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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)

pauldana 2004-07-30

changed /trunk/pfaat/src/com/neogenesis/pfaat/AboutDialog.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/AlignmentFrame.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/AlignmentNamePanel.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/Sequence.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/io/AlignmentLoader.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/j3d/BasicCanvas.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/pdb/PdbFrame.java
changed /trunk/pfaat/src/com/neogenesis/pfaat/print/PrintPSDialog.java
changed /trunk/pfaat/src/forester/atv/ATVgraphic.java
changed /trunk/pfaat/src/forester/atv/ATVjframe.java
changed /trunk/pfaat/src/forester/tree/Node.java
changed /trunk/pfaat/src/forester/tree/Tree.java
/trunk/pfaat/src/com/neogenesis/pfaat/AboutDialog.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/AlignmentFrame.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/AlignmentNamePanel.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/Sequence.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/io/AlignmentLoader.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/j3d/BasicCanvas.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/pdb/PdbFrame.java Diff Switch to side-by-side view
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/trunk/pfaat/src/com/neogenesis/pfaat/print/PrintPSDialog.java Diff Switch to side-by-side view
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/trunk/pfaat/src/forester/atv/ATVgraphic.java Diff Switch to side-by-side view
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/trunk/pfaat/src/forester/atv/ATVjframe.java Diff Switch to side-by-side view
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/trunk/pfaat/src/forester/tree/Node.java Diff Switch to side-by-side view
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/trunk/pfaat/src/forester/tree/Tree.java Diff Switch to side-by-side view
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