| line |
true |
false |
branch |
|
59
|
0 |
34 |
unless (eval {
do {
require warnings;
1
}
}) |
|
97
|
8 |
28 |
if (defined $$self{'_nhx_obj'}) |
|
166
|
1017 |
3 |
if (defined $_[0]{'parent'}) { } |
|
200
|
1703 |
1066 |
if (defined $_[0]{'length'}) { } |
|
239
|
0 |
44 |
if (defined $bootstrap and not _is_number($bootstrap)) { } |
|
|
1 |
43 |
elsif (not defined $bootstrap) { } |
|
295
|
0 |
0 |
if (defined $_[0]{'xcoord'}) { } |
|
379
|
2963 |
4715 |
defined $$self{'children'} ? : |
|
409
|
0 |
6 |
unless (defined $node2) |
|
416
|
0 |
6 |
if ($node1 eq $node2) |
|
437
|
16 |
0 |
if (defined $$tmp_node2{'parent'}) |
|
447
|
3 |
0 |
if (defined $$tmp_node1{'parent'}) |
|
472
|
63 |
1096 |
$out_format =~ /NHX/i ? : |
|
479
|
491 |
668 |
if (@children) { } |
|
488
|
479 |
12 |
if (defined $name and not $remove_inode_names) |
|
489
|
272 |
219 |
if (defined $length) |
|
490
|
81 |
410 |
if (defined $comment) |
|
497
|
0 |
668 |
unless (defined $name) |
|
504
|
488 |
180 |
if (defined $length) |
|
505
|
35 |
633 |
if (defined $comment) |
|
539
|
2827 |
2820 |
if $$self{'children'} |
|
560
|
409 |
2783 |
if (not $name) { } |
|
|
0 |
4613 |
elsif (not $self->is_otu and $name =~ /^\d+$/) { } |
|
572
|
1362 |
1830 |
if (@children) |
|
574
|
2953 |
0 |
if $child |
|
617
|
0 |
0 |
if ($child->is_otu) { } |
|
621
|
0 |
0 |
if @$children |
|
642
|
0 |
0 |
if $self->get_name |
|
646
|
0 |
0 |
if $self->get_length |
|
651
|
0 |
0 |
if $self->nhx_command_to_string |
|
677
|
0 |
0 |
unless ($words or @$words) |
|
682
|
82 |
1443 |
unless $pos |
|
689
|
461 |
2320 |
if ($word eq '(') { } |
|
|
521 |
1799 |
elsif ($word eq ',') { } |
|
|
461 |
1338 |
elsif ($word eq ')') { } |
|
|
676 |
662 |
elsif ($word eq ':') { } |
|
739
|
88 |
3369 |
if ($word =~ s/\[(.*)\]//) |
|
746
|
46 |
42 |
if (defined $nhx_obj->to_string) { } |
|
752
|
42 |
0 |
if defined $comment_str |
|
788
|
0 |
676 |
unless defined $length |
|
790
|
0 |
676 |
unless (_is_number($length)) |
|
797
|
4 |
672 |
if ($length =~ /e/i) |
|
819
|
0 |
42 |
unless (_is_number($bootstrap)) |
|
825
|
42 |
0 |
if defined _sci_to_dec($bootstrap) |
|
844
|
27 |
169 |
if $self->get_name eq $name |
|
847
|
71 |
94 |
if $result |
|
867
|
4 |
1 |
if ($self->is_otu) |
|
868
|
3 |
1 |
if ($OTUlist =~ /\s+$name\s+/) { } |
|
882
|
3 |
1 |
if ($result eq 'keep') |
|
887
|
0 |
1 |
if ($#newchildren == -1) |
|
894
|
0 |
1 |
if ($#children == 0) |
|
903
|
0 |
0 |
if defined $$child{'_nhx_obj'} |
|
909
|
0 |
0 |
if ($child->is_otu) |
|
936
|
12 |
204 |
if ($self->is_otu and not $other->is_otu or not $self->is_otu and $other->is_otu) |
|
945
|
115 |
89 |
if ($self->is_otu and $other->is_otu) |
|
946
|
81 |
34 |
if ($self->_same_attributes($other)) { } |
|
961
|
2 |
87 |
unless ($self->_same_attributes($other)) |
|
965
|
2 |
85 |
if (scalar @self_children != scalar @other_children) { } |
|
984
|
123 |
68 |
if ($self_children[$self_index]->equals($other_children[$other_index])) |
|
999
|
29 |
123 |
if ($found eq 'false') |
|
1014
|
2 |
202 |
unless defined $self->get_length and defined $other->get_length or not defined $self->get_length || defined $other->get_length |
|
1018
|
132 |
70 |
if (defined $self->get_length and defined $other->get_length) |
|
1019
|
2 |
130 |
if ($self->get_length != $other->get_length) |
|
1024
|
113 |
87 |
if ($self->is_otu and $other->is_otu) |
|
1025
|
30 |
83 |
if ($self->get_name ne $other->get_name) |
|
1028
|
13 |
157 |
if (defined $self->get_nhx_obj and defined $other->get_nhx_obj) |
|
1029
|
1 |
12 |
unless ($self->get_nhx_obj->equals($other->get_nhx_obj)) |
|
1033
|
0 |
169 |
if (not defined $self->get_nhx_obj and defined $other->get_nhx_obj) |
|
1036
|
1 |
168 |
if (defined $self->get_nhx_obj and not defined $other->get_nhx_obj) |
|
1055
|
1 |
1 |
unless defined $self->get_parent |
|
1059
|
1 |
1 |
if ($potential_sibling ne $self) |
|
1078
|
0 |
2 |
unless (defined $node2) |
|
1086
|
0 |
1 |
if defined $parent1 and defined $parent2 and $parent1 eq $parent2 |
|
1112
|
0 |
0 |
if ($oldparent) |
|
1117
|
0 |
0 |
if defined $$newparent{'_nhx_obj'} |
|
1137
|
0 |
982 |
if ($overwrite_children) { } |
|
1162
|
0 |
0 |
if defined $$child{'_nhx_obj'} |
|
1167
|
0 |
0 |
if @{$child->get_children;} > 0 |
|
1187
|
0 |
0 |
if $self->is_otu |
|
1189
|
0 |
0 |
if ($child->is_otu) { } |
|
1217
|
0 |
0 |
unless defined $child->_get_ycoord |
|
1239
|
603 |
461 |
if $self->is_otu |
|
1273
|
66 |
379 |
if $length or $length = 0 |
|
1275
|
63 |
300 |
if $child->find_lengths |
|
1292
|
0 |
0 |
unless ($otu1->is_otu or $otu2->is_otu) |
|
1312
|
2 |
12 |
if ($inode eq $currentnode) |
|
1342
|
0 |
0 |
if (grep {$_->get_name eq $inp_otu;} @{$node_otus;}) |
|
1344
|
0 |
0 |
if $eq_count == scalar @inp_otus |
|
1348
|
0 |
0 |
if ($eq_count == scalar @inp_otus) |
|
1352
|
0 |
0 |
if $child->is_otu |
|
1356
|
0 |
0 |
if (scalar @{$ancestors;}) |
|
1365
|
0 |
0 |
if $Bio::NEXUS::Node::AUTOLOAD =~ /DESTROY$/ |
|
1391
|
0 |
0 |
if (defined $synonym_for{$Bio::NEXUS::Node::AUTOLOAD}) { } |
|
1417
|
3 |
0 |
if (defined $$self{'_nhx_obj'}) |
|
1435
|
1 |
0 |
if (defined $$self{'_nhx_obj'}) { } |
|
1456
|
71 |
1035 |
if (defined $$self{'_nhx_obj'} and $$self{'_nhx_obj'}->contains_tag($tag_name)) { } |
|
1478
|
0 |
47 |
unless (defined $tag_name or not defined $tag_values) |
|
1483
|
0 |
47 |
if (ref $tag_values ne 'ARRAY') |
|
1488
|
44 |
3 |
unless defined $$self{'_nhx_obj'} |
|
1507
|
0 |
3 |
unless defined $$self{'_nhx_obj'} |
|
1525
|
0 |
0 |
if (defined $$self{'_nhx_obj'}) |
|
1544
|
0 |
0 |
if defined $$self{'_nhx_obj'} |
|
1559
|
55 |
13 |
if (defined $$self{'_nhx_obj'}) { } |
|
1579
|
8 |
0 |
if (defined $$self{'_nhx_obj'}) { } |
|
1602
|
1 |
0 |
if defined $$self{'_nhx_obj'} |