Mercurial > repos > bgruening > antismash
diff test-data/index.2.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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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/index.2.html Wed Feb 07 06:22:58 2018 -0500 @@ -0,0 +1,273 @@ +<!doctype html> +<html> + <head> + <title>ARBH01000003.1 - 1 clusters - antiSMASH results</title> + <link rel="stylesheet" type="text/css" href="css/bacteria.css"> + <meta charset="utf-8"> + </head> + <body> + <div id="header"> + <div class="top-header"> + <img class="antismash-logo" src="images/bacteria_logo.png" alt="antiSMASH"> + <span class="antismash-title"><a class="main-link" href="http://antismash.secondarymetabolites.org/">antibiotics & Secondary Metabolite Analysis SHell</a><br> + <span class="white">Version <span id="antismash-version">4.0.2</span></span> + </span> + <div id="icons"> + <a class="main-link" href="http://antismash.secondarymetabolites.org/"><img src="images/bacteria_home.png" alt="home" title="Go to start page"></a> + <a class="help-link" href="http://antismash.secondarymetabolites.org/#!/help"><img src="images/bacteria_help.png" alt="help" title="Get help using antiSMASH"></a> + <a class="about-link" href="http://antismash.secondarymetabolites.org/#!/about"><img src="images/bacteria_about.png" alt="about" title="About antiSMASH"></a> + <a href="#" id="download"><img src="images/bacteria_download.png" alt="download" title="Download results"></a> + <div id="downloadmenu"> + <ul id="downloadoptions"> + <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> + </div> + </div> + </div> + <div id="buttons"> + <span id="cluster-type">Select Gene Cluster:</span> + <ul id="clusterbuttons"> + <li><div class="arrow-left" id="prev-cluster"></div></li> + <li class="clbutton"><a href="#">Overview</a></li> + <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> + </ul> + </div> + </div> + + <!-- overview page --> + <div class="page" id="overview"> + <h3>Identified secondary metabolite clusters<span id="truncated"></span></h3> + <table id="cluster-overview"> + <thead> + <tr> + <th>Cluster</th> + <th>Type</th> + <th>From</th> + <th>To</th> + <th>Most similar known cluster</th> + <th>MIBiG BGC-ID</th> + </tr> + </thead> + <tbody> + <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> + </table> + </div> + + <div class="page" id="cluster-1"><h3>ARBH01000003 - 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 - 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"> + <div id="logos"> + <table id="logo-table"> + <tr> + <td> + <img src="images/tueblogo.gif"> + </td> + <td> + <img src="images/ruglogo.gif"> + </td> + <td> + <img src="images/ucsflogo.gif"> + </td> + <td> + <img src="images/wur-logo.png"> + </td> + </tr> + <tr> + <td> + <img src="images/uomlogo.jpg"> + </td> + <td> + <img src="images/dziflogo.png"> + </td> + <td> + <img src="images/cfb-logo.png"> + </td> + <td> + </td> + </tr> + </table> + </div> + <div id="copyright"> + If you have found antiSMASH useful, please <a href="http://antismash.secondarymetabolites.org/about">cite us</a>. + </div> + </div> + + <script src="js/jquery.js"></script> + <script src="js/purl.js"></script> + <script src="js/d3.v2.js"></script> + <script src="js/svgene.js"></script> + <script src="js/jsdomain.js"></script> + <script src="js/clusterblast.js"></script> + <script src="js/domainalign.js"></script> + <script src="geneclusters.js"></script> + <script type="text/javascript"> +function toggle_downloadmenu(event) { + event.preventDefault(); + $("#downloadmenu").fadeToggle("fast", "linear"); +} + +function switch_to_cluster() { + setTimeout(function() { + var url = $.url(); + $(".page").hide(); + $("li.clbutton").removeClass("active"); + var anchor = url.data.attr.fragment; + if (anchor == "") { + anchor = "overview"; + } + $("#" + anchor).show(); + if (anchor != "overview") { + $("li.clbutton." + anchor).addClass("active"); + } + + if (geneclusters[anchor] !== undefined) { + svgene.drawClusters(anchor+"-svg", [geneclusters[anchor]], 20, 700); + } + if ($("#" + anchor + "-details-svg").length > 0) { + jsdomain.drawDomains(anchor+ "-details-svg", details_data[anchor], 40, 700); + } + $("#" + anchor + " .clusterblast-selector").change(); + $("#" + anchor + " .domainalign-selector").change(); + }, 1); +} + +function next_cluster() { + var num_clusters = Object.keys(geneclusters).length; + var url = $.url(); + var anchor = url.data.attr.fragment; + var href = "#" + anchor; + if (anchor == "" || anchor == "overview") { + anchor = "cluster-0"; + } + var cluster_number = parseInt(anchor.split('-')[1]); + var next_cluster_number = cluster_number + 1; + if (next_cluster_number <= num_clusters) { + href = "#cluster-" + next_cluster_number; + } else { + href = "#overview"; + } + window.location.href = href; + switch_to_cluster(); +} + +function previous_cluster() { + var num_clusters = Object.keys(geneclusters).length; + var url = $.url(); + var anchor = url.data.attr.fragment; + var href = "#" + anchor; + if (anchor == "" || anchor == "overview") { + anchor = "cluster-0"; + } + var cluster_number = parseInt(anchor.split('-')[1]); + var prev_cluster_number = cluster_number - 1; + if (prev_cluster_number == 0 ) { + href = "#overview"; + } else if (prev_cluster_number < 0){ + href = "#cluster-" + num_clusters; + } else { + href = "#cluster-" + prev_cluster_number; + } + window.location.href = href; + switch_to_cluster(); +} + +function toggle_cluster_rules(ev) { + ev.preventDefault(); + var id = $(this).attr('id').replace(/-header/, ''); + var rules = $('#' + id); + if (rules.css('display') == "none") { + $(this).text('Hide pHMM detection rules used'); + } else { + $(this).text('Show pHMM detection rules used'); + } + rules.fadeToggle("fast", "linear"); +} + +function map_type_to_desc(type) { + switch(type) { + case "nrps": return "NRPS"; + case "t1pks": return "Type I PKS"; + case "t2pks": return "Type II PKS"; + case "t3pks": return "Type III PKS"; + case "t4pks": return "Type IV PKS"; + default: return type; + } +} + +function copyToClipboard (text) { + window.prompt ("Copy to clipboard: Ctrl+C, Enter", text); +} + +$(document).ready(function() { + + $("#download").click(toggle_downloadmenu); + + $("#next-cluster").click(next_cluster); + $("#prev-cluster").click(previous_cluster); + + $(".clbutton").click(function() { + /* Make sure that even if user missed the link and clicked the + background we still have the correct anchor */ + var href = $(this).children().first().attr('href'); + + if (href === undefined) { + return; + } + window.location.href = href; + + switch_to_cluster(); + }).mouseover(function() { + /* Set the select cluster label text to cluster type */ + var classes = $(this).attr('class').split(' '); + if (classes.length < 2) { + return; + } + if (classes[1] == 'separator') { + return; + } + var cluster_type = map_type_to_desc(classes[1]); + var label = $('#cluster-type'); + label.data("orig_text", label.text()); + label.text(cluster_type + ":"); + }).mouseout(function() { + /* and reset the select cluster label text */ + var label = $('#cluster-type'); + label.text(label.data("orig_text")); + }); + + $('.clusterblast-selector').change(function() { + var id = $(this).attr('id').replace('-select', ''); + var url = $(this).val(); + $.get(url, function(data) { + $('#' + id + '-svg').html(data); + clusterblast.init(id + '-svg'); + // id = + }, 'html'); + $('#' + id + '-download').off('click'); + $('#' + id + '-download').click(function () { + var url = $("#" + id + "-select").val(); + window.open(url, '_blank'); + }); + }); + + $('.domainalign-selector').change(function() { + var id = $(this).attr('id').replace('-select', ''); + var url = $(this).val(); + $.get(url, function(data) { + $('#' + id + '-svg').html(data); + domainalign.init(id + '-svg'); + // id = + }, 'html'); + $('#' + id + '-download').off('click'); + $('#' + id + '-download').click(function () { + var url = $("#" + id + "-select").val(); + window.open(url, '_blank'); + }); + }); + + $('.cluster-rules-header').click(toggle_cluster_rules); + + switch_to_cluster(); + +}); + </script> + + </body> +</html> \ No newline at end of file