam of Seq Annot,ResAnnot,ColumnFilter
* Fix for Column Selection after hiding columns
* PRint selected nodes bug
* Visible Clusters vs Clusters for Verticle Bar
* default block size change
* control + arrow key for shifting seq

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