| line |
true |
false |
branch |
|
87
|
14 |
710 |
unless ($LOADED_WRAPPERS)
|
|
88
|
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) { }
|
|
89
|
0 |
14 |
if $@
|
|
126
|
0 |
0 |
if ($seqstring and $seqstring =~ /\S/)
|
|
128
|
0 |
0 |
if ($@ and &looks_like_instance($@, 'Bio::Phylo::Util::Exceptions::InvalidData'))
|
|
149
|
0 |
0 |
if defined $name
|
|
153
|
0 |
0 |
if defined $desc
|
|
157
|
0 |
0 |
if $seq->can($field)
|
|
196
|
69 |
644 |
ref $_[0] ? :
|
|
200
|
69 |
644 |
if (&looks_like_instance($arg, 'ARRAY')) { }
|
|
217
|
7 |
706 |
if ($@)
|
|
271
|
715 |
747 |
if (@data) { }
|
|
272
|
691 |
24 |
wantarray ? :
|
|
275
|
747 |
0 |
wantarray ? :
|
|
302
|
0 |
0 |
if $_ ne $gap
|
|
303
|
0 |
0 |
if (@data) { }
|
|
304
|
0 |
0 |
wantarray ? :
|
|
307
|
0 |
0 |
wantarray ? :
|
|
326
|
39 |
584 |
if (my $matrix = $self->_get_container) { }
|
|
351
|
0 |
50 |
if $offset > $index
|
|
353
|
50 |
0 |
defined $val ? :
|
|
379
|
0 |
0 |
if ($is_numerical) { }
|
|
380
|
0 |
0 |
if $obj == $ent
|
|
383
|
0 |
0 |
if $obj eq $ent
|
|
412
|
719 |
0 |
if (my $obj = $self->get_type_object) { }
|
|
413
|
0 |
719 |
if ($obj->isa('Bio::Phylo::Matrices::Datatype::Mixed')) { }
|
|
416
|
0 |
0 |
if (&looks_like_implementor($datum, 'get_char')) { }
|
|
|
0 |
0 |
elsif (&looks_like_instance($datum, 'ARRAY')) { }
|
|
435
|
0 |
0 |
if $subtype->is_valid($split[$i - 1])
|
|
484
|
0 |
23 |
if (@_) { }
|
|
488
|
0 |
0 |
if (exists $focus{$c})
|
|
489
|
0 |
0 |
if (not exists $counts{$c}) { }
|
|
501
|
80 |
21 |
if (not exists $counts{$c}) { }
|
|
536
|
0 |
0 |
if $c1[$i] eq $m or $c1[$i] eq $g or $c2[$i] eq $m or $c2[$i] eq $g
|
|
540
|
0 |
0 |
$total ? :
|
|
568
|
10 |
0 |
unless (exists $args{"-$arg"})
|
|
576
|
5 |
0 |
if ($total > 0)
|
|
639
|
0 |
0 |
unless defined $newchars[$i]
|
|
681
|
0 |
0 |
if $c eq $m or $c eq $g
|
|
687
|
0 |
0 |
if (@states) { }
|
|
696
|
0 |
0 |
wantarray ? :
|
|
716
|
3 |
749 |
if (not $self->get_type_object->is_valid($self))
|
|
743
|
0 |
0 |
if (my $taxon = $self->get_taxon)
|
|
749
|
0 |
0 |
if (not $args{'-compact'}) { }
|
|
752
|
0 |
0 |
if ($missing ne $char[$i] and $gap ne $char[$i]) { }
|
|
|
0 |
0 |
elsif ($missing eq $char[$i] or $gap eq $char[$i]) { }
|
|
753
|
0 |
0 |
if ($char_ids and $char_ids->[$i]) { }
|
|
759
|
0 |
0 |
if ($state_ids and $$state_ids{uc $char[$i]}) { }
|
|
767
|
0 |
0 |
if ($char_ids and $char_ids->[$i]) { }
|
|
773
|
0 |
0 |
if ($special and $$special{$char[$i]}) { }
|
|
820
|
0 |
0 |
if (&looks_like_instance($dom, 'SCALAR') and $dom->_type == 18) { }
|
|
827
|
0 |
0 |
unless ($dom)
|
|
836
|
0 |
0 |
if (my $taxon = $self->get_taxon)
|
|
842
|
0 |
0 |
if (not $args{'-compact'}) { }
|
|
844
|
0 |
0 |
if ($missing ne $char[$i] and $gap ne $char[$i]) { }
|
|
|
0 |
0 |
elsif ($missing eq $char[$i] or $gap eq $char[$i]) { }
|
|
846
|
0 |
0 |
if ($char_ids and $char_ids->[$i]) { }
|
|
852
|
0 |
0 |
if ($state_ids and $$state_ids{uc $char[$i]}) { }
|
|
865
|
0 |
0 |
if ($char_ids and $char_ids->[$i]) { }
|
|
871
|
0 |
0 |
if ($special and $$special{$char[$i]}) { }
|
|
934
|
0 |
133 |
if (my $matrix = $self->get_matrix)
|