def __init__(self, sequences, reference_species, meta_data=None):
MultipleSequenceAlignment.__init__(self, sequences, meta_data)<EOL>ref_index = None<EOL>for i in range(<NUM_LIT:0>, len(sequences)):<EOL><INDENT>if sequences[i].name[<NUM_LIT:0>:len(reference_species)] == reference_species:<EOL><INDENT>if ref_index is not None:<EOL><INDENT>raise GenomeAlignmentError("<STR_LIT>" +<EOL>"<STR_LIT>" +<EOL>sequences[i] + "<STR_LIT>" +<EOL>sequences[ref_index])<EOL><DEDENT>ref_index = i<EOL><DEDENT><DEDENT>self.reference_sequence_name = sequences[ref_index].name<EOL>name_parts = self.reference_sequence_name.split("<STR_LIT:.>")<EOL>if len(name_parts) != <NUM_LIT:2>:<EOL><INDENT>raise GenomeAlignmentError("<STR_LIT>" +<EOL>sequences[ref_index].name + "<STR_LIT>" +<EOL>"<STR_LIT>")<EOL><DEDENT>self._chrom = name_parts[<NUM_LIT:1>]<EOL>self.reference_species = reference_species<EOL>
Constructor; see class docstring for parameter details.