| 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) |