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<!DOCTYPE html>
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<head>
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    <meta charset="utf-8" />
    <meta name="viewport" content="width=device-width, initial-scale=1.0" />
    <link rel="shortcut icon" href="./images/favicon-v.ico" type="image/x-icon">
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    <link rel="stylesheet" type="text/css" href="css/icons/fontello/css/animation.css" />
    <link id="seg_highlight" rel="stylesheet" type="text/css" href="css/segmenter_highlight.css" />
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    <link rel="stylesheet" type="text/css" href="css/segmenter_page.css" />
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    <title>Analyze V(D)J recombinations — Vidjil</title>
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</head>
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<body>
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    <div id="body">
        <header id="header_panel" class="panel">
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            <div id='updateIcon' style="display: none; align-items: center; background: blue; width:1px; height:1px; position:absolute;"></div>
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            <h1 id="app_title">Vidjil</h1>
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            <h2 id="tool_title">V(D)J analysis tool</h2>
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            <p>This tool quickly checks the V(D)J designation of a small number of sequences with (possibly incomplete) V(D)J recombinations. To analyze complete NGS RepSeq datasets, use the <a href="http://app.vidjil.org/">full Vidjil platform</a>. Reference: <a href="http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0166126">(Duez, 2016)</a>.
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            </p>
        </header>

        <div id="body_panel" class="flexbox">
            <div id="form_panel" class="panel twopanels_left">
                <form id="form_block" name="form_sequences">
                    <textarea autofocus id="form_sequences" name="sequences" rows="10" cols="80" placeholder="Enter up to 10 sequences in FASTA format..."></textarea>
                    <div id="bottom_form">
                        <input id="form_submit" type="button" value="Submit" />
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                        <button id="btn_exportfasta" class="btn_feature">Export results to FASTA</button>
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                    </div>
                </form>
            </div>

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            <div id="scatter_panel" class="panel twopanels_right">
                <div id="scatter_container" class="vidjil_view visible">
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                </div>
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            </div>
        </div>
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        <div id="segmenter_panel" class="panel">
            <div id="segmenter_container" class="vidjil_view visible">
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            </div>
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        </div>
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        <form id="form"></form>
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        <script data-main="js/app.js" src="js/lib/require.js"></script>
        <script src="js/eventListenerComp.js"></script>
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        <script src="js/segmenter_page.js"></script>
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</body>
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<template id='aligner'>
    <div class="aligner">
            <div class="bot-bar">
                    <div id="cluster" class="aligner-menu" title="Merge the selected clones into a unique cluster"
                            onclick="javascript:self.m.merge()"> Cluster </div>

                    <div id="align" class="aligner-menu" title="Align the sequences"
                            onclick="javascript:segment.toggleAlign()"> Align
                    </div>

                    <div id="segmenter_axis_menu" class="aligner-menu pointer" title="Data columns"> 
                            <span  ><i class="icon-pause-1"></i></span>
                    <span class="menu-content">
                            <div id="segmenter_axis_select">

                            </div>
                    </span>
                    </div>

                    <div id="align-settings" class="aligner-menu" title="Alignement settings">
                            <span ><i class="icon-cog"></i></span>
                            <div class="menu-content">
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                                <label for="highlight_match" title="matches">
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                                            <span><input type="checkbox" id="highlight_match" autocomplete="off"></span>
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                                            <span>Show only mutations</span>
                                </label>    
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                            </div>
                    </div>

                    <div id="align-external-tool" class="aligner-menu" title="External analyis" ><i class="icon-forward-1"></i>
                            <div class="menu-content">
                                    <a id="toIMGT" title="Send sequences to IMGT/V-QUEST and see the results in a new tab"
                                            class="aligner-button" onclick="javascript:segment.sendTo('imgt');"><i class="icon-forward-1"></i> IMGT/V-QUEST</a>
                                    <a id="toIgBlast" title="Send sequences to NCBI IgBlast and see the results in a new tab"
                                            class="aligner-button" onclick="javascript:segment.sendTo('igBlast');"><i class="icon-forward-1"></i> IgBlast</a>
                                    <span class="devel-mode"><a id="toARResT"
                                                    title="Send sequences to ARResT/CompileJunctions and see the results in a new tab"
                                                    class="aligner-button"
                                                    onclick="javascript:segment.sendTo('arrest');"><i class="icon-forward-1"></i> ARResT/CJ</a></span>
                                    <span class="devel-mode"><a id="toCloneDB"
                                                    title="Send sequences to EC-NGS/CloneDB in the background"
                                                    class="aligner-button"
                                                    onclick="javascript:db.callCloneDB(m.getSelected());"><i class="icon-forward-1"></i> CloneDB</a></span>
                                    <a id="toBlast" title="Send sequences to Ensembl Blast and see the results in a new tab"
                                            class="aligner-button" onclick="javascript:segment.sendTo('blast');"><i class="icon-forward-1"></i> Blast</a>
                                    <a id="toAssignSubsets"
                                            title="Send sequences to ARResT/AssignSubsets to classify IGH sequence in a CLL subset"
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                                            class="aligner-button" onclick="javascript:segment.sendTo('assignSubsets');"><i class="icon-forward-1"></i> AssignSubsets</a>
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                            </div>
                    </div>

                    <div id="align-segment-info" class="aligner-menu" title="Sequence features">
                            <span  ><i class="icon-menu"></i></span>
                            <div class="menu-content">
     
                            </div>
                    </div>

                    <div id="align-imgt" class="aligner-menu"
                    title="Sequence features from IMGT [click to reload]" onclick="javascript:segment.sendTo('IMGTSeg');"> <i class="icon-menu"></i> IMGT
                       <span title="reload IMGT info" ></span><i class="demo-icon icon-arrows-ccw"></i></span>
                       <div class="menu-content">

                       </div>
                    </div>
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                    <div class="focus cloneName"></div>
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                    <div id="aligner-stats" class="stats"><span  title="">
                            <span class="stats_content"></span>
                            <a class="focus_selected" id="focus_selected">(focus)</a> 
                            <a class="focus_selected" id="hide_selected">(hide)</a>
                            <span class="button" id="star_selected" title="Tag selected clones">
                                    <i id="tag_icon__multiple" class="icon-star-2"></i></span>
                            <span id="fixsegmenter" class="button">
                                    <i title="fix the segmenter in his position" class="icon-pin-outline"></i></span>
                    </div>
            </div>

            <div class="segmenter" style="height: 100px;">
                    <ul id="listSeq">

                    </ul>
            </div>
    </div>
</template>

<template id="aligner-sequence">
    <li class="sequence-line" style="display: none;">
            <div class="sequence-holder" style="position:relative;">
                    <div class="seq-fixed"></div>
            </div>
    </li>
</template>

<template id="aligner-F">
    <div class="seq-fixed cloneName">
            <span class="nameBox" title="clone name">
                    <span class="delBox"><i class="icon-cancel" title="Unselect this clone"></i></span>
                    <span class="nameBox2"></span>
            </span>
            <span class="axisBox"></span>
            <span class="starBox" id="color60"><i id="tag_icon_60" title="clone_tag" class="icon-star-2"></i></span>
            <span class="infoBox"><i class="icon-info" title="clone information"></i></span>
    </div>
</template>

<template id="aligner-M">
    <div class="seq-mobil">
            <div class="sequence-holder2" style="position:relative;">
                    <div>
                            <div class="seq_layer seq_layer_test"></div>
                            <div class="seq_layer_nuc"></div>
                    </div>

            </div>
    </div>
</template>


<template id="aligner-checkbox">
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        <label title="" class="aligner-checkbox-label" for="highlight_mutation">
            <span><input class="aligner-checkbox-input" type="checkbox" id="highlight_mutation" autocomplete="off" checked></span>
            <span class="aligner-checkbox-text" >Highlight mutation</span>
        </label>
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</template>

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