| line |
true |
false |
branch |
|
89
|
29 |
167 |
unless ($LOADED_WRAPPERS)
|
|
90
|
0 |
0 |
if $node->$field and $node->$field eq $value
|
|
|
0 |
0 |
if defined $node->id
|
|
|
0 |
0 |
unless (@_)
|
|
|
0 |
0 |
if (@_ == 1) { }
|
|
|
0 |
0 |
elsif (@_ == 2) { }
|
|
|
0 |
0 |
if (@nodes > 1)
|
|
|
0 |
0 |
if (wantarray) { }
|
|
|
0 |
0 |
if ($tips)
|
|
|
0 |
0 |
if ($args{'-order'} and $args{'-order'} =~ /^b/)
|
|
|
0 |
0 |
if (@_)
|
|
|
0 |
0 |
if ($order eq 'depth') { }
|
|
|
0 |
0 |
if (my $root = $self->get_root)
|
|
|
0 |
0 |
unless $nodect
|
|
|
0 |
0 |
if (@_)
|
|
|
0 |
0 |
unless (ref $node)
|
|
|
0 |
0 |
if ($node->is_terminal) { }
|
|
|
0 |
0 |
if ($new_root) { }
|
|
|
0 |
0 |
if (@_)
|
|
|
0 |
0 |
if (my $desc = $node->get_descendants)
|
|
|
0 |
0 |
if (ref $args{$key}) { }
|
|
|
0 |
0 |
if (ref $args{$key}) { }
|
|
|
0 |
0 |
if ($key =~ /^-keep_(.+)$/) { }
|
|
|
0 |
0 |
elsif ($key =~ /^-remove_(.+)$/) { }
|
|
|
0 |
0 |
if $remove->get_id == $keep->get_id
|
|
|
0 |
0 |
if (@names) { }
|
|
|
0 |
0 |
elsif (@keep_names) { }
|
|
|
0 |
0 |
if (ref $args[0]) { }
|
|
|
0 |
0 |
if $level < 0
|
|
119
|
0 |
0 |
if (&blessed($bptree) and $bptree->isa('Bio::Tree::TreeI')) { }
|
|
126
|
0 |
0 |
if defined $name
|
|
130
|
0 |
0 |
if defined $score
|
|
156
|
0 |
0 |
if ($parent)
|
|
203
|
115 |
1749 |
if ($firstp and $nextp and $firstp == $nextp)
|
|
204
|
6 |
109 |
unless ($first->get_next_sister)
|
|
207
|
6 |
109 |
unless ($next->get_previous_sister)
|
|
218
|
220 |
9 |
if ($p)
|
|
219
|
105 |
115 |
unless ($_->get_next_sister)
|
|
223
|
105 |
10 |
unless ($_->get_previous_sister)
|
|
257
|
0 |
1 |
unless $nB
|
|
265
|
1 |
1 |
if ($cdist > $middist) { }
|
|
269
|
1 |
0 |
if (my $parent = $current->get_parent) { }
|
|
305
|
121 |
30 |
if (my $root = $self->get_root) { }
|
|
309
|
2421 |
2062 |
if ($node->is_terminal)
|
|
319
|
0 |
0 |
if ($n->is_terminal)
|
|
375
|
3 |
7 |
if (scalar @children == 2)
|
|
378
|
2 |
0 |
unless (@{$children[0]->get_children;} or @{$children[1]->get_children;})
|
|
416
|
0 |
0 |
if ($anc->[0])
|
|
420
|
0 |
0 |
if $anc->[0]
|
|
452
|
1745 |
59 |
if ($root) { }
|
|
460
|
0 |
0 |
if (my $parent = $node->get_parent) { }
|
|
462
|
0 |
0 |
unless $children_of{$parent_id}
|
|
470
|
0 |
0 |
unless (exists $node_by_id{$parent})
|
|
472
|
0 |
0 |
if (scalar @children > 1)
|
|
520
|
3 |
0 |
if ($self->calc_tree_length) { }
|
|
529
|
16 |
0 |
if (my $path = $tip->$criterion)
|
|
530
|
4 |
12 |
if ($path > $height)
|
|
557
|
1 |
4 |
if ($is_taxa and not $@) { }
|
|
566
|
15 |
10 |
if (my $taxon = $node->get_taxon)
|
|
567
|
11 |
4 |
if $ids{$taxon->get_id}
|
|
591
|
0 |
0 |
if (not $nodes && @{$nodes;}) { }
|
|
|
0 |
0 |
elsif (scalar @{$nodes;} == 1) { }
|
|
606
|
0 |
0 |
if ($anc1->[$i]->get_id == $anc2->[$j]->get_id)
|
|
643
|
1 |
32 |
if $count != 0 and $count != 2
|
|
683
|
796 |
44 |
if (my $parent = $node->get_parent) { }
|
|
691
|
446 |
394 |
if $node->is_terminal
|
|
698
|
15 |
2001 |
unless $path{$id2}
|
|
699
|
4 |
1997 |
if abs 1 - $path{$id1} / $path{$id2} > $margin
|
|
728
|
2 |
0 |
if (@_ == 2) { }
|
|
|
0 |
0 |
elsif (@_ == 4) { }
|
|
739
|
1 |
3 |
if $mrca->is_ancestor_of($outgroup)
|
|
763
|
0 |
0 |
if (@_ == 2) { }
|
|
|
0 |
0 |
elsif (@_ == 4) { }
|
|
771
|
0 |
0 |
unless $tree->is_monophyletic($nodes, $outgroup)
|
|
775
|
0 |
0 |
scalar @{$tips;} == scalar @all ? :
|
|
803
|
0 |
3 |
if ($is_taxa and not $@)
|
|
809
|
3 |
0 |
if ($is_node_array and not $@) { }
|
|
817
|
0 |
3 |
$mrca ? :
|
|
820
|
2 |
1 |
scalar @{$mrca->get_terminals;} == scalar @{$tips;} ? :
|
|
843
|
0 |
0 |
if defined $node->get_branch_length
|
|
923
|
0 |
2 |
$normalize ? :
|
|
977
|
265 |
406 |
if (@children and $node->get_parent) { }
|
|
1022
|
128 |
5 |
if (exists $lengths_other{$split}) { }
|
|
1034
|
4 |
128 |
unless (exists $lengths_self{$split})
|
|
1176
|
4 |
0 |
if (my $parent = $tip->get_parent)
|
|
1177
|
4 |
0 |
if ($parent->is_preterminal)
|
|
1179
|
4 |
0 |
if (scalar @{$children;} == 2)
|
|
1267
|
55 |
64 |
if (@children == 2) { }
|
|
|
63 |
1 |
elsif (@children == 0) { }
|
|
1288
|
0 |
5 |
if ($n < 3) { }
|
|
1314
|
0 |
0 |
unless ($self->is_binary)
|
|
1326
|
0 |
0 |
if ($fd->is_internal) { }
|
|
1328
|
0 |
0 |
if ($_->is_terminal) { }
|
|
1339
|
0 |
0 |
if ($ld->is_internal) { }
|
|
1341
|
0 |
0 |
if ($_->is_terminal) { }
|
|
1352
|
0 |
0 |
unless $ftips + $ltips - 2
|
|
1355
|
0 |
0 |
if ($maxic == 0) { }
|
|
1422
|
0 |
0 |
if ($@)
|
|
1480
|
7 |
1 |
if ($node->get_parent)
|
|
1489
|
1 |
0 |
if ($nnodes) { }
|
|
1523
|
1 |
2 |
if $self->calc_resolution < 1
|
|
1525
|
1 |
1 |
unless $self->calc_tree_length
|
|
1544
|
7 |
1 |
if (my $parent = $node->get_parent)
|
|
1556
|
2 |
5 |
unless ($hj)
|
|
1619
|
1 |
5 |
if (not $self->is_ultrametric(0.01)) { }
|
|
1629
|
65 |
60 |
if (not $seen_tip or $node->is_internal)
|
|
1631
|
60 |
5 |
if (my $parent = $node->get_parent)
|
|
1636
|
5 |
60 |
if ($node->is_terminal)
|
|
1704
|
2 |
3 |
if (my $child = $node->get_child(0))
|
|
1738
|
1 |
1 |
unless ($self->is_ultrametric(0.01))
|
|
1780
|
9 |
123 |
unless $tuple->[2]
|
|
1782
|
3 |
18 |
$normalize ? :
|
|
1946
|
0 |
0 |
unless my $terminals = $self->get_terminals
|
|
1990
|
0 |
0 |
unless my $terminals = $self->get_terminals
|
|
2011
|
0 |
0 |
if ($el->{'terminals'}{$name}) { }
|
|
2038
|
0 |
0 |
unless $index
|
|
2047
|
0 |
0 |
if ($previous and $index->is_terminal)
|
|
2054
|
0 |
0 |
unless $child ne $previous
|
|
2059
|
0 |
0 |
if ($parent ne $previous)
|
|
2065
|
0 |
0 |
unless ($is_root)
|
|
2069
|
0 |
0 |
$direction eq 'root' ? :
|
|
2160
|
141 |
0 |
if (my $root = $self->get_root)
|
|
2229
|
3 |
0 |
if (my $root = $tree->get_root) { }
|
|
2274
|
4 |
3 |
unless (scalar @{$children;})
|
|
2309
|
0 |
0 |
if ($node->is_terminal) { }
|
|
2321
|
0 |
0 |
if $node->is_root
|
|
2328
|
0 |
0 |
if ($total)
|
|
2330
|
0 |
0 |
if ($rho)
|
|
2359
|
44 |
2 |
if (my $parent = $node->get_parent) { }
|
|
2441
|
5 |
4 |
if ($path_to_root > $tallest)
|
|
2480
|
16 |
1 |
if ($bl)
|
|
2508
|
1 |
13 |
if (scalar @children > 2)
|
|
2512
|
2 |
0 |
unless $anonymous
|
|
2560
|
0 |
0 |
if (&looks_like_class('Statistics::R') and &looks_like_class('Bio::Phylo::Generator'))
|
|
2566
|
0 |
0 |
if (my $seed = $args{'-seed'})
|
|
2592
|
0 |
0 |
if ($genus =~ /(..)$/)
|
|
2602
|
0 |
0 |
unless $args{'-rootedge'}
|
|
2607
|
0 |
0 |
if ($args{'-genera'})
|
|
2619
|
0 |
0 |
if ($rank)
|
|
2620
|
0 |
0 |
if ($rank eq 'genus')
|
|
2661
|
0 |
0 |
if --$size <= 1
|
|
2664
|
0 |
0 |
if ($node{$size}) { }
|
|
2677
|
0 |
0 |
if $n->is_terminal
|
|
2679
|
0 |
0 |
if (my $array = $node{$i})
|
|
2682
|
0 |
0 |
@filtered ? :
|
|
2704
|
0 |
0 |
int rand 2 ? :
|
|
2749
|
0 |
0 |
unless $genera{$genus}
|
|
2756
|
0 |
0 |
if $skip{$genus}
|
|
2760
|
0 |
0 |
if (scalar @$tips == 1) { }
|
|
2762
|
0 |
0 |
if $args{'-monotypic'}
|
|
2778
|
0 |
0 |
if ($clade_size == $tip_count) { }
|
|
2787
|
0 |
0 |
if ($args{'-polypara'})
|
|
2824
|
114 |
6 |
unless ($prune{$tip->get_id})
|
|
2850
|
0 |
24 |
if (&blessed($arg)) { }
|
|
2854
|
0 |
0 |
if $self->contains($node)
|
|
2866
|
121 |
16 |
if (&blessed($thing)) { }
|
|
2867
|
0 |
121 |
if ($thing->_type == $TAXON) { }
|
|
|
121 |
0 |
elsif ($thing->_type == $NODE) { }
|
|
2870
|
0 |
0 |
if $self->contains($node)
|
|
2874
|
111 |
10 |
if $self->contains($thing)
|
|
2880
|
16 |
0 |
if (my $tip = $self->get_by_name($thing))
|
|
2901
|
237 |
108 |
if (not exists $seen{$id}) { }
|
|
2918
|
25 |
237 |
unless (exists $seen{$nid})
|
|
2919
|
24 |
1 |
if $p
|
|
2922
|
24 |
1 |
if (defined $p)
|
|
2924
|
14 |
10 |
if (exists $seen{$pid})
|
|
2932
|
12 |
225 |
if (scalar @children == 1 and $seen{$nid} > 0)
|
|
2936
|
6 |
6 |
if defined $cbl and defined $bl
|
|
2939
|
8 |
4 |
if $p
|
|
2965
|
0 |
17 |
if ($bl and $bl < 0)
|
|
3004
|
10 |
6 |
if ($child->is_terminal) { }
|
|
3019
|
0 |
18 |
if ($right) { }
|
|
3069
|
0 |
4 |
UNIVERSAL::can($taxa, 'get_entities') ? :
|
|
3071
|
0 |
24 |
UNIVERSAL::can($_, 'get_name') ? :
|
|
3078
|
10 |
24 |
if (@children) { }
|
|
3113
|
0 |
0 |
if (not &looks_like_number($power)) { }
|
|
3140
|
0 |
0 |
unless (&looks_like_number($num))
|
|
3146
|
0 |
0 |
if ($length)
|
|
3168
|
0 |
0 |
if (not &looks_like_number($base)) { }
|
|
3176
|
0 |
0 |
if ($@) { }
|
|
3213
|
558 |
583 |
if (@children)
|
|
3216
|
0 |
558 |
if ($node->is_root and 1 == @children) { }
|
|
3223
|
0 |
0 |
if defined $clength
|
|
3224
|
0 |
0 |
if defined $glength
|
|
3225
|
0 |
0 |
if defined $length
|
|
3245
|
1 |
1185 |
if (1 == scalar @grandchildren)
|
|
3251
|
0 |
1 |
if defined $clength
|
|
3252
|
0 |
1 |
if defined $glength
|
|
3253
|
0 |
1 |
if defined $length
|
|
3300
|
0 |
0 |
if not $seen{$node->get_id}
|
|
3305
|
0 |
0 |
if (scalar @delete)
|
|
3330
|
0 |
0 |
if (scalar @children < 3) { }
|
|
3331
|
0 |
0 |
unless ($collapsible)
|
|
3409
|
0 |
0 |
if (my $parent = $node->get_parent)
|
|
3484
|
0 |
0 |
if (defined $length and not $length =~ /^[+-]?\d+$/)
|
|
3490
|
0 |
0 |
if (my $root = $self->get_root)
|
|
3534
|
0 |
0 |
unless (&looks_like_object($dom, 18))
|
|
3540
|
0 |
0 |
if (defined $length and not $length =~ /^[+-]?\d+$/)
|
|
3546
|
0 |
0 |
if (my $root = $self->get_root)
|