Protein Family Alignment Annotation Tool svncode

Now exports residue annotations for residues that are non-standard residues or a gap in addition to the 20 standard residues

1) Changed Sequence.ResidueAnnotation.residueAnnotations from hashMap to TreeMap. This change ensures that residue annotation names are always returned and consequently always displayed in alphanumeric order. This change in type led to various changes in the method signatures within Sequence and consequently led to changes in the many files that are part of this commit. 2) Renamed the static class Sequence.ColumnAnnotation to Sequence.ResidueAnnotation, 3) Renamed other variables and method to more accurate names. 4) Moved the various getter methods within Sequence.ResidueAnnotation next to each other for clarity. 5) Removed Sequence.getLengthWithoutGaps2 which was not used. 6) Added javadoc to some methods in Sequence.java when the function of the method was unclear.

remove implements that was temporarily added while exploring upcoming sort functionality

rename getAnnotation to getAnnotationSettingsName to reflect actual function since version 2 and other stuff that was mentioned in the comment for revision 1763 but not savedin file prior to commit

rename annotation annotationSettingsName and getAnnotation() to getAnnotationSettingsName() to reflect their actual function since version 2

Improved and clearer usage

Add boolean param for getAllResidueAnnotations.

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