| line |
true |
false |
branch |
|
358
|
0 |
7 |
defined $spaces ? : |
|
361
|
0 |
7 |
$handler ? : |
|
366
|
0 |
7 |
if $linelength |
|
385
|
9 |
0 |
if ($line =~ /^\#\s*STOCKHOLM\s+/mosx) |
|
397
|
17 |
712 |
if ($line =~ /^\s*$/mosx) |
|
403
|
9 |
703 |
if (index($line, '//') == 0) { } |
|
|
386 |
317 |
elsif ($line =~ /^\#=([A-Z]{2})\s+([^\n]+?)\s*$/mosx) { } |
|
|
317 |
0 |
elsif ($line =~ /^(\S+)\s+([^\s]+)\s*/) { } |
|
407
|
8 |
1 |
if $self->alphabet |
|
415
|
61 |
325 |
if ($primary_tag eq 'GS' or $primary_tag eq 'GR') { } |
|
420
|
309 |
77 |
$primary_tag eq 'GF' || $primary_tag eq 'GR' ? : |
|
437
|
193 |
510 |
if (exists $MAPPING{$feat} and ref $MAPPING{$feat} eq 'ARRAY') { } |
|
|
485 |
25 |
elsif (exists $MAPPING{$feat}) { } |
|
440
|
85 |
108 |
$MAPPING{$feat}[0] eq $MAPPING{$feat}[1] ? : |
|
441
|
64 |
129 |
$last_feat eq $feat ? : |
|
445
|
4 |
105 |
if ($align and $name eq 'ACCESSION' and not $self->alphabet) |
|
446
|
4 |
0 |
if ($data =~ /^(P|R)F/) |
|
447
|
2 |
0 |
$1 eq 'P' ? : |
|
|
2 |
2 |
$1 eq 'R' ? : |
|
451
|
18 |
5 |
$primary_tag eq 'GC' ? : |
|
|
2 |
23 |
$primary_tag eq 'GR' ? : |
|
469
|
545 |
50 |
if ($isa_primary and defined $data_chunk and not $concat) |
|
475
|
64 |
639 |
defined $data_chunk->{$secondary_tag} ? : |
|
477
|
378 |
325 |
if $nse |
|
478
|
20 |
366 |
if ($name eq 'SEQUENCE' or $name eq 'NAMED_META' or $name eq 'CONSENSUS_META') |
|
480
|
20 |
317 |
if $name ne 'SEQUENCE' |
|
518
|
0 |
2 |
unless $aln and $aln->isa('Bio::Align::AlignI') |
|
524
|
0 |
2 |
unless $self->_print("# $STKVERSION\n") |
|
525
|
2 |
0 |
if $self->spaces |
|
532
|
0 |
44 |
unless $coll |
|
535
|
0 |
44 |
unless exists $WRITEMAP{$param} |
|
538
|
6 |
38 |
if ($key eq 'Method') { } |
|
548
|
0 |
18 |
if ($tag eq 'RX') { } |
|
|
1 |
17 |
elsif ($tag eq 'XX') { } |
|
|
1 |
16 |
elsif ($tag eq 'SQ') { } |
|
|
1 |
15 |
elsif ($tag eq 'DR') { } |
|
554
|
0 |
0 |
if ($rkey eq 'ref_number') { } |
|
559
|
0 |
0 |
unless $data |
|
561
|
0 |
0 |
unless $self->_print("$text\n") |
|
582
|
0 |
1 |
exists $LINK_CB{$db} ? : |
|
588
|
9 |
6 |
ref $ann ? : |
|
590
|
2 |
16 |
unless $data |
|
592
|
0 |
16 |
unless $self->_print("$text\n") |
|
599
|
17 |
0 |
if (my $acc = $seq->accession_number) |
|
602
|
0 |
17 |
unless $self->_print($text) |
|
609
|
0 |
0 |
if (my(@links) = $sf->annotation->get_Annotations('dblink')) |
|
612
|
0 |
0 |
exists $LINK_CB{$db} ? : |
|
617
|
0 |
0 |
unless $self->_print($text) |
|
622
|
2 |
0 |
if $self->spaces |
|
628
|
0 |
2 |
if ($blocklen) { } |
|
635
|
0 |
0 |
unless $blockstart >= $alnlen |
|
641
|
0 |
2 |
unless $self->_print("//\n") |
|
643
|
2 |
0 |
if $self->_flush_on_write and defined $self->_fh |
|
662
|
0 |
2 |
if (defined $value) |
|
681
|
7 |
4 |
if @_ |
|
697
|
7 |
9 |
if ($handler) |
|
698
|
0 |
7 |
unless ref $handler and $handler->isa('Bio::HandlerBaseI') |
|
720
|
0 |
17 |
unless $self->_print(sprintf("%-*s%s\n", $maxlen + $metalen, $namestr, $seq->seq)) |
|
723
|
11 |
6 |
if ($seq->isa('Bio::Seq::MetaI')) |
|
725
|
0 |
0 |
unless $self->_print(sprintf("%-*s%s\n", $maxlen + $metalen, $seq_meta . ' ' . $namestr . ' ' . $mname, $seq->named_meta($mname))) |
|
733
|
1 |
1 |
if ($ameta) |
|
735
|
0 |
1 |
unless $self->_print(sprintf("%-*s%s\n", $maxlen + $metalen, $aln_meta . ' ' . $mname, $ameta->named_meta($mname))) |