Protein Family Alignment Annotation Tool svncode

Changed method signatures to faciliate refactoring of code and use by FileActionEventHandler.java

Small changes to facilitate debugging and amake code more readable

Trivial changes

added some java doc

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