| line |
true |
false |
branch |
|
88
|
14 |
710 |
unless ($LOADED_WRAPPERS)
|
|
89
|
0 |
0 |
if (defined $desc)
|
|
|
0 |
0 |
if (defined $end)
|
|
|
0 |
0 |
if (defined $end) { }
|
|
|
0 |
0 |
unless defined $self->id
|
|
|
0 |
0 |
unless defined $self->start
|
|
|
0 |
0 |
unless defined $self->end
|
|
|
0 |
0 |
unless $_ eq $DEFAULT_NAME
|
|
|
0 |
0 |
if $names->{$DEFAULT_NAME}
|
|
|
0 |
0 |
if (defined $start)
|
|
|
0 |
0 |
if (defined $strand)
|
|
|
0 |
0 |
if ($subloc->strand < 0)
|
|
|
0 |
0 |
if ($start > $end)
|
|
|
0 |
0 |
if ($start <= 0)
|
|
|
0 |
0 |
if ($end > $self->length)
|
|
|
0 |
0 |
if (defined $replace) { }
|
|
|
0 |
0 |
if (ref $start and $start->isa('Bio::LocationI')) { }
|
|
|
0 |
0 |
elsif (defined $start and defined $end) { }
|
|
90
|
0 |
14 |
if $@
|
|
127
|
0 |
0 |
if ($seqstring and $seqstring =~ /\S/)
|
|
129
|
0 |
0 |
if ($@ and &looks_like_instance($@, 'Bio::Phylo::Util::Exceptions::InvalidData'))
|
|
150
|
0 |
0 |
if defined $name
|
|
154
|
0 |
0 |
if defined $desc
|
|
158
|
0 |
0 |
if $seq->can($field)
|
|
197
|
69 |
644 |
ref $_[0] ? :
|
|
201
|
69 |
644 |
if (&looks_like_instance($arg, 'ARRAY')) { }
|
|
218
|
7 |
706 |
if ($@)
|
|
272
|
715 |
747 |
if (@data) { }
|
|
273
|
691 |
24 |
wantarray ? :
|
|
276
|
747 |
0 |
wantarray ? :
|
|
303
|
0 |
0 |
if $_ ne $gap
|
|
304
|
0 |
0 |
if (@data) { }
|
|
305
|
0 |
0 |
wantarray ? :
|
|
308
|
0 |
0 |
wantarray ? :
|
|
327
|
39 |
584 |
if (my $matrix = $self->_get_container) { }
|
|
352
|
0 |
50 |
if $offset > $index
|
|
354
|
50 |
0 |
defined $val ? :
|
|
380
|
0 |
0 |
if ($is_numerical) { }
|
|
381
|
0 |
0 |
if $obj == $ent
|
|
384
|
0 |
0 |
if $obj eq $ent
|
|
413
|
719 |
0 |
if (my $obj = $self->get_type_object) { }
|
|
414
|
0 |
719 |
if ($obj->isa('Bio::Phylo::Matrices::Datatype::Mixed')) { }
|
|
417
|
0 |
0 |
if (&looks_like_implementor($datum, 'get_char')) { }
|
|
|
0 |
0 |
elsif (&looks_like_instance($datum, 'ARRAY')) { }
|
|
436
|
0 |
0 |
if $subtype->is_valid($split[$i - 1])
|
|
485
|
0 |
23 |
if (@_) { }
|
|
489
|
0 |
0 |
if (exists $focus{$c})
|
|
490
|
0 |
0 |
if (not exists $counts{$c}) { }
|
|
502
|
80 |
21 |
if (not exists $counts{$c}) { }
|
|
537
|
0 |
0 |
if $c1[$i] eq $m or $c1[$i] eq $g or $c2[$i] eq $m or $c2[$i] eq $g
|
|
541
|
0 |
0 |
$total ? :
|
|
569
|
10 |
0 |
unless (exists $args{"-$arg"})
|
|
577
|
5 |
0 |
if ($total > 0)
|
|
640
|
0 |
0 |
unless defined $newchars[$i]
|
|
682
|
0 |
0 |
if $c eq $m or $c eq $g
|
|
688
|
0 |
0 |
if (@states) { }
|
|
697
|
0 |
0 |
wantarray ? :
|
|
717
|
3 |
749 |
if (not $self->get_type_object->is_valid($self))
|
|
744
|
0 |
0 |
if (my $taxon = $self->get_taxon)
|
|
750
|
0 |
0 |
if (not $args{'-compact'}) { }
|
|
753
|
0 |
0 |
if ($missing ne $char[$i] and $gap ne $char[$i]) { }
|
|
|
0 |
0 |
elsif ($missing eq $char[$i] or $gap eq $char[$i]) { }
|
|
754
|
0 |
0 |
if ($char_ids and $char_ids->[$i]) { }
|
|
760
|
0 |
0 |
if ($state_ids and $$state_ids{uc $char[$i]}) { }
|
|
768
|
0 |
0 |
if ($char_ids and $char_ids->[$i]) { }
|
|
774
|
0 |
0 |
if ($special and $$special{$char[$i]}) { }
|
|
821
|
0 |
0 |
if (&looks_like_instance($dom, 'SCALAR') and $dom->_type == 18) { }
|
|
828
|
0 |
0 |
unless ($dom)
|
|
837
|
0 |
0 |
if (my $taxon = $self->get_taxon)
|
|
843
|
0 |
0 |
if (not $args{'-compact'}) { }
|
|
845
|
0 |
0 |
if ($missing ne $char[$i] and $gap ne $char[$i]) { }
|
|
|
0 |
0 |
elsif ($missing eq $char[$i] or $gap eq $char[$i]) { }
|
|
847
|
0 |
0 |
if ($char_ids and $char_ids->[$i]) { }
|
|
853
|
0 |
0 |
if ($state_ids and $$state_ids{uc $char[$i]}) { }
|
|
866
|
0 |
0 |
if ($char_ids and $char_ids->[$i]) { }
|
|
872
|
0 |
0 |
if ($special and $$special{$char[$i]}) { }
|
|
935
|
0 |
133 |
if (my $matrix = $self->get_matrix)
|