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), )