| line |
true |
false |
branch |
|
165
|
3 |
0 |
unless $eng |
|
166
|
0 |
3 |
if ($eng->isa('Bio::Ontology::OntologyI')) |
|
168
|
0 |
0 |
if $eng->can('engine') |
|
172
|
0 |
3 |
if $name |
|
189
|
3 |
3 |
if @_ |
|
213
|
3 |
0 |
unless $self->term_factory |
|
247
|
0 |
1021 |
unless ($term->identifier and $term->name) |
|
260
|
850 |
187 |
unless defined $oname and defined $t_ns |
|
261
|
169 |
18 |
if ($oname eq $t_ns) |
|
268
|
2 |
1019 |
if ($new_ontology_flag and $term->namespace) |
|
283
|
97 |
893 |
unless ($self->_has_term($parent_term)) |
|
295
|
130 |
9 |
if ($self->_ont_engine->get_relationship_type($relationship)) { } |
|
309
|
66 |
175 |
unless ($self->_has_term($parent_term)) |
|
338
|
3 |
3 |
unless exists $self->{'_ontologies'} |
|
341
|
6 |
0 |
if (exists $self->{'_ontologies'}) |
|
343
|
5 |
1 |
if ($ont) |
|
382
|
3 |
2 |
unless exists $self->{'_ontologies'} |
|
384
|
0 |
5 |
unless ref $ont and $ont->isa('Bio::Ontology::OntologyI') |
|
388
|
0 |
5 |
unless $ont->name |
|
396
|
947 |
237 |
if $ont and not $term->ontology |
|
461
|
3 |
6133 |
if (defined $value) |
|
506
|
3 |
21 |
unless ($line) |
|
507
|
0 |
3 |
unless ($format_version_header_flag) |
|
517
|
0 |
21 |
if ($line =~ /\[\w*\]/) |
|
526
|
21 |
0 |
if ($line =~ /^(\[|format-version:
|data-version:
|typeref:
|version:
|date:
|saved-by:
|auto-generated-by:
|default-namespace:
|remark:
|subsetdef:
|import:
|synonymtypedef:
|idspace:
|default-relationship-id-prefix:
|id-mapping:
)/x) |
|
544
|
21 |
0 |
if ($line =~ /^([\w\-]+)\:\s*(.*)/) |
|
548
|
3 |
18 |
if ($tag =~ /format-version/) { } |
|
|
3 |
15 |
elsif ($tag =~ /default-namespace/) { } |
|
558
|
3 |
18 |
if ($tag =~ /default-namespace/i) |
|
576
|
1021 |
5569 |
if (not $line and $term) |
|
581
|
1039 |
4530 |
if ($line =~ /^\[(\w+)\]\s*(.*)/) |
|
582
|
1021 |
18 |
if (uc $1 eq 'TERM') { } |
|
|
18 |
0 |
elsif (uc $1 eq 'TYPEDEF') { } |
|
606
|
86 |
4444 |
if not $line =~ /^(\[|id:
|is_anonymous:
|name:
|namespace:
|alt_id:
|def:
|comment:
|subset:
|synonym:
|xref:
|is_a:
|intersection_of:
|union_of:
|disjoint_from:
|relationship:
|is_obsolete:
|replaced_by:
|consider:
|created_by:
|creation_date:
)/x or $skip_stanza_flag |
|
630
|
4444 |
0 |
if ($line =~ /^([\w\-]+)\:\s*(.*)/) |
|
634
|
0 |
4444 |
unless ($val) |
|
645
|
1021 |
3423 |
if ($tag eq 'ID') { } |
|
|
1021 |
2402 |
elsif ($tag eq 'NAME') { } |
|
|
0 |
2402 |
elsif ($tag eq 'XREF_ANALOG') { } |
|
|
0 |
2402 |
elsif ($tag eq 'XREF_UNKNOWN') { } |
|
|
10 |
2392 |
elsif ($tag eq 'NAMESPACE') { } |
|
|
575 |
1817 |
elsif ($tag eq 'DEF') { } |
|
|
293 |
1524 |
elsif ($tag eq 'SYNONYM') { } |
|
|
1 |
1523 |
elsif ($tag eq 'ALT_ID') { } |
|
|
6 |
1517 |
elsif ($tag =~ /XREF/i) { } |
|
|
19 |
1498 |
elsif ($tag eq 'IS_OBSOLETE') { } |
|
|
44 |
1454 |
elsif ($tag eq 'COMMENT') { } |
|
|
241 |
1213 |
elsif ($tag eq 'RELATIONSHIP') { } |
|
|
990 |
223 |
elsif ($tag eq 'IS_A') { } |
|
647
|
163 |
858 |
if ($self->_has_term($term)) |
|
655
|
0 |
0 |
unless ($term->has_dbxref($val)) |
|
681
|
19 |
0 |
if ($val eq 'true') { } |
|
|
0 |
0 |
elsif ($val eq 'false') { } |
|
719
|
0 |
4444 |
if ($str =~ /(.*)\s+(\{.*\})\s*$/) { } |
|
722
|
0 |
0 |
if ($extr) |
|
725
|
0 |
0 |
if (/(\w+)=\"(.*)\"/) { } |
|
|
0 |
0 |
elsif (/(\w+)=\'(.*)\'/) { } |
|
750
|
0 |
575 |
if ($prefix) |
|
757
|
0 |
575 |
if ($rem =~ /(\w+)\s+(\[.*)/) |
|
764
|
575 |
479 |
unless $extr |
|
767
|
479 |
0 |
if $extr |
|
794
|
0 |
4551 |
if ($line and not $line =~ /:/) |
|
806
|
0 |
241 |
$parts[1] =~ /\^(w+)\s+\!/ ? : |
|
813
|
0 |
575 |
unless $links |