Mercurial > repos > bgruening > antismash

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    <title>ARBH01000003.1 - 1 clusters - antiSMASH results</title>
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        <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 &amp; Secondary Metabolite Analysis SHell</a><br>
            <span class="white">Version <span id="antismash-version">4.0.2</span></span>
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            <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>
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        <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>
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    <!-- 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 &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">
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        If you have found antiSMASH useful, please <a href="http://antismash.secondarymetabolites.org/about">cite us</a>.
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    <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>

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author	bgruening
date	Wed, 07 Feb 2018 06:22:58 -0500
parents
children	5784e268efca