| line |
true |
false |
branch |
|
188
|
4 |
0 |
unless $eng |
|
189
|
0 |
4 |
if ($eng->isa('Bio::Ontology::OntologyI')) |
|
191
|
0 |
0 |
if $eng->can('engine') |
|
196
|
0 |
4 |
if (defined $defs_file_name and defined $defs_url) { } |
|
199
|
2 |
2 |
if defined $defs_file_name |
|
200
|
0 |
4 |
if defined $defs_url |
|
203
|
0 |
4 |
if (defined $files and defined $url) { } |
|
|
1 |
3 |
elsif (defined $files) { } |
|
|
0 |
3 |
elsif (defined $url) { } |
|
205
|
0 |
1 |
ref $files ? : |
|
|
1 |
0 |
$files ? : |
|
211
|
0 |
4 |
if $name |
|
230
|
3 |
11 |
if @_ |
|
256
|
0 |
4 |
unless $self->term_factory |
|
275
|
1 |
3 |
unless ($self->_fh) |
|
276
|
0 |
1 |
if ($self->url) { } |
|
|
1 |
0 |
elsif ($self->_flat_files) { } |
|
277
|
0 |
0 |
if (ref $self->url eq 'ARRAY') { } |
|
298
|
0 |
4 |
if (@{$self->_flat_files;}) { } |
|
329
|
4 |
1 |
unless exists $self->{'_ontologies'} |
|
331
|
5 |
0 |
if (exists $self->{'_ontologies'}) |
|
333
|
4 |
1 |
if ($ont) |
|
355
|
2 |
0 |
if (@_) |
|
358
|
0 |
2 |
if $self->_defs_io |
|
359
|
2 |
0 |
if (defined $f) |
|
369
|
0 |
0 |
if (defined $val) |
|
372
|
0 |
0 |
if $self->_defs_io |
|
381
|
0 |
1 |
if (defined $val) |
|
412
|
2 |
2 |
if $self->_defs_io |
|
434
|
3 |
3 |
unless exists $self->{'_flat_files'} |
|
457
|
2 |
83 |
if @_ |
|
463
|
4 |
0 |
unless exists $self->{'_ontologies'} |
|
465
|
0 |
4 |
unless ref $ont and $ont->isa('Bio::Ontology::OntologyI') |
|
469
|
4 |
0 |
unless $ont->name |
|
477
|
227 |
0 |
if $ont and not $term->ontology |
|
540
|
26 |
222 |
if ($line =~ /^!/) |
|
547
|
218 |
4 |
if $termspecs[0] =~ /^\s*$/ |
|
556
|
77 |
4 |
if $cross_ref eq $current_term |
|
565
|
25 |
11 |
if (index($parent, '%') == 0) { } |
|
|
11 |
0 |
elsif (index($parent, '<') == 0) { } |
|
574
|
204 |
18 |
unless ($self->_has_term($current_term)) |
|
586
|
218 |
4 |
unless ($line =~ /^\$/) |
|
590
|
11 |
14 |
unless ($self->_has_term($parent)) |
|
604
|
3 |
8 |
unless ($self->_has_term($parent)) |
|
619
|
116 |
106 |
if ($current_spaces != $prev_spaces) |
|
621
|
75 |
41 |
if ($current_spaces == $prev_spaces + 1) { } |
|
|
41 |
0 |
elsif ($current_spaces < $prev_spaces) { } |
|
637
|
218 |
4 |
if (index($line, '$') != 0) |
|
639
|
0 |
218 |
unless ($line =~ /^\s*([<%~]|\@\w+?\@)/) |
|
647
|
36 |
182 |
if ($relstring eq '<') { } |
|
|
182 |
0 |
elsif ($relstring eq '%') { } |
|
|
0 |
0 |
elsif ($relstring eq '~') { } |
|
655
|
0 |
0 |
if ($self->_ont_engine->get_relationship_type($relstring)) { } |
|
680
|
258 |
0 |
if ($line =~ /;\s*([A-Z_]{1,8}:\d{1,})/) { } |
|
696
|
218 |
0 |
if ($line =~ /([^;<%~]+);\s*$termid/) { } |
|
704
|
3 |
215 |
if (index($name, '$') == 0) |
|
707
|
3 |
0 |
unless $self->ontology_name |
|
744
|
183 |
81 |
if ($ref =~ /synonym/ or $ref =~ /[A-Z]{1,8}:\d{3,}/) |
|
752
|
81 |
0 |
if defined $ref |
|
778
|
218 |
4 |
if ($line =~ /^(\s+)/) { } |
|
791
|
4 |
9 |
if ($self->_done == 1 or not $self->_defs_io) |
|
804
|
26 |
36 |
if (not $line =~ /\S/ or $line =~ /^\s*!/) { } |
|
|
9 |
27 |
elsif ($line =~ /^\s*term:\s*(.+)/) { } |
|
|
9 |
18 |
elsif ($line =~ /^\s*[a-z]{0,8}id:\s*(.+)/) { } |
|
|
9 |
9 |
elsif ($line =~ /^\s*definition:\s*(.+)/) { } |
|
|
9 |
0 |
elsif ($line =~ /^\s*definition_reference:\s*(.+)/) { } |
|
|
0 |
0 |
elsif ($line =~ /^\s*comment:\s*(.+)/) { } |
|
810
|
7 |
2 |
if $self->_not_first_record |
|
819
|
0 |
9 |
if index($def, 'OBSOLETE') == 0 |
|
828
|
2 |
7 |
unless $line |
|
839
|
4 |
1235 |
if (defined $value) |
|
852
|
0 |
227 |
if (not defined $obsolete and index(lc $name, 'obsolete') == 0) |
|
872
|
6 |
9 |
if (defined $value) |
|
885
|
6 |
13 |
if (defined $value) |
|
897
|
13 |
9 |
if (defined $value) |
|
907
|
218 |
231 |
unless $links |