| line |
true |
false |
branch |
|
137
|
0 |
4 |
unless $u_name |
|
140
|
1 |
3 |
if defined $desc |
|
163
|
6 |
4 |
if ($u_name and defined $Bio::Map::Gene::GENES->{$u_name}) |
|
164
|
0 |
6 |
if $desc |
|
185
|
4 |
28 |
if (defined $value) |
|
186
|
0 |
4 |
if $self->{'_uname'} |
|
351
|
0 |
320 |
unless $map and $self->in_map($map) |
|
354
|
353 |
320 |
if $pos->isa('Bio::Map::GenePosition') |
|
381
|
0 |
2 |
unless $pos and $pos->isa('Bio::Map::GenePosition') |
|
384
|
0 |
2 |
unless $self->in_map($map) |
|
386
|
1 |
1 |
if (@transcripts == 0) |
|
388
|
0 |
1 |
if ($pos->start != 0) |
|
405
|
2 |
0 |
if ($increase > 0) |
|
433
|
0 |
174 |
unless $map |
|
436
|
166 |
8 |
if (@transcripts > 0) |
|
437
|
3 |
163 |
if (defined $int) { } |
|
438
|
3 |
0 |
if ($int > 0 and $int <= @transcripts) { } |
|
448
|
163 |
0 |
if (defined $self->{'active_transcript'}{$map}) { } |
|
475
|
0 |
276 |
unless $map |
|
476
|
0 |
276 |
unless $map->isa('Bio::Map::GeneMap') |
|
496
|
0 |
99 |
unless $map |
|
499
|
4 |
95 |
if (@transcripts == 0 and $value == 0) |
|
535
|
0 |
12 |
unless ref $thing |
|
540
|
2 |
10 |
if ($thing->isa('Bio::Map::PositionI')) |
|
543
|
1 |
1 |
if ($existing_pos) |
|
591
|
0 |
22 |
unless $map |
|
617
|
9 |
11 |
if (@exons == 0 and $exon_num == 1) |
|
659
|
0 |
5 |
unless $map |
|
710
|
0 |
0 |
unless $USE_ENSEMBL |
|
711
|
0 |
0 |
unless 'Bio::Tools::Run::Ensembl'->registry_setup |
|
712
|
0 |
0 |
unless defined $bool |
|
714
|
0 |
0 |
unless (ref $self) |
|
733
|
9 |
0 |
unless $SET_FROM_DB or $self->{'_set_from_db'} |
|
755
|
0 |
0 |
unless ($trans_ref and @{$trans_ref;} > 0) |
|
762
|
0 |
0 |
if ($pos->isa('Bio::Map::GenePosition')) |
|
769
|
0 |
0 |
$strand == -1 ? : |
|
785
|
0 |
0 |
$strand == -1 ? : |
|
787
|
0 |
0 |
$strand == -1 ? : |
|
796
|
0 |
0 |
if ($length > $longest_trans) |
|
805
|
0 |
0 |
if $start > $end |
|
812
|
0 |
0 |
$strand == -1 ? : |
|
815
|
0 |
0 |
if (defined $transcript->coding_region_start) |
|
818
|
0 |
0 |
if $atg > $stop |
|
828
|
0 |
0 |
if $start > $end |
|
830
|
0 |
0 |
ref $species ? : |
|
831
|
0 |
0 |
unless defined $end |
|
840
|
0 |
0 |
if $start > $end |
|
857
|
37 |
280 |
if (defined $transcript_number and $transcript_number == 0) |
|
863
|
317 |
1633 |
unless $pos->isa('Bio::Map::GenePosition') |
|
864
|
1068 |
565 |
unless $pos->type eq $type |
|
866
|
41 |
524 |
if (defined $transcript_number) |
|
868
|
0 |
41 |
unless $rel->type eq 'transcript' |
|
870
|
1 |
40 |
unless $rel_transcript_num == $transcript_number |
|
880
|
41 |
276 |
if (defined $transcript_number) { } |
|
890
|
13 |
263 |
unless $self->{'t_order'}{$map} |
|
891
|
13 |
263 |
unless @known_order |
|
894
|
263 |
0 |
if @known_order == @positions |
|
898
|
0 |
0 |
unless exists $exists{$pos} |
|
909
|
0 |
110 |
unless $wanted and $wanted > 0 |
|
910
|
2 |
108 |
unless @list > 0 |
|
912
|
107 |
1 |
if ($index >= 0 and $index <= $#list) |
|
921
|
0 |
6 |
unless $pos and $pos->isa('Bio::Map::GenePosition') |
|
924
|
0 |
6 |
unless $self->in_map($map) |
|
930
|
0 |
6 |
unless $transcript_pos->end |
|
931
|
0 |
6 |
unless $pos->end |
|
932
|
0 |
6 |
unless ($transcript_pos->contains($pos)) |
|
945
|
1 |
1 |
unless $thing |
|
947
|
0 |
1 |
if (ref $thing and $thing->isa('Bio::Map::GeneMap')) |
|
951
|
0 |
1 |
if ($map and $map->isa('Bio::Map::GeneMap')) { } |
|
963
|
0 |
7 |
unless $map |
|
965
|
0 |
7 |
if (defined $self->{'_ensembl'}{$uid}) |