Mercurial > repos > bgruening > antismash
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 |
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| 0:5db064bbb3be | 1:593bb8f5488b |
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| 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 & 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 & PKS_AT) or (ene_KS & PKS_AT) or (mod_KS & PKS_AT) or (hyb_KS & PKS_AT) or (itr_KS & PKS_AT) or (tra_KS & 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> |