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 ):
n = self.mTableNeighbours.GetNumNeighbours( nid )
if n >= self.mMinProfileSize:
profile = alignlib.makeEmptyProfile( self.mRegularizor, self.mLogOddor )
pairsdblib.fillProfileNeighbours( profile,
self.mConnectionPairsdb,
nid,
self.mTableNameNeighbours,
self.mMaxLinesMali,
0,
self.mMaxLevel,
self.mMinLevel )
if self.mLogLevel >= 3:
print "# ------> using profile for rep %i" % nid
else:
profile = pairsdblib.makeSequenceFromPicasso( self.mConnectionPairsdb, nid )
if self.mLogLevel >= 3:
print "# ------> using sequence for rep %i" % nid
profile.useSegment( nrdb_from, nrdb_to )
return profile, (str(n),)
def GetAlignandum(self, nid, nrdb_from, nrdb_to):
n = self.mTableNeighbours.GetNumNeighbours(nid)
if n >= self.mMinProfileSize:
profile = alignlib.makeEmptyProfile(self.mRegularizor,
self.mLogOddor)
pairsdblib.fillProfileNeighbours(profile, self.mConnectionPairsdb,
nid, self.mTableNameNeighbours,
self.mMaxLinesMali, 0,
self.mMaxLevel, self.mMinLevel)
if self.mLogLevel >= 3:
print "# ------> using profile for rep %i" % nid
else:
profile = pairsdblib.makeSequenceFromPicasso(
self.mConnectionPairsdb, nid)
if self.mLogLevel >= 3:
print "# ------> using sequence for rep %i" % nid
profile.useSegment(nrdb_from, nrdb_to)
return profile, (str(n), )
