| line |
true |
false |
branch |
|
103
|
5 |
2 |
if $in |
|
104
|
5 |
2 |
if $out |
|
105
|
1 |
6 |
if $cds |
|
106
|
0 |
7 |
if $exons and ref($exons) =~ /ARRAY/i |
|
107
|
1 |
6 |
if $peptide_offset |
|
108
|
0 |
7 |
if $nozero |
|
109
|
0 |
7 |
if $strict |
|
117
|
16 |
0 |
if (defined $value) |
|
120
|
0 |
16 |
unless defined $COORDINATE_SYSTEMS{$value} |
|
130
|
22 |
0 |
if (defined $value) |
|
133
|
0 |
22 |
unless defined $COORDINATE_SYSTEMS{$value} |
|
143
|
0 |
2 |
if (defined $value) |
|
144
|
0 |
0 |
$value ? : |
|
154
|
2 |
0 |
if (defined $value) |
|
157
|
0 |
2 |
unless defined $Bio::Coordinate::GeneMapper::NOZERO_VALUES->{$value} |
|
168
|
7 |
0 |
if (defined $value) |
|
169
|
0 |
7 |
unless $value->isa('Bio::Coordinate::Graph') |
|
179
|
0 |
0 |
if (defined $value) |
|
180
|
0 |
0 |
unless $value->isa('Bio::LocationI') |
|
183
|
0 |
0 |
unless defined $value->start |
|
187
|
0 |
0 |
unless defined $value->end |
|
209
|
2 |
0 |
if (defined $offset) |
|
210
|
0 |
2 |
unless $offset =~ /^[+-]?\d+$/ |
|
214
|
0 |
2 |
if (defined $len) |
|
215
|
0 |
0 |
unless $len =~ /^[+-]?\d+$/ |
|
231
|
0 |
0 |
if (defined $len) |
|
232
|
0 |
0 |
if defined $len and not $len =~ /^[+-]?\d+$/ |
|
253
|
5 |
0 |
if (@value) |
|
254
|
0 |
5 |
if (ref $value[0] and $value[0]->isa('Bio::SeqFeatureI') and $value[0]->location->isa('Bio::Location::SplitLocationI')) { } |
|
259
|
0 |
5 |
unless ref \@value eq 'ARRAY' |
|
261
|
0 |
5 |
unless ref $value[0] and $value[0]->isa('Bio::LocationI') |
|
270
|
2 |
3 |
if (defined $value[0]->strand and $value[0]->strand == -1) { } |
|
277
|
0 |
2 |
unless ($self->cds) |
|
292
|
0 |
3 |
unless ($self->cds) |
|
312
|
5 |
0 |
if (defined $self->{'_mappers'}{$gene_mapper}) { } |
|
369
|
5 |
10 |
if ($exon->start <= 1 and $exon->end >= 1) |
|
378
|
10 |
5 |
if (defined $prev_exon_end) |
|
456
|
4 |
1 |
if ($coffset) |
|
478
|
0 |
150 |
unless $loc->isa('Bio::Location::Simple') |
|
494
|
6 |
5 |
if (defined $value) |
|
495
|
3 |
3 |
if ($value =~ /^[+-]?\d+$/) { } |
|
|
3 |
0 |
elsif (ref $value and $value->isa('Bio::RangeI')) { } |
|
509
|
6 |
0 |
if defined $self->{'_cds'}->end |
|
520
|
0 |
6 |
if (defined $self->{'_chr_exons'}) |
|
532
|
0 |
1 |
unless ref $value and $value->isa('Bio::Location::Simple') || $value->isa('Bio::Location::SplitLocationI') || $value->isa('Bio::SeqFeatureI') |
|
539
|
0 |
35 |
unless $self->{'_in'} |
|
541
|
0 |
35 |
unless $self->{'_out'} |
|
544
|
0 |
35 |
unless $self->{'_in'} != $self->{'_out'} |
|
548
|
0 |
35 |
if $value->isa('Bio::SeqFeatureI') |
|
553
|
1 |
3 |
if (defined $self->{'_nozero'} and $self->{'_nozero'} == 1 || $self->{'_nozero'} == 3) |
|
555
|
0 |
1 |
if defined $value->start and $value->start < 1 |
|
557
|
0 |
1 |
if defined $value->end and $value->end < 1 |
|
566
|
2 |
43 |
if ($mapper eq $TRANSLATION) { } |
|
|
0 |
43 |
elsif (not defined $self->{'_mappers'}{$mapper}) { } |
|
567
|
2 |
0 |
if ($self->direction == 1) { } |
|
590
|
16 |
27 |
if $value and $value->isa('Bio::Location::SplitLocationI') and $value->can('gap') |
|
594
|
0 |
43 |
if $value and $self->verbose > 0 |
|
601
|
1 |
3 |
if (defined $value and defined $self->{'_nozero'} and $self->{'_nozero'} == 2 || $self->{'_nozero'} == 3) |
|
604
|
1 |
0 |
if defined $value->start and $value->start < 1 |
|
606
|
1 |
0 |
if defined $value->end and $value->end < 1 |
|
612
|
7 |
28 |
if (ref $value eq 'Bio::Coordinate::Result' and $value->each_match > 1) { } |
|
|
5 |
46 |
elsif (ref $value eq 'Bio::Coordinate::Result' and $value->each_match == 1) { } |
|
618
|
7 |
9 |
unless ($prevloc) |
|
623
|
5 |
4 |
if ($prevloc->end == $loc->start - 1 and $prevloc->seq_id eq $loc->seq_id) { } |
|
632
|
4 |
3 |
if ($merging) |
|
633
|
0 |
4 |
if (@matches > 1) { } |
|
685
|
0 |
0 |
if (defined $self->cds) |
|
686
|
0 |
0 |
if defined $self->cds->end |
|
754
|
0 |
0 |
$self->direction ? : |
|
811
|
0 |
3 |
unless defined $value and $value->isa('Bio::Location::Simple') || $value->isa('Bio::Location::SplitLocationI') |
|
818
|
0 |
3 |
if ($value->isa('Bio::Location::SplitLocationI')) { } |
|
846
|
0 |
1 |
unless defined $value and $value->isa('Bio::Location::Simple') || $value->isa('Bio::Location::SplitLocationI') |
|
853
|
0 |
1 |
if ($value->isa('Bio::Location::SplitLocationI')) { } |
|
880
|
0 |
1 |
unless defined $value and $value->isa('Bio::Location::Simple') || $value->isa('Bio::Location::SplitLocationI') |
|
887
|
0 |
1 |
if ($value->isa('Bio::Location::SplitLocationI')) { } |
|
917
|
3 |
32 |
if $self->{'_in'} > $self->{'_out'} |
|
919
|
4 |
31 |
unless ($new_direction == $self->{'_direction'}) |
|
937
|
3 |
32 |
if ($start > $end) |
|
943
|
18 |
17 |
if (exists $self->{'_previous_path'} and $self->{'_previous_path'} eq "$start$end") { } |
|
959
|
3 |
32 |
$reverse ? : |