def GetAlignandum(self, nid):
if self.mTableSource.GetNumNeighbours(
nid, max_filter=self.mFilter) >= self.mMinProfileSize:
if self.mLogLevel >= 3:
print "# using profile for nid %i" % nid
sys.stdout.flush()
profile = alignlib.makeEmptyProfile(self.mRegularizor,
self.mLogOddor)
pairsdblib.fillProfileNeighbours(profile, self.mConnectionPairsdb,
nid, self.mTableNameSource,
self.mMaxLinesMali)
self.mIsProfile[nid] = 1
else:
if self.mLogLevel >= 3:
print "# using sequence for nid %i" % nid
sys.stdout.flush()
profile = pairsdblib.makeSequenceFromPairsdb(
self.mConnectionPairsdb, nid)
self.mIsProfile[nid] = 0
if self.mMask:
self.MaskAlignandum(nid, profile)
profile.Prepare()
if self.mLogLevel >= 5:
print "# alignandum for rep %i" % nid
print profile.Write()
sys.stdout.flush()
return profile
def GetAlignandum(self, nid, nrdb_from, nrdb_to):
alignandum = pairsdblib.makeSequenceFromPairsdb(
self.mConnectionPairsdb, nid)
alignandum.useSegment(nrdb_from, nrdb_to)
return alignandum, None
def GetAlignandum( self, nid, nrdb_from, nrdb_to ):
alignandum = pairsdblib.makeSequenceFromPairsdb( self.mConnectionPairsdb, nid )
alignandum.useSegment( nrdb_from, nrdb_to )
return alignandum, None
