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)