Protein Family Alignment Annotation Tool svncode

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.

Made the code more readable in various ways such as renaming field and method names, adding braces to if statements etc.

1. Added Find Sequences With The Same Annotation Values... menu item (Currently just finds sequences using pre-existing AlignmentSearchDialog). 2. Extracted a new method named scrollToFoundSequences (Sequence[] seqs) from findSequences() as this will be used by the new menut item described in #1. 3. Changed the 1st letter of each word in the menu items to upper case so most should be consistent now. 4. 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

1. Added more helpful error message when the number of seq annot values in the seqAnnots.csv file are not consistent with the number header values. 2. Added additional journal column-width sizes for .ps export

1. Added more journal column-width options. 2. Append / replace file extension with .ps when user specifies .pdf or nothing when exporting. This ensures the os recognizes the exported file as postscript.