Protein Family Alignment Annotation Tool svncode

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

1. Created various getters and setters to facilitate future development of class and addition of more colors. 2. Made constant colors like PINKY_AND_PERKY_FOR_P_VALS public to facilitate bug-free maintenance of default dropdown for colors. 3. Made the help that reports RGBs and score ranges 100% automated which will eliminate human errors in help

1. Added Pinky and Perky for p-vals colorscheme. 2. Added Perky for p-vals colorscheme. 3. Reworked colorscheme names to be constants to faciliate easier adding of colors in the future. 4. Added more console echos to explain how to hide, show, and delete the surefaces that are cereated by these methods. 5. Hide any surfaces named chainInPfaat* prior to rendering new surfaces and otherwise the surfaces blend together and do not look as expected. 6.

Rename MapConservationDialog to MapConservationToStructureDialog.java and MapConservationOptions.java to MapConservationToStructureOptions.java