HappyDoc Generated Documentation ./MultAlignViewer/structAssoc.py

. / MultAlignViewer / structAssoc.py 

Functions   
  oldTryAssoc 
oldTryAssoc (
        alignSeq,
        molSeq,
        gappedMseq,
        maxErrors=None,
        )
Exceptions   

ValueError, "bad assoc"

  makeForcedMatch 
makeForcedMatch (
        side,
        aseq,
        mseq,
        aseqStart,
        aseqLength,
        mseqStart,
        mseqLength,
        )
  nwAssoc 
nwAssoc ( alignSeq,  molSeq )
  tryAssoc 
tryAssoc (
        alignSeq,
        mseq,
        segments,
        gaps,
        estLen,
        maxErrors=None,
        )
Exceptions   

ValueError, "bad assoc"

  gappedMatch 
gappedMatch (
        aseq,
        mseq,
        segments,
        gaps,
        estLen,
        maxErrors,
        )
Exceptions   

ValueError, "bad assoc"

  dragMatch 
dragMatch (
        aseq,
        gappedMseq,
        maxErrors,
        )

mseq longer than aseq can still be gaps in mseq

Exceptions   

ValueError, "bad assoc"

  constrainedMatch 
constrainedMatch (
        aseq,
        mseq,
        segments,
        maxErrors,
        )

all the segments should fit in aseq

Exceptions   

ValueError, "bad assoc"
AssertionError, "Internal match problem: segments (%d) != offsets (%d)" %(len( segments ), len( offsets ) )

Classes   

Matchup


This document was automatically generated Wed Jul 9 15:49:36 2008 by HappyDoc version 3.1