Protein Family Alignment Annotation Tool svncode

Y value scaling transform added. Automatic scaling of Y value by its standard deviation was also coded to happen when the maximum absolute value of Y is very small (less than 1e-3) but the feature is temporarily disabled again.

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Updated to add the following
1. rename sort sequence menu items
2. add confirmation dialog before close window, alignment and window close button
3. read property files

Updated to add the following:
1. Add confirmation dialog at Close window, close Alignment, window close button.
2. Rename Sort Sequence menu and submenu items
3. read property files

Enables to read property files

ColumnSelector roughly working.

ColumnSelector being debugged.

Column selection feature added.

Merged the change.

Added bootstrap (0.632, 0.632+) and monte-carlo cross-validation methods. Coding of the class PermutationTest is on the way.