comparison test-data/index.html @ 1:593bb8f5488b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/antismash commit 654a4f3b3a1602cec2510d51fb953fd456427e08
author bgruening
date Wed, 07 Feb 2018 06:22:58 -0500
parents
children 5784e268efca
comparison
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0:5db064bbb3be 1:593bb8f5488b
1 <!doctype html>
2 <html>
3 <head>
4 <title>ARBH01000003.1 - 1 clusters - antiSMASH results</title>
5 <link rel="stylesheet" type="text/css" href="css/bacteria.css">
6 <meta charset="utf-8">
7 </head>
8 <body>
9 <div id="header">
10 <div class="top-header">
11 <img class="antismash-logo" src="images/bacteria_logo.png" alt="antiSMASH">
12 <span class="antismash-title"><a class="main-link" href="http://antismash.secondarymetabolites.org/">antibiotics &amp; Secondary Metabolite Analysis SHell</a><br>
13 <span class="white">Version <span id="antismash-version">4.0.2</span></span>
14 </span>
15 <div id="icons">
16 <a class="main-link" href="http://antismash.secondarymetabolites.org/"><img src="images/bacteria_home.png" alt="home" title="Go to start page"></a>
17 <a class="help-link" href="http://antismash.secondarymetabolites.org/#!/help"><img src="images/bacteria_help.png" alt="help" title="Get help using antiSMASH"></a>
18 <a class="about-link" href="http://antismash.secondarymetabolites.org/#!/about"><img src="images/bacteria_about.png" alt="about" title="About antiSMASH"></a>
19 <a href="#" id="download"><img src="images/bacteria_download.png" alt="download" title="Download results"></a>
20 <div id="downloadmenu">
21 <ul id="downloadoptions">
22 <li><a href="ARBH01000003.1.zip">Download all results</a></li><li><a href="ARBH01000003.1.geneclusters.xls">Download XLS overview file</a></li><li><a href="ARBH01000003.1.final.embl">Download EMBL summary file</a></li><li><a href="ARBH01000003.1.final.gbk">Download GenBank summary file</a></li></ul>
23 </div>
24 </div>
25 </div>
26 <div id="buttons">
27 <span id="cluster-type">Select Gene Cluster:</span>
28 <ul id="clusterbuttons">
29 <li><div class="arrow-left" id="prev-cluster"></div></li>
30 <li class="clbutton"><a href="#">Overview</a></li>
31 <li class="clbutton t1pks cluster-1"><a href="#cluster-1">1</a></li><li id="last-clbutton"><div class="arrow-right" id="next-cluster"></div></li>
32 </ul>
33 </div>
34 </div>
35
36 <!-- overview page -->
37 <div class="page" id="overview">
38 <h3>Identified secondary metabolite clusters<span id="truncated"></span></h3>
39 <table id="cluster-overview">
40 <thead>
41 <tr>
42 <th>Cluster</th>
43 <th>Type</th>
44 <th>From</th>
45 <th>To</th>
46 <th>Most similar known cluster</th>
47 <th>MIBiG BGC-ID</th>
48 </tr>
49 </thead>
50 <tbody>
51 <tr class="separator-row"><td class="separator-text" colspan="2">The following clusters are from record ARBH01000003.1:</td></tr><tr><td class="clbutton t1pks"><a href="#cluster-1">Cluster 1</a></td><td><a href="http://antismash.secondarymetabolites.org/help#t1pks" target="_blank">T1pks</a></td><td class="digits">1</td><td class="digits">3500</td><td>-</td><td>-</td></tr></tbody>
52 </table>
53 </div>
54
55 <div class="page" id="cluster-1"><h3>ARBH01000003.1 - Cluster 1 - T1pks</h3><div class="sidepanel"><div class="structure"><h3>Predicted core structure</h3><a href="images/nostructure_icon.png" target="_new"><img src="images/nostructure_icon.png"></a><div class="as-structure-warning">Rough prediction of core scaffold based on assumed PKS/NRPS colinearity; tailoring reactions not taken into account</div></div><div class="more-details"><h3>Prediction details</h3><dl class="prediction-text"><dt>Monomers prediction:</dt><dd>(mal)</dd><dt>ctg1_1</dt><dd>PKS signature: mal<br></dd><dd>Minowa: mal<br></dd><dd>consensus: mal<br></dd></dl></div></div><div class="content"><div class="description-container"><h3>Gene cluster description</h3><div class="cluster-download"><a href="ARBH01000003.1.cluster001.gbk">Download cluster GenBank file</a></div><div class="description-text">ARBH01000003.1 - Gene Cluster 1. Type = t1pks. Location: 1 - 3500 nt. Click on genes for more information.</div><a class="cluster-rules-header" id="cluster-1-rules-header" href="#cluster-1">Show pHMM detection rules used</a><div class="cluster-rules" id="cluster-1-rules">t1pks: ((PKS_KS &amp; PKS_AT) or (ene_KS &amp; PKS_AT) or (mod_KS &amp; PKS_AT) or (hyb_KS &amp; PKS_AT) or (itr_KS &amp; PKS_AT) or (tra_KS &amp; PKS_AT))<br></div><div id="cluster-1-svg"></div></div><div class="legend"><h4>Legend:</h4><div><div><div class="legend-field legend-type-biosynthetic"></div><div class="legend-label">core biosynthetic genes</div></div><div><div class="legend-field legend-type-biosynthetic-additional"></div><div class="legend-label">additional biosynthetic genes</div></div><div><div class="legend-field legend-type-transport"></div><div class="legend-label">transport-related genes</div></div><div><div class="legend-field legend-type-regulatory"></div><div class="legend-label">regulatory genes</div></div><div><div class="legend-field legend-type-other"></div><div class="legend-label">other genes</div></div></div></div><div class="details"><h3>Detailed annotation</h3><div class="details-svg" id="cluster-1-details-svg"></div></div></div></div><div id="footer">
56 <div id="logos">
57 <table id="logo-table">
58 <tr>
59 <td>
60 <img src="images/tueblogo.gif">
61 </td>
62 <td>
63 <img src="images/ruglogo.gif">
64 </td>
65 <td>
66 <img src="images/ucsflogo.gif">
67 </td>
68 <td>
69 <img src="images/wur-logo.png">
70 </td>
71 </tr>
72 <tr>
73 <td>
74 <img src="images/uomlogo.jpg">
75 </td>
76 <td>
77 <img src="images/dziflogo.png">
78 </td>
79 <td>
80 <img src="images/cfb-logo.png">
81 </td>
82 <td>
83 </td>
84 </tr>
85 </table>
86 </div>
87 <div id="copyright">
88 If you have found antiSMASH useful, please <a href="http://antismash.secondarymetabolites.org/about">cite us</a>.
89 </div>
90 </div>
91
92 <script src="js/jquery.js"></script>
93 <script src="js/purl.js"></script>
94 <script src="js/d3.v2.js"></script>
95 <script src="js/svgene.js"></script>
96 <script src="js/jsdomain.js"></script>
97 <script src="js/clusterblast.js"></script>
98 <script src="js/domainalign.js"></script>
99 <script src="geneclusters.js"></script>
100 <script type="text/javascript">
101 function toggle_downloadmenu(event) {
102 event.preventDefault();
103 $("#downloadmenu").fadeToggle("fast", "linear");
104 }
105
106 function switch_to_cluster() {
107 setTimeout(function() {
108 var url = $.url();
109 $(".page").hide();
110 $("li.clbutton").removeClass("active");
111 var anchor = url.data.attr.fragment;
112 if (anchor == "") {
113 anchor = "overview";
114 }
115 $("#" + anchor).show();
116 if (anchor != "overview") {
117 $("li.clbutton." + anchor).addClass("active");
118 }
119
120 if (geneclusters[anchor] !== undefined) {
121 svgene.drawClusters(anchor+"-svg", [geneclusters[anchor]], 20, 700);
122 }
123 if ($("#" + anchor + "-details-svg").length > 0) {
124 jsdomain.drawDomains(anchor+ "-details-svg", details_data[anchor], 40, 700);
125 }
126 $("#" + anchor + " .clusterblast-selector").change();
127 $("#" + anchor + " .domainalign-selector").change();
128 }, 1);
129 }
130
131 function next_cluster() {
132 var num_clusters = Object.keys(geneclusters).length;
133 var url = $.url();
134 var anchor = url.data.attr.fragment;
135 var href = "#" + anchor;
136 if (anchor == "" || anchor == "overview") {
137 anchor = "cluster-0";
138 }
139 var cluster_number = parseInt(anchor.split('-')[1]);
140 var next_cluster_number = cluster_number + 1;
141 if (next_cluster_number <= num_clusters) {
142 href = "#cluster-" + next_cluster_number;
143 } else {
144 href = "#overview";
145 }
146 window.location.href = href;
147 switch_to_cluster();
148 }
149
150 function previous_cluster() {
151 var num_clusters = Object.keys(geneclusters).length;
152 var url = $.url();
153 var anchor = url.data.attr.fragment;
154 var href = "#" + anchor;
155 if (anchor == "" || anchor == "overview") {
156 anchor = "cluster-0";
157 }
158 var cluster_number = parseInt(anchor.split('-')[1]);
159 var prev_cluster_number = cluster_number - 1;
160 if (prev_cluster_number == 0 ) {
161 href = "#overview";
162 } else if (prev_cluster_number < 0){
163 href = "#cluster-" + num_clusters;
164 } else {
165 href = "#cluster-" + prev_cluster_number;
166 }
167 window.location.href = href;
168 switch_to_cluster();
169 }
170
171 function toggle_cluster_rules(ev) {
172 ev.preventDefault();
173 var id = $(this).attr('id').replace(/-header/, '');
174 var rules = $('#' + id);
175 if (rules.css('display') == "none") {
176 $(this).text('Hide pHMM detection rules used');
177 } else {
178 $(this).text('Show pHMM detection rules used');
179 }
180 rules.fadeToggle("fast", "linear");
181 }
182
183 function map_type_to_desc(type) {
184 switch(type) {
185 case "nrps": return "NRPS";
186 case "t1pks": return "Type I PKS";
187 case "t2pks": return "Type II PKS";
188 case "t3pks": return "Type III PKS";
189 case "t4pks": return "Type IV PKS";
190 default: return type;
191 }
192 }
193
194 function copyToClipboard (text) {
195 window.prompt ("Copy to clipboard: Ctrl+C, Enter", text);
196 }
197
198 $(document).ready(function() {
199
200 $("#download").click(toggle_downloadmenu);
201
202 $("#next-cluster").click(next_cluster);
203 $("#prev-cluster").click(previous_cluster);
204
205 $(".clbutton").click(function() {
206 /* Make sure that even if user missed the link and clicked the
207 background we still have the correct anchor */
208 var href = $(this).children().first().attr('href');
209
210 if (href === undefined) {
211 return;
212 }
213 window.location.href = href;
214
215 switch_to_cluster();
216 }).mouseover(function() {
217 /* Set the select cluster label text to cluster type */
218 var classes = $(this).attr('class').split(' ');
219 if (classes.length < 2) {
220 return;
221 }
222 if (classes[1] == 'separator') {
223 return;
224 }
225 var cluster_type = map_type_to_desc(classes[1]);
226 var label = $('#cluster-type');
227 label.data("orig_text", label.text());
228 label.text(cluster_type + ":");
229 }).mouseout(function() {
230 /* and reset the select cluster label text */
231 var label = $('#cluster-type');
232 label.text(label.data("orig_text"));
233 });
234
235 $('.clusterblast-selector').change(function() {
236 var id = $(this).attr('id').replace('-select', '');
237 var url = $(this).val();
238 $.get(url, function(data) {
239 $('#' + id + '-svg').html(data);
240 clusterblast.init(id + '-svg');
241 // id =
242 }, 'html');
243 $('#' + id + '-download').off('click');
244 $('#' + id + '-download').click(function () {
245 var url = $("#" + id + "-select").val();
246 window.open(url, '_blank');
247 });
248 });
249
250 $('.domainalign-selector').change(function() {
251 var id = $(this).attr('id').replace('-select', '');
252 var url = $(this).val();
253 $.get(url, function(data) {
254 $('#' + id + '-svg').html(data);
255 domainalign.init(id + '-svg');
256 // id =
257 }, 'html');
258 $('#' + id + '-download').off('click');
259 $('#' + id + '-download').click(function () {
260 var url = $("#" + id + "-select").val();
261 window.open(url, '_blank');
262 });
263 });
264
265 $('.cluster-rules-header').click(toggle_cluster_rules);
266
267 switch_to_cluster();
268
269 });
270 </script>
271
272 </body>
273 </html>