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>';
}
}
<?php
require_once dirname(dirname(__FILE__)) . '/lib.php';
require_once dirname(__FILE__) . '/nexus.php';
require_once dirname(__FILE__) . '/tree2svg.php';
$have_tree = false;
if (isset($_POST['tree'])) {
$tree = $_POST['tree'];
$tree = stripcslashes($tree);
$obj = parse_nexus($tree);
$have_tree = true;
}
if (isset($_GET['url'])) {
$nexus = get($_GET['url']);
if ($nexus != '') {
$obj = parse_nexus($nexus);
$have_tree = true;
}
}
if ($have_tree) {
// Make SVG
echo '<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8" />
<title>Untitled</title>';
echo '<script>
function node_info(otu)
{
var info = document.getElementById("info");
info.innerHTML = otu;
$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;
}
$have_tree = false;
if (isset($_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>
6 \'AF261253 Mantidactylus horridus 16S ribosomal RNA gene, partial sequence; mitochondrial gene for mitochondrial product\',
7 \'GU975157 Gephyromantis ventrimaculatus voucher ZCMV 4591 16S ribosomal RNA gene, partial sequence; mitochondrial\',
8 \'FJ559200 Gephyromantis ventrimaculatus voucher ZCMV 3362 16S ribosomal RNA gene, partial sequence; mitochondrial\',
9 \'AY848373 Gephyromantis striatus voucher FA_m53 16S ribosomal RNA gene, partial sequence; mitochondrial\',
10 \'AJ314807 Mantidactylus malagasius mitochondrial partial 16S rRNA gene\',
11 \'HM364637 Gephyromantis aff. malagasius \'\'Betampona\'\' voucher MSNT<ITA-Torino\',
12 \'GU975158 Gephyromantis ventrimaculatus voucher ZCMV 4927 16S ribosomal RNA gene, partial sequence; mitochondrial\',
13 \'FJ559189 Gephyromantis cf. \'\'malagasius\'\' MV-2009 voucher FAZC-Andranobe 16S ribosomal RNA gene, partial sequence; mitochondrial\',
14 \'AJ314797 Mantidactylus malagasius mitochondrial partial 16S rRNA gene, variety coastal\',
15 \'AB325878 Gephyromantis klemmeri mitochondrial DNA, cytb gene to tRNA-Ala gene\',
16 \'FJ559237 Mantidactylus guttulatus voucher ZSM 644/2001 16S ribosomal RNA gene, partial sequence; mitochondrial\',
17 \'AY454390 Mantidactylus malagasius 16S ribosomal RNA gene, partial sequence; mitochondrial\',
18 \'AY848172 Mantidactylus guttulatus voucher FA_m23 16S ribosomal RNA gene, partial sequence; mitochondrial\',
19 \'AY848170 Mantidactylus grandidieri voucher FA_M17 16S ribosomal RNA gene, partial sequence; mitochondrial\',
20 \'AY848121 Mantidactylus grandidieri voucher RAN 42628 16S ribosomal RNA gene, partial sequence; mitochondrial\',
21 \'EF100468 Gephyromantis silvanus 16S ribosomal RNA gene, partial sequence; mitochondrial\',
22 \'AY848369 Gephyromantis silvanus voucher 2002A80 16S ribosomal RNA gene, partial sequence; mitochondrial\',
23 \'AY848370 Gephyromantis silvanus voucher 2002A81 16S ribosomal RNA gene, partial sequence; mitochondrial\',
24 \'AY848366 Gephyromantis silvanus voucher 2001_1379 16S ribosomal RNA gene, partial sequence; mitochondrial\',
25 \'AB325884 Mantidactylus grandidieri mitochondrial DNA, D-loop to tRNA-Ala gene\',
26 \'AF215314 Mantidactylus grandidieri 16S ribosomal RNA gene, partial sequence; mitochondrial\',
27 \'AY341712 Mantidactylus grandidieri 16S ribosomal RNA gene, partial sequence; mitochondrial\',
28 \'HM364634 Gephyromantis sp. 23 MV-2009 voucher MRSN:A6610 16S ribosomal RNA gene, partial sequence; mitochondrial\',
29 \'HM364633 Gephyromantis sp. 23 MV-2009 voucher MRSN:A6383 16S ribosomal RNA gene, partial sequence; mitochondrial\'
;
tree PAUP_1 = [&R] (((((1:0.021912,(2:0,3:0):0.028696):0.010761,(5:0,6:0):0.047194):0.011291,15:0.053600):0.003991,(((4:0.000173,17:0.002118):0.006109,9:0.009697):0.029928,(((7:0,8:0):-0.000237,12:0.000237):0.035129,((10:0.024184,(13:0,14:0):0.022665):0.002323,11:0.030023):0.010171):0.009920):0.002340):0,(((16:0.006860,18:0.011460):0.007728,(((19:0,20:0):0.003029,26:0.003106):0.011626,(25:0.000211,27:0.001817):0.013968):0.004472):0.039654,((((21:0,22:0):0,23:0):0,24:0):0.046011,(28:0,29:0):0.041474):0.013986):0.007324);
End;
';
$obj = parse_nexus($str);
print_r($obj);
}
