P2T2/index.html at master · MTZimmermann/P2T2 · GitHub

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<!DOCTYPE html>
<html>

<head>
    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
    <!-- FROM: http://getbootstrap.com/ -->
    <link href="bootstrap-3.3.5-dist/css/bootstrap.min.css" rel="stylesheet">
    <link href="https://cdnjs.cloudflare.com/ajax/libs/intro.js/2.6.0/introjs.min.css" rel="stylesheet">

    <script src="https://ajax.googleapis.com/ajax/libs/jquery/2.2.0/jquery.min.js"></script>
    <script src="bootstrap-3.3.5-dist/js/bootstrap.min.js"></script>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/d3/3.5.17/d3.js"></script>
    <script src="https://cdnjs.cloudflare.com/ajax/libs/intro.js/2.6.0/intro.min.js"></script>
    <script type="text/javascript" language="javascript" src="lib_misc.js"></script>
    <script type="text/javascript" language="javascript" src="data.js"></script>
    <script type="text/javascript" language="javascript" src="data_model.js"></script>
    <script type="text/javascript" language="javascript" src="laneProteinSequence.js"></script>
    <script type="text/javascript" language="javascript" src="laneExac.js"></script>
    <script type="text/javascript" language="javascript" src="laneGeneric.js"></script>
    <script type="text/javascript" language="javascript" src="laneAlignment.js"></script>
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    <script type="text/javascript" language="javascript" src="laneHiding.js"></script>
    <script type="text/javascript" language="javascript" src="view_d3.js"></script>

    <style type="text/css">
        #graph-container {
            margin: 10px 0;
            overflow-x: scroll;
        }

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        .x.axis line, .y.axis line {
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        .x.axis .minor, .y.axis .minor {
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        }

        .x.axis path, .y.axis path {
            display: none;
        }

        .y.axis text {
            font-size: 10px;
        }

        .protein-sequence text {
            dominant-baseline: central;
            text-anchor: middle;
            font-family: monospace;
        }

        .spinner {
            width: 30px;
            display: inline-block;
            height: 30px;
            visibility: hidden;
            background-image: url(images/ajax-loader.gif);
            background-repeat: no-repeat;
            background-position: center;
        }

        .brush .extent {
            fill-opacity: .125;
            shape-rendering: crispEdges;
        }

        .EXaC circle {
            fill: gray;
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        .siteSpecific, .ipsMotifs, .elmMotifs, .pdbHomology {
            stroke-width: 2px;
            stroke-linecap: round;
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        .siteSpecific {
            stroke-width: 4px;
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        .rowGroupLabel {
            dominant-baseline: hanging;
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            fill-opacity: .25;
            shape-rendering: crispEdges;
            pointer-events: none;
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        .overlay {
            fill: none;
            pointer-events: all;
        }

        .protein-sequence-lane-highlight rect {
            fill: green;
        }

        .aa-letter {
            background-color: orange;
            color: black;
            padding: 3px;
            border-radius: 5px;
        }

        .protein-sequence-lane-highlight text {
            dominant-baseline: central;
            text-anchor: middle;
            font-family: monospace;
            fill: white;
        }

        .alignment-lane text {
            dominant-baseline: central;
            text-anchor: middle;
            font-family: monospace;
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        .alignment-lane-highlight text {
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            font-family: monospace;
        }

        .highlight-closest-line {
            stroke-width: 6px;
            stroke-linecap: round;
            stroke-opacity: 0.75;
        }

        .highlight-closest-text {
            stroke: white;
            stroke-opacity: 0.75;
            stroke-width: 2px;
            paint-order: stroke;
            font-size: 12px;
        }

        .annotation-font-bold {
            font-weight: bold;
        }

        body {
            padding-top: 60px;
        }

        .line-title {
            font-size: 8px;
            font-weight: bold;
            dominant-baseline: hanging;
            text-anchor: end;
        }

        .mult-align-table tbody tr td {
            padding: 0 5px;
        }

        .mult-align-table tbody tr td.mult-align-annotation {
            padding-left: 15px;
            padding-bottom: 5px;
            font-style: italic;
        }

        /* Try to fix intro.js  as per https://github.com/usablica/intro.js/issues/216 */
        .introjs-fixParent, #modal--composer.introjs-fixParent {
            position: absolute;
        }
    </style>

    <!-- Piwik monitoring code. Ask Neil Ihrke and Courtney Kramer about access to piwik-ima.cloudapp.net -->
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</head>

<body>
<nav class="navbar navbar-default navbar-fixed-top">
    <div class="navbar-header">
        <button type="button" class="navbar-toggle collapsed" data-toggle="collapse" data-target="#navbar"
                aria-expanded="false" aria-controls="navbar">
            <span class="sr-only">Toggle navigation</span>
            <span class="icon-bar"></span>
            <span class="icon-bar"></span>
            <span class="icon-bar"></span>
        </button>
        <a class="navbar-brand" href="#" title="Protein Panoramic Annotation Tool"
          data-intro="Welcome to Protein Panoramic Annotation Tool"><b>P<sup>2</sup>T<sup>2</sup></b></a>
    </div>

    <div class="navbar-header">
        <form class="navbar-form navbar-left" id="form_gene">
            <div class="dropdown">
                <input type="text" id="txt_gene_search" class="form-control"
                       placeholder="Please enter a gene symbol"
                       size="30"
                       aria-haspopup="true" aria-expanded="false"
                       data-intro="Type a gene name here and select from the search results. Annotations for the selected gene will be displayed, many of which are links.<br>Click-and-drag to zoom in.<br>Double-click to zoom out.">

                <ul class="dropdown-menu" id="tbl_results" aria-labelledby="txt_gene_search"></ul>
                <input type="submit" id="btn_gene_search" class="btn btn-default" value="Submit">

                <div class="form-group">
                    <div class="spinner">
                    </div>
                </div>

                MSA:
                <select class="form-control" id="msa_seq_type">
                    <option value="Paralogs">Paralogs</option>
                    <!-- <option value="Orthologs">Orthologs</option> -->
                </select>
                <select class="form-control" id="msa_ann_type">
                    <option value="Sites">Sites</option>
                    <!-- <option value="Regions">Regions</option> -->
                </select>

                <div class="form-group">
                    <p id='checkBrowserTypeResult'></p>
                </div>

            </div>
        </form>
        <form class="navbar-form navbar-right" id="form_mark" onsubmit="return false;">
            <div class="form-group">
                <input type="text" id="txt_aa_mark" class="form-control"
                       placeholder="AA position"
                       size="10"
                       data-intro="You can mark a position of interest by typing it here and then clicking [Mark], or shift-clicking any open position in the plot.<br>Clicking on points and lines will bring you to the information source.">
                <input type="submit" id="btn_aa_mark" class="btn btn-default" value="Mark">
                &nbsp;

                <a href="#" class="btn btn-default" onclick="window.location.href='help.html'" data-intro="Check our help page!">
                    <span class="glyphicon glyphicon-info-sign" style="color: #5bc0de"></span>
                    Help
                </a>

                <a href="#" class="btn btn-default" onclick="introJs().setOption('showStepNumbers','false').start();">
                    Intro
                </a>
            </div>
        </form>
    </div> <!-- class="navbar-header" -->
</nav>

<div class="container-fluid">

    <div class="row">
        <div class="col-sm-10">
            <h4 id="status"></h4>

            <div id="graph-container">
                <svg id="graph">
                </svg>
            </div>

            <div class="alert alert-warning" id="warnings" role="alert" style="display:none"></div>
            <div class="alert alert-info" id="notes" role="alert" style="display:none"></div>

            <script>
              $(document).ready(setupView);
              // Check if viewing in supported browsers
              function checkBrowserType() {
                var isChrome = !!window.chrome && !!window.chrome.webstore;
                var isSafari = /^((?!chrome|android).)*safari/i.test(navigator.userAgent);
                var isFirefox = typeof InstallTrigger !== 'undefined';
                if (isChrome || isSafari || isFirefox) {
                  document.getElementById('checkBrowserTypeResult').innerHTML = '';
                }
                else {
                  document.getElementById('checkBrowserTypeResult').innerHTML = '<small>*This visualization was optimized for the Chrome browser.<br>*Use Chrome for more reliable performance.</small>';
                }
              }
              checkBrowserType();
            </script>
        </div> <!-- left column -->
        <div class="col-sm-2" id="details">
        </div> <!-- right column -->

    </div> <!-- row -->
</div> <!-- content container -->

</body>

</html>