Protein Family Alignment Annotation Tool svncode

Changes default color to a nice orange

Makes oval and symbol smaller and thus visible when printing

Fixes issue where top ruler panel was not being printed to ps and would make rest of image too big when font was greater than ~4 or 5 . Also , fixes issue where file could not be specified for export sequence annots

aded sha1 to oracle siging but not sure it is needed

break other jars into separate jnlp

Slightly better error handling when loading a.fa file that is mislabelled as .aln

Now connect directly to uniprot and retrieves residue annotations as well as sequence annotations

Command line program to get JMOL or PyMOL residue coloring commands based on residue annotations mapped to structure.

updates

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