| line |
true |
false |
branch |
|
142
|
0 |
3 |
if ($tag =~ /^optimal/o) { } |
|
|
1 |
2 |
elsif ($tag =~ /^cai/o) { } |
|
|
1 |
1 |
elsif ($tag =~ /^tai/o) { } |
|
|
0 |
1 |
elsif ($tag =~ /^base/o) { } |
|
146
|
0 |
0 |
ref $val eq 'HASH' ? : |
|
151
|
0 |
1 |
ref $val eq 'HASH' ? : |
|
157
|
0 |
1 |
ref $val eq 'HASH' ? : |
|
162
|
0 |
0 |
if (ref $val eq 'ARRAY' or $val =~ /^seq/) { } |
|
239
|
13 |
13 |
if ($type =~ /cai/i) { } |
|
|
13 |
0 |
elsif ($type =~ /tai/i) { } |
|
251
|
0 |
26 |
unless ($xaiHash) |
|
258
|
0 |
26 |
unless my $codonList = $self->get_codon_list($seq) |
|
267
|
26 |
1560 |
unless $$codonList{$codon} |
|
269
|
26 |
1534 |
if $nonDegCodons{$codon} and $type =~ /cai/i |
|
270
|
13 |
1521 |
unless (exists $$xaiHash{$codon}) |
|
272
|
0 |
0 |
$self->no_atg ? : |
|
|
0 |
0 |
if $self->debug and $self->no_atg ? $codon ne 'ATG' : 1 |
|
282
|
0 |
26 |
unless $xai |
|
305
|
0 |
0 |
unless my $optimalCodons = $$self{'_optimal_codons'} |
|
308
|
0 |
0 |
unless my $codonList = $self->get_codon_list($seq) |
|
318
|
0 |
0 |
if not $withNonDeg and $nonDegCodons{$codon} |
|
319
|
0 |
0 |
if $$optimalCodons{$codon} |
|
478
|
0 |
26 |
unless defined $minTotal |
|
482
|
0 |
26 |
unless my $codonList = $self->get_codon_list($seq) |
|
488
|
0 |
26 |
if ($correctBaseComp) |
|
490
|
0 |
0 |
unless (defined $baseComposition) |
|
492
|
0 |
0 |
unless my $defaultBaseComp = $self->base_composition |
|
495
|
0 |
0 |
if ($defaultBaseComp eq 'seq') { } |
|
|
0 |
0 |
elsif ($defaultBaseComp eq 'seq3') { } |
|
514
|
0 |
0 |
unless $expectedCodonFreq |
|
529
|
26 |
468 |
if ($redundancy == 1) |
|
540
|
26 |
1508 |
unless exists $$codonList{$_} |
|
546
|
4 |
464 |
if $AAcnt < $minTotal or $AAcnt < 2 |
|
549
|
0 |
464 |
if ($correctBaseComp) { } |
|
576
|
22 |
1504 |
unless $codonCnt |
|
585
|
130 |
0 |
if ($numAAInClass > 0) |
|
591
|
130 |
0 |
if $Fsum > 0 |
|
604
|
130 |
0 |
if (exists $FavgByClass{$redundancy}) |
|
606
|
0 |
130 |
unless $FavgByClass{$redundancy} |
|
613
|
0 |
0 |
$F_EstimateMethod eq 'mean' ? : |
|
616
|
0 |
0 |
unless ($estimatedFavg) |
|
633
|
0 |
0 |
if $redundancy == 1 |
|
635
|
0 |
0 |
if ($equalRatio) { } |
|
641
|
0 |
0 |
if $r < 2 |
|
646
|
0 |
0 |
if ($cnt > 0) { } |
|
657
|
0 |
0 |
if ($redundancy == 3) { } |
|
699
|
0 |
0 |
if (ref $seq eq 'HASH') { } |
|
707
|
0 |
0 |
if ($pos) { } |
|
709
|
0 |
0 |
unless $pos > 0 and $pos < 4 |
|
711
|
0 |
0 |
if ($codonList) { } |
|
734
|
0 |
0 |
if ($codonList) { } |
|
755
|
0 |
0 |
wantarray ? : |
|
810
|
0 |
0 |
if (uc $baseComp eq 'NA') |
|
816
|
0 |
0 |
unless $baseComp and ref $baseComp eq 'ARRAY' |
|
824
|
0 |
0 |
if $$baseComp[$_] == 0 |
|
830
|
0 |
0 |
$compSum > 2 ? : |