Branch Coverage

Bio/SearchIO/Writer/HTMLResultWriter.pm
Criterion Covered Total %
branch 61 140 43.5


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 $qstrand)
357 21 0 if ($hstrand) { }
362 5 16 $hstrand < 0 ? :
364 21 0 if ($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 @_