<commit_before><div id="config" ng-controller="TooltipCtrl">
  <form name="configForm">
    <h2 style="font-size: 24px;">Graph Controls <span uib-tooltip-template="'helpTool'" tooltip-placement="right" tooltip-class="customClass" tooltip-append-to-body="true" class="glyphicon glyphicon-question-sign" style="float: right; cursor: pointer"></span></h2>

    <script type="text/ng-template" id="helpTool"><p>To pan left or right you can either use the <b>left and right arrow keys</b> or <b>click and drag</b> on graph</p><p><b>Double click</b> on a graph to zoom into that point. Hold <b>shift and double click</b> on a graph to zoom out.</p>
    </script>

    <div><a href="?" class="btn btn-default btn-sm" target="_self">Reset to defaults</a>
    </div>
    <div>
      <label>Zoom:
        <input class="form-control" type="number" name="basesPerGraph"
               style="width:5em;"
               min="100" required
               ng-model="gc.basesPerGraph"
               ng-model-options="{ updateOn: 'default blur', debounce: { 'default': 600, 'blur': 0 } }">
        bases/line
      </label>
      <div class="error" ng-messages="configForm.basesPerGraph.$error">
        <div ng-message="min">Cannot zoom in that far.</div>
        <div ng-message="required">Must specify a zoom level</div>
      </div>
    </div>
    <div>
      <label>Range:</label>
      <input class="form-control" type="number" name="startBase" style="width:6em;"
             min="0" max="{{gc.length}}"
             ng-model="gc.startBase"
             ng-model-options="{ updateOn: 'default blur', debounce: { 'default': 600, 'blur': 0 } }">
      <span>to</span>
      <input class="form-control" type="number" name="endBase" style="width:6em;"
             min="0" max="{{gc.length}}"
             ng-model="gc.endBase"
             ng-model-options="{ updateOn: 'default blur', debounce: { 'default': 600, 'blur': 0 } }">
    </div>
    <div>
      <label>Goto:
        <input class="form-control" type="number" name="gotoBase" style="width:6em;"
               min="0" max="{{gc.length}}"
               ng-model="gc.gotoBase"
               ng-model-options="{ updateOn: 'default blur', debounce: { 'default': 600, 'blur': 0 } }">
      </label>
    </div>
    <div>
      <label>Find ORF by name:<br/>
        <input class="form-control" type="text" name="findORF" style="width:9em;"
               ng-model="gc.findORF"
               ng-model-options="{ updateOn: 'default blur', debounce: { 'default': 1200, 'blur': 0 } }"
               npact-orf-finder
        >
      </label>
      <span ng-show="results && results.length > 0">
        <button ng-click="resultsIndex = resultsIndex - 1" class="arrowbutton">&lt;</button>
        <button ng-click="resultsIndex = resultsIndex + 1" class="arrowbutton">&gt;</button>
        {{resultsIndex + 1}} of {{results.length}}
      </span>
      <span ng-show="results && results.length == 0">
        No results found
      </span>
    </div>
    <div>
      <label>
        <input type="checkbox" ng-model="gc.colorBlindFriendly"
               ng-change="gc.cookiePersist()">
        Color-blind friendly
      </label>
      <br>
      <label>
        <input type="checkbox" ng-model="gc.mycoplasma">
        Mycoplasma
      </label>
    </div>

    <h3>Tracks <a class="small" href="#downloads-tracks" >Download tracks</a></h3>
    <div>
      <div ng-repeat="t in gc.tracks track by t.filename">
        <label class="track-label" title="{{t.filename}}"><input ng-model="t.active" type="checkbox" /> {{t.name}}</label>&nbsp;<small>{{t.id()}}</small>
      </div>
      <div><button class="btn btn-default btn-xs" target="_self">Upload a track</button></div>

    </div>

    <h3>N-Profile Options</h3>
    <div class="nprofile-options">
      <label>Base types profiled:</label><br>
      <checkbox-list id="profile-options" ng-model="gc.nucleotides"
                     title="nucleotide type(s) represented in frame analysis"
                     options="['A', 'C', 'G', 'T']">
    </div>
  </form>
</div>
<commit_msg>remove annotations from track names<commit_after><div id="config" ng-controller="TooltipCtrl">
  <form name="configForm">
    <h2 style="font-size: 24px;">Graph Controls <span uib-tooltip-template="'helpTool'" tooltip-placement="right" tooltip-class="customClass" tooltip-append-to-body="true" class="glyphicon glyphicon-question-sign" style="float: right; cursor: pointer"></span></h2>

    <script type="text/ng-template" id="helpTool"><p>To pan left or right you can either use the <b>left and right arrow keys</b> or <b>click and drag</b> on graph</p><p><b>Double click</b> on a graph to zoom into that point. Hold <b>shift and double click</b> on a graph to zoom out.</p>
    </script>

    <div><a href="?" class="btn btn-default btn-sm" target="_self">Reset to defaults</a>
    </div>
    <div>
      <label>Zoom:
        <input class="form-control" type="number" name="basesPerGraph"
               style="width:5em;"
               min="100" required
               ng-model="gc.basesPerGraph"
               ng-model-options="{ updateOn: 'default blur', debounce: { 'default': 600, 'blur': 0 } }">
        bases/line
      </label>
      <div class="error" ng-messages="configForm.basesPerGraph.$error">
        <div ng-message="min">Cannot zoom in that far.</div>
        <div ng-message="required">Must specify a zoom level</div>
      </div>
    </div>
    <div>
      <label>Range:</label>
      <input class="form-control" type="number" name="startBase" style="width:6em;"
             min="0" max="{{gc.length}}"
             ng-model="gc.startBase"
             ng-model-options="{ updateOn: 'default blur', debounce: { 'default': 600, 'blur': 0 } }">
      <span>to</span>
      <input class="form-control" type="number" name="endBase" style="width:6em;"
             min="0" max="{{gc.length}}"
             ng-model="gc.endBase"
             ng-model-options="{ updateOn: 'default blur', debounce: { 'default': 600, 'blur': 0 } }">
    </div>
    <div>
      <label>Goto:
        <input class="form-control" type="number" name="gotoBase" style="width:6em;"
               min="0" max="{{gc.length}}"
               ng-model="gc.gotoBase"
               ng-model-options="{ updateOn: 'default blur', debounce: { 'default': 600, 'blur': 0 } }">
      </label>
    </div>
    <div>
      <label>Find ORF by name:<br/>
        <input class="form-control" type="text" name="findORF" style="width:9em;"
               ng-model="gc.findORF"
               ng-model-options="{ updateOn: 'default blur', debounce: { 'default': 1200, 'blur': 0 } }"
               npact-orf-finder
        >
      </label>
      <span ng-show="results && results.length > 0">
        <button ng-click="resultsIndex = resultsIndex - 1" class="arrowbutton">&lt;</button>
        <button ng-click="resultsIndex = resultsIndex + 1" class="arrowbutton">&gt;</button>
        {{resultsIndex + 1}} of {{results.length}}
      </span>
      <span ng-show="results && results.length == 0">
        No results found
      </span>
    </div>
    <div>
      <label>
        <input type="checkbox" ng-model="gc.colorBlindFriendly"
               ng-change="gc.cookiePersist()">
        Color-blind friendly
      </label>
      <br>
      <label>
        <input type="checkbox" ng-model="gc.mycoplasma">
        Mycoplasma
      </label>
    </div>

    <h3>Tracks <a class="small" href="#downloads-tracks" >Download tracks</a></h3>
    <div>
      <div ng-repeat="t in gc.tracks track by t.filename">
        <label class="track-label" title="{{t.filename}}"><input ng-model="t.active" type="checkbox" /> {{t.name}}</label>
      </div>
      <div><button class="btn btn-default btn-xs" target="_self">Upload a track</button></div>

    </div>

    <h3>N-Profile Options</h3>
    <div class="nprofile-options">
      <label>Base types profiled:</label><br>
      <checkbox-list id="profile-options" ng-model="gc.nucleotides"
                     title="nucleotide type(s) represented in frame analysis"
                     options="['A', 'C', 'G', 'T']">
    </div>
  </form>
</div>

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