function ncbi_lca($tax_id_1, $tax_id_2)
{
global $db;
// If tax_id is the same, then return as lca
if ($tax_id_1 == $tax_id_2) {
return $tax_id_1;
}
$path_1 = ncbi_ancestors($tax_id_1);
$path_2 = ncbi_ancestors($tax_id_2);
$path_1 = array_reverse($path_1);
$path_2 = array_reverse($path_2);
// ensure tax_ids are part of this path (handle case where one node is lca of itself and other node)
$path_1[] = $tax_id_1;
$path_2[] = $tax_id_2;
$i = 0;
$m = count($path_1);
$n = count($path_2);
$x = min($m, $n);
//print_r($path_1);
//print_r($path_2);
while ($path_1[$i] == $path_2[$i] && $i < $x) {
$i++;
}
$lca = $path_1[$i - 1];
return $lca;
}
function get_span(&$tree)
{
if (!isset($tree->translations->tax_id)) {
return;
}
$tree->classification->span = array();
foreach ($tree->translations->tax_id as $k => $v) {
$tree->classification->span[] = (int) $v;
}
// What is tree about?
// Get majority rule taxon
$c = array();
$stack = array();
foreach ($tree->classification->span as $tax_id) {
$ancestors = ncbi_ancestors($tax_id);
if (count($ancestors) != 0) {
$ancestors = array_reverse($ancestors);
foreach ($ancestors as $anc) {
if (!isset($c[$anc])) {
$c[$anc] = 0;
}
$c[$anc]++;
// Store nodes in stack. This is really a partial order (i.e., a tree), but because we
// visit nodes from root to tip, we preserve the order that matters
if (!in_array($anc, $stack)) {
$stack[] = $anc;
}
}
}
}
// Compute threshold for majority of taxa
$num_taxa = $c[$stack[0]];
$threshold = round($num_taxa / 2);
if ($num_taxa % 2 == 0) {
$threshold++;
}
// Go down the stack until we hit a node that is more frequent than the majority rule theshold,
// this is what the study is "about"
$majority = array_pop($stack);
while ($c[$majority] < $threshold) {
$majority = array_pop($stack);
}
//
$tree->classification->majority_taxon = get_ncbi_taxon($majority);
// Path from majority to root
$tree->classification->majority_path = array_reverse(ncbi_ancestors($majority));
// LCA of all taxa in tree
$lca = $majority;
while ($c[$lca] < $num_taxa) {
$lca = array_pop($stack);
}
// Now make span comprise just unique taxa. We don't do this above because we want to take
// the relavtive frequencies of each tax_id into account when computing majority_taxon
$tree->classification->span = array_values(array_unique($tree->classification->span));
$tree->classification->lca = $lca;
}
$paths = array();
$tree_objs = array();
$result = $db->Execute($sql);
if ($result == false) {
die("failed [" . __LINE__ . "]: " . $sql);
}
while (!$result->EOF) {
$tree = new stdclass();
$tree->id = $result->fields['id'];
$tree->left = $result->fields['left'];
$tree->right = $result->fields['right'];
$tree->majority_taxon_tax_id = $result->fields['majority_taxon_tax_id'];
$tree->publication = json_decode($result->fields['publication']);
$tree_objs[$result->fields['id']] = $tree;
// Store path for this tree
$paths[$result->fields['id']] = array_reverse(ncbi_ancestors($result->fields['majority_taxon_tax_id'], $tax_id));
$paths[$result->fields['id']][] = $result->fields['majority_taxon_tax_id'];
$result->MoveNext();
}
// compute layout...
// Construct a tree of the majority taxa and use it to arrange trees in "layers"
$t = new Tree();
$node_list = array();
// list of nodes in path tree
$tree_list = array();
// list of trees assigned to each node
$first = true;
foreach ($paths as $k => $path) {
//print_r($path);
$n = count($path);
if ($first) {
