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<title>All Classes</title>
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<h1 class="bar">All Classes</h1>
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<ul>
<li><a href="edu/msu/cme/rdp/classifier/comparison/AbstractNode.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">AbstractNode</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/distance/BoxPlotUtils.html" title="class in edu.msu.cme.rdp.classifier.train.validation.distance" target="classFrame">BoxPlotUtils</a></li>
<li><a href="edu/msu/cme/rdp/classifier/rrnaclassifier/ClassificationParser.html" title="class in edu.msu.cme.rdp.classifier.rrnaclassifier" target="classFrame">ClassificationParser</a></li>
<li><a href="edu/msu/cme/rdp/classifier/ClassificationResult.html" title="class in edu.msu.cme.rdp.classifier" target="classFrame">ClassificationResult</a></li>
<li><a href="edu/msu/cme/rdp/classifier/io/ClassificationResultFormatter.html" title="class in edu.msu.cme.rdp.classifier.io" target="classFrame">ClassificationResultFormatter</a></li>
<li><a href="edu/msu/cme/rdp/classifier/io/ClassificationResultFormatter.FORMAT.html" title="enum in edu.msu.cme.rdp.classifier.io" target="classFrame">ClassificationResultFormatter.FORMAT</a></li>
<li><a href="edu/msu/cme/rdp/classifier/Classifier.html" title="class in edu.msu.cme.rdp.classifier" target="classFrame">Classifier</a></li>
<li><a href="edu/msu/cme/rdp/classifier/ClassifierCmd.html" title="class in edu.msu.cme.rdp.classifier" target="classFrame">ClassifierCmd</a></li>
<li><a href="edu/msu/cme/rdp/classifier/utils/ClassifierFactory.html" title="class in edu.msu.cme.rdp.classifier.utils" target="classFrame">ClassifierFactory</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/gridware/ClassifierGridware.html" title="class in edu.msu.cme.rdp.multicompare.gridware" target="classFrame">ClassifierGridware</a></li>
<li><a href="edu/msu/cme/rdp/classifier/cli/ClassifierMain.html" title="class in edu.msu.cme.rdp.classifier.cli" target="classFrame">ClassifierMain</a></li>
<li><a href="edu/msu/cme/rdp/classifier/utils/ClassifierSequence.html" title="class in edu.msu.cme.rdp.classifier.utils" target="classFrame">ClassifierSequence</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/ClassifierTraineeMaker.html" title="class in edu.msu.cme.rdp.classifier.train" target="classFrame">ClassifierTraineeMaker</a></li>
<li><a href="edu/msu/cme/rdp/taxatree/utils/ClassifierTreeBuilder.html" title="class in edu.msu.cme.rdp.taxatree.utils" target="classFrame">ClassifierTreeBuilder</a></li>
<li><a href="edu/msu/cme/rdp/taxatree/utils/ClassifierTreeBuilder.ClassifierTaxonFactory.html" title="interface in edu.msu.cme.rdp.taxatree.utils" target="classFrame"><i>ClassifierTreeBuilder.ClassifierTaxonFactory</i></a></li>
<li><a href="edu/msu/cme/rdp/classifier/cli/CmdOptions.html" title="class in edu.msu.cme.rdp.classifier.cli" target="classFrame">CmdOptions</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/leaveoneout/CompareMisclassified.html" title="class in edu.msu.cme.rdp.classifier.train.validation.leaveoneout" target="classFrame">CompareMisclassified</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/distance/CompareTrainingSets.html" title="class in edu.msu.cme.rdp.classifier.train.validation.distance" target="classFrame">CompareTrainingSets</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/ComparisonBrowserBean.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">ComparisonBrowserBean</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/ComparisonBrowserNode.html" title="interface in edu.msu.cme.rdp.classifier.comparison" target="classFrame"><i>ComparisonBrowserNode</i></a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/ComparisonCmd.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">ComparisonCmd</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/ComparisonResultTreeSet.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">ComparisonResultTreeSet</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/ComparisonResultTreeSet.ComparisonResultComparator.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">ComparisonResultTreeSet.ComparisonResultComparator</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/CopyNumberParser.html" title="class in edu.msu.cme.rdp.classifier.train" target="classFrame">CopyNumberParser</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/CorrectAssignment.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">CorrectAssignment</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/crossvalidate/CrossValidate.html" title="class in edu.msu.cme.rdp.classifier.train.validation.crossvalidate" target="classFrame">CrossValidate</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/crossvalidate/CrossValidateMain.html" title="class in edu.msu.cme.rdp.classifier.train.validation.crossvalidate" target="classFrame">CrossValidateMain</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/DecisionMaker.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">DecisionMaker</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/visitors/DefaultPrintVisitor.html" title="class in edu.msu.cme.rdp.multicompare.visitors" target="classFrame">DefaultPrintVisitor</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/visitors/EstimateSPrintVisitor.html" title="class in edu.msu.cme.rdp.multicompare.visitors" target="classFrame">EstimateSPrintVisitor</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/movingwindow/FindWindowFrame.html" title="class in edu.msu.cme.rdp.classifier.train.validation.movingwindow" target="classFrame">FindWindowFrame</a></li>
<li><a href="edu/msu/cme/rdp/classifier/GenusWordConditionalProb.html" title="class in edu.msu.cme.rdp.classifier" target="classFrame">GenusWordConditionalProb</a></li>
<li><a href="edu/msu/cme/rdp/classifier/io/GenusWordProbFileParser.html" title="class in edu.msu.cme.rdp.classifier.io" target="classFrame">GenusWordProbFileParser</a></li>
<li><a href="edu/msu/cme/rdp/classifier/HierarchyTree.html" title="class in edu.msu.cme.rdp.classifier" target="classFrame">HierarchyTree</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/HierarchyTree.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">HierarchyTree</a></li>
<li><a href="edu/msu/cme/rdp/classifier/utils/HierarchyVersion.html" title="class in edu.msu.cme.rdp.classifier.utils" target="classFrame">HierarchyVersion</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/leaveoneout/LeaveOneOutTester.html" title="class in edu.msu.cme.rdp.classifier.train.validation.leaveoneout" target="classFrame">LeaveOneOutTester</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/leaveoneout/LeaveOneOutTesterMain.html" title="class in edu.msu.cme.rdp.classifier.train.validation.leaveoneout" target="classFrame">LeaveOneOutTesterMain</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/LineageSequence.html" title="class in edu.msu.cme.rdp.classifier.train" target="classFrame">LineageSequence</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/LineageSequenceParser.html" title="class in edu.msu.cme.rdp.classifier.train" target="classFrame">LineageSequenceParser</a></li>
<li><a href="edu/msu/cme/rdp/classifier/io/LogWordPriorFileParser.html" title="class in edu.msu.cme.rdp.classifier.io" target="classFrame">LogWordPriorFileParser</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/Main.html" title="class in edu.msu.cme.rdp.multicompare" target="classFrame">Main</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/movingwindow/MainMovingWindow.html" title="class in edu.msu.cme.rdp.classifier.train.validation.movingwindow" target="classFrame">MainMovingWindow</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/MCSample.html" title="class in edu.msu.cme.rdp.multicompare" target="classFrame">MCSample</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/MCSamplePrintUtil.html" title="class in edu.msu.cme.rdp.multicompare" target="classFrame">MCSamplePrintUtil</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/MCSampleResult.html" title="class in edu.msu.cme.rdp.multicompare" target="classFrame">MCSampleResult</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/taxon/MCTaxon.html" title="class in edu.msu.cme.rdp.multicompare.taxon" target="classFrame">MCTaxon</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/MergeTaxonCount.html" title="class in edu.msu.cme.rdp.multicompare" target="classFrame">MergeTaxonCount</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/MultiClassifier.html" title="class in edu.msu.cme.rdp.multicompare" target="classFrame">MultiClassifier</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/MultiClassifierResult.html" title="class in edu.msu.cme.rdp.multicompare" target="classFrame">MultiClassifierResult</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/NameRankDupException.html" title="class in edu.msu.cme.rdp.classifier.train" target="classFrame">NameRankDupException</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/NBClassifier.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">NBClassifier</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/distance/PairwiseSeqDistance.html" title="class in edu.msu.cme.rdp.classifier.train.validation.distance" target="classFrame">PairwiseSeqDistance</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/PixelCalculatorBean.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">PixelCalculatorBean</a></li>
<li><a href="edu/msu/cme/rdp/classifier/io/ProbIndexFileParser.html" title="class in edu.msu.cme.rdp.classifier.io" target="classFrame">ProbIndexFileParser</a></li>
<li><a href="edu/msu/cme/rdp/classifier/RankAssignment.html" title="class in edu.msu.cme.rdp.classifier" target="classFrame">RankAssignment</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/RawGenusWordConditionalProb.html" title="class in edu.msu.cme.rdp.classifier.train" target="classFrame">RawGenusWordConditionalProb</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/RawHierarchyTree.html" title="class in edu.msu.cme.rdp.classifier.train" target="classFrame">RawHierarchyTree</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/crossvalidate/RdmSelectTaxon.html" title="class in edu.msu.cme.rdp.classifier.train.validation.crossvalidate" target="classFrame">RdmSelectTaxon</a></li>
<li><a href="edu/msu/cme/rdp/multicompare/Reprocess.html" title="class in edu.msu.cme.rdp.multicompare" target="classFrame">Reprocess</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/Score.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">Score</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/SeqErrorBean.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">SeqErrorBean</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/SeqInfo.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">SeqInfo</a></li>
<li><a href="edu/msu/cme/rdp/classifier/ShortSequenceException.html" title="class in edu.msu.cme.rdp.classifier" target="classFrame">ShortSequenceException</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/SigCalculator.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">SigCalculator</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/SortedROCSet.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">SortedROCSet</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/SortedROCSet.PredictionCount.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">SortedROCSet.PredictionCount</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/SortedROCSet.ResultComparator.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">SortedROCSet.ResultComparator</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/StatusCount.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">StatusCount</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/StatusCountUtils.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">StatusCountUtils</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/distance/TaxaSimilarityMain.html" title="class in edu.msu.cme.rdp.classifier.train.validation.distance" target="classFrame">TaxaSimilarityMain</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/Taxon.html" title="interface in edu.msu.cme.rdp.classifier.comparison" target="classFrame"><i>Taxon</i></a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/Taxonomy.html" title="class in edu.msu.cme.rdp.classifier.train" target="classFrame">Taxonomy</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/Taxonomy.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">Taxonomy</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/TaxonTree.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">TaxonTree</a></li>
<li><a href="edu/msu/cme/rdp/classifier/TrainingDataException.html" title="class in edu.msu.cme.rdp.classifier" target="classFrame">TrainingDataException</a></li>
<li><a href="edu/msu/cme/rdp/classifier/TrainingInfo.html" title="class in edu.msu.cme.rdp.classifier" target="classFrame">TrainingInfo</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/TreeFactory.html" title="class in edu.msu.cme.rdp.classifier.train" target="classFrame">TreeFactory</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/TreeFactory.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">TreeFactory</a></li>
<li><a href="edu/msu/cme/rdp/classifier/io/TreeFileParser.html" title="class in edu.msu.cme.rdp.classifier.io" target="classFrame">TreeFileParser</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/UncNode.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">UncNode</a></li>
<li><a href="edu/msu/cme/rdp/unifrac/Unifrac.html" title="class in edu.msu.cme.rdp.unifrac" target="classFrame">Unifrac</a></li>
<li><a href="edu/msu/cme/rdp/unifrac/UnifracTaxon.html" title="class in edu.msu.cme.rdp.unifrac" target="classFrame">UnifracTaxon</a></li>
<li><a href="edu/msu/cme/rdp/taxatree/UnifracTree.html" title="class in edu.msu.cme.rdp.taxatree" target="classFrame">UnifracTree</a></li>
<li><a href="edu/msu/cme/rdp/taxatree/UnifracTree.UnifracResult.html" title="class in edu.msu.cme.rdp.taxatree" target="classFrame">UnifracTree.UnifracResult</a></li>
<li><a href="edu/msu/cme/rdp/unifrac/UnifracTreeBuilder.html" title="class in edu.msu.cme.rdp.unifrac" target="classFrame">UnifracTreeBuilder</a></li>
<li><a href="edu/msu/cme/rdp/unifrac/UnifracTreeBuilder.UnifracSample.html" title="class in edu.msu.cme.rdp.unifrac" target="classFrame">UnifracTreeBuilder.UnifracSample</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/ValidationClassificationResult.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">ValidationClassificationResult</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/ValidClassificationResultFacade.html" title="class in edu.msu.cme.rdp.classifier.train.validation" target="classFrame">ValidClassificationResultFacade</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/movingwindow/Window.html" title="class in edu.msu.cme.rdp.classifier.train.validation.movingwindow" target="classFrame">Window</a></li>
<li><a href="edu/msu/cme/rdp/classifier/train/validation/movingwindow/WindowTester.html" title="class in edu.msu.cme.rdp.classifier.train.validation.movingwindow" target="classFrame">WindowTester</a></li>
<li><a href="edu/msu/cme/rdp/classifier/comparison/Ztable.html" title="class in edu.msu.cme.rdp.classifier.comparison" target="classFrame">Ztable</a></li>
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