| line |
true |
false |
branch |
|
137
|
0 |
2 |
unless (defined $aln and ref $aln and $aln->isa('Bio::Align::AlignI')) |
|
161
|
765 |
4787 |
if ($char eq $GAP or $j >= $dnalen) { } |
|
200
|
0 |
1 |
unless (defined $dna_aln and ref $dna_aln and $dna_aln->isa('Bio::Align::AlignI')) |
|
213
|
0 |
14 |
if scalar(@aln_str) % 3 |
|
219
|
4754 |
762 |
if ($triplet =~ /^[GATC]+$/i) { } |
|
|
762 |
0 |
elsif ($triplet =~ /^[$Bio::LocatableSeq::GAP_SYMBOLS]+$/) { } |
|
369
|
0 |
1 |
unless $self |
|
371
|
0 |
2 |
unless $_->isa('Bio::Align::AlignI') |
|
373
|
0 |
2 |
unless $_->is_flush |
|
381
|
0 |
14 |
if exists $unique{$seq->id} |
|
393
|
0 |
14 |
if ($new_seq->isa('Bio::Seq::MetaI')) |
|
401
|
0 |
14 |
if (@cat_seq == 0) |
|
408
|
0 |
14 |
if (@cat_seq > 1) |
|
423
|
0 |
14 |
if ($cat_seq->isa('Bio::Seq::Meta::Array')) { } |
|
|
0 |
14 |
elsif ($cat_seq->isa('Bio::Seq::Meta')) { } |
|
424
|
0 |
0 |
unless ($new_seq->isa('Bio::Seq::Meta::Array')) |
|
429
|
0 |
0 |
if ($new_seq->isa('Bio::Seq::Meta')) |
|
451
|
0 |
0 |
if ($new_seq->isa('Bio::Seq::Meta::Array')) { } |
|
459
|
0 |
0 |
unless ($new_seq->isa('Bio::Seq::Meta')) |
|
477
|
0 |
1 |
if ($cons_meta) |
|
487
|
0 |
1 |
if ($cat_cons_meta) |
|
488
|
0 |
0 |
unless $new_cons_meta |
|
499
|
0 |
1 |
if $new_cons_meta |
|
523
|
0 |
0 |
unless my $align = shift() |
|
533
|
0 |
0 |
unless $case_sensitive |
|
534
|
0 |
0 |
if ++$counts{$seq} > $max |