Protein Family Alignment Annotation Tool svncode

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

no message

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Paul's 6th round of ATV changes and
Sequence Annotation import and
misc fixes

Changes marked with // phdana atv6 ->
or marked with // phdana seq ann ->

Changes include:

* ATV advanced search
* ATV export
* ATV print selectd nodes bug fix
* Import Sequence Annotation
* Sequence Annotation Dialog
* Rename/add stuff in Pfaat Edit menu
* Rename stuff on Edit Annotations Dialog
* misc bug fixes

Paul Dana's 6th round of ATV changes

changes marked witih // phdana atv6 ->

Changes include
* fix for Print Selected -> sizes correctly
* Export Tags -> exports all possible tags to .csv vile
* Import Tags -> can accept the output of Export tags