function tree2kml($obj, $default_labels = 'taxa')
{
$t = new Tree();
$t->Parse($obj->tree->newick);
$t->BuildWeights($t->GetRoot());
// compute KML coordinates
$attr = array();
$td = new KmlTreeDrawer($t, $attr);
$td->CalcCoordinates();
// raw labels (OTUs)
// $port->StartGroup('otu', (('otu' == $default_labels) || !isset($obj->translations)) );
$kml = '';
$kml .= "<?xml version =\"1.0\" encoding=\"UTF-8\"?>\n";
$kml .= "<kml xmlns=\"http://earth.google.com/kml/2.1\">\n";
$kml .= "<Document>\n";
$kml .= "<Style id=\"treeLine\">\n";
$kml .= "<LineStyle><color>7fffffff</color><width>2</width></LineStyle>\n";
$kml .= "</Style>\n";
$kml .= "<Style id=\"whiteBall\">\n";
$kml .= "<IconStyle>\n";
$kml .= "<Icon>\n";
$kml .= "<href>http://iphylo.org/~rpage/phyloinformatics/images/whiteBall.png</href>\n";
$kml .= "</Icon>\n";
$kml .= "</IconStyle>\n";
$kml .= "<LineStyle>\n";
$kml .= "<width>2</width>\n";
$kml .= "</LineStyle>\n";
$kml .= "</Style>\n";
$td->Draw(null);
$kml .= $td->kml;
$kml .= "<Folder>\n";
$kml .= "<name>Labels</name>\n";
// labels
$ni = new NodeIterator($t->getRoot());
$q = $ni->Begin();
while ($q != NULL) {
if ($q->IsLeaf()) {
$kml .= "<Placemark>\n";
$kml .= "<name>" . $q->Getlabel() . "</name>\n";
$kml .= "<styleUrl>#whiteBall</styleUrl>\n";
$kml .= "<Point>\n";
$kml .= "<altitudeMode>absolute</altitudeMode>\n";
$kml .= "<extrude>1</extrude>\n";
$kml .= "<coordinates>\n";
$kml .= $q->GetAttribute('long') . "," . $q->GetAttribute('lat') . "," . $q->GetAttribute('altitude') . "\n";
$kml .= "</coordinates>\n";
$kml .= "</Point>\n";
$kml .= "</Placemark>\n";
}
$q = $ni->Next();
}
$kml .= "</Folder>\n";
$kml .= "</Document>\n";
$kml .= "</kml>\n";
echo $kml;
}
function main()
{
global $matching_path;
$have_tree = false;
$have_taxa = false;
$have_table = false;
$newick = '';
if (isset($_POST['tree'])) {
$obj = parse_nexus(stripcslashes($_POST['tree']));
$taxa = get_taxa_from_tree($obj);
$newick = $obj->tree->newick;
//echo $newick;
//print_r($obj);
$t = new Tree();
$t->Parse($newick);
$ni = new NodeIterator($t->getRoot());
$q = $ni->Begin();
while ($q != NULL) {
if ($q->IsLeaf()) {
if (isset($obj->translations->translate)) {
$q->SetLabel($obj->translations->translate[$q->GetLabel()]);
}
}
$q = $ni->Next();
}
$newick = $t->WriteNewick();
//echo $newick;
$have_tree = true;
}
if (isset($_POST['taxa'])) {
$have_taxa = true;
}
if (isset($_POST['table'])) {
$table = $_POST['table'];
$have_table = true;
}
if (isset($_POST['newick'])) {
$newick = $_POST['newick'];
}
if ($have_tree || $have_taxa) {
if ($have_table) {
// get taxa
$taxa = explode("\n", stripcslashes($_POST['taxa']));
$n = count($taxa);
for ($i = 0; $i < $n; $i++) {
$taxa[$i] = trim($taxa[$i]);
}
// get table data
$table = stripcslashes($_POST['table']);
// Interpret table automatically...
// assume column one contains OTUs, and some other column(s) have lat and long
$data = extract_table($table);
//print_r($data);
if (count($taxa) != count($data)) {
echo '<html>
<head>
<meta charset="utf-8" />
<style type="text/css" title="text/css">
body { font-family:sans-serif;padding:20px; }
</style>
<title>Create KML tree - Error</title>
</head>
<body>
<a href=".">Back</a>
<h1>Error</h1>
<p>The number of taxa in the tree (' . count($taxa) . ') does not match the number in the table (' . count($data) . ')</p>
</body>
</html>';
exit;
}
$data_lookup_by_label = array();
foreach ($data as $d) {
$data_lookup_by_label[$d->label] = $d;
}
// show matching...
/*
echo ' <form method="post" action=".">
<table border="1">';
echo '<tr><th>Taxa in tree</th><th>Taxa in table</th><th>Latitude</th><th>Longitude</th></tr>';
$nrows = count($data);
for ($i=0;$i < $nrows; $i++)
{
echo '<tr>';
echo '<td>' . $taxa[$i] . '</td>';
echo '<td>' . $data[$i]->label . '</td>';
echo '<td>' . $data[$i]->latlong['latitude'] . '</td>';
echo '<td>' . $data[$i]->latlong['longitude'] . '</td>';
echo '</td></tr>';
}
echo '</table>
<input type="submit" value="Go"></input>
</form>';
*/
// build graph for matching
// Create GML file for graph linking taxon labels in tree and table
// Taxon labels in table
$b = array();
foreach ($data as $row) {
$b[] = $row->label;
}
$filename = 'tmp/' . uniqid() . '.gml';
$gml = create_graph($taxa, $b);
file_put_contents($filename, $gml);
//echo $gml;
// Compute maximum weight bipartite matching
$command = $matching_path . 'matching ' . $filename;
$output = array();
exec($command, $output);
//echo $command;
$json = join("", $output);
//echo $json;
$match = json_decode($json);
if (0) {
echo '<pre>';
$n = count($taxa);
foreach ($match->matching as $pair) {
echo $taxa[$pair[0]] . "|\t" . $b[$pair[1] - $n] . "\n";
}
echo '</pre>';
}
// Mapping between tree labels and table labels
$match_by_label = array();
$n = count($taxa);
foreach ($match->matching as $pair) {
$match_by_label[$taxa[$pair[0]]] = $b[$pair[1] - $n];
}
// match and build KML file
$t = new Tree();
$t->Parse($newick);
$t->BuildWeights($t->GetRoot());
//echo $newick;
$ni = new NodeIterator($t->getRoot());
$q = $ni->Begin();
while ($q != NULL) {
if ($q->IsLeaf()) {
$data = $data_lookup_by_label[$match_by_label[$q->GetLabel()]];
$q->SetAttribute('lat', $data->latlong['latitude']);
$q->SetAttribute('long', $data->latlong['longitude']);
}
$q = $ni->Next();
}
// KML...
//echo '<pre>';
//$t->Dump();
//echo '</pre>';
$kml = tree2kml($t);
echo '<html>
<head>
<meta charset="utf-8" />
<style type="text/css" title="text/css">
body { font-family:sans-serif;padding:20px; }
</style>
<title>Create KML tree - Step 3</title>
<script type="text/javascript" src="https://www.google.com/jsapi"> </script>
<script type="text/javascript">
var ge;
google.load("earth", "1");
function init() {
google.earth.createInstance(\'map3d\', initCB, failureCB);
}
function initCB(instance) {
ge = instance;
ge.getWindow().setVisibility(true);
var treeDoc = ge.parseKml(';
$kml_lines = explode("\n", $kml);
$k = join(" ", $kml_lines);
echo "'" . $k . "'";
echo ');
ge.getFeatures().appendChild(treeDoc);
}
function failureCB(errorCode) {
}
google.setOnLoadCallback(init);
</script>
</head>
<body>
<a href=".">Home</a>
<h1>Step 3: Match tree to table and create KML</h1>';
// Display mapping
echo '<h2>Tree and table matching</h2>';
echo '<table border="1">';
echo '<tr><th>Taxa in tree</th><th>Taxa in table</th><th>Latitude</th><th>Longitude</th></tr>';
$n = count($taxa);
foreach ($match->matching as $pair) {
echo '<tr>';
echo '<td>';
echo $taxa[$pair[0]];
echo '</td>';
$data = $data_lookup_by_label[$match_by_label[$taxa[$pair[0]]]];
echo '<td>' . $data->label . '</td>';
echo '<td>' . $data->latlong['latitude'] . '</td>';
echo '<td>' . $data->latlong['longitude'] . '</td>';
echo '</tr>';
}
echo '</table>';
echo '<h2>KML</h2>';
echo '<textarea rows="30" cols="100">';
echo $kml;
echo '</textarea>';
echo '<h2>Google Earth plugin</h2>';
echo ' <div id="map3d" style="height: 400px; width: 600px;"></div>';
echo '</body>
</html>';
} else {
// We have the tree but no data yet
echo '<html>
<head>
<meta charset="utf-8" />
<style type="text/css" title="text/css">
body { font-family:sans-serif;padding:20px; }
</style>
<title>Create KML tree - Step 2</title>
</head>
<body>
<a href=".">Home</a>
<h1>Step 2: Add table</h1>
<form method="post" action=".">
<input name="newick" type="hidden" value="' . $newick . '">
<table>
<tr><th>Taxa in tree</th><th>Paste in table with taxa (in first column), and latitude and longitude.<br/>The first row of the table must contain column headings.</th></tr>
<tr>
<td>
<textarea id="taxa" name="taxa" rows="30" cols="60" readonly="readonly">' . join("\n", $taxa) . '</textarea>
</td>
<td>
<textarea id="table" name="table" rows="30" cols="60"></textarea>
</td>
</tr>
</table>
<input type="submit" value="Next step"></input>
</form>
</body>
</html>';
}
} else {
// Starting point, get tree
echo '<html>
<head>
<meta charset="utf-8" />
<style type="text/css" title="text/css">
body { font-family:sans-serif;padding:20px; }
</style>
<title>Create KML tree - Step 1</title>
</head>
<body>
<h1>Step 1: Paste in a tree in NEXUS format</h1>
<form method="post" action=".">
<textarea id="tree" name="tree" rows="30" cols="60"></textarea>
<br />
<input type="submit" value="Next step"></input>
</form>
</body>
</html>';
}
}
/**
* @begin Draw tree and labels in SVG
*
* @param width Width (pixels) to draw tree + labels in
* @param height
* @param label_space Width (pixels) of space to draw leaf labels in
* @param font_height Height of font to use to draw labels
* @param default_labels Name of group of labels to show by default
*
*/
function tree2svg($obj, $width = 400, $height = 400, $label_space = 150, $font_height = 10, $force_height = false, $default_labels = 'taxa')
{
//----------------------------------------------------------------------------------------------
$t = new Tree();
$t->Parse($obj->tree->newick);
$t->BuildWeights($t->GetRoot());
$tree_width = $width - $label_space;
if (!$force_height) {
// adjust height to accomodate tree
$height = $t->GetNumLeaves() * ($font_height + $font_height / 3);
$inset = $font_height;
} else {
$inset = 0;
}
// Drawing properties
$attr = array();
$attr['inset'] = $inset;
$attr['width'] = $tree_width;
$attr['height'] = $height;
$attr['font_height'] = $font_height;
$attr['line_width'] = 1;
// Don't draw labels (we do this afterwards)
$attr['draw_leaf_labels'] = false;
$attr['draw_internal_labels'] = false;
$td = NULL;
if ($t->HasBranchLengths()) {
$td = new PhylogramTreeDrawer($t, $attr);
} else {
$td = new RectangleTreeDrawer($t, $attr);
}
$td->CalcCoordinates();
if (!$force_height) {
$port = new SVGPort('', $width, $td->max_height + $attr['font_height']);
} else {
$port = new SVGPort('', $width, $height + 2);
}
$port->StartGroup('tree');
$td->Draw($port);
$port->EndGroup();
// labels
if ($label_space > 0) {
$ni = new NodeIterator($t->getRoot());
// raw labels (OTUs)
$port->StartGroup('otu', 'otu' == $default_labels || !isset($obj->translations));
$q = $ni->Begin();
while ($q != NULL) {
if ($q->IsLeaf()) {
$p0 = $q->GetAttribute('xy');
$p0['x'] += $font_height / 3;
$text = $q->Getlabel();
$text = str_replace("_", " ", $text);
$action = 'onclick="node_info(\'' . htmlentities($text) . '\');"';
$port->DrawText($p0, $text, $action);
}
$q = $ni->Next();
}
$port->EndGroup();
if ($obj->translations) {
// Tree has a one or more translation tables
foreach ($obj->translations as $k => $v) {
// Draw labels as a separate group
$port->StartGroup($k, $k == $default_labels ? true : false);
$q = $ni->Begin();
while ($q != NULL) {
if ($q->IsLeaf()) {
$p0 = $q->GetAttribute('xy');
$p0['x'] += $font_height / 3;
$label = $q->Getlabel();
if (is_array($v)) {
if (isset($v[$label])) {
$label = $v[$label];
} else {
// No translation for this OTU
$label = '[' . $label . ']';
}
} else {
if (isset($v->{$label})) {
$label = $v->{$label};
} else {
// No translation for this OTU
$label = '[' . $label . ']';
}
}
$action = 'onclick="node_info(\'' . $q->Getlabel() . '\');"';
$port->DrawText($p0, $label, $action);
}
$q = $ni->Next();
}
$port->EndGroup();
}
}
}
$svg = $port->GetOutput();
return $svg;
}
function ToSQL()
{
$n = new NodeIterator($this->root);
$a = $n->Begin();
while ($a != NULL) {
$sql = 'INSERT INTO t (name, id, parent_id, weight, path, is_leaf) VALUES(';
$sql .= '"' . $a->GetLabel() . '",' . $a->GetId() . ',';
if ($a->GetAncestor()) {
$sql .= $a->GetAncestor()->GetId();
} else {
$sql .= '0';
}
$sql .= ',' . $a->GetAttribute('weight');
$sql .= ',"' . $a->GetAttribute('path') . '"';
$sql .= ',';
if ($a->IsLeaf()) {
$sql .= '1';
} else {
$sql .= '0';
}
$sql .= ');';
echo $sql . "\n";
$a = $n->Next();
}
}
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();
}
}
