| line |
true |
false |
branch |
|
81
|
0 |
3 |
unless defined $locus and UNIVERSAL::can($locus, 'isa') and $locus->isa('Bio::Polloc::LocusI')
|
|
83
|
0 |
3 |
if defined $$locus{'_gff3_line'} and not $force
|
|
85
|
3 |
0 |
defined $locus->seq_name ? :
|
|
90
|
3 |
0 |
defined $locus->score ? :
|
|
93
|
3 |
0 |
if defined $locus->id
|
|
94
|
3 |
0 |
if defined $locus->name
|
|
95
|
0 |
3 |
if defined $locus->aliases
|
|
96
|
0 |
3 |
if defined $locus->parents
|
|
97
|
0 |
3 |
if defined $locus->genome and defined $locus->genome->name
|
|
99
|
0 |
3 |
if (defined $locus->target)
|
|
105
|
3 |
0 |
if defined $locus->comments
|
|
106
|
0 |
3 |
if defined $locus->xrefs
|
|
107
|
0 |
3 |
if defined $locus->ontology_terms_str
|
|
116
|
3 |
0 |
if $a
|
|
135
|
87 |
7 |
unless $ln =~ /^\s*#/ or $ln =~ /^\s*$/
|
|
137
|
3 |
87 |
unless $ln
|
|
151
|
0 |
229 |
unless $c =~ /(.+?)=(.*)/
|
|
159
|
87 |
0 |
if defined $atts{'note'}
|
|
161
|
87 |
0 |
$f eq 'repeat' || $f eq 'vntr' || $f =~ /tandem.?repeat/ || lc $source eq 'trf' || lc $source eq 'mreps' ? :
|
|
|
0 |
87 |
$f eq 'pattern' || $f eq 'domain' ? :
|
|
|
0 |
87 |
$f eq 'crispr' ? :
|
|
|
0 |
87 |
$f eq 'composition' ? :
|
|
|
0 |
87 |
$f eq 'amplicon' || $f eq 'amplification' ? :
|
|
168
|
34 |
53 |
if grep {/Extended feature/;} @comments
|
|
178
|
215 |
83 |
if ($comm =~ /^(.+?)=(.+)$/) { }
|
|
|
34 |
49 |
elsif ($type eq 'extend' and $comm =~ /Based on group [^:]+: (.*)/) { }
|
|
180
|
207 |
8 |
if ($k and $v and $locus->can($k))
|
|
185
|
0 |
8 |
if not defined $genome_name and $k =~ /^organism(?:_name)?$/ || $k =~ /^genome(?:_name)?$/
|
|
189
|
34 |
0 |
if defined $self->_locus_by_id($b)
|
|
193
|
2 |
85 |
if (defined $genomes)
|
|
196
|
2 |
0 |
if (defined $genome_name)
|
|
198
|
2 |
0 |
if $g->name eq $genome_name
|
|
199
|
2 |
0 |
if defined $genome
|
|
203
|
0 |
2 |
unless (defined $genome)
|
|
205
|
0 |
0 |
if defined $g->search_sequence($seqid)
|
|
206
|
0 |
0 |
if defined $genome
|
|
222
|
1 |
2 |
unless ($$self{'_header'})
|
|
250
|
0 |
9 |
unless defined $value
|
|
251
|
3 |
6 |
if (ref $value and ref($value) =~ /array/i)
|
|
256
|
3 |
0 |
if $out
|
|
285
|
0 |
45 |
unless defined $value
|
|
315
|
0 |
925 |
unless defined $value
|