| line |
true |
false |
branch |
|
116
|
0 |
10786 |
if (exists $args{'-leaf'})
|
|
119
|
0 |
10786 |
if (exists $args{'-id'})
|
|
124
|
0 |
10786 |
if (exists $args{'-nhx'})
|
|
135
|
29 |
10757 |
unless ($LOADED_WRAPPERS)
|
|
136
|
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 (@_)
|
|
175
|
0 |
0 |
if defined $name
|
|
179
|
0 |
0 |
if defined $branch_length
|
|
183
|
0 |
0 |
if defined $desc
|
|
187
|
0 |
0 |
if defined $bootstrap and &looks_like_number($bootstrap)
|
|
238
|
116 |
0 |
if (my $parent = $self->get_parent) { }
|
|
241
|
116 |
0 |
if (my(@children) = @{$self->get_children;}) { }
|
|
246
|
232 |
0 |
if (defined $length)
|
|
259
|
116 |
0 |
if (my $tree = $self->get_tree)
|
|
333
|
6 |
230 |
if ($ps and &looks_like_object($ps, $TYPE_CONSTANT))
|
|
334
|
6 |
0 |
if (my $parent = $self->get_parent)
|
|
338
|
6 |
7 |
if ($children->[$i] == $self)
|
|
343
|
6 |
0 |
if $j == -1
|
|
369
|
6 |
230 |
if ($ns and &looks_like_object($ns, $TYPE_CONSTANT))
|
|
370
|
6 |
0 |
if (my $parent = $self->get_parent)
|
|
375
|
6 |
10 |
if ($children->[$i] == $self)
|
|
403
|
0 |
0 |
if ($self->is_root)
|
|
449
|
1 |
8 |
if $node->get_id == $root->get_id
|
|
450
|
1 |
7 |
if $node->get_parent and $node->get_parent->get_id == $root->get_id and not $force
|
|
465
|
0 |
7 |
if $dist < 0 or $dist > $tmp
|
|
497
|
7 |
0 |
if (scalar @children == 2) { }
|
|
513
|
0 |
0 |
if $j != $i
|
|
517
|
0 |
0 |
if @children
|
|
580
|
230 |
0 |
if (my $parent = $self->get_parent)
|
|
583
|
119 |
161 |
if ($children->[$i]->get_id == $id)
|
|
607
|
7119 |
215 |
if (my $parent = $self->get_parent)
|
|
610
|
7119 |
3954 |
if ($children->[$i]->get_id == $id)
|
|
637
|
69 |
2 |
if ($node = $node->get_parent) { }
|
|
664
|
3 |
0 |
if (my $anc = $self->get_ancestors) { }
|
|
689
|
2 |
1 |
$patristic ? :
|
|
692
|
3 |
0 |
if (my $terminals = $root->get_terminals) { }
|
|
696
|
13 |
11 |
if ($distance > $furthest_distance)
|
|
726
|
2 |
0 |
if (my $parent = $self->get_parent)
|
|
749
|
0 |
45223 |
unless defined $i
|
|
809
|
34314 |
0 |
if ($children)
|
|
833
|
0 |
530 |
if ($self->is_terminal) { }
|
|
860
|
1 |
0 |
if (@{$desc;})
|
|
862
|
6 |
8 |
if ($_->is_internal)
|
|
887
|
7 |
33 |
if ($self->get_id == $other_node->get_id)
|
|
895
|
32 |
168 |
if ($self_anc_id == $other_anc->[$j]->get_id)
|
|
922
|
6 |
4 |
if (my $grand_daughter = $daughter->get_first_daughter) { }
|
|
952
|
16 |
4 |
if (my $grand_daughter = $daughter->get_last_daughter) { }
|
|
985
|
0 |
0 |
if (my $parent = $node->get_parent)
|
|
986
|
0 |
0 |
if (my $pclone = $parent->get_generic('clone')) { }
|
|
1031
|
1008 |
896 |
if (not @child) { }
|
|
|
0 |
896 |
elsif (@child != 2) { }
|
|
1043
|
16 |
880 |
if ($found_ul and $found_vl)
|
|
1048
|
24 |
856 |
if ($found_ur and $found_vr)
|
|
1058
|
82 |
774 |
if $found_ul
|
|
1059
|
82 |
774 |
if $found_vl
|
|
1060
|
60 |
796 |
if $found_ur
|
|
1061
|
60 |
796 |
if $found_vr
|
|
1062
|
142 |
714 |
if ($found_u and not $found_v) { }
|
|
|
142 |
1032 |
elsif ($found_v and not $found_u) { }
|
|
1068
|
112 |
744 |
if $node->is_equal($u)
|
|
1069
|
112 |
744 |
if $node->is_equal($v)
|
|
1140
|
1 |
10 |
if $child->is_internal
|
|
1225
|
116146 |
10801 |
if (my $parent = $self->get_parent) { }
|
|
1231
|
3 |
116143 |
if ($self->get_id == $ancestor_id)
|
|
1256
|
3 |
10800 |
if ($child->is_descendant_of($self)) { }
|
|
1285
|
1 |
3 |
if ($self_parent and $sister_parent and $self_parent->get_id == $sister_parent->get_id) { }
|
|
1315
|
557 |
10552 |
if (my $parent = $self->get_parent)
|
|
1346
|
1 |
1 |
if $mrca->is_ancestor_of($outgroup)
|
|
1377
|
0 |
22155 |
if $type != $_->_type
|
|
1409
|
379 |
0 |
if (defined $branch_length)
|
|
1412
|
298 |
81 |
if (my $parent = $node->get_parent) { }
|
|
1443
|
1 |
1 |
if ($parent)
|
|
1444
|
1 |
0 |
if (my $cntr = $parent->calc_nodes_to_root)
|
|
1478
|
7 |
1 |
if ($nodes > $maxnodes)
|
|
1510
|
2 |
32 |
if (not $minnodes or $nodes < $minnodes)
|
|
1540
|
35 |
33 |
if (defined $branch_length)
|
|
1545
|
7 |
9 |
if ($length > $maxlength)
|
|
1575
|
35 |
33 |
if (defined $branch_length)
|
|
1580
|
9 |
7 |
unless ($minlength)
|
|
1583
|
0 |
16 |
if ($length < $minlength)
|
|
1612
|
37 |
1 |
if (defined $branch_length)
|
|
1619
|
43 |
5 |
if (defined $branch_length)
|
|
1674
|
704 |
468 |
if (shift())->is_terminal
|
|
1700
|
108 |
250 |
unless @child
|
|
1701
|
84 |
166 |
if $node->is_equal($u)
|
|
1705
|
58 |
108 |
if ($x->[0])
|
|
1709
|
0 |
58 |
if (not $child[1]) { }
|
|
1720
|
34 |
74 |
if ($y->[0]) { }
|
|
1724
|
0 |
34 |
if (not $child[0]) { }
|
|
1849
|
0 |
56 |
unless ($found_u and $found_v)
|
|
1857
|
13 |
43 |
if $root->is_equal($u)
|
|
1858
|
13 |
30 |
if $root->is_equal($v)
|
|
1971
|
0 |
143 |
if ($args{'-order'} and $args{'-order'} =~ /^rtl$/i) { }
|
|
1987
|
1025 |
3204 |
if $args{'-pre'}
|
|
1988
|
2001 |
2228 |
if (my $daughter = $node->$daughter_method) { }
|
|
1990
|
0 |
2001 |
if $args{'-with_relatives'}
|
|
1991
|
0 |
2001 |
if $args{'-pre_daughter'}
|
|
1993
|
7 |
1989 |
if $args{'-post_daughter'}
|
|
1996
|
10 |
2218 |
if $args{'-no_daughter'}
|
|
1998
|
0 |
4224 |
if $args{'-in'}
|
|
1999
|
2085 |
2139 |
if (my $sister = $node->$sister_method) { }
|
|
2001
|
0 |
2085 |
if $args{'-with_relatives'}
|
|
2002
|
0 |
2085 |
if $args{'-pre_sister'}
|
|
2004
|
0 |
2081 |
if $args{'-post_sister'}
|
|
2007
|
0 |
2139 |
if $args{'-no_sister'}
|
|
2009
|
3195 |
1025 |
if $args{'-post'}
|
|
2061
|
0 |
0 |
if ($args{'-order'} and $args{'-order'} =~ /rtl/i) { }
|
|
2077
|
0 |
0 |
if $args{'-pre'}
|
|
2078
|
0 |
0 |
if (my $sister = $node->$sister_method) { }
|
|
2079
|
0 |
0 |
if $args{'-pre_sister'}
|
|
2081
|
0 |
0 |
if $args{'-post_sister'}
|
|
2084
|
0 |
0 |
if $args{'-no_sister'}
|
|
2086
|
0 |
0 |
if $args{'-in'}
|
|
2087
|
0 |
0 |
if (my $daughter = $node->$daughter_method) { }
|
|
2088
|
0 |
0 |
if $args{'-pre_daughter'}
|
|
2090
|
0 |
0 |
if $args{'-post_daughter'}
|
|
2093
|
0 |
0 |
if $args{'-no_daughter'}
|
|
2095
|
0 |
0 |
if $args{'-post'}
|
|
2114
|
360 |
0 |
if (&looks_like_instance($sub, 'CODE')) { }
|
|
2119
|
5430 |
0 |
if (my $children = $node->get_children)
|
|
2156
|
0 |
0 |
if (my $taxon = $node->get_taxon)
|
|
2159
|
0 |
0 |
if ($node->is_root)
|
|
2166
|
0 |
0 |
if (my $length = shift(@nodes)->get_branch_length)
|
|
2189
|
0 |
0 |
if defined $length
|
|
2216
|
29 |
2775 |
unless $root_id
|
|
2221
|
2593 |
211 |
if ($node->is_terminal or $args{'-nodelabels'})
|
|
2222
|
35 |
2558 |
if (ref $args{'-nodelabels'} and ref $args{'-nodelabels'} eq 'CODE') { }
|
|
|
2558 |
0 |
elsif (not $args{'-tipnames'}) { }
|
|
|
0 |
0 |
elsif ($args{'-tipnames'} =~ /^internal$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-tipnames'} =~ /^taxon/i and $node->get_taxon) { }
|
|
2224
|
18 |
17 |
if ($node->is_terminal) { }
|
|
2239
|
0 |
0 |
if ($args{'-tipnames'} =~ /^taxon_internal$/i) { }
|
|
|
0 |
0 |
elsif ($args{'-tipnames'} =~ /^taxon$/i) { }
|
|
2249
|
0 |
35 |
if ($args{'-translate'} and exists $args{'-translate'}{$name})
|
|
2258
|
2572 |
232 |
if (defined($branch_length = $node->get_branch_length))
|
|
2259
|
0 |
2572 |
if ($args{'-blformat'})
|
|
2267
|
215 |
2589 |
if ($args{'-nhxkeys'})
|
|
2269
|
0 |
215 |
if ($args{'-nhxstyle'} =~ /^mesquite$/i) { }
|
|
2283
|
625 |
235 |
if $value
|
|
2285
|
215 |
0 |
if (@nhx) { }
|
|
2295
|
1372 |
1432 |
if (my $first_daughter = $node->get_first_daughter)
|
|
2301
|
1372 |
1432 |
if $node->get_first_daughter
|
|
2302
|
2593 |
211 |
if defined $name
|
|
2303
|
2572 |
232 |
if defined $branch_length
|
|
2304
|
215 |
2589 |
if $nhx
|
|
2305
|
29 |
2775 |
if ($root_id == $node->get_id) { }
|
|
|
1403 |
1372 |
elsif (my $next_sister = $node->get_next_sister) { }
|
|
2338
|
0 |
0 |
unless (&looks_like_object($dom, 18))
|
|
2346
|
0 |
0 |
if (my $taxon = $node->get_taxon)
|
|
2349
|
0 |
0 |
if ($node->is_root)
|
|
2356
|
0 |
0 |
if (my $length = shift(@nodes)->get_branch_length)
|
|
2384
|
0 |
0 |
if defined $length
|