Branch Coverage

blib/lib/Bio/DB/Das/Chado/Segment.pm
Criterion Covered Total %
branch 0 340 0.0


line true false branch
123 0 0 if $feature_id
133 0 0 unless (defined $name)
138 0 0 $base_start ? :
155 0 0 $factory->default_class ? :
161 0 0 if defined $target
163 0 0 if (defined $ref_feature_id) { }
167 0 0 if defined $refclass
170 0 0 unless $self->factory->allow_obsolete
172 0 0 if $self->factory->organism_id
215 0 0 if (ref $ref eq 'ARRAY') { }
0 0 elsif (ref $ref eq 'SCALAR') { }
223 0 0 unless $fetch_uniquename_query->execute($feature_id)
228 0 0 if $$hashref{'is_obsolete'} and not $self->factory->allow_obsolete
235 0 0 $base_start ? :
236 0 0 $stop ? :
241 0 0 unless defined $base_start and defined $stop and defined $db_id
259 0 0 if (@segments < 2) { }
0 0 elsif (wantarray) { }
276 0 0 unless $srcfeature_query->execute($landmark_feature_id)
280 0 0 $$hash_ref{'srcfeature_id'} ? :
289 0 0 unless defined $target
292 0 0 if ($landmark_feature_id == $srcfeature_id) { }
294 0 0 unless $landmark_is_src_query->execute($landmark_feature_id)
302 0 0 if $$hash_ref{'is_obsolete'} and not $self->factory->allow_obsolete
309 0 0 if ($$hash_ref{'fmin'})
318 0 0 if (defined $interbase_start and $interbase_start < 0)
325 0 0 if (defined $stop and defined $length and $stop > $length)
330 0 0 $stop ? :
410 0 0 unless ref $self
428 0 0 if @_
429 0 0 if $$self{'feature_id'}
445 0 0 if ($org_id)
451 0 0 if $sth->rows > 1
477 0 0 if @_
500 0 0 unless defined(my $id = $self->id)
525 0 0 unless $self->factory->allow_obsolete
527 0 0 if $self->factory->organism_id
531 0 0 if ($feature_id) { }
0 0 elsif ($db_id) { }
549 0 0 unless $sth->execute
552 0 0 if $self->factory->organism_id
554 0 0 unless $self->factory->allow_obsolete
558 0 0 if ($rows_returned == 0) { }
0 0 elsif ($rows_returned == 1) { }
561 0 0 if ($self->factory->use_all_feature_names) { }
564 0 0 if ($fulltext) { }
583 0 0 if ($fulltext) { }
599 0 0 unless $isth->execute
602 0 0 if ($rows_returned == 0) { }
0 0 elsif ($rows_returned == 1) { }
606 0 0 if ($fulltext) { }
619 0 0 unless $isth->execute
624 0 0 if $rows_returned == 0
626 0 0 if ($rows_returned == 1) { }
700 0 0 if @_
733 0 0 unless ref $self
734 0 0 if @_
735 0 0 if $$self{'start'}
768 0 0 unless ref $self
769 0 0 if @_
770 0 0 if $$self{'end'}
895 0 0 if (ref $self and $self->factory->do2Level) { }
899 0 0 if ($sub_args[0] and $sub_args[0] =~ /^-/)
901 0 0 if $args{-'factory'}
902 0 0 if $args{-'feature_id'}
907 0 0 if (ref $self and $sub_args[0] and $sub_args[0] =~ /^-/) { }
0 0 elsif (defined $factory and $sub_args[0] and $sub_args[0] =~ /^-/) { }
942 0 0 if ($type_placeholder and not $types)
943 0 0 if (ref $type_placeholder eq 'ARRAY') { }
952 0 0 if defined $types and 0
961 0 0 unless ($feature_id)
966 0 0 defined $base_start ? :
969 0 0 defined $end ? :
990 0 0 if ($types and scalar @$types != 0)
994 0 0 if (ref $$types[0] eq 'ARRAY')
1001 0 0 if ($$types[0] =~ /(.*):(.*)/)
1007 0 0 unless $valid_type
1010 0 0 if ($temp_source and $temp_dbxref) { }
1016 0 0 if (scalar @$types > 1)
1021 0 0 if ($$types[$i] =~ /(.*):(.*)/)
1028 0 0 unless $valid_type
1031 0 0 if ($temp_source and $temp_dbxref) { }
1043 0 0 if ref $self
1044 0 0 if (not $srcfeature_id and defined $seq_id)
1047 0 0 if $factory->organism_id
1068 0 0 if ($feature_id) { }
1083 0 0 if (defined $refclass_feature_id and defined $srcfeature_id) { }
0 0 elsif ($refclass) { }
1094 0 0 unless $sth->execute($feature_id, $refclass)
1097 0 0 if defined $srcfeature_id
1103 0 0 if ($factory->srcfeatureslice and $srcfeature_id and defined $interbase_start and defined $rend) { }
0 0 elsif (defined $interbase_start and defined $rend) { }
1113 0 0 if defined $srcfeature_id
1121 0 0 if defined $sql_types
1123 0 0 if $morewhere
1129 0 0 if ref $self and $self->factory->organism_id
1137 0 0 if ($factory->recursivMapping and not $feature_id)
1154 0 0 unless $feature_query->execute
1158 0 0 if ($feature_query->rows < 1 and $sql_types and not defined $interbase_start and not defined $rend)
1168 0 0 unless $feature_query->execute
1200 0 0 if $$hashref{'is_obsolete'} and not $self->factory->allow_obsolete
1202 0 0 if ($feature_id and defined $stop and $stop != $$hashref{'fmax'}) { }
0 0 elsif (defined $$hashref{'seqlen'}) { }
1211 0 0 if ($feature_id and defined $base_start and defined $$hashref{'fmin'} and $base_start != $$hashref{'fmin'} + 1) { }
0 0 elsif (defined $$hashref{'seqlen'}) { }
1228 0 0 if (defined $$hashref{'seqlen'}) { }
1244 0 0 $feature_id ? :
0 0 $feature_id ? :
1272 0 0 if ($iterator) { }
0 0 elsif (wantarray) { }
0 0 elsif (@features > 0) { }
1274 0 0 if @features
1306 0 0 if ($_[0] and $_[0] =~ /^-/) { }
1324 0 0 if ($type_placeholder and not $types)
1328 0 0 if defined $types and 0
1336 0 0 unless ($feature_id)
1348 0 0 if (scalar @$types != 0)
1354 0 0 if ($$types[0] =~ /(.*):(.*)/)
1360 0 0 unless $valid_type
1363 0 0 if ($temp_source and $temp_dbxref) { }
1369 0 0 if (scalar @$types > 1)
1374 0 0 if ($$types[$i] =~ /(.*):(.*)/)
1381 0 0 unless $valid_type
1384 0 0 if ($temp_source and $temp_dbxref) { }
1408 0 0 if ($feature_id) { }
1416 0 0 if $self->factory->organism_id
1426 0 0 if (defined $refclass_feature_id) { }
0 0 elsif ($refclass) { }
1437 0 0 unless $sth->execute($feature_id)
1440 0 0 if defined $srcfeature_id
1446 0 0 if ($factory->srcfeatureslice) { }
1478 0 0 unless $sth->execute
1490 0 0 if $$hashref{'is_obsolete'} and not $self->factory->allow_obsolete
1492 0 0 if (not defined $feat->feature_id or $feat->feature_id != $$hashref{'feature_id'})
1494 0 0 if (defined $feat->feature_id and $feat->feature_id != $$hashref{'feature_id'})
1499 0 0 if ($feature_id and defined $stop and $stop != $$hashref{'fmax'}) { }
1505 0 0 if ($feature_id and defined $base_start and $base_start != $$hashref{'fmin'} + 1) { }
1520 0 0 $feature_id ? :
0 0 $feature_id ? :
1540 0 0 if ($$hashref{'sfeature_id'})
1541 0 0 if ($feature_id and defined $stop and $stop != $$hashref{'sfmax'}) { }
1547 0 0 if ($feature_id and defined $base_start and $base_start != $$hashref{'sfmin'} + 1) { }
1562 0 0 $feature_id ? :
1589 0 0 if (@features > 0 and $features[-1]->feature_id ne $feat->feature_id)
1594 0 0 if ($iterator) { }
0 0 elsif (wantarray) { }
1596 0 0 if @features
1643 0 0 if ($arg{'self'})
1646 0 0 if $self->verbose
1652 0 0 unless $sth->execute($r_id)
1667 0 0 if ($has_start and $has_stop and $base_start > $stop) { }
0 0 elsif ($strand and $strand < 0) { }
1675 0 0 if (not $has_start || $has_stop) { }
0 0 elsif (not $has_start) { }
0 0 elsif (not $has_stop) { }
1694 0 0 unless $sth->execute
1700 0 0 if ($reversed)
1768 0 0 unless ref $self
1785 0 0 if @_
1805 0 0 if @_
1806 0 0 if defined $$self{'source'}
1815 0 0 unless $sth->execute($self->feature_id, $self->factory->gff_source_db_id)
1867 0 0 if defined $$self{'desc'}
1881 0 0 if defined $$self{'species'}
1942 0 0 if $features
1981 0 0 if $$self{'sourceseq'}
1987 0 0 unless $sourceseq_query->execute($self->srcfeature_id)
1990 0 0 if $sourceseq_query->rows < 1
2071 0 0 unless (ref $self)
2073 0 0 unless ref $self