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var newRefLimit = "50"; set_badges(newQueryLimit, newRefLimit); set_state_ref_controls("show"); recover_query_ids(); } // recovering the original query IDs function recover_query_ids() { var queryAccs = document.getElementById('queryAccessions').value; var refAccs = document.getElementById('refAccessions').value; var queryArr = queryAccs.split("\n"); var refArr = refAccs.split("\n"); if (typeof queryArr == 'undefined' || queryArr.length < 1) { queryArr = []; } if (typeof refArr == 'undefined' || refArr.length < 1) { refArr = []; } var arrDiff = queryArr.filter(x => refArr.indexOf(x) === -1); // get unique array items var joinedAccsArr = arrDiff.filter(function(item, pos){ return arrDiff.indexOf(item)== pos; }); joinedAccsArr = joinedAccsArr.sort(); joinedAccsString = joinedAccsArr.join("\n"); joinedAccsString = joinedAccsString.trim(); document.getElementById('queryAccessions').value = joinedAccsString; } function similarities_only() { var newQueryLimit = "10"; var newRefLimit = "50"; set_badges(newQueryLimit, newRefLimit); // now show all previously unnecessary controls again: set_state_ref_controls("show"); recover_query_ids(); } function tree_only() { var newQueryLimit = "60"; var newRefLimit = "0"; // "50"; set_badges(newQueryLimit, newRefLimit); set_state_ref_controls("hide"); // adding accessions from both the query and reference accession fields var queryAccs = document.getElementById('queryAccessions').value; var refAccs = document.getElementById('refAccessions').value; var queryArr = queryAccs.split("\n"); var refArr = refAccs.split("\n"); if (typeof queryArr == 'undefined' || queryArr.length < 1) { queryArr = []; } if (typeof refArr == 'undefined' || refArr.length < 1) { refArr = []; } var joinedAccsArr = queryArr.concat(refArr); // get unique array items joinedAccsArr = joinedAccsArr.filter(function(item, pos){ return joinedAccsArr.indexOf(item)== pos; }); joinedAccsArr = joinedAccsArr.sort(); joinedAccsString = joinedAccsArr.join("\n"); joinedAccsString = joinedAccsString.trim(); document.getElementById('queryAccessions').value = joinedAccsString; } // this function simply sets the visible state of all controls // related to the reference function set_state_ref_controls(visibleState) { if (visibleState == "hide") { // show it: $("#refAccessions").addClass('hidden'); $("#refAccessionsLabel").addClass('hidden'); $("#refAccessionsTooltip").addClass('hidden'); $("#refSequences").addClass('hidden'); $("#refGenomesTooltip").addClass('hidden'); $("#refGenomesLabel").addClass('hidden'); $("#textRefBadge").addClass('hidden'); $("#numRefBadge").addClass('hidden'); } else if (visibleState == "show") { // hide it: remove all unnecessary controls: $("#refAccessions").removeClass('hidden'); $("#refAccessionsLabel").removeClass('hidden'); $("#refAccessionsTooltip").removeClass('hidden'); $("#refSequences").removeClass('hidden'); $("#refGenomesTooltip").removeClass('hidden'); $("#refGenomesLabel").removeClass('hidden'); $("#textRefBadge").removeClass('hidden'); $("#numRefBadge").removeClass('hidden'); } } function set_badges(newQueryLimit, newRefLimit) { // finding the inline span element and changing // the value of the **query badge** var span = document.getElementById('numQueryBadge'); while (span.firstChild) { span.removeChild(span.firstChild); } span.appendChild(document.createTextNode(newQueryLimit)); // finding the inline span element and changing // the value of the **reference badge** var span = document.getElementById('numRefBadge'); while (span.firstChild) { span.removeChild(span.firstChild); } span.appendChild(document.createTextNode(newRefLimit)); } </script>  <div class="container"> <div class="page-header"> <h1>Phylogeny Server<small> Gene phylogenies and similarities</small></h1> </div> <div class="alert alert-warning" role="alert"> <span class="glyphicon glyphicon-exclamation-sign"></span> <b>Note:</b> the primary citation for the DSMZ single-gene phylogeny server has changed. Details are found <a href="phylogeny-service_background.php" class="ing">here</a>. <button type="button" class="close" data-dismiss="alert" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="alert alert-info" role="alert"> <span class="glyphicon glyphicon-exclamation-sign"></span> Want to analyze <b><a href="ggdc.php">microbial</a></b> or <b><a href="victor.php">viral</a></b> genomes instead? <button type="button" class="close" data-dismiss="alert" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="panel panel-primary">  <div class="panel-heading" id="submissionForm"> Submission Form <div class="pull-right"> <span class="badge badge-pill badge-danger"><a href="https://ggdc-test.dsmz.de/phylogeny-service_background.php" class="ing">How to cite</a></span> </div> </div> <div class="panel-body"> <form class="form-horizontal" role="form" method="post" action="submit_phylo_job.php" enctype="multipart/form-data" name="Form"> <fieldset>  <div class="form-group"> <label class="col-md-4 control-label" for="selectbasic">Requested calculations</label> <div class="col-md-4"> <div class="text-center">  <div class="btn-group" data-toggle="buttons"> <label class="btn btn-primary active"> <input type="radio" name="options" id="option1" autocomplete="off" value="both" onchange="tree_and_similarities()">tree & similarities </label> <label class="btn btn-primary"> <input type="radio" name="options" id="option2" autocomplete="off" value="similarities" onchange="similarities_only()">similarities only </label> <label class="btn btn-primary"> <input type="radio" name="options" id="option3" autocomplete="off" value="tree" onchange="tree_only()">tree only </label> </div> </div> </div>  <a href="#"><span class="glyphicon glyphicon-question-sign" data-toggle="tooltip" data-original-title="Select the type of analysis you need"></span></a> </div>  <div class="form-group"> <label class="col-md-4 control-label" id="queryAccessionsLabel" for="textarea">Query accessions</label> <div class="col-md-4"> <textarea class="form-control" id="queryAccessions" name="queryAccessions" rows="4" placeholder="one row per organism (see FAQ for valid formats)"></textarea> </div>  <a href="#"><span class="glyphicon glyphicon-question-sign" data-toggle="tooltip" data-original-title="Enter one GenBank accession per line for each query organism you want to investigate. If similarity calculation is selected, the query accessions/sequences will be compared against the reference sequences."></span></a> </div>  <div class="form-group"> <label class="col-md-4 control-label" for="filebutton">Query sequences</label> <div class="col-md-4"> <input id="querySequences" name="querySequences" class="input-file" type="file"> </div>  <a href="#"><span class="glyphicon glyphicon-question-sign" data-toggle="tooltip" data-original-title="Select a single multi-FASTA file with the sequences of all query organisms you want to investigate. If similarity calculation is selected, the query sequences/accessions will be compared against the reference sequences."></span></a> </div>  <div class="form-group"> <label class="col-md-4 control-label"></label> <div class="col-md-4"> <button class="btn btn-default disabled" type="button" id="textQueryBadge" name="textQueryBadge"> Max. query accessions: <span class="badge" id="numQueryBadge" name="numQueryBadge">10</span> </button> </div> </div>  <div class="form-group"> <label class="col-md-4 control-label" id="refAccessionsLabel" for="textarea">Reference accessions</label> <div class="col-md-4"> <textarea class="form-control" id="refAccessions" name="refAccessions" rows="4" placeholder="one row per organism (see FAQ for valid formats)"> KP893899 </textarea> </div>  <a href="#"><span class="glyphicon glyphicon-question-sign" id="refAccessionsTooltip" data-toggle="tooltip" data-original-title="Enter one GenBank accession per line for each reference organism you want to investigate."></span></a> </div>  <div class="form-group"> <label class="col-md-4 control-label" id="refGenomesLabel" for="filebutton">Reference sequences</label> <div class="col-md-4"> <input id="refSequences" name="refSequences" class="input-file" type="file"> </div>  <a href="#"><span class="glyphicon glyphicon-question-sign" id="refGenomesTooltip" data-toggle="tooltip" data-original-title="Select a single multi-FASTA file with the sequences of all reference organisms you want to investigate."></span></a> </div>  <div class="form-group"> <label class="col-md-4 control-label"></label> <div class="col-md-4"> <button class="btn btn-default disabled" type="button" id="textRefBadge" name="textRefBadge"> Max. reference accessions/sequences: <span class="badge" id="numRefBadge">50</span> </button> </div> </div> <div class="form-group"> <label class="col-md-4 control-label" for="inputEmail">Contact details</label> <label for="inputEmail" class="sr-only">Email address</label> <div class="col-md-4"> <input type="email" name="email" id="email" class="form-control" placeholder="mail@example.com" required autofocus> </div>  <a href="#"><span class="glyphicon glyphicon-question-sign" data-toggle="tooltip" data-original-title="Please check your e-mail spam folder if the GGDC results message does not arrive in time."></span></a> </div>  <div class="form-group"> <label class="col-md-4 control-label" for="singlebutton"></label> <div class="col-md-4"> <div class="text-center"> <button id="singlebutton" name="singlebutton" class="btn btn-primary">Submit</button> </div> </div> </div>  <div class="form-group"> <label class="col-md-4 control-label" for="progressbar">Current slot usage</label> <div class="col-md-4"> </br> <div class="progress"> <div class="progress-bar progress-bar-success" role="progressbar" aria-valuenow="4" aria-valuemin="0" aria-valuemax="100" style="width: 4%;"> 4% </div> </div> </div> </div> </div>  </div>     <footer> <div class="footer-logo"> <a href="http://www.dsmz.de"><img src="img/DSMZLogo.svg" height="75px"></a> <p>  © 2012-2024 Leibniz Institute DSMZ · <a href="faq.php#qgen0">Privacy</a> · <a href="legalnotice.php">Terms</a></p> <p class="pull-right"><a href="#">Back to top   </a></p> </div> </footer> </div>     <script src="assets/js/vendor/jquery.min.js"></script> <script src="dist/js/bootstrap.min.js"></script>  <script src="assets/js/vendor/holder.min.js"></script>  <script src="assets/js/ie10-viewport-bug-workaround.js"></script> <script src="js/enable_supplementary_functions.js"></script> </body> </html>

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