Protein Family Alignment Annotation Tool svncode

Move various classes from src/forester/atv/ to src/org/pfaat/gui/tree/component

Move ATVgraphic.java from src/forester/atv/ to src/org/pfaat/gui/tree/component/

Move SequenceSelectionDialog.java and ItemSelectionDialog.java to src/org/pfaat/gui/common/dialogs/

Add java doc

Moved to org.pfaat.tree. See additional detail in previos commit

Move ATVjframe.java to org.pfaat. Needed to make several methods in atv classes public to facilitate this

Replace Comparison* with PercentIdentityMatrix*

replaced with PercentIdentiyMatrixFrame.java

moved to org.pfaat and name PercentIdentityMatrixxxx

small changes