| line |
true |
false |
branch |
|
113
|
0 |
207 |
unless (defined $type) |
|
123
|
40 |
167 |
if (not defined $field) { } |
|
136
|
1961 |
1018 |
if $_->can($type) and defined $_->$type |
|
139
|
56 |
151 |
if (wantarray) { } |
|
142
|
0 |
151 |
if (@nodes > 1) |
|
163
|
0 |
0 |
do {
not $input->isa('Bio::Tree::NodeI')
} ? : |
|
|
0 |
1 |
ref $input ? : |
|
171
|
0 |
1 |
if (not $node->ancestor and $self->get_root_node->internal_id != $node->internal_id) { } |
|
197
|
599 |
0 |
if (ref $input) { } |
|
198
|
0 |
599 |
unless ($input->isa('Bio::Tree::NodeI')) |
|
215
|
338 |
4469 |
if $node eq $root |
|
240
|
0 |
0 |
do {
not $input->isa('Bio::Tree::NodeI')
} ? : |
|
|
0 |
0 |
ref $input ? : |
|
253
|
0 |
0 |
if ($node_name =~ /$sep/) |
|
298
|
0 |
12 |
unless @args > 0 |
|
301
|
8 |
4 |
if (ref $args[0]) { } |
|
302
|
0 |
8 |
unless $args[0]->isa('Bio::Tree::NodeI') |
|
306
|
0 |
4 |
unless @args % 2 == 0 |
|
312
|
2 |
3 |
ref $value ? : |
|
314
|
3 |
2 |
if ($key =~ s/remove_//) { } |
|
|
2 |
0 |
elsif ($key =~ s/keep_//) { } |
|
|
0 |
0 |
elsif ($key =~ /preserve/) { } |
|
330
|
1 |
3 |
if ($remove_all) |
|
331
|
0 |
1 |
if (@keep_nodes == 0) |
|
338
|
2 |
2 |
if (@keep_nodes > 0) { } |
|
341
|
3 |
8 |
unless exists $keep_iids{$node->internal_id} |
|
356
|
0 |
0 |
unless ($ancestor or $reroot) |
|
364
|
0 |
49 |
if (exists $root_descs{$node->internal_id}) |
|
376
|
0 |
46 |
if $preserve_lengths |
|
380
|
0 |
12 |
if ($reroot) |
|
382
|
0 |
0 |
unless @candidates > 0 |
|
383
|
0 |
0 |
unless @candidates == 1 |
|
406
|
2 |
8 |
if (ref $nodes eq 'ARRAY') { } |
|
412
|
0 |
10 |
unless @nodes >= 2 |
|
423
|
0 |
23 |
unless (ref $node and $node->isa('Bio::Tree::NodeI')) |
|
429
|
0 |
10 |
unless @paths >= 2 |
|
437
|
0 |
78 |
unless (defined $node_id) |
|
443
|
24 |
10 |
if (keys %node_ids == 1) { } |
|
455
|
8 |
2 |
if ($lca and $self->number_nodes > 0) |
|
457
|
8 |
0 |
if $own_lca |
|
496
|
0 |
0 |
unless ref $thing |
|
499
|
0 |
0 |
if ($thing->isa('Bio::Tree::TreeI')) { } |
|
|
0 |
0 |
elsif ($thing->isa('Bio::Tree::NodeI')) { } |
|
501
|
0 |
0 |
unless @leaves == 1 |
|
505
|
0 |
0 |
unless $thing->ancestor |
|
517
|
0 |
0 |
if (defined $node) |
|
523
|
0 |
0 |
unless ($merged) |
|
579
|
44 |
60 |
if ($node->ancestor and $node->each_Descendent == 1) |
|
583
|
8 |
0 |
if @remove |
|
584
|
0 |
8 |
if ($reroot) |
|
587
|
0 |
0 |
if (@descs == 1) |
|
615
|
2 |
27 |
unless @descs == 2 or @descs == 0 |
|
622
|
1 |
28 |
if $binary < 0 |
|
695
|
2 |
10 |
if (@descs > 2) { } |
|
|
0 |
10 |
elsif (@descs == 1) { } |
|
705
|
1 |
1 |
if $half > int $half |
|
766
|
0 |
0 |
$node->is_Leaf && !($id =~ /^artificial/) ? : |
|
788
|
0 |
0 |
if ($key eq '_desc' or $key eq '_ancestor') |
|
802
|
0 |
0 |
unless defined $node |
|
810
|
0 |
0 |
if (@data) { } |
|
|
0 |
0 |
elsif ($id) { } |
|
811
|
0 |
0 |
unless (exists ${$paired;}{join $", @data} or @data == 1) |
|
839
|
0 |
0 |
if (not defined $nodes) { } |
|
|
0 |
0 |
elsif (ref $nodes eq 'ARRAY') { } |
|
|
0 |
0 |
elsif (@args == 2) { } |
|
853
|
0 |
0 |
unless @{$nodes;} == 2 |
|
856
|
0 |
0 |
unless ($lca) |
|
865
|
0 |
0 |
if $current_node eq $lca |
|
866
|
0 |
0 |
if ($current_node->branch_length) { } |
|
|
0 |
0 |
elsif (not $warned) { } |
|
899
|
0 |
6 |
unless (defined $nodes and defined $outgroup) |
|
904
|
0 |
6 |
unless (ref($nodes) =~ /ARRAY/i) |
|
909
|
0 |
6 |
unless (defined $clade_root) |
|
916
|
2 |
10 |
if ($og_ancestor->internal_id == $clade_root->internal_id) |
|
946
|
0 |
2 |
unless (defined $nodes and defined $outgroup) |
|
950
|
0 |
2 |
unless (ref($nodes) =~ /ARRAY/i) |
|
965
|
0 |
2 |
unless (defined $clade_root) |
|
974
|
0 |
4 |
if ($og_ancestor->internal_id == $clade_root->internal_id) |
|
984
|
4 |
4 |
unless $n->is_Leaf |
|
988
|
1 |
3 |
unless $nodehash{$n->internal_id} |
|
1006
|
0 |
18 |
unless (defined $new_root and $new_root->isa('Bio::Tree::NodeI')) |
|
1012
|
1 |
17 |
if ($new_root == $old_root) |
|
1017
|
0 |
17 |
unless ($anc) |
|
1031
|
9 |
34 |
if defined $next->bootstrap |
|
1066
|
0 |
0 |
unless (defined $node and $node->isa('Bio::Tree::NodeI')) |
|
1072
|
0 |
0 |
if (defined $id) |
|
1073
|
0 |
0 |
if ref $id |
|
1074
|
0 |
0 |
if defined $id and not ref $id |
|
1099
|
0 |
0 |
if ($rootnode->id and $rootnode->id eq $id) |
|
1104
|
0 |
0 |
if ($node->id and $node->id eq $id) |
|
1124
|
3 |
1 |
defined $node->id ? : |
|
1159
|
0 |
3 |
unless open my $TRAIT, '<', $file |
|
1166
|
3 |
51 |
if ($first_line) |
|
1173
|
0 |
51 |
if not defined $id or $id eq '' |
|
1177
|
18 |
33 |
if not defined $value or $value eq '' |
|
1188
|
2 |
1 |
unless defined $ignore |
|
1192
|
2 |
1 |
if (defined $trait_name) |
|
1197
|
0 |
32 |
if $node->id =~ /^['"]+(.*)['"]+$/ |
|
1199
|
1 |
31 |
unless (exists $$trait_values{$node->id}) |
|
1200
|
1 |
0 |
if ($ignore) { } |