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VisualizeUploadedData.html
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<!doctype html>
<html ng-app="IPSA">
<head>
<meta charset="utf-8"/>
<!-- jQuery -->
<script src="support/js/external/jquery.min.js"></script>
<!-- angularJS scripts -->
<script src="support/js/external/angular.min.js"></script>
<script src="support/js/external/angular-animate.min.js"></script>
<script src="support/js/external/angular-sanitize.min.js"></script>
<!-- Various angular wrappers -->
<!-- Bootstrap -->
<script src="support/js/external/ui-bootstrap-tpls-2.5.0.min.js"></script>
<!-- Select2 -->
<script src="support/js/external/select.min.js"></script>
<!-- Handsontable -->
<script src="support/js/external/handsontable.full.min.js"></script>
<script src="support/js/external/ngHandsontable.min.js"></script>
<!-- D3 -->
<script src="support/js/external/d3.v3.min.js" charset="utf-8"></script>
<script src="support/js/external/d3-ease.v1.min.js"></script>
<!-- LoDash, object manipulation -->
<script src="support/js/external/lodash.min.js" charset="utf-8"></script>
<!-- mini-colors -->
<script src="support/js/external/jquery.minicolors.min.js"></script>
<script src="support/js/external/angular-minicolors.min.js"></script>
<!-- SVG Downloader Thx Hypercubed -->
<script src="support/js/external/angular-downloadsvg-directive.js"></script>
<!-- ngStorage -->
<script src="support/js/external/ngStorage.js"></script>
<!-- Dain Scripts -->
<script src="support/js/internal/VisualizeUploadedData.js"></script>
<script src="support/js/internal/bulk_controllers.js"></script>
<script src="support/js/internal/IPSA.js"></script>
<!-- D3-Tip -->
<script src="support/js/external/d3-tip.js"></script>
<!-- css links here -->
<link href="support/css/external/bootstrap.min.css" rel="stylesheet">
<link href="support/css/external/select.min.css" rel="stylesheet">
<link href="support/css/external/handsontable.full.min.css" rel="stylesheet">
<link href="support/css/external/jquery.minicolors.min.css" rel="stylesheet">
<link href="support/css/external/Montserrat.css" rel="stylesheet">
<link href="support/css/external/Open+Sans.css" rel="stylesheet">
<link href="support/css/external/Inconsolata.css" rel="stylesheet">
<link href="support/css/internal/PeptideAnnotator.css" rel="stylesheet">
</head>
<body>
<nav class="navbar navbar-default navbar-static-top" role="navigation">
<div class="navbar-header">
<a class="navbar-brand">
IPSA
</a>
</div>
<ul class="nav navbar-nav">
<li class="divider-vertical"></li>
<li><a href="PeptideAnnotator.html">Single Spectrum Annotator</a></li>
<li class="divider-vertical"></li>
<li><a href="BulkDataUpload.html">Bulk Data Upload</a></li>
<li class="divider-vertical"></li>
<li class="active"><a href="VisualizeUploadedData.html">Visualize Uploaded Data</a></li>
<li class="divider-vertical"></li>
<li><a href="support/css/external/woff2/Fonts.zip">Download Used Fonts</a></li>
</ul>
<ul class="nav navbar-nav navbar-right">
<ul><a href="http://coonlabs.com"><img src="support/images/CoonLogo.png"></a></ul>
</ul>
</nav>
<div class="container-fluid">
<div ng-controller="MasterCtrl">
<div class="row">
<div ng-controller="PeptideCtrl">
<div ng-controller="GraphCtrl">
<div class="col-md-5">
<div class="panel panel-default">
<div class="panel-heading">
<h3 class="panel-title">Annotation Options</h3>
</div>
<div class="panel-body">
<div class="col-md-12">
<div class="row">
<div class="col-md-12">
<label>Select Uploaded Sequence</label>
<div class="form-group">
<ui-select ng-model="idObject.selectedSequence" search-enabled="true">
<ui-select-match placeholder="Click and type/scroll to search for peptide by sequence, scan, etc.">
<span ng-bind-html="formatUploadedIdOption(idObject.selectedSequence)"></span>
</ui-select-match>
<ui-select-choices repeat="id in ids | filter: $select.search | orderBy:'scanNumber'| limitTo: 100">
<span ng-bind-html="formatUploadedIdOption(id)"></span>
</ui-select-choices>
</ui-select>
</div>
</div>
</div>
<div class="row">
<div class="col-md-9">
<label>Peptide Sequence</label>
<div class="input-group-md">
<input type="text" class="form-control" placeholder="Enter sequence here..." ng-model="peptide.sequence" ng-blur="validateSequence()">
</div>
</div>
<div class="col-md-3">
<label>Precursor Charge</label>
<div class="input-group-md">
<input type="number" class="form-control" placeholder="Undefined..." ng-model="idObject.selectedSequence.charge" readonly>
</div>
</div>
</div>
<br/>
<div ng-controller="DataCtrl">
<div class="row">
<div class="col-md-4">
<label for="charge">Max Fragment Charge</label>
<div class="input-group-md">
<input type="number" class="form-control" id="charge" placeholder=1 min="{{peptide.fragmentMin}}" max="{{peptide.fragmentMax}}" ng-model="peptide.charge" ng-blur="validateFragmentCharge()">
</div>
</div>
<div class="col-md-4">
<label>Fragment Tolerance (+/-)</label>
<div class="input-group">
<input type="number" class="form-control" ng-model="cutoffs.tolerance" min="0" ng-blur="validateTolerance()">
<span class="input-group-btn">
<button class="btn btn-primary" type="button" ng-click="swapToleranceType()" >{{cutoffs.toleranceType}}</button>
</span>
</div>
</div>
<div class="col-md-4">
<label>Matching Threshold</label>
<div class="input-group">
<input type="number" class="form-control" ng-model="cutoffs.matchingCutoff" min="0" ng-blur="validateThreshold()">
<span class="input-group-btn">
<button class="btn btn-primary" type="button" ng-click="swapMatchingType()">{{cutoffs.matchingType}}</button>
</span>
</div>
</div>
</div>
<br/>
<div class="row">
<div class="col-md-4">
<label>N-terminal</label>
<div class="btn-group">
<label class="btn btn-fragment" ng-model="checkModel.a.selected" uib-btn-checkbox>{{checkModel.a.label}}</label>
<label class="btn btn-fragment" ng-model="checkModel.b.selected" uib-btn-checkbox>{{checkModel.b.label}}</label>
<label class="btn btn-fragment" ng-model="checkModel.c.selected" uib-btn-checkbox>{{checkModel.c.label}}</label>
<label class="btn btn-fragment" ng-model="checkModel.C.selected" uib-btn-checkbox>{{checkModel.C.label}}</label>
</div>
</div>
<div class="col-md-4">
<label>C-terminal</label>
<div class="btn-group">
<label class="btn btn-fragment" ng-model="checkModel.x.selected" uib-btn-checkbox>{{checkModel.x.label}}</label>
<label class="btn btn-fragment" ng-model="checkModel.y.selected" uib-btn-checkbox>{{checkModel.y.label}}</label>
<label class="btn btn-fragment" ng-model="checkModel.z.selected" uib-btn-checkbox>{{checkModel.z.label}}</label>
<label class="btn btn-fragment" ng-model="checkModel.Z.selected" uib-btn-checkbox>{{checkModel.Z.label}}</label>
</div>
</div>
<div class="col-md-4">
<label>Neutral Losses</label>
<div class="btn-group">
<label class="btn btn-fragment" ng-model="checkModel.H2O.selected" uib-btn-checkbox>-H<sub>2</sub>O</label>
<label class="btn btn-fragment" ng-model="checkModel.NH3.selected" uib-btn-checkbox>-NH<sub>3</sub></label>
<label class="btn btn-fragment" ng-model="checkModel.CO2.selected" uib-btn-checkbox>-CO<sub>2</sub></label>
</div>
</div>
</div>
<br/>
<div class="row">
<div class="col-md-12">
<label for="dataFormat">Select Peptide Modifications</label>
</div>
<div class="col-md-12">
<div ng-controller="ModCtrl">
<div class="form-group-lg">
<ui-select multiple ng-model="peptide.mods" search-enabled="true">
<ui-select-match placeholder="Select peptide modifications..."> <span ng-bind-html="formatModificationOption($item)"></span> </ui-select-match>
<ui-select-choices repeat="mod in mods | filter: $select.search | orderBy:'name' | limitTo: 250" > <span ng-mouseenter="$select.setActiveItem()" ng-bind-html="formatModificationOption(mod)"></span> </ui-select-choices>
</ui-select>
</div>
</div>
</div>
</div>
<br/>
<div ng-controller="ColorCtrl">
<div class="row">
<div class="col-md-3" ng-hide="!checkModel.a.selected">
<label for="wheel-demo">{{checkModel.a.label}}</label>
<input minicolors="wheelsettings" id="wheel-demo" class="form-control" type="text" ng-model="checkModel.a.color">
</div>
<div class="col-md-3" ng-hide="!checkModel.b.selected">
<label for="wheel-demo">{{checkModel.b.label}}</label>
<input minicolors="wheelsettings" id="wheel-demo" class="form-control" type="text" ng-model="checkModel.b.color">
</div>
<div class="col-md-3" ng-hide="!checkModel.c.selected">
<label for="wheel-demo">{{checkModel.c.label}}</label>
<input minicolors="wheelsettings" id="wheel-demo" class="form-control" type="text" ng-model="checkModel.c.color">
</div>
<div class="col-md-3" ng-hide="!checkModel.C.selected">
<label for="wheel-demo">{{checkModel.C.label}}</label>
<input minicolors="wheelsettings" id="wheel-demo" class="form-control" type="text" ng-model="checkModel.C.color">
</div>
<div class="col-md-3" ng-hide="!checkModel.x.selected">
<label for="wheel-demo">{{checkModel.x.label}}</label>
<input minicolors="wheelsettings" id="wheel-demo" class="form-control" type="text" ng-model="checkModel.x.color">
</div>
<div class="col-md-3" ng-hide="!checkModel.y.selected">
<label for="wheel-demo">{{checkModel.y.label}}</label>
<input minicolors="wheelsettings" id="wheel-demo" class="form-control" type="text" ng-model="checkModel.y.color">
</div>
<div class="col-md-3" ng-hide="!checkModel.z.selected">
<label for="wheel-demo">{{checkModel.z.label}}</label>
<input minicolors="wheelsettings" id="wheel-demo" class="form-control" type="text" ng-model="checkModel.z.color">
</div>
<div class="col-md-3" ng-hide="!checkModel.Z.selected">
<label for="wheel-demo">{{checkModel.Z.label}}</label>
<input minicolors="wheelsettings" id="wheel-demo" class="form-control" type="text" ng-model="checkModel.Z.color">
</div>
<div class="col-md-3">
<label for="wheel-demo">Precursor</label>
<input
minicolors="wheelsettings"
id="wheel-demo"
class="form-control"
type="text"
ng-model="checkModel.precursor.color">
</div>
<div class="col-md-3">
<label for="wheel-demo">Unassigned</label>
<input
minicolors="wheelsettings"
id="wheel-demo"
class="form-control"
type="text"
ng-model="checkModel.unassigned.color">
</div>
</div>
</div>
<br/>
<div class="row">
<div class="col-md-12">
<button type="submit" class="btn btn-success" ng-click="processData()" ng-disabled="!idObject.selectedSequence">Generate Chart</button>
<button class="btn btn-primary" ng-click="downloadData()" ng-disabled="!idObject.selectedSequence">Export Data</button>
<button svg-download title="{{peptide.sequence}}" class="btn btn-primary">Download as SVG</button>
<button class="btn btn-danger" type="button" ng-disabled="ids.length <= 0 || isProcessing" ng-click="AnnotateAllData()">
<Span ng-hide="isProcessing">Export Fragment Ion Statistics</Span>
<Span ng-show="isProcessing">Processing. This May Take a Few Minutes...</Span>
</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div class="col-md-7">
<div annotated-spectrum plotdata="set.plotData" peptide="set.peptide" settings="set.settings" class="content"></div>
<form role="form" ng-init="randomize()"></form>
</div>
</div>
</div>
</div>
</div>
</div>
</body>
</html>