| line |
true |
false |
branch |
|
156
|
15 |
15 |
if $id |
|
157
|
0 |
30 |
if $sysname |
|
158
|
0 |
30 |
if $trivname |
|
159
|
0 |
30 |
if $chr |
|
160
|
0 |
30 |
if $gene_symbol |
|
161
|
0 |
30 |
if $desc |
|
162
|
0 |
30 |
if $alphabet |
|
163
|
0 |
30 |
if $numbering |
|
164
|
15 |
15 |
if $offset |
|
165
|
0 |
30 |
if $rna_offset |
|
166
|
0 |
30 |
if $rna_id |
|
167
|
0 |
30 |
if $cds_end |
|
169
|
0 |
30 |
if $dna_ori |
|
170
|
0 |
30 |
if $dna_mut |
|
171
|
0 |
30 |
if $rna_ori |
|
172
|
0 |
30 |
if $rna_mut |
|
173
|
0 |
30 |
if $aa_ori |
|
174
|
0 |
30 |
if $aa_mut |
|
205
|
28 |
38 |
if (defined $value) { } |
|
235
|
1 |
33 |
if (defined $value) { } |
|
|
16 |
17 |
elsif (not defined $self->{'sysname'}) { } |
|
243
|
17 |
30 |
if ($mut->isa('Bio::Variation::DNAMutation')) |
|
245
|
16 |
1 |
if ($c == 1) { } |
|
253
|
1 |
15 |
if $c > 1 |
|
281
|
1 |
33 |
if (defined $value) { } |
|
|
20 |
13 |
elsif (not defined $self->{'trivname'}) { } |
|
289
|
17 |
42 |
if ($mut->isa('Bio::Variation::AAChange')) |
|
291
|
16 |
1 |
if ($c == 1) { } |
|
299
|
1 |
19 |
if $c > 1 |
|
326
|
2 |
1 |
if (defined $value) { } |
|
352
|
1 |
1 |
if (defined $value) { } |
|
379
|
1 |
1 |
if (defined $value) { } |
|
406
|
20 |
132 |
if (defined $value) |
|
407
|
20 |
0 |
if ($type{$value}) { } |
|
436
|
6 |
12 |
if (defined $value) { } |
|
466
|
21 |
64 |
if (defined $value) { } |
|
|
0 |
64 |
elsif (not defined $self->{'offset'}) { } |
|
499
|
0 |
0 |
if (defined $value) { } |
|
527
|
5 |
15 |
if (defined $value) { } |
|
557
|
1 |
1 |
if (defined $value) { } |
|
|
0 |
1 |
elsif (not defined $self->{'rna_offset'}) { } |
|
586
|
1 |
5 |
if (defined $value) { } |
|
614
|
61 |
0 |
if (defined $value) { } |
|
615
|
0 |
61 |
if (not $value->isa('Bio::Variation::VariantI')) { } |
|
672
|
0 |
0 |
if (defined $value) { } |
|
673
|
0 |
0 |
if (not $value->isa('Bio::LiveSeq::Gene')) { } |
|
726
|
6 |
1 |
if (defined $value) { } |
|
754
|
5 |
1 |
if (defined $value) { } |
|
758
|
1 |
0 |
unless $self->{'dna_mut'} |
|
766
|
0 |
1 |
unless $self->{'dna_ori'} and $self->each_Variant |
|
770
|
0 |
2 |
unless $_->isa('Bio::Variation::DNAMutation') |
|
771
|
0 |
2 |
unless $_->isMutation |
|
775
|
2 |
0 |
if ($_->start < 25) { } |
|
782
|
0 |
2 |
unless $_->allele_ori->seq |
|
786
|
2 |
0 |
if ($_->end + 25 > length $self->{'dna_mut'}) { } |
|
821
|
6 |
1 |
if (defined $value) { } |
|
847
|
6 |
1 |
if (defined $value) { } |
|
873
|
6 |
1 |
if (defined $value) { } |
|
899
|
7 |
1 |
if (defined $value) { } |
|
930
|
1 |
2 |
unless $valid_obj{$value} |
|
935
|
2 |
0 |
if $self->rna_id |
|
936
|
1 |
1 |
if $alphabet eq 'aa' |
|
942
|
1 |
1 |
if $self->{$value} |
|
970
|
0 |
0 |
if ($mut->isa('Bio::Variation::RNAChange')) |
|
985
|
0 |
0 |
if ($mut->DNAMutation->label =~ /point/) { } |
|
|
0 |
0 |
elsif ($mut->DNAMutation->label =~ /deletion/) { } |
|
986
|
0 |
0 |
if ($cposd == 1) { } |
|
|
0 |
0 |
elsif ($cposd == 2) { } |
|
|
0 |
0 |
elsif ($cposd == 3) { } |
|
1008
|
0 |
0 |
if ($cposd == 2) |
|
1015
|
0 |
0 |
if (length $rseqorid == 3) |
|
1022
|
0 |
0 |
if ($rseqorid) |
|
1033
|
0 |
0 |
if $i > $maxflanklen |
|
1043
|
0 |
0 |
if (length $rseqorid == 3 and length $rseqorid == 3) |
|
1048
|
0 |
0 |
if (length $rseqoriu == 3 and length $rseqoriu == 3) |
|
1064
|
0 |
0 |
unless $mut->AAChange |
|
1076
|
0 |
0 |
if length $rseqori[$i] == 3 |
|
1078
|
0 |
0 |
if (length $a != 1 or $apos - ($maxflanklen / 2 - 1) + $i < 1 or $apos - ($maxflanklen / 2 - 1) + $i > $aposmax) { } |
|
1086
|
0 |
0 |
if (length $rseqmut[$i] == 3) |
|
1087
|
0 |
0 |
if ($rseqmut[$i] eq ' ') { } |
|
1093
|
0 |
0 |
if ($b ne $a and length $b == 1 and $apos - ($maxflanklen / 2 - 1) + $i >= 1 or $apos - ($maxflanklen / 2 - 1) + $i >= $aposmax and $mut->label =~ /termination/) { } |
|
1104
|
0 |
0 |
if ($i == 0 and length $rseqori[$i] != 3) |
|
1109
|
0 |
0 |
if $rseqori[$i] ne '' |
|
1110
|
0 |
0 |
if $rseqmut[$i] ne '' |