Protein Family Alignment Annotation Tool svncode

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.