Protein Family Alignment Annotation Tool svncode

tweaked doStandardDevScale to deal with potentially unremoved 0 variance columns

added MATLAB equivalent of ones()
tweaked fixedWidthString

Affine scoring added: Gap opening and gap extension provides better alignment
Bug Fix: Numbering PDB was incorrect when the pdb sequence to be associated with a sequence could not be aligned perfectly

Affine scoring added: Gap opening and gap extension provides better alignment

Bug Fix: Numbering PDB was incorrect when the pdb sequence to be associated with a sequence could not be aligned perfectly

Fix bug that was causing same chain to be counted more than once

Changed gap opening and gap extension values

rename some fields

Fix bug that was causing same chain to be counted more than once

tweaked/added a couple of output format functions