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conceptMap.php
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<!DOCTYPE html>
<!--Part of code modified from Jam Cellar 2014-05-06-->
<!--Navigation panel on the concept map is from reactome-->
<head>
<meta charset="utf-8">
<meta name="name" content="Concept Map" />
<title>Concept Map</title>
<style>
/** {*/
/*margin: 0;*/
/*padding: 0*/
/*}*/
/*body {*/
/*font-family: "Helvetica Neue", Arial, Helvetica, sans-serif;*/
/*background-color: #ffffff;*/
/*margin: 0px;*/
/*overflow: hidden;*/
/*}*/
svg {
position: absolute;
font: 12px sans-serif;
}
text {
/*pointer-events: none;*/
}
.inner_node rect {
pointer-events: all;
}
.inner_node rect.highlight {
stroke: #315B7E;
stroke-width: 2px;
}
.outer_node circle {
/*fill: #fff;*/
stroke: steelblue;
stroke-width: 1.5px;
pointer-events: all;
}
.outer_node circle.highlight {
stroke: #315B7E;
stroke-width: 2px;
}
.link {
fill: none;
}
.dragheader { background-color:#666666;color:#fff; font-weight:bold;text-align: left;left:0px;top:0px;
cursor:move; position:relative; }
.dragheader:hover {color:red z-index:120;}
.widget { float:left; background:#aec7e8; z-index:120;}
.widget .close { color:red; font-size:0.7em;float:right; text-align: center }
.widget .close:hover { color:greenyellow;cursor:pointer; }
</style>
</head>
<body>
<table class="GG5EBMLCKI" style="position: absolute; left: 6px; top: 6px; z-index: 1000">
<colgroup>
<col>
</colgroup>
<tbody>
<tr>
<td id="reset" rowspan="2"><img
src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAAMCAYAAABWdVznAAAARUlEQVR42mNgYGD4Tyy+du0aiGb4TwygngYYH5s4hgaYW9HZWDXg8yxWDVAOsgScjdNJMIUwmihPw0ykbrCSFNMgghQMAIlEf5Ic/Z/LAAAAAElFTkSuQmCC"
width="12" height="12" class="gwt-Image" alt="reset" title="reset"></td>
<td rowspan="2"><img id="zoomIn"
src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAAMCAYAAABWdVznAAAAPUlEQVR42mNgYGD4Tyw+c+YMiGb4TwzAqwGXGJ014PMsVg0gDgzDJGGYKCfBFBLtB5I0EIwHkmIa2XPEYABjqIzoNxHTuAAAAABJRU5ErkJggg=="
width="12" height="12" class="gwt-Image" alt="zoom in" title="zoom in"></td>
<td rowspan="2"><img id="zoomOut"
src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAAMCAYAAABWdVznAAAALUlEQVR42mNgYGD4Tyw+c+YMiGb4TwwYChrweRarBhAHFx4KniYppvF5FhsGACZcn28f7AIaAAAAAElFTkSuQmCC"
width="12" height="12" class="gwt-Image" alt="zoom out" title="zoom out"></td>
<td rowspan="2"><img id="moveLeft"
src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAAMCAYAAABWdVznAAAAQklEQVR42mNgYGD4Tyw+c+YMiGb4TwygngZcBmDVAHMrURrweRarBigHLoGMcToJpgmmiChPY1NMebCSFNPoHiSEARyJjOip0asqAAAAAElFTkSuQmCC"
width="12" height="12" class="gwt-Image" alt="move left" title="move left"></td>
<td><img id="moveUp"
src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAAMCAYAAABWdVznAAAAOUlEQVR42mNgYGD4Tyw+c+YMiGb4TwzAqwEmSZQGdCfg1YDL3UQ7iaANZPmBPhoIxgNJMQ0LDWIxAKWrjOj75HeuAAAAAElFTkSuQmCC"
width="12" height="12" class="gwt-Image" alt="move up" title="move up"></td>
<td rowspan="2"><img id="moveRight"
src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAAMCAYAAABWdVznAAAAQElEQVR42mNgYGD4Tyw+c+YMiGb4TwygvgZ0caI0IMthaMDnWawaQBxkjBwyRDsJppgoDciKKQ9WkmIa3bOEMABhH42Buzog1wAAAABJRU5ErkJggg=="
width="12" height="12" class="gwt-Image" alt="move right" title="move right"></td>
</tr>
<tr>
<td><img id="moveDown"
src="data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAwAAAAMCAYAAABWdVznAAAAN0lEQVR42mNgYGD4Tyw+c+YMiGb4TwzAqwEmOQg1IGvCqgFXyOC1AZti6vuBYDyQFNOw0CAWAwDNAozowTErvwAAAABJRU5ErkJggg=="
width="12" height="12" class="gwt-Image" alt="move down" title="move down"></td>
</tr>
</tbody>
</table>
<input id="myInput" type="file" style="visibility:hidden; "/>
<script src="http://d3js.org/d3.v3.min.js"></script>
<script src="http://ajax.googleapis.com/ajax/libs/jquery/1/jquery.min.js"></script>
<script src="//code.jquery.com/ui/1.11.2/jquery-ui.js"></script>
<link rel="stylesheet" href="//code.jquery.com/ui/1.11.2/themes/smoothness/jquery-ui.css">
<script type="text/javascript" src="jsLib/dat.gui.js"></script>
<link rel="stylesheet" href="css-ui/dat_gui.css">
<script src="conceptMapJS/concept_fns.js?version=5"></script>
<?php
//$jsonFile = $_GET['fileName'];
//$jsonData = file_get_contents($jsonFile);
require_once('display_fns.php');
if(preg_match("/[A-Za-z0-9\_]+/", $_GET['fileName']) == TRUE){
$outfile = '/var/www/data/'.test_input($_GET['fileName']).'.txt';
}else{
exit();
}
if(preg_match("/[A-Za-z0-9\_]+/", $_GET['flag_egift']) == TRUE){
$flag_egift = test_input($_GET['flag_egift']);
}else{
exit();
}
if(!$_GET['conceptName']){
$conceptName = '';
}
else{
$conceptName = $_GET['conceptName'];
}
//$flag_egift = $_GET['flag_egift']; //check whehter it's egift data or customized data
//$conceptName = $_GET['conceptName'];
$list = file_get_contents($outfile);
$list = preg_replace('/\r\n|\r|\n/',"\n",$list);
$list_arr = explode("\n",$list);
$json_arr = array();
$json_data ='';
foreach ($list_arr as $d) {
$data = explode("\t",$d);
if($data[0] && $data[1]){
$json_arr['"'.$data[0].'"'][] = '"'.$data[1].'"';
}
}
//print_r($json_arr);
foreach ($json_arr as $key=>$value){
$string = '['.$key . ',['.implode(',',$value).']]';
//echo $string.'-----</br>';
$json_data[]=$string;
}
$json_data_string = '['.implode(',',$json_data).']';
//echo $json_data_string;
//fwrite($fh_json,$json_data_string) or die("cannot open this json_arr file");
//fclose($fh_json);
?>
<script>
//
// Generated by the Exaile Playlist Analyzer plugin.
// (C) 2014 Dustin Spicuzza <[email protected]>
//
// This work is licensed under the Creative Commons Attribution 4.0
// International License. To view a copy of this license, visit
// http://creativecommons.org/licenses/by/4.0/.
//
// Inspired by http://www.findtheconversation.com/concept-map/
// Loosely based on http://bl.ocks.org/mbostock/4063550
//
//var data = [[120, ["like", "call response", "dramatic intro", "has breaks", "male vocalist", "silly", "swing"]], [150, ["brassy", "like", "calm energy", "female vocalist", "swing", "fun"]], [170, ["calm energy", "instrumental", "swing", "like", "happy"]], [140, ["has breaks", "male vocalist", "swing", "piano", "banjo", "chill"]], [160, ["calm energy", "instrumental", "swing", "like", "interesting"]], [140, ["brassy", "like", "energy", "dramatic intro", "male vocalist", "baseball", "swing"]], [170, ["instrumental", "interesting", "high energy", "like", "swing"]], [140, ["instrumental", "energy", "like", "swing"]], [200, ["instrumental", "brassy", "dramatic intro", "like", "swing"]], [160, ["male vocalist", "brassy", "swing", "like", "my favorites"]], [130, ["like", "interesting", "dramatic intro", "male vocalist", "silly", "swing", "gospel"]], [160, ["like", "long intro", "announcer", "energy", "swing", "female vocalist"]], [170, ["instrumental", "swing", "bass", "like"]], [150, ["like", "interesting", "has breaks", "instrumental", "chunky", "swing", "banjo", "trumpet"]], [170, ["like", "has breaks", "male vocalist", "silly", "swing", "banjo"]], [190, ["instrumental", "banjo", "swing"]], [130, ["instrumental", "brassy", "banjo", "like", "swing"]], [160, ["brassy", "like", "energy", "instrumental", "big band", "jam", "swing"]], [150, ["like", "male vocalist", "live", "swing", "piano", "banjo", "chill"]], [150, ["like", "trick ending", "instrumental", "chunky", "swing", "chill"]], [120, ["brassy", "like", "female vocalist", "swing", "chill", "energy buildup"]], [150, ["brassy", "like", "interesting", "instrumental", "swing", "piano"]], [190, ["brassy", "like", "long intro", "energy", "baseball", "swing", "female vocalist"]], [180, ["calm energy", "female vocalist", "live", "like", "swing"]], [200, ["banjo", "like", "long intro", "interesting", "energy", "my favorites", "male vocalist", "silly", "swing", "fun", "balboa"]], [150, ["brassy", "calm energy", "chunky", "instrumental", "old-timey", "live", "swing"]], [160, ["like", "call response", "interesting", "instrumental", "calm energy", "swing"]], [180, ["interesting", "swing", "fast", "male vocalist"]], [150, ["calm energy", "chunky", "swing", "female vocalist", "like"]], [180, ["like", "has breaks", "male vocalist", "chunky", "silly", "swing"]], [140, ["instrumental", "brassy", "dramatic intro", "swing", "chill"]], [150, ["male vocalist", "trumpet", "like", "swing"]], [150, ["instrumental", "energy", "like", "has breaks", "swing"]], [180, ["brassy", "like", "energy", "has breaks", "instrumental", "has calm", "swing"]], [150, ["female vocalist", "swing"]], [170, ["instrumental", "brassy", "energy", "swing"]], [170, ["calm energy", "instrumental", "energy", "like", "swing"]], [190, ["brassy", "like", "instrumental", "high energy", "swing", "trumpet"]], [160, ["male vocalist", "energy", "swing", "old-timey"]], [170, ["like", "oldies", "my favorites", "fast", "male vocalist", "high energy", "swing"]]];
var data = <?php echo $json_data_string; ?>;
window.conceptFile_name = <?php echo "'".$conceptName."'"; ?>;
var flag_egift = <?php echo $flag_egift; ?>;
console.log(window.conceptFile_name);
var xValue=0;
var yValue=0;
var zoomValue=1.0;
window.gui_flag = false;
window._data = null;
var CUSTOMEDATA = ! flag_egift;
var SymbolInInner = true;
renderNodes(data);
//pass concept map name to concept_fns.js
var concept_name = '';
var concept_name = 'Pineal';
function compare(a, b) {
if (a.name.length > b.name.length)
return -1;
if (a.name.length < b.name.length)
return 1;
return 0;
}
function renderNodes(data) {
var outer = d3.map();
var inner = [];
var links = [];
var outerId = [0];
data.forEach(function (d) {
if (d == null)
return;
i = { id: 'i' + inner.length, name: d[0], related_links: [] }; //to do, we can sort the inner array
i.related_nodes = [i.id];
inner.push(i);
if (!Array.isArray(d[1]))
d[1] = [d[1]];
d[1].forEach(function (d1) {
o = outer.get(d1);
if (o == null) {
o = { name: d1, id: 'o' + outerId[0], related_links: [] };
o.related_nodes = [o.id];
outerId[0] = outerId[0] + 1;
outer.set(d1, o);
}
// create the links
l = { id: 'l-' + i.id + '-' + o.id, inner: i, outer: o }
links.push(l);
// and the relationships
i.related_nodes.push(o.id);
i.related_links.push(l.id);
o.related_nodes.push(i.id);
o.related_links.push(l.id);
});
});
inner = inner.sort(compare);
var inner_even = [];
var inner_odd = [];
for (var i = 0; i < inner.length; i++) {
if (i % 2) {
inner_odd.push(inner[i]);
} else {
inner_even.push(inner[i]);
}
}
inner = inner_odd.reverse().concat(inner_even);
data = {
inner: inner, //{ id: 'i' + inner.length, name: d[0], related_links: [] };
outer: outer.values(), //only the value part { name: d1, id: 'o' + outerId[0], related_links: [] };
links: links
}
d3.text("./ratelimitsymbol.txt", function (error, rateLimitSymbols) {
rateLimitSymbols = rateLimitSymbols.replace(/\r\n/g, '\n');
rateLimitSymbols = rateLimitSymbols.replace(/\r/g, '\n');
var rateLimit_Symbols = rateLimitSymbols.split("\n");
if (!SymbolInInner) {
for (var i = 0; i < data.outer.length; ++i) {
var index = rateLimit_Symbols.indexOf(data.outer[i].name);
if (index > -1) {
data.outer[i].rateLimit = true;
}
}
}
else {
for (var i = 0; i < data.inner.length; ++i) {
var index = rateLimit_Symbols.indexOf(data.inner[i].name);
if (index > -1) {
data.inner[i].rateLimit = true;
}
}
}
loadData(data,flag_egift);
});
}
</script>