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