def __init__(self, chrom, genomic_start, genomic_end, consensus_match_strand,
               consensus_start, consensus_end, consensus_len, retrotransposon,
               pairwise_alignment=None, uniq_id=None):
    """
    Constructor for RetrotransposonOccurrence objects; see class docstring
    for parameter defs.
    """
    GenomicInterval.__init__(self, chrom, genomic_start, genomic_end,
                             retrotransposon.name, 0, "+")
    self.consensus_start = consensus_start
    self.consensus_end = consensus_end
    # TODO check that consensus length is at least as long as end index
    self.consensus_len = consensus_len
    self.consensus_match_strand = consensus_match_strand
    self.retrotransposon = retrotransposon
    self.uniq_id = uniq_id
    # TODO would be good to provide some error-checking here to make sure the
    # alignment matches up properly with this occurrence...
    self.pairwise_alignment = pairwise_alignment
def __init__ ( self , chrom , genomic_start , genomic_end , consensus_match_strand , consensus_start , consensus_end , consensus_len , retrotransposon , pairwise_alignment = None , uniq_id = None ) : GenomicInterval . __init__ ( self , chrom , genomic_start , genomic_end , retrotransposon . name , 0 , "+" ) self . consensus_start = consensus_start self . consensus_end = consensus_end self . consensus_len = consensus_len self . consensus_match_strand = consensus_match_strand self . retrotransposon = retrotransposon self . uniq_id = uniq_id self . pairwise_alignment = pairwise_alignment
Constructor for RetrotransposonOccurrence objects; see class docstring
    for parameter defs.