Protein Family Alignment Annotation Tool svncode

rename annotation annotationSettingsName and getAnnotation() to getAnnotationSettingsName() to reflect their actual function since version 2

Improved and clearer usage

Add boolean param for getAllResidueAnnotations.

1) Add boolean param for getAllResidueAnnotations. 2) parameterize ArrayList and others in Alignment.java

A) Addressed all of the warings in this class by: 1 Removing various imports that were no longer used. 2 Paramatizing Hashmap, Vector, Set, Iterator etc. 3 Replace new Integer(someInt) with Integer.valueOf(someInt). 4. Use BufferedReader instead of DataInputStream. B) Remove unused code that was commented out for a long time. C ) Add braces to one-line if statements that lacked them for code readability

Improved logic for various option combos and improved description of the options and usage

This package is for testing new lines of code. Any classes created in this package should NOT be added or committed to the repository

1. Change ... to the more explicit browse... in various dialogs. 2 Added default file names for File -> export-> x...

small change to message after creating mac pkg

1. Make Dialogs a bit wider so they fit in more verbose color names. 2. Renamed various fields and constants so coloring using a consistent naming convention and it is easier to distinguish one color type from others in the code. 3. Fixed small bug where color names for solid rainbow for Probabilities appeared in the wrong order in the help. 4. Added solidRainbowThreeColorsPvalsStartpointsForScores solidRainbowThreeColorsProbsDiscretePaletteColorsInHuman