Protein Family Alignment Annotation Tool svncode

Changed some variable names and added comments to improve code readability

Added javadoc and renamed some variables so the code is easier to understand

Added multiSequenceSelector method that was in AlignmentFrame and is somewhat redundant. Also added an additional constructor to support new method. Need to consolidate these methods in the future but decided to keep as disictinct methods for now so as no bugs are introduced.

Add java doc TODOs that document the fact/Bad practice that the methods related to alignment are duplicated in FileSequenceActionEventHandler

Created/extracted method loadPfaatProperties and call it before createMenuBarAndMenuItems . The code was previously buried in initializeFileMenu

Renamed to ColorSequenceNameAndResiduesDialog.java and StartOfUserDefinedNumberDialog.java

Renamed to better reflect their purpose. Were previously known as StartIndexDialog.java and ColorSequenceDialog.java

added short comment

1. Added FileSequenceActionEventHandler to handle events from Right-click seq and File-> Sequence-> * 2. Added SequenceSelectorDialog.java which will gradually replace AlignmentNamePanel.sequenceSelector

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