add_alignment - method for adding the alignment to an annotation

        :param ref_seq: List of reference sequences
        :type ref_seq: List
        :param annotation: The complete annotation
        :type annotation: Annotation

        :rtype: Annotation

def add_alignment(self, ref_seq, annotation) -> Annotation:
        """
        add_alignment - method for adding the alignment to an annotation

        :param ref_seq: List of reference sequences
        :type ref_seq: List
        :param annotation: The complete annotation
        :type annotation: Annotation

        :rtype: Annotation
        """
        seq_features = get_seqs(ref_seq)
        annoated_align = {}
        allele = ref_seq.description.split(",")[0]
        locus = allele.split("*")[0].split("-")[1]
        for feat in seq_features:
            if feat in annotation.annotation:
                if isinstance(annotation.annotation[feat], DBSeq):
                    seq_len = len(str(annotation.annotation[feat]))
                    ref_len = len(seq_features[feat])
                else:
                    seq_len = len(str(annotation.annotation[feat].seq))
                    ref_len = len(seq_features[feat])
                if seq_len == ref_len:
                    seq = list(annotation.annotation[feat].seq)
                    gaps = self.refdata.annoated_alignments[locus][allele][feat]['Gaps']
                    if self.verbose and self.verbosity > 0:
                        self.logger.info(self.logname + " Lengths match for " + feat)
                        self.logger.info(self.logname + " Gaps at " + feat)
                        self.logger.info(self.logname +
                                         "-".join([",".join([str(s)
                                                             for s in g])
                                                   for g in gaps]))
                    for i in range(0, len(gaps)):
                        for j in gaps[i]:
                            loc = j
                            seq.insert(loc, '-')
                    nseq = ''.join(seq)
                    annoated_align.update({feat: nseq})
                else:
                    in_seq = str(annotation.annotation[feat].seq)
                    ref_seq = self.refdata.annoated_alignments[locus][allele][feat]['Seq']
                    alignment = pairwise2.align.globalxx(in_seq, ref_seq)
                    if self.verbose and self.verbosity > 0:
                        self.logger.info(self.logname + " Align2 -> in_seq != ref_len " + feat)
                        self.logger.info(self.logname + " " + str(len(in_seq)) + " == " + str(ref_len))
                    annoated_align.update({feat: alignment[0][0]})
            else:
                nseq = ''.join(list(repeat('-', len(seq_features[feat]))))
                annoated_align.update({feat: nseq})
        annotation.aligned = annoated_align
        return annotation