Protein Family Alignment Annotation Tool svncode

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.