Protein Family Alignment Annotation Tool svncode

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

Removed classes that are no longer necessary due to rearchitecting of PdbUtilities

Rearchitected and no longer contains static methods

Renamed method to be consistent with menu item

rm WRSTORE.*; jar -cvf Jmol4pfaat.jar *

fix for [ 1497036 ] CTRL select focus

fix for: [ 1517736 ] mouse wheel does not scroll alignment down
fix for: [ 1514485 ] Mouse over residue annot (follow up)

delete

move to properties folder