Returns a mapping between the sequences ONLY IF there are exactly two. This restriction makes the code much simpler.

def get_residue_mapping(self):
        '''Returns a mapping between the sequences ONLY IF there are exactly two. This restriction makes the code much simpler.'''
        if len(self.sequence_ids) == 2:
            if not self.alignment_output:
                self.align()
            assert(self.alignment_output)
            return self._create_residue_map(self._get_alignment_lines(), self.sequence_ids[1], self.sequence_ids[2])
        else:
            return None