Lines Matching refs:hseq
353 my $hseq = $aln->get_seq_by_pos(2);
355 $hstart ||= $hseq->start;
365 $beg = $aln->column_from_residue_number($hseq->id, $intvl->[0]);
366 $end = $aln->column_from_residue_number($hseq->id, $intvl->[1]);
372 $hseq = $aln->get_seq_by_pos(2);
374 $hinc = $hseq->length - $hseq->num_gaps($Bio::LocatableSeq::GAP_SYMBOLS);
392 -strand => $hseq->strand,
396 -tag => { subject_id => $hseq->id,
397 subject_desc => $hseq->desc,
398 subject_start => $hstart + (($hseq->strand && $hseq->strand < 0) ? -1 : 1)*$hlen,
399 subject_end => $hstart + (($hseq->strand && $hseq->strand < 0) ? -1 : 1)*($hlen+$hinc-1)
403 $hit_string .= $hseq->seq;
414 my $hseq = Bio::LocatableSeq->new( -id => 'subject',
416 $hseq->add_SeqFeature(@hfeats);
418 $taln->add_seq($hseq);