| line |
true |
false |
branch |
|
88
|
29 |
151 |
unless ($LOADED_WRAPPERS) |
|
89
|
0 |
0 |
if defined $node->id |
|
|
0 |
0 |
if $node->$field and $node->$field eq $value |
|
|
0 |
0 |
unless (@_) |
|
|
0 |
0 |
if (@_ == 1) { } |
|
|
0 |
0 |
elsif (@_ == 2) { } |
|
|
0 |
0 |
if (@nodes > 1) |
|
|
0 |
0 |
if (wantarray) { } |
|
|
0 |
0 |
if ($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 $level < 0 |
|
118
|
0 |
0 |
if (&blessed($bptree) and $bptree->isa('Bio::Tree::TreeI')) { } |
|
125
|
0 |
0 |
if defined $name |
|
129
|
0 |
0 |
if defined $score |
|
155
|
0 |
0 |
if ($parent) |
|
202
|
115 |
1746 |
if ($firstp and $nextp and $firstp == $nextp) |
|
203
|
6 |
109 |
unless ($first->get_next_sister) |
|
206
|
6 |
109 |
unless ($next->get_previous_sister) |
|
217
|
220 |
9 |
if ($p) |
|
218
|
105 |
115 |
unless ($_->get_next_sister) |
|
222
|
105 |
10 |
unless ($_->get_previous_sister) |
|
256
|
0 |
1 |
unless $nB |
|
264
|
1 |
1 |
if ($cdist > $middist) { } |
|
268
|
1 |
0 |
if (my $parent = $current->get_parent) { } |
|
304
|
121 |
30 |
if (my $root = $self->get_root) { } |
|
308
|
2721 |
2388 |
if ($node->is_terminal) |
|
318
|
0 |
0 |
if ($n->is_terminal) |
|
374
|
3 |
7 |
if (scalar @children == 2) |
|
377
|
2 |
0 |
unless (@{$children[0]->get_children;} or @{$children[1]->get_children;}) |
|
415
|
0 |
0 |
if ($anc->[0]) |
|
419
|
0 |
0 |
if $anc->[0] |
|
451
|
2048 |
59 |
if ($root) { } |
|
459
|
0 |
0 |
if (my $parent = $node->get_parent) { } |
|
461
|
0 |
0 |
unless $children_of{$parent_id} |
|
469
|
0 |
0 |
unless (exists $node_by_id{$parent}) |
|
471
|
0 |
0 |
if (scalar @children > 1) |
|
519
|
3 |
0 |
if ($self->calc_tree_length) { } |
|
528
|
16 |
0 |
if (my $path = $tip->$criterion) |
|
529
|
4 |
12 |
if ($path > $height) |
|
556
|
1 |
4 |
if ($is_taxa and not $@) { } |
|
565
|
15 |
10 |
if (my $taxon = $node->get_taxon) |
|
566
|
11 |
4 |
if $ids{$taxon->get_id} |
|
590
|
0 |
0 |
if (not $nodes && @{$nodes;}) { } |
|
|
0 |
0 |
elsif (scalar @{$nodes;} == 1) { } |
|
605
|
0 |
0 |
if ($anc1->[$i]->get_id == $anc2->[$j]->get_id) |
|
642
|
1 |
32 |
if $count != 0 and $count != 2 |
|
682
|
868 |
48 |
if (my $parent = $node->get_parent) { } |
|
690
|
486 |
430 |
if $node->is_terminal |
|
697
|
15 |
2181 |
unless $path{$id2} |
|
698
|
4 |
2177 |
if abs 1 - $path{$id1} / $path{$id2} > $margin |
|
727
|
2 |
0 |
if (@_ == 2) { } |
|
|
0 |
0 |
elsif (@_ == 4) { } |
|
738
|
1 |
3 |
if $mrca->is_ancestor_of($outgroup) |
|
762
|
0 |
0 |
if (@_ == 2) { } |
|
|
0 |
0 |
elsif (@_ == 4) { } |
|
770
|
0 |
0 |
unless $tree->is_monophyletic($nodes, $outgroup) |
|
774
|
0 |
0 |
scalar @{$tips;} == scalar @all ? : |
|
802
|
0 |
3 |
if ($is_taxa and not $@) |
|
808
|
3 |
0 |
if ($is_node_array and not $@) { } |
|
816
|
0 |
3 |
$mrca ? : |
|
819
|
2 |
1 |
scalar @{$mrca->get_terminals;} == scalar @{$tips;} ? : |
|
842
|
0 |
0 |
if defined $node->get_branch_length |
|
922
|
0 |
2 |
$normalize ? : |
|
976
|
265 |
406 |
if (@children and $node->get_parent) { } |
|
1021
|
128 |
5 |
if (exists $lengths_other{$split}) { } |
|
1033
|
4 |
128 |
unless (exists $lengths_self{$split}) |
|
1175
|
4 |
0 |
if (my $parent = $tip->get_parent) |
|
1176
|
4 |
0 |
if ($parent->is_preterminal) |
|
1178
|
4 |
0 |
if (scalar @{$children;} == 2) |
|
1266
|
55 |
64 |
if (@children == 2) { } |
|
|
63 |
1 |
elsif (@children == 0) { } |
|
1287
|
0 |
5 |
if ($n < 3) { } |
|
1313
|
0 |
0 |
unless ($self->is_binary) |
|
1325
|
0 |
0 |
if ($fd->is_internal) { } |
|
1327
|
0 |
0 |
if ($_->is_terminal) { } |
|
1338
|
0 |
0 |
if ($ld->is_internal) { } |
|
1340
|
0 |
0 |
if ($_->is_terminal) { } |
|
1351
|
0 |
0 |
unless $ftips + $ltips - 2 |
|
1354
|
0 |
0 |
if ($maxic == 0) { } |
|
1421
|
0 |
0 |
if ($@) |
|
1479
|
7 |
1 |
if ($node->get_parent) |
|
1488
|
1 |
0 |
if ($nnodes) { } |
|
1522
|
1 |
2 |
if $self->calc_resolution < 1 |
|
1524
|
1 |
1 |
unless $self->calc_tree_length |
|
1543
|
7 |
1 |
if (my $parent = $node->get_parent) |
|
1555
|
2 |
5 |
unless ($hj) |
|
1618
|
1 |
5 |
if (not $self->is_ultrametric(0.01)) { } |
|
1628
|
65 |
60 |
if (not $seen_tip or $node->is_internal) |
|
1630
|
60 |
5 |
if (my $parent = $node->get_parent) |
|
1635
|
5 |
60 |
if ($node->is_terminal) |
|
1703
|
2 |
3 |
if (my $child = $node->get_child(0)) |
|
1737
|
1 |
1 |
unless ($self->is_ultrametric(0.01)) |
|
1779
|
9 |
123 |
unless $tuple->[2] |
|
1781
|
3 |
18 |
$normalize ? : |
|
1945
|
0 |
0 |
unless my $terminals = $self->get_terminals |
|
1989
|
0 |
0 |
unless my $terminals = $self->get_terminals |
|
2010
|
0 |
0 |
if ($el->{'terminals'}{$name}) { } |
|
2037
|
0 |
0 |
unless $index |
|
2046
|
0 |
0 |
if ($previous and $index->is_terminal) |
|
2053
|
0 |
0 |
unless $child ne $previous |
|
2058
|
0 |
0 |
if ($parent ne $previous) |
|
2064
|
0 |
0 |
unless ($is_root) |
|
2068
|
0 |
0 |
$direction eq 'root' ? : |
|
2159
|
145 |
0 |
if (my $root = $self->get_root) |
|
2228
|
3 |
0 |
if (my $root = $tree->get_root) { } |
|
2273
|
4 |
3 |
unless (scalar @{$children;}) |
|
2308
|
0 |
0 |
if ($node->is_terminal) { } |
|
2320
|
0 |
0 |
if $node->is_root |
|
2327
|
0 |
0 |
if ($total) |
|
2329
|
0 |
0 |
if ($rho) |
|
2358
|
44 |
2 |
if (my $parent = $node->get_parent) { } |
|
2440
|
5 |
4 |
if ($path_to_root > $tallest) |
|
2479
|
16 |
1 |
if ($bl) |
|
2507
|
1 |
13 |
if (scalar @children > 2) |
|
2511
|
2 |
0 |
unless $anonymous |
|
2559
|
0 |
0 |
if (&looks_like_class('Statistics::R') and &looks_like_class('Bio::Phylo::Generator')) |
|
2565
|
0 |
0 |
if (my $seed = $args{'-seed'}) |
|
2591
|
0 |
0 |
if ($genus =~ /(..)$/) |
|
2601
|
0 |
0 |
unless $args{'-rootedge'} |
|
2606
|
0 |
0 |
if ($args{'-genera'}) |
|
2618
|
0 |
0 |
if ($rank) |
|
2619
|
0 |
0 |
if ($rank eq 'genus') |
|
2660
|
0 |
0 |
if --$size <= 1 |
|
2663
|
0 |
0 |
if ($node{$size}) { } |
|
2676
|
0 |
0 |
if $n->is_terminal |
|
2678
|
0 |
0 |
if (my $array = $node{$i}) |
|
2681
|
0 |
0 |
@filtered ? : |
|
2703
|
0 |
0 |
int rand 2 ? : |
|
2748
|
0 |
0 |
unless $genera{$genus} |
|
2755
|
0 |
0 |
if $skip{$genus} |
|
2759
|
0 |
0 |
if (scalar @$tips == 1) { } |
|
2761
|
0 |
0 |
if $args{'-monotypic'} |
|
2777
|
0 |
0 |
if ($clade_size == $tip_count) { } |
|
2786
|
0 |
0 |
if ($args{'-polypara'}) |
|
2823
|
112 |
6 |
unless ($prune{$tip->get_id}) |
|
2849
|
0 |
24 |
if (&blessed($arg)) { } |
|
2853
|
0 |
0 |
if $self->contains($node) |
|
2865
|
117 |
16 |
if (&blessed($thing)) { } |
|
2866
|
0 |
117 |
if ($thing->_type == $TAXON) { } |
|
|
117 |
0 |
elsif ($thing->_type == $NODE) { } |
|
2869
|
0 |
0 |
if $self->contains($node) |
|
2873
|
111 |
6 |
if $self->contains($thing) |
|
2879
|
16 |
0 |
if (my $tip = $self->get_by_name($thing)) |
|
2900
|
235 |
108 |
if (not exists $seen{$id}) { } |
|
2917
|
23 |
235 |
unless (exists $seen{$nid}) |
|
2918
|
22 |
1 |
if $p |
|
2921
|
22 |
1 |
if (defined $p) |
|
2923
|
12 |
10 |
if (exists $seen{$pid}) |
|
2931
|
10 |
225 |
if (scalar @children == 1 and $seen{$nid} > 0) |
|
2935
|
4 |
6 |
if defined $cbl and defined $bl |
|
2938
|
6 |
4 |
if $p |
|
2964
|
0 |
17 |
if ($bl and $bl < 0) |
|
3003
|
10 |
6 |
if ($child->is_terminal) { } |
|
3018
|
0 |
18 |
if ($right) { } |
|
3068
|
0 |
4 |
UNIVERSAL::can($taxa, 'get_entities') ? : |
|
3070
|
0 |
24 |
UNIVERSAL::can($_, 'get_name') ? : |
|
3077
|
10 |
24 |
if (@children) { } |
|
3112
|
0 |
0 |
if (not &looks_like_number($power)) { } |
|
3139
|
0 |
0 |
unless (&looks_like_number($num)) |
|
3145
|
0 |
0 |
if ($length) |
|
3167
|
0 |
0 |
if (not &looks_like_number($base)) { } |
|
3175
|
0 |
0 |
if ($@) { } |
|
3212
|
717 |
733 |
if (@children) |
|
3215
|
0 |
717 |
if ($node->is_root and 1 == @children) { } |
|
3222
|
0 |
0 |
if defined $clength |
|
3223
|
0 |
0 |
if defined $glength |
|
3224
|
0 |
0 |
if defined $length |
|
3244
|
1 |
1490 |
if (1 == scalar @grandchildren) |
|
3250
|
0 |
1 |
if defined $clength |
|
3251
|
0 |
1 |
if defined $glength |
|
3252
|
0 |
1 |
if defined $length |
|
3299
|
0 |
0 |
if not $seen{$node->get_id} |
|
3304
|
0 |
0 |
if (scalar @delete) |
|
3329
|
0 |
0 |
if (scalar @children < 3) { } |
|
3330
|
0 |
0 |
unless ($collapsible) |
|
3408
|
0 |
0 |
if (my $parent = $node->get_parent) |
|
3483
|
0 |
0 |
if (defined $length and not $length =~ /^[+-]?\d+$/) |
|
3489
|
0 |
0 |
if (my $root = $self->get_root) |
|
3533
|
0 |
0 |
unless (&looks_like_object($dom, 18)) |
|
3539
|
0 |
0 |
if (defined $length and not $length =~ /^[+-]?\d+$/) |
|
3545
|
0 |
0 |
if (my $root = $self->get_root) |