|
|
oldTryAssoc
|
oldTryAssoc (
alignSeq,
molSeq,
gappedMseq,
maxErrors=None,
)
|
|
|
makeForcedMatch
|
makeForcedMatch (
side,
aseq,
mseq,
aseqStart,
aseqLength,
mseqStart,
mseqLength,
)
|
|
|
nwAssoc
|
nwAssoc ( alignSeq, molSeq )
|
|
|
tryAssoc
|
tryAssoc (
alignSeq,
mseq,
segments,
gaps,
estLen,
maxErrors=None,
)
|
|
|
gappedMatch
|
gappedMatch (
aseq,
mseq,
segments,
gaps,
estLen,
maxErrors,
)
|
|
|
dragMatch
|
dragMatch (
aseq,
gappedMseq,
maxErrors,
)
mseq longer than aseq
can still be gaps in mseq
|
|
|
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 ) )
|
|
|