Protein Family Alignment Annotation Tool svncode

add more details to report usage

change default sizes for font, node and branch thickness

initial commit

support graceful handling of seq annots with no match in msa.

gracefully reports seq annots that do not have match in MSA but still imports the seq annots with matches. Reworded message when opening tree

tweaked message to help user

changes to tooltip mouse-over help for residue annotations . Might be over the top and require tweaks

Helps with gracefulreporting of sequence annotations that did not have matching sequences in the MSA. ie it imports the rest of them without barfing

writeResidueDistancesToFile takes extra param, added additional jsap opts related to annotations

refactored to use toNewHampshire with extra param