| line |
true |
false |
branch |
|
117
|
0 |
9575 |
if (exists $args{'-leaf'})
|
|
120
|
0 |
9575 |
if (exists $args{'-id'})
|
|
125
|
0 |
9575 |
if (exists $args{'-nhx'})
|
|
136
|
29 |
9546 |
unless ($LOADED_WRAPPERS)
|
|
137
|
0 |
0 |
if (@_)
|
|
|
0 |
0 |
if (@_)
|
|
|
0 |
0 |
if (defined $bs and &looks_like_number($bs))
|
|
|
0 |
0 |
if (@_)
|
|
|
0 |
0 |
if (my $desc = get_descendants())
|
|
|
0 |
0 |
if (@_)
|
|
|
0 |
0 |
if (my $children = $self->get_children)
|
|
|
0 |
0 |
if (my $desc = $self->get_descendants)
|
|
|
0 |
0 |
ref $values ? :
|
|
|
0 |
0 |
if (@_)
|
|
176
|
0 |
0 |
if defined $name
|
|
180
|
0 |
0 |
if defined $branch_length
|
|
184
|
0 |
0 |
if defined $desc
|
|
188
|
0 |
0 |
if defined $bootstrap and &looks_like_number($bootstrap)
|
|
239
|
110 |
0 |
if (my $parent = $self->get_parent) { }
|
|
242
|
110 |
0 |
if (my(@children) = @{$self->get_children;}) { }
|
|
247
|
220 |
0 |
if (defined $length)
|
|
260
|
110 |
0 |
if (my $tree = $self->get_tree)
|
|
334
|
6 |
230 |
if ($ps and &looks_like_object($ps, $TYPE_CONSTANT))
|
|
335
|
6 |
0 |
if (my $parent = $self->get_parent)
|
|
339
|
6 |
7 |
if ($children->[$i] == $self)
|
|
344
|
6 |
0 |
if $j == -1
|
|
370
|
6 |
230 |
if ($ns and &looks_like_object($ns, $TYPE_CONSTANT))
|
|
371
|
6 |
0 |
if (my $parent = $self->get_parent)
|
|
376
|
6 |
10 |
if ($children->[$i] == $self)
|
|
404
|
0 |
0 |
if ($self->is_root)
|
|
450
|
1 |
8 |
if $node->get_id == $root->get_id
|
|
451
|
1 |
7 |
if $node->get_parent and $node->get_parent->get_id == $root->get_id and not $force
|
|
466
|
0 |
7 |
if $dist < 0 or $dist > $tmp
|
|
498
|
7 |
0 |
if (scalar @children == 2) { }
|
|
514
|
0 |
0 |
if $j != $i
|
|
518
|
0 |
0 |
if @children
|
|
581
|
230 |
0 |
if (my $parent = $self->get_parent)
|
|
584
|
119 |
161 |
if ($children->[$i]->get_id == $id)
|
|
608
|
7914 |
217 |
if (my $parent = $self->get_parent)
|
|
611
|
7914 |
4383 |
if ($children->[$i]->get_id == $id)
|
|
638
|
69 |
2 |
if ($node = $node->get_parent) { }
|
|
665
|
3 |
0 |
if (my $anc = $self->get_ancestors) { }
|
|
690
|
2 |
1 |
$patristic ? :
|
|
693
|
3 |
0 |
if (my $terminals = $root->get_terminals) { }
|
|
697
|
13 |
11 |
if ($distance > $furthest_distance)
|
|
727
|
2 |
0 |
if (my $parent = $self->get_parent)
|
|
750
|
0 |
50998 |
unless defined $i
|
|
810
|
44170 |
0 |
if ($children)
|
|
834
|
0 |
585 |
if ($self->is_terminal) { }
|
|
861
|
1 |
0 |
if (@{$desc;})
|
|
863
|
6 |
8 |
if ($_->is_internal)
|
|
888
|
7 |
33 |
if ($self->get_id == $other_node->get_id)
|
|
896
|
32 |
168 |
if ($self_anc_id == $other_anc->[$j]->get_id)
|
|
923
|
6 |
4 |
if (my $grand_daughter = $daughter->get_first_daughter) { }
|
|
953
|
16 |
4 |
if (my $grand_daughter = $daughter->get_last_daughter) { }
|
|
986
|
0 |
0 |
if (my $parent = $node->get_parent)
|
|
987
|
0 |
0 |
if (my $pclone = $parent->get_generic('clone')) { }
|
|
1032
|
1008 |
896 |
if (not @child) { }
|
|
|
0 |
896 |
elsif (@child != 2) { }
|
|
1044
|
16 |
880 |
if ($found_ul and $found_vl)
|
|
1049
|
24 |
856 |
if ($found_ur and $found_vr)
|
|
1059
|
82 |
774 |
if $found_ul
|
|
1060
|
82 |
774 |
if $found_vl
|
|
1061
|
60 |
796 |
if $found_ur
|
|
1062
|
60 |
796 |
if $found_vr
|
|
1063
|
142 |
714 |
if ($found_u and not $found_v) { }
|
|
|
142 |
1032 |
elsif ($found_v and not $found_u) { }
|
|
1069
|
112 |
744 |
if $node->is_equal($u)
|
|
1070
|
112 |
744 |
if $node->is_equal($v)
|
|
1141
|
1 |
10 |
if $child->is_internal
|
|
1226
|
132813 |
9609 |
if (my $parent = $self->get_parent) { }
|
|
1232
|
3 |
132810 |
if ($self->get_id == $ancestor_id)
|
|
1257
|
3 |
9608 |
if ($child->is_descendant_of($self)) { }
|
|
1286
|
1 |
3 |
if ($self_parent and $sister_parent and $self_parent->get_id == $sister_parent->get_id) { }
|
|
1316
|
547 |
9370 |
if (my $parent = $self->get_parent)
|
|
1347
|
1 |
1 |
if $mrca->is_ancestor_of($outgroup)
|
|
1378
|
0 |
19759 |
if $type != $_->_type
|
|
1410
|
379 |
0 |
if (defined $branch_length)
|
|
1413
|
298 |
81 |
if (my $parent = $node->get_parent) { }
|
|
1444
|
1 |
1 |
if ($parent)
|
|
1445
|
1 |
0 |
if (my $cntr = $parent->calc_nodes_to_root)
|
|
1479
|
7 |
1 |
if ($nodes > $maxnodes)
|
|
1511
|
2 |
32 |
if (not $minnodes or $nodes < $minnodes)
|
|
1541
|
35 |
33 |
if (defined $branch_length)
|
|
1546
|
7 |
9 |
if ($length > $maxlength)
|
|
1576
|
35 |
33 |
if (defined $branch_length)
|
|
1581
|
9 |
7 |
unless ($minlength)
|
|
1584
|
0 |
16 |
if ($length < $minlength)
|
|
1613
|
37 |
1 |
if (defined $branch_length)
|
|
1620
|
43 |
5 |
if (defined $branch_length)
|
|
1675
|
704 |
468 |
if (shift())->is_terminal
|
|
1701
|
108 |
250 |
unless @child
|
|
1702
|
84 |
166 |
if $node->is_equal($u)
|
|
1706
|
58 |
108 |
if ($x->[0])
|
|
1710
|
0 |
58 |
if (not $child[1]) { }
|
|
1721
|
34 |
74 |
if ($y->[0]) { }
|
|
1725
|
0 |
34 |
if (not $child[0]) { }
|
|
1850
|
0 |
56 |
unless ($found_u and $found_v)
|
|
1858
|
13 |
43 |
if $root->is_equal($u)
|
|
1859
|
13 |
30 |
if $root->is_equal($v)
|
|
1972
|
0 |
141 |
if ($args{'-order'} and $args{'-order'} =~ /^rtl$/i) { }
|
|
1988
|
987 |
3479 |
if $args{'-pre'}
|
|
1989
|
2112 |
2354 |
if (my $daughter = $node->$daughter_method) { }
|
|
1991
|
0 |
2112 |
if $args{'-with_relatives'}
|
|
1992
|
0 |
2112 |
if $args{'-pre_daughter'}
|
|
1994
|
7 |
2100 |
if $args{'-post_daughter'}
|
|
1997
|
10 |
2344 |
if $args{'-no_daughter'}
|
|
1999
|
0 |
4461 |
if $args{'-in'}
|
|
2000
|
2213 |
2248 |
if (my $sister = $node->$sister_method) { }
|
|
2002
|
0 |
2213 |
if $args{'-with_relatives'}
|
|
2003
|
0 |
2213 |
if $args{'-pre_sister'}
|
|
2005
|
0 |
2209 |
if $args{'-post_sister'}
|
|
2008
|
0 |
2248 |
if $args{'-no_sister'}
|
|
2010
|
3470 |
987 |
if $args{'-post'}
|
|
2062
|
0 |
0 |
if ($args{'-order'} and $args{'-order'} =~ /rtl/i) { }
|
|
2078
|
0 |
0 |
if $args{'-pre'}
|
|
2079
|
0 |
0 |
if (my $sister = $node->$sister_method) { }
|
|
2080
|
0 |
0 |
if $args{'-pre_sister'}
|
|
2082
|
0 |
0 |
if $args{'-post_sister'}
|
|
2085
|
0 |
0 |
if $args{'-no_sister'}
|
|
2087
|
0 |
0 |
if $args{'-in'}
|
|
2088
|
0 |
0 |
if (my $daughter = $node->$daughter_method) { }
|
|
2089
|
0 |
0 |
if $args{'-pre_daughter'}
|
|
2091
|
0 |
0 |
if $args{'-post_daughter'}
|
|
2094
|
0 |
0 |
if $args{'-no_daughter'}
|
|
2096
|
0 |
0 |
if $args{'-post'}
|
|
2115
|
360 |
0 |
if (&looks_like_instance($sub, 'CODE')) { }
|
|
2120
|
5672 |
0 |
if (my $children = $node->get_children)
|
|
2157
|
0 |
0 |
if (my $taxon = $node->get_taxon)
|
|
2160
|
0 |
0 |
if ($node->is_root)
|
|
2167
|
0 |
0 |
if (my $length = shift(@nodes)->get_branch_length)
|
|
2190
|
0 |
0 |
if defined $length
|
|
2217
|
29 |
3335 |
unless $root_id
|
|
2222
|
3153 |
211 |
if ($node->is_terminal or $args{'-nodelabels'})
|
|
2223
|
35 |
3118 |
if (ref $args{'-nodelabels'} and ref $args{'-nodelabels'} eq 'CODE') { }
|
|
|
3118 |
0 |
elsif (not $args{'-tipnames'}) { }
|
|
|
0 |
0 |
elsif ($args{'-tipnames'} =~ /^internal$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-tipnames'} =~ /^taxon/i and $node->get_taxon) { }
|
|
2225
|
18 |
17 |
if ($node->is_terminal) { }
|
|
2240
|
0 |
0 |
if ($args{'-tipnames'} =~ /^taxon_internal$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-tipnames'} =~ /^taxon$/i) { }
|
|
2250
|
0 |
35 |
if ($args{'-translate'} and exists $args{'-translate'}{$name})
|
|
2259
|
3132 |
232 |
if (defined($branch_length = $node->get_branch_length))
|
|
2260
|
0 |
3132 |
if ($args{'-blformat'})
|
|
2268
|
215 |
3149 |
if ($args{'-nhxkeys'})
|
|
2270
|
0 |
215 |
if ($args{'-nhxstyle'} =~ /^mesquite$/i) { }
|
|
2284
|
625 |
235 |
if $value
|
|
2286
|
215 |
0 |
if (@nhx) { }
|
|
2296
|
1652 |
1712 |
if (my $first_daughter = $node->get_first_daughter)
|
|
2302
|
1652 |
1712 |
if $node->get_first_daughter
|
|
2303
|
3153 |
211 |
if defined $name
|
|
2304
|
3132 |
232 |
if defined $branch_length
|
|
2305
|
215 |
3149 |
if $nhx
|
|
2306
|
29 |
3335 |
if ($root_id == $node->get_id) { }
|
|
|
1683 |
1652 |
elsif (my $next_sister = $node->get_next_sister) { }
|
|
2339
|
0 |
0 |
unless (&looks_like_object($dom, 18))
|
|
2347
|
0 |
0 |
if (my $taxon = $node->get_taxon)
|
|
2350
|
0 |
0 |
if ($node->is_root)
|
|
2357
|
0 |
0 |
if (my $length = shift(@nodes)->get_branch_length)
|
|
2385
|
0 |
0 |
if defined $length
|