本文整理汇总了PHP中Tree::GetRoot方法的典型用法代码示例。如果您正苦于以下问题：PHP Tree::GetRoot方法的具体用法？PHP Tree::GetRoot怎么用？PHP Tree::GetRoot使用的例子？那么恭喜您, 这里精选的方法代码示例或许可以为您提供帮助。您也可以进一步了解该方法所在类Tree的用法示例。
在下文中一共展示了Tree::GetRoot方法的4个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的PHP代码示例。
示例1: tree2kml
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;
}示例2: main
//.........这里部分代码省略.........
$b = array();
foreach ($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);
}
示例3: tree2svg
/**
* @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();
}
//.........这里部分代码省略.........
示例4: array
}
}
/*
echo '<pre>';
$t->Dump();
echo $t->WriteDot();
print_r($tree_list);
echo '</pre>';
*/
// We now have a tree of trees, we want to assign these to a linear order of layers for drawing.
// Nodes that have no trees are "ignored"
$layers = array();
$depth = 0;
$p = new PreorderIterator($t->GetRoot());
$q = $p->Begin();
while ($q != NULL) {
if ($q == $t->GetRoot()) {
// Do any studies map to this node?
if (isset($tree_list[$q->GetLabel()])) {
$q->SetAttribute('depth', 0);
if (!isset($layers[$depth])) {
$layers[$depth] = array();
}
$layers[$depth][] = $q->GetLabel();
} else {
$q->SetAttribute('depth', -1);
}
} else {
$anc = $q->GetAncestor();