Protein Family Alignment Annotation Tool svncode

LOTS of fixes and improvements to sequence and now residue annotations retrieved from uniprot

now saves to location of original file

made changes to error

changed error. not sure if this code is still used

made residue annot oval on each residue smaller so it is completely visible when printed to ps

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