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<!doctype html>
<html>
<head profile="http://www.w3.org/2005/10/profile">
<meta charset="utf-8">
<title>MaMD Analytical</title>
<link rel="stylesheet" href="assets/css/bootstrap.custom.css">
<link rel="stylesheet" href="assets/css/index.css">
<link rel="stylesheet" href="assets/css/all.min.css" />
<link rel="stylesheet" href="assets/css/jquery.toast.min.css" />
<script type="text/javascript" src="assets/js/all.min.js"></script>
</head>
<body>
<nav class="navbar navbar-expand-lg navbar-dark bg-primary fixed-top d-print-none">
<a class="navbar-brand" href="#">MaMD Analytical (<span id="app-version"></span>)</a>
<button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarColor01" aria-controls="navbarColor01" aria-expanded="false" aria-label="Toggle navigation">
<span class="navbar-toggler-icon"></span>
</button>
<div class="collapse navbar-collapse" id="navbarColor01">
<ul class="navbar-nav mr-auto">
<li class="nav-item active">
<a class="nav-link" href="#"></a>
</li>
</ul>
<form class="my-2 my-lg-0">
<a id="new-button" class="btn btn-secondary" href="#"><i class="far fa-plus-square"></i> New</a>
<a id="open-button" class="btn btn-secondary" href="#"><i class="far fa-folder-open"></i> Open</a>
<a id="save-button" class="btn btn-secondary" href="#"><i class="far fa-save"></i> Save</a>
</form>
</div>
</nav>
<section id="section-setup" class="setup" style="display:none;">
<div class="container">
<div class="row">
<div class="col text-center">
<h1>Welcome to MaMD Analytical</h1>
<p class="small">Before you can begin using this analysis tool, we need to configure a few things first.</p>
<p class="small"><strong>Note: </strong> This may take several minutes to complete.</p>
</div>
</div>
<div class="row">
<div class="col">
<div class="card card-default">
<div class="card-body">
<!-- <div id="setup-rtools" class="setup-item">
<div class="row">
<div class="col text-left">
<span class="setup-item-name">1) RTools</span>
</div>
<div class="col-2 text-right">
<span class="setup-item-status"></span>
</div>
</div>
<div class="pb row">
<div class="col">
<div class="progress">
<div class="progress-bar bg-success" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100">
<span class="sr-only">0% Complete</span>
</div>
</div>
</div>
</div>
<div class="err row" style="display:none;">
<div class="col">
<pre></pre>
</div>
</div>
</div> -->
<div id="setup-r" class="setup-item">
<div class="row">
<div class="col text-left">
<span class="setup-item-name">1) R (v3.6.2)</span>
</div>
<div class="col-2 text-right">
<span class="setup-item-status"></span>
</div>
</div>
<div class="pb row">
<div class="col">
<div class="progress">
<div class="progress-bar bg-success" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100">
<span class="sr-only">0% Complete</span>
</div>
</div>
</div>
</div>
<div class="err row" style="display:none;">
<div class="col">
<pre></pre>
</div>
</div>
</div>
<div id="setup-packages" class="setup-item">
<div class="row">
<div class="col text-left">
<span class="setup-item-name">2) Required R packages <span class="setup-item-package"></span>
</div>
<div class="col-2 text-right">
<span class="setup-item-status">0 of 5</span>
</div>
</div>
<div class="pb row">
<div class="col">
<div class="progress">
<div class="progress-bar bg-success" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100">
<span class="sr-only">0% Complete</span>
</div>
</div>
</div>
</div>
<div class="err row" style="display:none;">
<div class="col">
<pre></pre>
</div>
</div>
</div>
<div class="row">
<div class="col">
<p class="text-center">
<strong>Note: </strong> You may be asked to approve changes a few times during this process.<br />
This is required to configure MaMD Analytical.
</p>
<div id="setup-error-log" style="display:none;">
<div class="col">
<pre></pre>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="row">
<div class="col text-center">
<button id="setup-start" class="btn btn-lg btn-success">Get Started</button>
</div>
</div>
</div>
</section>
<section id="section-main" class="main" style="display:none;">
<div class="container">
<div class="alerts-container d-print-none">
<div id="settings-alert" class="alert alert-danger" role="alert">
The setting for the RScript path is missing. Please check your settings before continuing.
</div>
<div id="offline-alert" class="alert alert-warning" role="alert">
You are currently working offline. Analysis can continue to be peformed, but no updates to the application can be downloaded and applied until an internet connection has been established.
</div>
<div id="update-alert" class="alert" role="alert"></div>
<div id="generic-alert" class="alert" role="alert"></div>
</div>
<ul class="nav nav-tabs d-print-none" id="tabs" role="tablist">
<!-- <li class="nav-item">
<a class="nav-link" id="settings-tab" data-toggle="tab" href="#settings" role="tab" aria-controls="settings" aria-selected="false">Settings</a>
</li> -->
<li class="nav-item">
<a class="nav-link" id="case-tab" data-toggle="tab" href="#case" role="tab" aria-controls="case" aria-selected="false">Case Info</a>
</li>
<li class="nav-item">
<a class="nav-link active" id="analysis-tab" data-toggle="tab" href="#analysis" role="tab" aria-controls="analysis" aria-selected="true">Analysis</a>
</li>
<li class="nav-item">
<a class="nav-link" id="results-tab" data-toggle="tab" href="#results" role="tab" aria-controls="results" aria-selected="false">Results</a>
</li>
</ul>
<div class="tab-content" id="tab-contents">
<div class="tab-pane fade show" id="case" role="tabpanel" aria-labelledby="case-tab">
<div class="card">
<div class="card-header">Case Info</div>
<div class="card-body">
<div class="row">
<div class="col">
<div>
<label for="case_number_input">Case #</label>
<input type="text" id="case_number_input" class="form-control" placeholder="Case #" />
</div>
<div>
<label for="observation_date_input">Observation Date</label>
<input type="text" id="observation_date_input" class="form-control" placeholder="Date" />
</div>
<div>
<label for="analyst_input">Analyst</label>
<input type="text" id="analyst_input" class="form-control" placeholder="Analyst" />
</div>
</div>
</div>
</div>
</div>
</div>
<div class="tab-pane fade show active" id="analysis" role="tabpanel" aria-labelledby="analysis-tab">
<div class="card">
<div class="card-header">Groups (select all that apply)</div>
<div class="card-body">
<div id="group-list"></div>
</div>
</div>
<div class="card">
<div class="card-header">MMS Traits</div>
<div class="card-body">
<div id="trait-list"></div>
</div>
</div>
<div class="card">
<div class="card-header">Run Analysis</div>
<div class="card-body">
<a id="analysis-button" href="#" class="btn btn-success">Run Analysis</a>
<span id="min-selection-warning" style="display:none;" class="inline-warning"></span>
<span id="min-group-warning" style="display:none;" class="inline-warning"></span>
</div>
</div>
</div>
<div class="tab-pane fade" id="results" role="tabpanel" aria-labelledby="results-tab">
<div id="analysis-pending" class="alert alert-warning" role="alert">
Use the Analysis tab to make your selections and click the "Run Analysis" button to see the results.
</div>
<div id="analysis-loading" class="alert alert-info" role="alert">
<p>Please wait while the analysis is running...</p>
<!-- <p>
<strong>Parameters:</strong><br />
<pre id="analysis-parameters"></pre>
</p> -->
</div>
<div id="analysis-error" class="alert alert-danger" role="alert">
<p>There was an error while running the analysis:</p>
<pre id="analysis-error-message"></pre>
</div>
<div id="analysis-results">
<div class="result-area">
<div class="row d-none d-print-block">
<div class="col">
<h2>MaMD Analysis <span id="results-app-version" class="small"></span></h2>
<h4>Case Info</h4>
<p>
<strong>Case #:</strong> <span id="results-case-number"></span><br />
<strong>Observation Date:</strong> <span id="results-observation-date"></span><br />
<strong>Analyst:</strong> <span id="results-analyst"></span><br />
<strong>Exported On:</strong> <span id="results-export-on"></span>
</p>
</div>
</div>
<div class="row">
<div class="col">
<h5>Predicted: <span id="results-ancestry"></span></h5>
<h6>Posterior Probability: <span id="results-probability"></span></h6>
<p>
<strong>Accuracy: </strong><span id="results-accuracy"></span><br />
<strong>95% CI: </strong><span id="results-ci"></span>
</p>
<p>
<strong>Sensitivity: </strong><span id="results-sensitivity"></span><br />
<strong>Specificity: </strong><span id="results-specificity"></span>
</p>
<p>
<button id="export-results-pdf" class="btn btn-success d-print-none">Export to PDF</button>
</p>
<p>
<table id="results-traits" class="table table-bordered table-sm">
<thead class="thead-dark">
<tr>
<th scope="col">Trait</th>
<th scope="col">Score</th>
</tr>
</thead>
<tbody></tbody>
</table>
</p>
</div>
<div class="col">
<canvas id="results-probabilities" width="200" height="200"></canvas>
</div>
</div>
<hr />
<div class="row">
<div class="col">
<table id="results-matrix" class="table table-bordered table-striped table-sm">
<thead></thead>
<tbody></tbody>
</table>
</div>
</div>
</div>
<!-- <h5>Predicted Ancestry</h5>
<pre id="analysis-results-1"></pre>
<h5>Posterior Probabilities</h5>
<pre id="analysis-results-2"></pre>
<h5>Classification Matrix</h5>
<pre id="analysis-results-3"></pre>
<h5>Statistics</h5>
<div id="analysis-results-4" class="result-area">
<div class="table-responsive">
<table class="table table-striped table-hover">
<thead>
<tr>
<th scope="col">Statistic</th>
<th scope="col">Value</th>
</tr>
</thead>
<tbody>
<tr>
<td>Accuracy</td>
<td>0.63347283</td>
</tr>
<tr>
<td>Accuracy</td>
<td>0.63347283</td>
</tr>
</tbody>
</table>
</div>
</div> -->
</div>
</div>
</div>
</div>
</section>
<div class="modal fade" id="settings-modal" role="dialog" tabindex="-1">
<div class="modal-dialog modal-dialog-scrollable modal-lg" role="document">
<div class="modal-content">
<div class="modal-header">
<h5 class="modal-title">Settings / Packages</h5>
<button type="button" class="close" data-dismiss="modal" aria-label="Close">
<span aria-hidden="true">×</span>
</button>
</div>
<div class="modal-body">
<div class="card">
<div class="card-header">Settings</div>
<div class="card-body">
<!-- <div class="row">
<div class="col">
<p>Use the button below to select the location of Rscript, or choose from the list below.</p>
<p><strong>Current RScript Path: </strong><span id="rscript-current-path"></span></p>
<p>
<input type="file" id="settings-rscript-button" value="Select Rscript" />
</p>
<div id="settings-found-rscript"></div>
</div>
</div> -->
<div class="row">
<div class="col">
<p><strong>Current RScript Path: </strong><span id="rscript-current-path"></span></p>
</div>
</div>
<div class="row">
<div class="col">
<div class="form-check">
<input type="checkbox" class="form-check-input" value="" id="settings-auto-update-check" />
<label class="form-check-label" for="settings-auto-update-check">
Automatically check for updates on application start
</label>
</div>
</div>
</div>
</div>
</div>
<div class="card">
<div class="card-header">Required R Packages</div>
<div class="card-body">
<div class="row">
<div class="col">
<p>The following R packages are required for the analysis to run. If you do not have them installed, use the buttons to install them.</p>
<div id="settings-r-packages"></div>
</div>
</div>
</div>
</div>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<div id="trait-template" class="template">
<div class="row">
<div class="col">
<span class="trait-name"></span> (<span class="trait-abbreviation"></span>)
<!-- <a href="#" class="trait-title" data-toggle="popover" data-placement="right"><i class="far fa-question-circle"></i></a> -->
</div>
<div class="col text-center trait-col1"></div>
<div class="col text-center trait-col2"></div>
<div class="col text-center trait-col3"></div>
<div class="col text-center trait-col4"></div>
<div class="col text-center trait-col5"></div>
</div>
</div>
<div id="trait-image-template" class="template">
<a href="#" class="btn btn-default trait-image-button">
<img class="trait-image img-fluid" /><br />
<!-- <a href="#">Details</a> -->
</a>
</div>
<div id="r-package-template" class="template">
<div class="r-package">
<strong class="r-package-name"></strong> <span class="badge"></span>
<a href="#" class="r-package-install-button">Install Package</a>
</div>
</div>
<!-- <script src="assets/js/jquery.min.js"></script>
<script src="assets/js/popper.min.js"></script>
<script src="assets/js/bootstrap.min.js"></script> -->
<script src="assets/js/app.js"></script>
<script src="assets/js/jquery.toast.min.js"></script>
</body>
</html>