| line |
true |
false |
branch |
|
135
|
50 |
2 |
if (defined $inds) |
|
136
|
0 |
50 |
if (not ref($inds) =~ /ARRAY/i) { } |
|
143
|
9 |
43 |
if defined $name |
|
144
|
4 |
48 |
if defined $source |
|
145
|
7 |
45 |
if defined $description |
|
146
|
3 |
49 |
defined $checkisa ? : |
|
164
|
9 |
34 |
if @_ |
|
181
|
7 |
34 |
if @_ |
|
198
|
4 |
34 |
if @_ |
|
214
|
0 |
0 |
unless $arg |
|
215
|
0 |
0 |
unless ref $arg and $arg->isa('Bio::AnnotationCollectionI') |
|
247
|
1 |
2 |
if (defined $frequencies) { } |
|
248
|
1 |
0 |
if (ref($frequencies) =~ /HASH/i) { } |
|
259
|
1 |
1 |
unless (defined $self->{'_allele_freqs'}{$name}) |
|
283
|
0 |
1404 |
unless defined $i |
|
285
|
1 |
1403 |
$self->{'_checkisa'} ? : |
|
|
0 |
1404 |
unless ($self->{'_checkisa'} ? $i->isa('Bio::PopGen::IndividualI') : 1) |
|
293
|
0 |
51 |
unless $self->{'_individuals'} |
|
313
|
0 |
1 |
unless $self->{'_individuals'} |
|
314
|
1 |
1 |
if $namehash{$ind->unique_id} |
|
322
|
0 |
1 |
unless $self->{'_individuals'} |
|
341
|
0 |
93 |
unless $self->{'_individuals'} |
|
342
|
0 |
93 |
unless @inds |
|
343
|
3 |
90 |
if (@args) |
|
347
|
1 |
2 |
if (defined $id) { } |
|
|
2 |
0 |
elsif (defined $marker) { } |
|
371
|
1240 |
0 |
if (defined $name) |
|
373
|
0 |
1240 |
unless $self->{'_individuals'} |
|
393
|
0 |
48 |
unless $self->{'_cached_markernames'} |
|
394
|
48 |
30 |
if not $force and defined $self->{'_cached_markernames'} |
|
400
|
2 |
28 |
if ($nms[0] =~ /^(Site|Codon)/) |
|
408
|
0 |
30 |
unless $self->{'_cached_markernames'} |
|
427
|
406 |
490 |
if (defined $self->{'_allele_freqs'} and defined($marker = $self->{'_allele_freqs'}{$markername})) { } |
|
434
|
0 |
490 |
if (not @genotypes) { } |
|
440
|
0 |
71266 |
if $al eq '?' |
|
469
|
0 |
1245 |
if ($self->{'_forced_set_individuals'}) |
|
473
|
30 |
1215 |
if (not defined $markername) { } |
|
474
|
0 |
30 |
unless $self->{'_individuals'} |
|
477
|
0 |
1215 |
unless $self->{'_individuals'} |
|
478
|
9063 |
0 |
if $individual->has_Marker($markername) |
|
522
|
0 |
405 |
unless defined $marker and defined $allelename |
|
525
|
0 |
0 |
$self->{'_checkisa'} ? : |
|
|
0 |
0 |
if defined $marker and ref $marker and $self->{'_checkisa'} ? $marker->isa('Bio::PopGen::MarkerI') : 1 |
|
531
|
1440 |
1581 |
if ($alleles{$allelename}) |
|
532
|
1440 |
0 |
if keys %alleles == 1 |
|
535
|
405 |
0 |
$total ? : |
|
552
|
0 |
0 |
unless defined $marker and defined $allelename |
|
554
|
0 |
0 |
$self->{'_checkisa'} ? : |
|
|
0 |
0 |
if defined $marker and ref $marker and $self->{'_checkisa'} ? $marker->isa('Bio::PopGen::MarkerI') : 1 |
|
556
|
0 |
0 |
if (ref $marker) |
|
565
|
0 |
0 |
if ($alleles{$allelename}) |
|
566
|
0 |
0 |
if keys %alleles == 2 |
|
569
|
0 |
0 |
$total ? : |