| line |
true |
false |
branch |
|
143
|
0 |
3 |
if ($tag =~ /^optimal/o) { } |
|
|
1 |
2 |
elsif ($tag =~ /^cai/o) { } |
|
|
1 |
1 |
elsif ($tag =~ /^tai/o) { } |
|
|
0 |
1 |
elsif ($tag =~ /^base/o) { } |
|
147
|
0 |
0 |
ref $val eq 'HASH' ? : |
|
152
|
0 |
1 |
ref $val eq 'HASH' ? : |
|
158
|
0 |
1 |
ref $val eq 'HASH' ? : |
|
163
|
0 |
0 |
if (ref $val eq 'ARRAY' or $val =~ /^seq/) { } |
|
240
|
13 |
13 |
if ($type =~ /cai/i) { } |
|
|
13 |
0 |
elsif ($type =~ /tai/i) { } |
|
252
|
0 |
26 |
unless ($xaiHash) |
|
259
|
0 |
26 |
unless my $codonList = $self->get_codon_list($seq) |
|
268
|
26 |
1560 |
unless $codonList->{$codon} |
|
270
|
26 |
1534 |
if $nonDegCodons{$codon} and $type =~ /cai/i |
|
271
|
13 |
1521 |
unless (exists $xaiHash->{$codon}) |
|
273
|
0 |
0 |
$self->no_atg ? : |
|
|
0 |
0 |
if $self->debug and $self->no_atg ? $codon ne 'ATG' : 1 |
|
283
|
0 |
26 |
unless $xai |
|
306
|
0 |
0 |
unless my $optimalCodons = $self->{'_optimal_codons'} |
|
309
|
0 |
0 |
unless my $codonList = $self->get_codon_list($seq) |
|
319
|
0 |
0 |
if not $withNonDeg and $nonDegCodons{$codon} |
|
320
|
0 |
0 |
if $optimalCodons->{$codon} |
|
479
|
0 |
26 |
unless defined $minTotal |
|
483
|
0 |
26 |
unless my $codonList = $self->get_codon_list($seq) |
|
484
|
26 |
0 |
&blessed($seq) && $seq->can('id') ? : |
|
489
|
0 |
26 |
if ($correctBaseComp) |
|
491
|
0 |
0 |
unless (defined $baseComposition) |
|
494
|
0 |
0 |
unless ($defaultBaseComp) |
|
500
|
0 |
0 |
if ($defaultBaseComp eq 'seq') { } |
|
|
0 |
0 |
elsif ($defaultBaseComp eq 'seq3') { } |
|
518
|
0 |
0 |
if $baseComposition |
|
520
|
0 |
0 |
unless $expectedCodonFreq |
|
535
|
26 |
468 |
if ($redundancy == 1) |
|
546
|
26 |
1508 |
unless exists $codonList->{$_} |
|
552
|
4 |
464 |
if $AAcnt < $minTotal or $AAcnt < 2 |
|
555
|
0 |
464 |
if ($correctBaseComp) { } |
|
582
|
22 |
1504 |
unless $codonCnt |
|
591
|
130 |
0 |
if ($numAAInClass > 0) |
|
597
|
130 |
0 |
if $Fsum > 0 |
|
610
|
130 |
0 |
if (exists $FavgByClass{$redundancy}) |
|
613
|
0 |
130 |
unless $FavgByClass{$redundancy} |
|
619
|
0 |
0 |
$F_EstimateMethod eq 'mean' ? : |
|
622
|
0 |
0 |
unless ($estimatedFavg) |
|
640
|
0 |
0 |
if $redundancy == 1 |
|
642
|
0 |
0 |
if ($equalRatio) { } |
|
648
|
0 |
0 |
if $r < 2 |
|
653
|
0 |
0 |
if ($cnt > 0) { } |
|
664
|
0 |
0 |
if ($redundancy == 3) { } |
|
706
|
0 |
0 |
if (ref $seq eq 'HASH') { } |
|
714
|
0 |
0 |
if ($pos) { } |
|
716
|
0 |
0 |
unless $pos > 0 and $pos < 4 |
|
718
|
0 |
0 |
if ($codonList) { } |
|
741
|
0 |
0 |
if ($codonList) { } |
|
762
|
0 |
0 |
wantarray ? : |
|
817
|
0 |
0 |
unless ($baseComp and ref $baseComp eq 'ARRAY') |
|
829
|
0 |
0 |
if $baseComp->[$_] == 0 |
|
835
|
0 |
0 |
$compSum > 2 ? : |