| line |
true |
false |
branch |
|
313
|
157 |
348 |
unless $id |
|
314
|
505 |
0 |
if $id |
|
335
|
644 |
25216 |
if (defined $value) |
|
336
|
1 |
643 |
if (not defined $Bio::Tools::CodonTable::TABLES[$value] or $Bio::Tools::CodonTable::TABLES[$value] eq '') |
|
382
|
40 |
12 |
if $name |
|
419
|
1 |
19901 |
unless defined $seq |
|
420
|
1 |
19900 |
unless $seq |
|
424
|
60 |
19840 |
if length($seq) % 3 == 2 |
|
429
|
5315 |
14585 |
if ($seq =~ /[^actg]/) { } |
|
432
|
1527 |
16252 |
if ($triplet eq $Bio::Tools::CodonTable::CODONGAP) { } |
|
|
10946 |
5306 |
elsif (exists $Bio::Tools::CodonTable::CODONS->{$triplet}) { } |
|
444
|
0 |
124418 |
if ($triplet eq $Bio::Tools::CodonTable::CODONGAP) |
|
447
|
124418 |
0 |
if (exists $Bio::Tools::CodonTable::CODONS->{$triplet}) { } |
|
454
|
7 |
19893 |
if ($partial == 2 and $complete_codon) |
|
456
|
0 |
7 |
if ($triplet eq $Bio::Tools::CodonTable::CODONGAP) { } |
|
|
0 |
7 |
elsif (exists $Bio::Tools::CodonTable::CODONS->{$triplet}) { } |
|
479
|
141 |
5172 |
if ($count == 1) { } |
|
|
13 |
5159 |
elsif ($count == 2) { } |
|
483
|
3 |
10 |
if ($aas{'D'} and $aas{'N'}) { } |
|
|
4 |
6 |
elsif ($aas{'E'} and $aas{'Q'}) { } |
|
489
|
1 |
5 |
$partial ? : |
|
492
|
1 |
5158 |
$partial ? : |
|
525
|
0 |
3 |
unless length $value == 3 |
|
527
|
0 |
3 |
unless defined $Bio::Tools::CodonTable::CODONS->{$value} |
|
558
|
5 |
130 |
if (length $value == 3) |
|
563
|
133 |
1 |
if (defined $value and $value =~ /$Bio::Tools::CodonTable::VALID_PROTEIN/ and length $value == 1) |
|
572
|
1 |
144 |
if $aa eq '*' |
|
580
|
1 |
134 |
if ($coding and uc $coding eq 'RNA') |
|
611
|
0 |
22 |
unless ($obj and $obj->isa('Bio::PrimarySeqI')) |
|
615
|
0 |
22 |
if ($obj->alphabet ne 'protein') |
|
623
|
21 |
1 |
if (not $cut || $threshold) { } |
|
626
|
7 |
68 |
if ($aa =~ /x/i) { } |
|
636
|
0 |
1 |
unless ($cut->isa('Bio::CodonUsage::Table')) |
|
642
|
1 |
20 |
if ($aa =~ /x/i) |
|
668
|
0 |
1 |
unless ($obj and $obj->isa('Bio::PrimarySeqI')) |
|
672
|
0 |
1 |
if ($obj->alphabet ne 'protein') |
|
676
|
0 |
1 |
if (!$cut | !$cut->isa('Bio::CodonUsage::Table')) |
|
687
|
1 |
20 |
if ($aa =~ /x/i) |
|
691
|
20 |
0 |
if (defined $cod_ref->{$aa}) { } |
|
736
|
1 |
612 |
if (length $value != 3) { } |
|
746
|
46 |
569 |
if ($m eq $Bio::Tools::CodonTable::TERMINATOR) { } |
|
767
|
0 |
718 |
unless length $value == 3 |
|
775
|
55 |
665 |
if ($m eq $key) |
|
797
|
2 |
1 |
unless $self->unambiguous_codons($value) |
|
852
|
0 |
1 |
unless length $table == 64 and length $starts == 64 |
|
864
|
0 |
22 |
if (ref $cod_ref ne 'ARRAY') |