| line |
true |
false |
branch |
|
63
|
1 |
0 |
if ($ntrees)
|
|
66
|
2 |
1 |
if $tree->is_clade($arg)
|
|
96
|
150 |
1 |
if ($self->can_contain(@_)) { }
|
|
99
|
0 |
150 |
if ($tree->is_default)
|
|
100
|
0 |
0 |
if (not $seen_default) { }
|
|
108
|
0 |
150 |
if ($seen_default)
|
|
109
|
0 |
0 |
if (my $tree = $self->get_default_tree)
|
|
139
|
0 |
0 |
if $tree->is_default
|
|
162
|
8 |
0 |
if (my $taxa = $self->get_taxa) { }
|
|
167
|
0 |
120 |
if $tip->get_taxon and $taxa->contains($tip->get_taxon)
|
|
169
|
78 |
42 |
unless ($tips{$name})
|
|
183
|
0 |
78 |
unless (exists $taxa{$name})
|
|
238
|
0 |
14 |
if defined $val
|
|
258
|
3 |
3 |
unless (exists $clade_lengths{$clade})
|
|
265
|
3 |
6 |
unless (exists $clade_lengths{$clade})
|
|
281
|
1 |
2 |
if ($seen_partitions{$partition} / $tree_count <= $perc)
|
|
291
|
0 |
1 |
if (@sorted == 0)
|
|
304
|
3 |
2 |
unless (exists $seen_nodes{$tip})
|
|
306
|
3 |
0 |
if ($branches =~ /^f/i) { }
|
|
323
|
2 |
0 |
if ($branches =~ /^f/i) { }
|
|
331
|
0 |
0 |
if ($args{'-summarize'} =~ /^f/i) { }
|
|
343
|
1 |
1 |
if ($old_parent)
|
|
393
|
0 |
0 |
unless exists $tip_values{$tipname}
|
|
396
|
0 |
0 |
if (exists $tip_values{$datumname}) { }
|
|
407
|
0 |
0 |
if (my $root = $tree->get_root)
|
|
412
|
0 |
0 |
if (my $data = $data{$datum->get_name})
|
|
413
|
0 |
0 |
if @{$data;}
|
|
436
|
0 |
4 |
if (my $taxa = $self->get_taxa) { }
|
|
445
|
65 |
16 |
unless ($taxa{$name})
|
|
451
|
4 |
0 |
if (%taxa)
|
|
527
|
1 |
0 |
if ($args{'-make_translate'})
|
|
532
|
18 |
0 |
if (not $args{'-tipnames'}) { }
|
|
|
0 |
0 |
elsif ($args{'-tipnames'} =~ /^internal$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-tipnames'} =~ /^taxon/i and $node->get_taxon) { }
|
|
541
|
0 |
0 |
if ($args{'-tipnames'} =~ /^taxon_internal$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-tipnames'} =~ /^taxon$/i) { }
|
|
552
|
18 |
0 |
unless exists $translate{$name}
|
|
565
|
1 |
0 |
if ($args{'-figtree'})
|
|
569
|
0 |
1 |
if ($args{'-links'})
|
|
572
|
0 |
0 |
if (my $taxa = $self->get_taxa)
|
|
578
|
1 |
0 |
if ($args{'-make_translate'})
|
|
585
|
1 |
17 |
if ($i == $#translate) { }
|
|
596
|
1 |
0 |
if ($tree->is_rooted) { }
|
|
597
|
0 |
1 |
if ($args{'-rooting'} =~ /^token$/i) { }
|
|
|
1 |
0 |
elsif ($args{'-rooting'} =~ /^comment$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-rooting'} =~ /^nhx/i) { }
|
|
612
|
0 |
0 |
if ($args{'-nhxkeys'}) { }
|
|
625
|
0 |
0 |
if ($args{'-rooting'} =~ /^token$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-rooting'} =~ /^comment$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-rooting'} =~ /^nhx/i) { }
|
|
640
|
0 |
0 |
if ($args{'-nhxkeys'}) { }
|