Protein Family Alignment Annotation Tool svncode

Now use org.pfaat.gui.msa.analysis.action.SimilarityMatrixEncoder instead of src/org/pfaat/gui/msa/analysis/seqspace/action/SeqSpaceEncoder.java

Never worked properly.

These were part of seqspace package. SimilarityMatrixEncoder was called something like SeqSpaceEncoder

THIS COMMIT CORRESPONDS TO THE MOVEMENT OF ~6000 LINES OF CODE FROM AlignmentFrame AND 1500 FROM SequenceAnnotation1Panel TO VARIOUS ActionEventHandlers. THERE IS ALSO ~400 LINES OF COMMENTED OUT DEADISH CODE AT THE END OF AlignmentFrame THAT CAN BE DELETED IN THE FUTURE. Specific changes in this commit are: 1) Moved Sort by sequence action methods from SequenceAnnotation1Panel.java to SortSequenceActionEventHandler. 2) Moved View-> Hide and View-> Show menu items from AlignmentFrame to ViewShowHideActionEventHandler.java.

Add java doc

Add java doc

Move to org.pfaat

Add java doc

1) renamed AlignmentNamePanel.java to SequenceAnnotation1Panel.java, AlignmentAnn2Panel.java to SequenceAnnotation2Panel.java , AlignmentAnn3Panel.java to SequenceAnnotation3Panel.java . 2) Add initial version of ViewShowHideActionEventHandler.java for 1st 2 menu items.

1) Moved initialization of Action Event Handlers to the begining of each initializeMenuName Method to improve code readability. 2) Added More verbose comments above each menu item to improve code readability.