| line |
l |
!l |
condition |
|
62
|
0 |
15 |
$opts{'input'} // "newick" |
|
63
|
1 |
14 |
$opts{'output'} // "newick" |
|
65
|
15 |
0 |
shift() || 'STDIN' |
|
80
|
0 |
0 |
$opts{'cut-sis'} || die("$0 --cut-sis \n") |
|
100
|
0 |
0 |
$edgeFile || die("can't read parent-child edge file\n") |
|
314
|
0 |
0 |
$label_file || die("label file not found\n") |
|
336
|
0 |
0 |
$label_file || die("label file not found\n") |
|
382
|
0 |
0 |
$nd->branch_length || 0 |
|
448
|
0 |
0 |
$node->branch_length || 0 |
|
456
|
0 |
0 |
$trait_table_file || die("no trait file: $trait_table_file\n") |
|
715
|
0 |
0 |
$tree->find_node($opts{'swap-otus'}) || die("node not found\n") |
|
907
|
5 |
0 |
$nd->branch_length || 0 |
|
908
|
5 |
0 |
$desc[0]->branch_length || 0 |
|
925
|
15 |
0 |
$_->branch_length || 0 |
|
1116
|
0 |
0 |
$opts{'del-low-boot'} || die('spcify cutoff, e.g., 0.75 or 75\\n') |
|
1122
|
0 |
0 |
$opts{'del-short-br'} || die('spcify cutoff, e.g., 0.02\\n') |
| line |
l |
!l&&r |
!l&&!r |
condition |
|
83
|
0 |
0 |
0 |
$nd->id || $nd->internal_id |
|
281
|
0 |
0 |
0 |
$opts{'cut-tree'} || 0.5 * $least_otu_height |
|
400
|
0 |
0 |
0 |
$node eq $current_node or $node eq $parent_node |
|
401
|
0 |
0 |
0 |
$node->{'ycoord'} < $current_ycoord || $node->{'ycoord'} > $parent_ycoord |
|
402
|
0 |
0 |
0 |
$node->{'ycoord'} > $current_ycoord || $node->{'ycoord'} < $parent_ycoord |
|
630
|
0 |
0 |
0 |
$nd->is_Leaf or $nd eq $rootnode |
|
1105
|
0 |
0 |
0 |
$curnode->id || $curnode->internal_id |
|
|
0 |
0 |
0 |
$last_curnode->id || $last_curnode->internal_id |
|
1142
|
0 |
0 |
0 |
$_->is_Leaf or $_ eq $node1 |
|
1219
|
0 |
0 |
15 |
$opts->{'clean-br'} or $opts->{'clean-boot'} |
|
1273
|
17 |
0 |
0 |
$tree->find_node('-id', $node_name) || $tree->find_node('-internal_id', $node_name) |
|
1331
|
0 |
0 |
0 |
$_->id || $_->internal_id |
|
1379
|
0 |
0 |
0 |
$curnode->id || $curnode->internal_id |
|
|
0 |
0 |
0 |
$_->id || $_->internal_id |
|
1389
|
0 |
0 |
0 |
$curnode->id || $curnode->internal_id |
|
|
0 |
0 |
0 |
$_->id || $_->internal_id |