Protein Family Alignment Annotation Tool svncode

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

Renaming ResidueSearchOptions to ResidueAnnotationSearchOptions

associated with renaming to method to SequenceAnnotListBase.java

renamed class to SequenceAnnotListBase.java

renamed the class

Renamed this class

1. Several method names related to sequence annotations were renamed as previously referred to as Properties and sometimes tags. Similar renames will appear in the next commit for other files. 2. There may be other things that I forgot about. They probably relate to renaming field and method names to improve readbility of code.