| line |
true |
false |
branch |
|
156
|
0 |
1 |
if (defined $filters) |
|
157
|
0 |
0 |
if (!ref($filters) =~ /HASH/i) { } |
|
185
|
0 |
82 |
unless (defined $type and $type =~ /^(P|N)/i) |
|
190
|
2 |
80 |
if (defined $value) |
|
214
|
0 |
1 |
unless defined $result |
|
219
|
0 |
1 |
if defined $resultfilter and not &{$resultfilter;}($result) |
|
224
|
1 |
0 |
if ($alg =~ /T(FAST|BLAST)([XY])/i) { } |
|
|
0 |
0 |
elsif ($alg =~ /T(FAST|BLAST)N/i) { } |
|
|
0 |
0 |
elsif ($alg =~ /(FAST|BLAST)N/i or $alg =~ /(WABA|EXONERATE)/i) { } |
|
|
0 |
0 |
elsif ($alg =~ /(FAST|BLAST)P/ or $alg =~ /SSEARCH|HMM(PFAM|SEARCH)/i) { } |
|
|
0 |
0 |
elsif ($alg =~ /(FAST|BLAST)[XY]/i) { } |
|
249
|
1 |
0 |
$dbtype eq 'translated' ? : |
|
|
1 |
0 |
$qtype eq 'translated' ? : |
|
253
|
1 |
0 |
if ($num <= 1) |
|
267
|
1 |
0 |
if ($result->can('rewind')) |
|
272
|
0 |
20 |
if $hitfilter and not &{$hitfilter;}($hit) |
|
275
|
0 |
20 |
unless $nm |
|
280
|
20 |
0 |
if (length $hit->description > $Bio::SearchIO::Writer::HTMLResultWriter::MaxDescLen - 3) { } |
|
292
|
0 |
20 |
if (not @hsps) { } |
|
294
|
0 |
0 |
defined $hsps[0] ? : |
|
|
0 |
0 |
$hit->bits ? : |
|
|
0 |
0 |
defined $hsps[0] ? : |
|
|
0 |
0 |
$hit->significance ? : |
|
305
|
0 |
0 |
defined $hsps[0] ? : |
|
|
20 |
0 |
$hit->bits ? : |
|
|
0 |
0 |
defined $hsps[0] ? : |
|
|
20 |
0 |
$hit->significance ? : |
|
319
|
0 |
21 |
if $hspfilter and not &{$hspfilter;}($hsp) |
|
324
|
0 |
21 |
if (defined $hsp->pvalue) |
|
334
|
21 |
0 |
if ($type eq 'PROTEIN') |
|
341
|
0 |
21 |
if ($hsp->gaps) |
|
354
|
21 |
0 |
if ($hstrand or $qstrand) |
|
357
|
0 |
21 |
if (not $hstrand) { } |
|
362
|
5 |
16 |
$hstrand < 0 ? : |
|
364
|
0 |
21 |
if (not $qstrand) { } |
|
368
|
7 |
14 |
$qstrand < 0 ? : |
|
373
|
0 |
21 |
if (defined $hframe and not defined $qframe) { } |
|
|
0 |
21 |
elsif (defined $qframe and not defined $hframe) { } |
|
383
|
0 |
21 |
if ($links and $hsp->can('links') and defined(my $lnks = $hsp->links)) |
|
390
|
14 |
7 |
$qstrand >= 0 ? : |
|
|
14 |
7 |
$qstrand >= 0 ? : |
|
|
16 |
5 |
$hstrand >= 0 ? : |
|
|
16 |
5 |
$hstrand >= 0 ? : |
|
438
|
42 |
21 |
if (defined $v->{'start'}) |
|
444
|
42 |
0 |
if (length $piece < $Bio::SearchIO::Writer::HTMLResultWriter::AlignmentLineWidth) |
|
469
|
1 |
0 |
if ($pav or $sav) |
|
472
|
1 |
0 |
if ($pav) |
|
480
|
1 |
0 |
if ($sav) |
|
510
|
0 |
20 |
if ($code) |
|
541
|
40 |
0 |
$result->algorithm =~ /(P|X|Y)$/i ? : |
|
544
|
40 |
0 |
length $self->remote_database_url($type) > 0 ? : |
|
576
|
0 |
20 |
if ($code) |
|
597
|
0 |
20 |
if ($code) |
|
627
|
20 |
0 |
$result->algorithm =~ /(P|X|Y)$/i ? : |
|
634
|
0 |
20 |
if ($sec =~ s/((?:gi\|(\d+)\|)? # optional GI
(\w+)\|([A-Z\d\.\_]+) # main
(\|[A-Z\d\_]+)?) # optional secondary ID
//msx) { } |
|
641
|
0 |
0 |
length $self->remote_database_url($type) > 0 ? : |
|
676
|
0 |
1 |
if ($code) |
|
726
|
0 |
1 |
if ($code) |
|
777
|
0 |
1 |
if ($code) |
|
856
|
0 |
60 |
if ($code) |
|
883
|
0 |
60 |
if ($string =~ s/gi\|(\d+)\|?//) |
|
886
|
60 |
0 |
if ($string =~ /(\w+)\|([A-Z\d\.\_]+)(\|[A-Z\d\_]+)?/) { } |
|
887
|
60 |
0 |
defined $2 ? : |
|
896
|
0 |
0 |
$a <=> $b ? : |
|
897
|
0 |
0 |
$a <=> $b ? : |
|
919
|
0 |
0 |
unless defined $result and ref $result and $result->isa('Bio::Search::Result::ResultI') |
|
921
|
0 |
0 |
if ($result->algorithm =~ /BLAST/i) { } |
|
|
0 |
0 |
elsif ($result->algorithm =~ /FAST/i) { } |
|
923
|
0 |
0 |
if ($result->algorithm_version =~ /WashU/i) { } |
|
984
|
1 |
1 |
if @_ |