Branch Coverage

Bio/LiveSeq/IO/Loader.pm
Criterion Covered Total %
branch 50 156 32.0


line true false branch
77 0 0 if (defined $getswissprotinfo) { }
78 0 0 if ($getswissprotinfo ne 0 and $getswissprotinfo ne 1)
86 0 0 unless ($hashref)
89 0 0 if ($test_transl)
151 0 6 unless ($gene_name or $cds_position)
155 0 6 if ($gene_name and $cds_position) { }
6 0 elsif ($gene_name) { }
164 0 6 if (defined $getswissprotinfo) { }
165 0 0 if ($getswissprotinfo ne 0 and $getswissprotinfo ne 1)
173 0 6 if (defined $flanking) { }
174 0 0 unless ($flanking >= 0)
182 0 6 unless ($hashref)
184 0 6 unless ($gene)
204 0 0 unless ($obj_transl eq $hash_transl)
234 0 0 if ($getswissprotinfo)
244 0 0 if ($swisshashes[$j])
271 0 6 if (index($input, 'cds-position:') == 0) { }
273 0 0 if ($cds_position >= 1 and $cds_position <= scalar @cds)
280 0 6 unless ($genefeatureshash and scalar @{$genefeatureshash->{'genefeatures'};})
293 6 0 if ($min - $flanking < 1) { }
298 6 0 if ($max + $flanking > $seqlength) { }
317 0 6 unless (@transcripts)
331 0 6 if ($ttables[$j])
336 0 6 if ($swisshashes[$j])
355 1 5 if (@exons)
360 9 0 if ($object != -1) { }
361 9 0 if defined $exondescs[$exoncount]
372 1 5 if (@introns)
377 8 0 if ($object != -1) { }
388 5 1 if (@prim_transcripts)
392 7 0 if ($object != -1)
398 0 6 if (@repeat_regions)
403 0 0 if ($object != -1) { }
415 0 6 if (@repeat_units)
420 0 0 if ($object != -1) { }
447 0 110 unless defined $element
448 0 110 if ($element < $min)
451 6 104 if ($element > $max)
479 6 0 if ($transcriptobj != -1)
509 0 0 unless ($entry)
526 0 0 if ($entry->{'Features'})
551 0 0 unless ($entry)
580 0 0 if ($featurename eq 'CDS') { }
618 0 0 unless ($entry)
625 0 0 if ($genename)
626 0 0 if (index($genenames, $genename) == -1)
648 0 0 if ($entry->{'Features'})
654 0 0 if ($feature->{'name'} eq 'INIT_MET' and $feature->{'location'} eq '0 0') { }
669 0 0 if (index($liveseq_aa, '-') != -1 or index($swiss_aa, '-') != -1)
682 0 0 if ($aarangeobj != -1)
730 6 0 if (scalar @cds == 1)
736 0 6 if ($cds_position)
741 0 0 unless ($skipgenematch)
748 0 0 if ($skipgenematch or $cds_position and $self->_checkfeatureproximity($entryfeature->{'range'}, $cds_begin, $cds_end, $proximity) or not $cds_position and $entryfeature->{'qualifiers'}{'gene'} eq "$gene_name")
754 6 24 if ($name eq 'CDS') { }
758 6 0 if ($getswissprotinfo)
777 0 24 if ($entryfeature->{'locationtype'} and $entryfeature->{'locationtype'} eq 'joined')
781 9 15 if ($name eq 'exon')
783 3 6 if ($entryfeature->{'qualifiers'}{'note'})
784 0 3 if ($desc) { }
793 8 16 if ($name eq 'intron')
795 0 8 if ($desc) { }
803 7 17 if ($name eq 'prim_transcript' or $name eq 'mRNA')
804 0 24 if ($name eq 'repeat_unit')
808 0 24 if ($name eq 'repeat_region')
815 0 6 unless ($gene_name)
846 0 0 if (ref $range[0] eq 'ARRAY') { }
851 0 0 if ($cds_begin > $cds_end)
854 0 0 if ($strand == -1)
857 0 0 if ($cds_begin - $end > $proximity)
861 0 0 if ($begin - $cds_end > $proximity)
877 0 0 $^O =~ /mswin/i ? :
882 0 0 unless open my $TMPFASTAFILE1, '>', $fastafile1
883 0 0 unless open my $TMPFASTAFILE2, '>', $fastafile2
923 0 0 if (@alt_codons) { }
946 0 0 if ($dice < $relativeusage + $partial) { }
953 0 0 unless ($chosen_codon)
975 0 0 unless ($gene)