| line |
true |
false |
branch |
|
142
|
1 |
3 |
if (@args) |
|
146
|
0 |
1 |
if ref $arg ne 'HASH' |
|
153
|
63 |
0 |
if (not exists $Bio::CodonUsage::Table::STRICTAA{$k}) { } |
|
|
0 |
0 |
elsif ($k =~ /[^ATCGatcg]/) { } |
|
160
|
0 |
1 |
if (not $is_codon_hash || $is_Aa_hash) { } |
|
|
0 |
1 |
elsif ($is_Aa_hash) { } |
|
|
1 |
0 |
elsif ($is_codon_hash) { } |
|
215
|
1 |
0 |
if ($self->_check_codon($cod)) { } |
|
241
|
65 |
0 |
if ($self->_check_codon($cod)) { } |
|
267
|
0 |
2 |
if (not $threshold or $threshold < 0 or $threshold > 100) |
|
275
|
95 |
32 |
if ($self->{'_table'}{$aa}{$codon}{'rel_freq'} > $threshold / 100) |
|
282
|
0 |
2 |
if (grep {scalar @{$return_hash{$_};} == 0;} keys %return_hash) |
|
312
|
0 |
21 |
unless (defined $self->{'_table'}{$aa}) |
|
318
|
37 |
27 |
if ($self->{'_table'}{$aa}{$codon}{'rel_freq'} > $rel_freq) |
|
342
|
65 |
0 |
if (@_) { } |
|
345
|
65 |
0 |
if ($self->_check_codon($cod)) { } |
|
374
|
0 |
5 |
if (not @_) { } |
|
381
|
5 |
0 |
if (exists $self->{'_coding_gc'}{$n}) { } |
|
|
0 |
0 |
elsif (exists $self->{'_coding_gc'}{'all'}) { } |
|
416
|
0 |
4 |
unless (grep {$key eq $_;} @allowed) |
|
437
|
3 |
1 |
if (@_) |
|
455
|
0 |
132 |
if (@_) |
|
457
|
0 |
0 |
if ($val < 0 or $val > 16 or $val =~ /[^\d]/ or $val == 7 or $val == 8) { } |
|
482
|
3 |
1 |
if (@_) |
|
484
|
0 |
3 |
if ($val < 0) { } |
|
493
|
0 |
4 |
unless exists $self->{'_cds_count'} |
|
517
|
0 |
2 |
unless (exists $Bio::CodonUsage::Table::STRICTAA{$aa} or exists $Bio::SeqUtils::ONECODE{$aa}) |
|
546
|
0 |
0 |
if ($self->_check_aa($aa)) { } |
|
552
|
0 |
0 |
$self->{'_table'}{$aa3}{$cod}{'rel_freq'} > $max ? : |
|
572
|
0 |
0 |
if ($self->_check_aa($aa)) { } |
|
578
|
0 |
0 |
$self->{'_table'}{$aa3}{$cod}{'rel_freq'} < $min ? : |
|
590
|
0 |
0 |
if (not exists $Bio::CodonUsage::Table::STRICTAA{$aa} || exists $Bio::SeqUtils::ONECODE{$aa}) { } |
|
601
|
0 |
131 |
if ($cod =~ /[^ATCG]/ or not $cod =~ /\w\w\w/) { } |
|
659
|
93 |
96 |
if (substr($cod, $index - 1, 1) =~ /g|c/io) |