html TreeFam基因树小部件
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"http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
<html xmlns="http://www.w3.org/1999/xhtml" lang="en-US" xml:lang="en-US">
<head>
<!-- Javascript files -->
<!--
<script type="text/javascript" src="../../main/javascript/Biojs.js"></script>
<script type="text/javascript" src="../../main/javascript/Biojs.Tree.js"></script>
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<script type="text/javascript">
//<![CDATA[
var mySequence;
window.onload = function() {
//$('.on_off :checkbox').iphoneStyle();
//$('.disabled :checkbox').iphoneStyle();
//$('.css_sized_container :checkbox').iphoneStyle({ resizeContainer: false, resizeHandle: false });
// set treefam family in header
var treefam_family = "TF101003";
var treefam_family_genes = "121";
var treefam_family_species = "21";
var treefam_family_alignment_conservation = "66";
var treefam_family_alignment_length = "1213";
//jQuery("#tf_family").text(treefam_family);
//jQuery("#tf_sequences").text(treefam_family_genes);
//jQuery("#tf_species").text(treefam_family_species);
//jQuery("#tf_alignment_length").text(treefam_family_alignment_conservation);
//jQuery("#tf_alignment_conservation").text(treefam_family_alignment_length);
jQuery("#cite_panel").html(
'TreeFam family '+treefam_family+' has '+treefam_family_genes+' from '+treefam_family_species+' species. '+
'The sequences were aligned using MCoffee. The final alignment was '+treefam_family_alignment_length+' AA long '+
'and on average '+treefam_family_alignment_conservation+'% conserved. '+
'TreeBest (1) was used to build a gene tree and reconcile it with the species tree. '+
'TreeBest build 5 source trees using nj and Phyml (2). It then merges them into one tree trying to minimize the number of duplications using a species tree.'+
'<p id="footnote-1">(1) Ruan,J., Li,H., Chen,Z., Coghlan,A., Coin,L.J.M., Guo,Y., Hériché,J.-K., Hu,Y., Kristiansen,K., Li,R., et al. (2008) TreeFam: 2008 Update. Nucleic Acids Res, 36, D735-40.<\/p> '+
'<p id="footnote-2">(2) Guindon,S., Dufayard,J.-F., Lefort,V., Anisimova,M., Hordijk,W. and Gascuel,O. (2010) New algorithms and methods to estimate maximum-likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol, 59, 307-321.<\/p> ');
jQuery("#treefam_family").text(treefam_family);
jQuery("#treefam_family").attr("href", "http://www.treefam.org/family/" +treefam_family);
jQuery("#tree_type_tooltip").tipsy({
gravity: 'nw',
html: true,
title: function() {
var text_string = "Beside the <b>full gene tree</b> for all species, TreeFam provides a pruned-down version focussing on <b>model</b> organims only";
return text_string;
}
});
jQuery("#branch_length_tooltip").tipsy({
gravity: 'nw',
html: true,
title: function() {
var text_string = "Switch between an cladogram and a phylogenetic tree.<br>"
text_string += "The cladogram shows the relationships between genes, but does not show real branch length.";
return text_string;
}
});
jQuery("#labels_tooltip").tipsy({
gravity: 'nw',
html: true,
title: function() {
var text_string = "Toggle between gene names and UniProt IDs";
return text_string;
}
});
jQuery("#inner_nodes_tooltip").tipsy({
gravity: 'nw',
html: true,
title: function() {
var text_string = "Click <i>Bootstrap</i> to see support values for inner nodes.<br>";
text_string += "<b>Taxonomy</b> displays internal taxonomic group names";
return text_string;
}
});
jQuery("#zooming_tooltip").tipsy({
gravity: 'nw',
html: true,
title: function() {
var text_string = "activate the zoom to use the mouse-wheel on the tree to zoom in.";
return text_string;
}
});
jQuery("#settings_panel").show();
//$(".show_hide").show();
jQuery('#cite_li').click(function(){
jQuery("#cite_panel").slideToggle();
});
jQuery('#settings_li').click(function(){
jQuery("#settings_panel").slideToggle();
});
/* jQuery('#toggle-view span').click(function () {
var text = jQuery(this).children('div.panel');
if (text.is(':hidden')) {
text.slideDown('200');
jQuery(this).children('span').html('-');
} else {
text.slideUp('200');
jQuery(this).children('span').html('+');
}
}); */
jQuery('.show_leaf_common_name').click(function(){
if (jQuery(this).is(':checked')){
myTree.show_gene_annotation();
}});
jQuery('.show_leaf_uniprot').click(function(){
if (jQuery(this).is(':checked')){
myTree.show_uniprot_annotation();
}});
jQuery( ".ultra_branch_length" ).click(function() {
console.log("toggle branch length");
myTree.toggle_branchlength();
});
jQuery( ".real_branch_length" ).click(function() {
console.log("toggle toggle_leaf_annotation");
myTree.toggle_branchlength();
});
// bootstrap
jQuery('#bootstrap_check').click(function() {
if(jQuery(this).is(":checked")) {myTree.show_bootstrap();}
else{myTree.hide_bootstrap();}
});
jQuery('#taxa_level').click(function() {
if(jQuery(this).is(":checked")) {myTree.show_taxlevel();}
else{myTree.hide_taxlevel();}
});
// zoom
jQuery('.zoom_on').click(function(){
console.log("adding zoom");
if (jQuery(this).is(':checked')){
myTree.addZoom();
}});
jQuery('.zoom_off').click(function(){
console.log("adding zoom");
if (jQuery(this).is(':checked')){
myTree.removeZoom();
}});
jQuery('.zoom_reset').click(function(){
console.log("adding zoom");
if (jQuery(this).is(':checked')){
myTree.resetZoom();
}});
/*var $slider = $('input[name="slider1"]');
$slider.bind('change', function(e) {
e.preventDefault();
console.log($(this).val());
myTree.slideZoom($(this).val());
});
*/
jQuery('#target').submit(function() {
alert('Handler for .submit() called.');
myTree = new Biojs.Tree({
target : "tree",
tv_contentcontainer : "tv_contentcontainer",
format : 'CODATA',
load_from_web : load_from_web,
formatOptions : {
title:false,
footer:false,
tree:'json',
},
id : 'P918283',
// tree parameters
//no_genes : no_genes,
//alignment_length : alignment_length,
json_tree : model_json_tree,
image_path : image_path,
newick_tree : newick_tree,
highlight_gene : highlight_gene,
json_tree_string : json_tree_string,
load_from_variable : load_from_variable,
show_controls : show_controls,
modelTreeOn : ""
});
return false;
});
// add cool toolbar
//jQuery('#user-toolbar').toolbar({
// content: '#user-toolbar-options',
// position: 'top'
//});
//console.log("ready to load stuff");
//var model_json_tree = "../../main/resources/dependencies/data/trees/TF105041_model.json";
//var full_json_tree = "../../main/resources/dependencies/data/trees/dump_model_tree";
//TF101002.json
//var model_json_tree = "../../main/resources/dependencies/data/trees/TF101002_model.json";
//var full_json_tree = "../../main/resources/dependencies/data/trees/TF101002_full.json";
//var wormbase_json_tree = "../../main/resources/dependencies/data/trees/TF101002_full.json";
//TF101107.
var model_json_tree = "TF101222_model.json";
var full_json_tree = "TF101222_full.json";
var wormbase_json_tree = "TF101222_wormbase.json";
//TF101011.
//var model_json_tree = "../../main/resources/dependencies/data/trees/treefam_trees/TF333268_model.json";
//var full_json_tree = "../../main/resources/dependencies/data/trees/treefam_trees/TF333268_full.json";
//var wormbase_json_tree = "../../main/resources/dependencies/data/trees/treefam_trees/TF333268_wormbase.json";
// TF101003
//var model_json_tree = "../../main/resources/dependencies/data/trees/treefam_trees/TF101001_model.json";
//var full_json_tree = "../../main/resources/dependencies/data/trees/treefam_trees/TF101001_full.json";
//var wormbase_json_tree = "../../main/resources/dependencies/data/trees/treefam_trees/TF101001_wormbase.json";
//TF101222.json
//var model_json_tree = "../../main/resources/dependencies/data/trees/TF101222_model.json";
//var full_json_tree = "../../main/resources/dependencies/data/trees/TF101222_full.json";
//TF101222.json
//var model_json_tree = "../../main/resources/dependencies/data/trees/TF352753_model.json";
//var full_json_tree = "../../main/resources/dependencies/data/trees/TF352753_full.json";
//var full_json_tree = "../../main/resources/dependencies/data/trees/TF106341.json";
//var json_tree = "../../main/resources/dependencies/data/trees/primates.json";
//var json_tree = "../../main/resources/dependencies/data/trees/toy_tree_original.json";
//var json_tree = "../../main/resources/dependencies/data/trees/toy_tree.json";
//var no_genes = 44 * 2;
//var alignment_length = 54 * 2;
var image_path = "http://www.treefam.org/static/images/species_pictures/species_files/";
//var highlight_gene = "ENSBTAP00000001311";
var highlight_gene = "";
//var newick_tree = "../data/trees/newick_tree.nh";
var newick_tree = "";
var load_from_variable = 0;
var load_from_web = 0;
var json_tree_string;
var show_controls = 1;
myTree = new Biojs.Tree({
target : "tree",
tv_contentcontainer : "tv_contentcontainer",
format : 'CODATA',
load_from_web : load_from_web,
formatOptions : {
title:false,
footer:false,
tree:'json',
},
id : 'P918283',
// tree parameters
//no_genes : no_genes,
//alignment_length : alignment_length,
json_tree : model_json_tree,
image_path : image_path,
newick_tree : newick_tree,
highlight_gene : highlight_gene,
json_tree_string : json_tree_string,
load_from_variable : load_from_variable,
show_controls : show_controls,
modelTreeOn : ""
});
$("#full_tree").click(function() {
myTree.clear_divs();
jQuery('#show_leaf_common_name').attr('checked', true);
jQuery('#show_leaf_uniprot').attr('checked', false);
jQuery('#bootstrap_check').attr('checked', false);
jQuery('#taxa_level').attr('checked', false);
jQuery('show_leaf_common_name').attr('checked', true);
//myTree.showFullTree();
myTree = new Biojs.Tree({
target : "tree",
tv_contentcontainer : "tv_contentcontainer",
format : 'CODATA',
formatOptions : {
title:false,
footer:false,
tree:'json',
},
id : 'P918283',
// tree parameters
json_tree : full_json_tree,
image_path : image_path,
newick_tree : newick_tree,
highlight_gene : highlight_gene,
json_tree_string : json_tree_string,
load_from_variable : load_from_variable,
show_controls : show_controls,
modelTreeOn : ""
});
});
$("#model_tree").click(function() {
myTree.clear_divs();
//myTree.showModelTree();
myTree = new Biojs.Tree({
target : "tree",
tv_contentcontainer : "tv_contentcontainer",
format : 'CODATA',
formatOptions : {
title:false,
footer:false,
tree:'json',
},
id : 'P918283',
// tree parameters
json_tree : model_json_tree,
image_path : image_path,
newick_tree : newick_tree,
highlight_gene : highlight_gene,
json_tree_string : json_tree_string,
load_from_variable : load_from_variable,
show_controls : show_controls,
modelTreeOn : ""
});
});
$("#wormbase_tree").click(function() {
myTree.clear_divs();
//myTree.showModelTree();
myTree = new Biojs.Tree({
target : "tree",
tv_contentcontainer : "tv_contentcontainer",
format : 'CODATA',
formatOptions : {
title:false,
footer:false,
tree:'json',
},
id : 'P918283',
// tree parameters
json_tree : wormbase_json_tree,
image_path : image_path,
newick_tree : newick_tree,
highlight_gene : highlight_gene,
json_tree_string : json_tree_string,
load_from_variable : load_from_variable,
show_controls : show_controls,
modelTreeOn : ""
});
});
};
//]]>
</script>
<title></title>
</head>
<body>
<div class="tv_contentcontainer" id="tv_contentcontainer">
<div class="tv_breadcrumbs">
<a class="settings-button pressed" id="button-right" name="button-right"></a>
<!--<a href="http://www.treefam.org"><img src="http://www.treefam.org/static/images/treefam_logo.png" alt="" width="" height="35" class="logo" /></a> -->
TreeFam gene tree for family <a id="treefam_family" href="" name="treefam_family"></a><br />
<ul id="toggle-view">
<li id="li_head">
<h3 id="cite_li">
How to cite this tree
</h3><span >+</span>
<div id="cite_panel" class="panel"></div>
</li>
<li id="li_head">
<h3 id="settings_li">
Control elements
</h3><span >+</span>
<div id="settings_panel" style="padding-left: 10px;" class="panel">
<div class="settings">
<div class="left">
<label for="tree_type" class="fixedwidth">Tree type</label>
<img id="tree_type_tooltip" title="Click for information about this field" src="http://cc.skoda-auto.com/che/style/ltr/nci_default/icon_info.png" style="vertical-align: bottom;" alt="info" width="10">
<ul>
<li>
<input type="radio" class="radioinput" name="tree_type" id="model_tree" value="model_tree" checked="checked">
<label for="model_tree" class="radiolabel">Model</label>
</li>
<li>
<input type="radio" class="radioinput" name="tree_type" id="wormbase_tree" value="wormbase_tree">
<label for="wormbase_tree" class="radiolabel">Wormbase</label>
</li>
<li>
<input type="radio" class="radioinput" name="tree_type" id="full_tree" value="full_tree">
<label for="full_tree" class="radiolabel">Full</label>
</li>
</ul>
</div>
<div class="middle">
<label for="branch_length" class="fixedwidth">Branch length</label>
<img id="branch_length_tooltip" title="Click for information about this field" src="http://cc.skoda-auto.com/che/style/ltr/nci_default/icon_info.png" style="vertical-align: bottom;" alt="info" width="10">
<ul>
<li>
<input type="radio" class="ultra_branch_length" name="br_length" id="branch_length" value="real_branch" checked="checked"> <label for="tran_code_22" class="branch_length">Cladogram</label>
</li>
<li>
<input type="radio" class="real_branch_length" name="br_length" id="branch_length" value="real_branch"> <label for="tran_code_21" class="branch_length">Real</label>
</li>
</ul>
</div>
<div class="right">
<label for="leaf_annotation" class="fixedwidth">Leaf labels</label>
<img id="labels_tooltip" title="Click for information about this field" src="http://cc.skoda-auto.com/che/style/ltr/nci_default/icon_info.png" style="vertical-align: bottom;" alt="info" width="10">
<ul>
<li>
<input type="radio" class="show_leaf_common_name" name="leaf_annot" id="show_leaf_common_name" value="leaf_annotation" checked="checked"> <label for="gene_label" class="leaf_annotation">Gene name</label>
</li>
<li>
<input type="radio" class="show_leaf_uniprot" name="leaf_annot" id="uniprot" value="leaf_annotation"> <label for="uniprot" class="leaf_annotation">UniProt</label>
</li>
</ul>
</div>
<div class="right3">
<label for="inner_nodes" class="fixedwidth">Internal labels</label>
<img id="inner_nodes_tooltip" title="Click for information about this field" src="http://cc.skoda-auto.com/che/style/ltr/nci_default/icon_info.png" style="vertical-align: bottom;" alt="info" width="10">
<ul>
<li>
<input type="checkbox" class="bootstrap_check" name="bootstrap" id="bootstrap_check" value="leaf_annotation" > <label for="gene_label" class="leaf_annotation">Bootstrap</label>
</li>
<li>
<input type="checkbox" class="int_names" name="taxa_level" id="taxa_level" value="leaf_annotation"> <label for="uniprot" class="leaf_annotation">Taxonomy</label>
</li>
</ul>
</div>
<div class="right2">
<label for="tran_code" class="fixedwidth">Mouse Zooming</label>
<img id="zooming_tooltip" title="Click for information about this field" src="http://cc.skoda-auto.com/che/style/ltr/nci_default/icon_info.png" style="vertical-align: bottom;" alt="info" width="10">
<ul>
<li>
<input type="radio" class="zoom_on" name="tran_code" id="zoom_on" value="zoom_on"> <label for="zoom_on" class="radiolabel">On</label>
</li>
<li>
<input type="radio" class="zoom_off" name="tran_code" id="zoom_off" value="zoom_off" checked="checked"> <label for="zoom_off" class="radiolabel">Off</label>
</li>
<!--<li>
<input type="radio" class="zoom_reset" name="tran_code" id="zoom_off" value="zoom_off" > <label for="zoom_off" class="radiolabel">Reset</label>
</li>-->
</ul>
</div>
</div>
</li>
</ul>
<div class="tv_homecontent">
<div class="tree_container" id="tree"></div>
</div>
<div class="clearfloat"></div>
</div>
</div>
</body>
</html>
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