Protein Family Alignment Annotation Tool svncode

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.

With these changes Find -> Sequences With The Same Annotation Values... is now fully operational

rename AlignmentSearchOptions as SequenceAnnotationSearchOptions.java