Protein Family Alignment Annotation Tool svncode

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

Fix bug where use of color wireframe command by user would prevent coloring of struct by res annots and conservation scores

Change menu item to be consistent with res annot label deltaRelativeRSA

Change order of labels color and surface so grouping is more logical.

1. Change order of labels color and surface so grouping is more logical. 2. Set Solid Rainbow for P-vals as default color for now

changes that reflect changes to Analysis -> Color Structure By ..

1. Rename MapConservationScoresToStAction.java to MapConservationScoresToStructureAction.java 2. Add more info to help. 3. deselect all chains after mapping res annots to struct

1. Small tweaks to help message for align/association of struct to sequene. 2. Small tweaks to menu items and help buttons to make things more intuitive for the user. 3. Make Capitalizeation of 1st letter of each word in menus consistent.