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>';
}
}
}
$kml .= "</Folder>\n";
$kml .= "</Document>\n";
$kml .= "</kml>\n";
echo $kml;
}
$have_tree = false;
if (isset($_POST['tree'])) {
$obj = parse_nexus($_POST['tree']);
$have_tree = true;
}
if ($have_tree) {
// Make KML
header('Content-disposition: attachment; filename=tree.kml');
header('Content-type: application/vnd.google-earth.kml+xml');
$kml = tree2kml($obj, 'translate');
} else {
echo '<html>
<head>
</head>
<body>
<p>Paste in a tree in NEXUS format.</p>
<form method="post" action="tkml.php">
<textarea id="tree" name="tree" rows="30" cols="60"></textarea>
<input type="submit" value="Go"></input>
</form>
<p>As an example copy and paste the NEXUS file below:</p>
<textarea cols="80" rows="20" readonly="readonly">
#NEXUS
