Protein Family Alignment Annotation Tool svncode

renamed, see previous commit

Renamed from src/com/neogenesis/pfaat/SequenceAnnComponent.java src/com/neogenesis/pfaat/SequenceNameComponent.java src/com/neogenesis/pfaat/AlignmentAnnPanel.java for clarity and to reflect actual function

The following changes were made to Edit sequence/Node annotations dialog: 1) Center the dialog relative to the tree graphic. 2) Set the size of the dialog relative to the tree graphic. 3) The show checkboxes are now on the left as they were not visible when the annotation values were long. 4) Made the text size bigger for annotation names and values. 5) Made the textfield for annotation values longer/bigger. 6) Changed the background color of all components to the default look and feel. 6). Move the show checkbox for spec/duplication to be leftmost.

1) Now calculates more accurate relative accessibilies for modified residues. 2) Prints warning whenever the max possible residue accessibility is exceeded or not set for a modified residue.

now part of src/com/neogenesis/pfaat/pdb/PdbAminoAcidCodeAndProperties.java

replaced with src/com/neogenesis/pfaat/pdb/PdbAminoAcidCodeAndProperties.java

Reordering of structure menu items based on predicted frequency of use.

small changes to usage

1) Renamed Sequence.getColumnAnnotation to Sequence.getResidueAnnotation. 2) The add annotions tab in EditResAnnDialog.java now provided enter text prompts, no longer has up or down buttons, provides warning if the user forgets to enter a residue annotation name or value after creating a row via the add button and then clicking save.

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