Protein Family Alignment Annotation Tool svncode

Fix bug where editing of a sequence would hang when it had a line annotations

1) Address some warnings related to types. 2) Made code more readable and easier to interpret during debugging.

Address warnings related to type

These 2 classes are now in the src/org/pfaat/gui/msa/file/action package

Rename HelpActionHandler to HelpActionEventHandler

Most of these changes will reflect the change in location of various references to org/pfaat

no longer used

1. Efficient /Recalculation/painting of information score during MSA editing. 2. Removal of unused code including Group panel, JNET sec struc analysis, old tree launcher,consensus 2 and 3, dropdown comboboxes in consensus. 3. Moved Action Event Handlers to src/org/pfaat/gui/msa/find/actioneventhandler , src/org/pfaat/gui/msa/analysis/actioneventhandler, src/org/pfaat/gui/msa/help/actioneventhandler. 4. Reorganized Analysis -> Conservation scores 5. Moved several Action methods related to File, Analysis and Find to src/org/pfaat/gui/msa/find/action/ and src/org/pfaat/gui/msa//file/action/ , src/org/pfaat/gui/msa//analysis/plsr/action, and src/org/pfaat/gui/msa//analysis/action that were part of the previous commit

New package structure

Moved from a analysis (I think)