Protein Family Alignment Annotation Tool svncode

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Comparison Matrix changes *mostly* done...everyhting works except for Inlude Gaps...waiting for daniel's help on the exact implemention of that

default of wireframe

Fix for "Launch PDB..." being alignment dependant

Fix for Res annot and Seq annotation that allows blank entries

Fix missing elemnts in coeff print out from Analysis->Correlate

improvements to the plugin architexture

Added plugin architecture and example plugin

Fix for speed of saving in file formats OTHER than pfaam
Pdb fixes

Blank Analysis menu