Protein Family Alignment Annotation Tool svncode

Fix bug that was causing same chain to be counted more than once

tweaked/added a couple of output format functions

pass chain to asaCalculator, clean up right click popup menu

make call to asaCalculator

Renamed some of fields and associated emthods in pfaat.pdb
Wrote base clas for AsaCalculator

fix for [ 1514489 ] Add residue annotation (rephrased)

Cleaned up AlignmentName class and extracted a few methods

Cleaned up class and extracted a few methods

Various changes to how pdb files are loaded and associated. Main rearchitecting and extracting methods to make code easier to follow and easier to use.

Modified so takes advantage of PdbUtilities rearchitecting.
extracted some method from associatePdbSequence and addPdbSequence