while (!isset($tree_list[$r->GetLabel()])) {
$r = $r->GetAncestor();
}
$depth += count($tree_list[$r->GetLabel()]);
}
$q->SetAttribute('depth', $depth);
if (!isset($layers[$depth])) {
$layers[$depth] = array();
}
$layers[$depth][] = $q->GetLabel();
} else {
$depth = $anc->GetAttribute('depth');
$q->SetAttribute('depth', $depth);
}
}
$q = $p->Next();
}
/*
echo '<pre>';
$t->Dump();
echo $t->WriteDot();
print_r($tree_list);
print_r($layers);
echo '</pre>';
*/
// Traverse in preorder...
// display trees
foreach ($layers as $layer_number => $taxids_in_this_layer) {
function CalcCoordinates()
{
$this->max_path_length = 0.0;
$this->t->GetRoot()->SetAttribute('path_length', $this->t->GetRoot()->GetAttribute('edge_length'));
// Get path lengths
$n = new PreorderIterator($this->t->getRoot());
$q = $n->Begin();
while ($q != NULL) {
$d = $q->GetAttribute('edge_length');
if ($d < 1.0E-5) {
$d = 0.0;
}
if ($q != $this->t->GetRoot()) {
$q->SetAttribute('path_length', $q->GetAncestor()->GetAttribute('path_length') + $d);
}
$this->max_path_length = max($this->max_path_length, $q->GetAttribute('path_length'));
$q = $n->Next();
}
$leaves = $this->t->GetNumLeaves();
$this->leaf_count = 0;
$n = new NodeIterator($this->t->getRoot());
$q = $n->Begin();
while ($q != NULL) {
if ($q->IsLeaf()) {
$this->CalcLeaf($q);
} else {
$this->CalcInternal($q);
}
$q = $n->Next();
}
}
