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TreeBASE phylogeny added
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@rdmpage
rdmpage committed Mar 2, 2016
1 parent 74f39dc commit 1aa1e82
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Showing 5 changed files with 1,232 additions and 14 deletions.
26 changes: 26 additions & 0 deletions config.inc.php
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@@ -0,0 +1,26 @@
<?php

// $Id: //

/**
* @file config.php
*
* Global configuration variables (may be added to by other modules).
*
*/

global $config;

// Date timezone
date_default_timezone_set('UTC');

// Proxy settings for connecting to the web-----------------------------------------------
// Set these if you access the web through a proxy server.
$config['proxy_name'] = '';
$config['proxy_port'] = '';

//$config['proxy_name'] = 'wwwcache.gla.ac.uk';
//$config['proxy_port'] = '8080';


?>
147 changes: 133 additions & 14 deletions index.html
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Expand Up @@ -23,6 +23,7 @@

<!-- phylogeny -->
<script src="jquery-svgpan.js"></script>
<script src="nexus.js"></script>
<script src="treelib.js"></script>

<script>
Expand Down Expand Up @@ -162,6 +163,33 @@

var ObjectLength =
Object.keys ? ObjectLength_Modern : ObjectLength_Legacy;

//--------------------------------------------------------------------------------
function treebase_trees(query) {
$.getJSON('treebase.php?q=' + query + "&type=trees&callback=?",
function(data){
var html = '';

html += '<select id="select_tree" onchange="show_treebase_tree(this);">';
html += '<option value="" disabled selected>View a tree</option>';

for (var i in data.items) {
html += '<option value="' + data.items[i].title + '">';

title = data.items[i].title;
if (data.items[i].study) {
title += ' [Study ' + data.items[i].study + ']';
}
html += title;
html += '</option>';
}
html += '</select>';

$('#treebase_tree_list').html(html);
}

);
}

//--------------------------------------------------------------------------------
function eol_images(eol) {
Expand Down Expand Up @@ -191,9 +219,31 @@
);
}

//--------------------------------------------------------------------------------
function show_treebase_tree(sel)
{
$.getJSON('treebase.php?q=' + sel.value + "&type=one_tree&callback=?",
function(data){
if (data.nexus) {
var nexus = parse_nexus(data.nexus);

if (nexus.status != NexusError.ok) {
} else {
if (nexus.treesblock.trees.length == 0) {
} else {
var newick = nexus.treesblock.trees[0].newick;
showtree('treebase_svg', newick);
}
}
}
}
);

}


//--------------------------------------------------------------------------------
function showtree(newick)
function showtree(element_id, newick)
{
var t = new Tree();
t.Parse(newick);
Expand All @@ -208,11 +258,18 @@

t.ComputeWeights(t.root);

var td = td = new RectangleTreeDrawer();
var td = null;

if (t.has_edge_lengths) {
td = new PhylogramTreeDrawer();
} else {
td = new RectangleTreeDrawer();
}

// clear existing diagram, if any
var viewport_id = element_id + '_viewport';

var svg = document.getElementById('svg');
var svg = document.getElementById(element_id);
while (svg.hasChildNodes())
{
svg.removeChild(svg.lastChild);
Expand All @@ -221,11 +278,11 @@


var g = document.createElementNS('http://www.w3.org/2000/svg','g');
g.setAttribute('id','viewport');
g.setAttribute('id',viewport_id);
svg.appendChild(g);


td.Init(t, {svg_id: 'viewport', width:200, height:400, fontHeight:10, root_length:0.1} );
td.Init(t, {svg_id: viewport_id, width:200, height:400, fontHeight:10, root_length:0.1} );

td.CalcCoordinates();
td.Draw();
Expand All @@ -252,7 +309,7 @@
{
if (q.IsLeaf())
{
drawText('viewport', q.xy, q.label);
drawText(viewport_id, q.xy, q.label);
}
q = n.Next();
}
Expand All @@ -269,7 +326,7 @@


// move drawing to centre of viewport
var viewport = document.getElementById('viewport');
var viewport = document.getElementById(viewport_id);
viewport.setAttribute('transform', 'translate(0 10) scale(' + scale + ')');

// pan
Expand All @@ -286,12 +343,18 @@
var query = $('#query').val();

// Clear stuff
$("#output").html('');
$("#results").html('');
$("#publications").html('');
$("#treebase").html('');
$('#treebase_tree_list').html('');

// Phylogeny
var svg = document.getElementById('svg');
var svg = document.getElementById('opentree_svg');
while (svg.hasChildNodes())
{
svg.removeChild(svg.lastChild);
}
svg = document.getElementById('treebase_svg');
while (svg.hasChildNodes())
{
svg.removeChild(svg.lastChild);
Expand Down Expand Up @@ -376,7 +439,7 @@

$.post('https://api.opentreeoflife.org/v2/tree_of_life/subtree', q,
function(data){
showtree(data.newick);
showtree('opentree_svg', data.newick);
}

);
Expand Down Expand Up @@ -441,7 +504,47 @@

}
}
);
);

// TreeBASE studies
$.getJSON('treebase.php?q=' + query + "&callback=?",
function(data){
var html = '';
html += '<ol style="font-size:12px;">';
for (var i in data.items) {
html += '<li>' + data.items[i].bibliographicCitation;


if (data.items[i].doi) {
html += ' <a href="http://dx.doi.org/' + data.items[i].doi + '" target="_new">' + 'http://dx.doi.org/' + data.items[i].doi + '</a>';
}

var id = data.items[i].id;
id = id.replace(/http:\/\/purl.org\/phylo\/treebase\/phylows\/study\/TB2:S/, '');
var url = 'https://treebase.org/treebase-web/search/study/summary.html?id=' + id;
html += ' <a href="' + url + '" target="_new">' + id + '</a>';



html += '</li>';
}
html += '</ol>';

$('#treebase').html(html);
//$('#publication_details').html('Data from <a href="http://search.crossref.org/?q=' + query + '" target="_new">CrossRef</a>');

// do we have studies, if so, we have trees
if (data.items.length > 0)
{
$('#treebase_details').html('Data from <a href="http://treebase.org" target="_new">TreeBASE</a>');

treebase_trees(query);
}
}

);




}
Expand All @@ -455,7 +558,6 @@ <h1>iSpecies</h1>
<p>Species</p>
<input type="text" id="query" value="" placeholder="Dermophis mexicanus">
<button id="find" onclick="find();">Find</button>
<div id="output" style="color:rgb(128,128,128);height:30px;">Status</div>
</div>

<h2>Map</h2>
Expand All @@ -471,10 +573,26 @@ <h2>References</h2>
<div id="publications"></div>

<h2>Phylogeny</h2>

<span id="treebase_details" style="font-size:10px;color:rgb(192,192,192);">Data from TreeBASE</span>
<!-- studies -->
<div id="treebase"></div>
<!-- trees -->
<div>
<div id="treebase_tree_list"></div>
<div style="width:500px;height:420px;background-color:white;border:1px solid rgb(228,228,228);">
<svg id="treebase_svg" xmlns="http://www.w3.org/2000/svg" version="1.1" height="500" width="500">
<g id="treebase_viewport">
</g>
</svg>
</div>
<div>


<span id="phylogeny_details" style="font-size:10px;color:rgb(192,192,192);">Phylogeny from Open Tree of Life</span>
<div style="width:500px;height:420px;background-color:white;border:1px solid rgb(228,228,228);">
<svg id="svg" xmlns="http://www.w3.org/2000/svg" version="1.1" height="500" width="500">
<g id="viewport">
<svg id="opentree_svg" xmlns="http://www.w3.org/2000/svg" version="1.1" height="500" width="500">
<g id="opentree_viewport">
</g>
</svg>
</div>
Expand All @@ -490,6 +608,7 @@ <h2>Phylogeny</h2>


create_map();

</script>

<script>
Expand Down

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