def __init__(self,
sequence,
hmmLength,
origSeqLength,
evalue,
seqStart=None,
seqEnd=None,
hmmStart=None,
hmmEnd=None):
"""Intialise HMMSequence with the hmmer unit. Must run align and
determineGapPositions.
Parameters:
unit - HMMUnit object.
hmmLength - int. length of the HMM.
align - boolean. Enables alignment algorithm based on HMM values.
See HMMSequence.align() for more info.
gaps - boolean. Enables gap counting algorithm to create pileup.
See HMMSequence.determineGapPositions()
"""
self.hmmLength = int(hmmLength)
self.gaps = [0] * self.hmmLength
self.origSeqLength = origSeqLength
self.evalue = evalue
self.seqStart = seqStart
self.seqEnd = seqEnd
self.hmmStart = hmmStart
self.hmmEnd = hmmEnd
HMMPileUp.total_seqs += 1
MutableSeq.__init__(self, sequence)
def __init__(self, sequence, hmmLength, origSeqLength, evalue, seqStart=None, seqEnd=None, hmmStart=None, hmmEnd=None):
"""Intialise HMMSequence with the hmmer unit. Must run align and
determineGapPositions.
Parameters:
unit - HMMUnit object.
hmmLength - int. length of the HMM.
align - boolean. Enables alignment algorithm based on HMM values.
See HMMSequence.align() for more info.
gaps - boolean. Enables gap counting algorithm to create pileup.
See HMMSequence.determineGapPositions()
"""
self.hmmLength = int(hmmLength)
self.gaps = [0]*self.hmmLength
self.origSeqLength = origSeqLength
self.evalue = evalue
self.seqStart = seqStart
self.seqEnd = seqEnd
self.hmmStart = hmmStart
self.hmmEnd = hmmEnd
HMMPileUp.total_seqs += 1
MutableSeq.__init__(self, sequence)
