Esempio n. 1
0
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;
}
Esempio n. 2
0
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>';
    }
}
Esempio n. 3
0
/**
 * @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;
}
Esempio n. 4
0
 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();
     }
 }
Esempio n. 5
0
 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();
     }
 }