All Classes
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All Classes Interface Summary Class Summary Enum Summary Exception Summary Class Description AbstractNode BoxPlotUtils ClassificationParser ClassificationResult This class holds the classification results for a query sequence.ClassificationResultFormatter ClassificationResultFormatter.FORMAT Classifier This is the class to do the classification.ClassifierCmd This is the legacy command line class to do the classification.ClassifierFactory A factory to create a classifier with the training information defined by the property file.ClassifierGridware ClassifierMain ClassifierSequence A Sequence containing the sequence information.ClassifierTraineeMaker A command line class to create training information from the raw data.ClassifierTreeBuilder<E extends edu.msu.cme.rdp.taxatree.Taxon> ClassifierTreeBuilder.ClassifierTaxonFactory<E extends edu.msu.cme.rdp.taxatree.Taxon> CmdOptions CompareMisclassified CompareTrainingSets ComparisonBrowserBean ComparisonBrowserNode ComparisonCmd ComparisonResultTreeSet ComparisonResultTreeSet.ComparisonResultComparator CopyNumberParser CorrectAssignment CrossValidate CrossValidateMain DecisionMaker DefaultPrintVisitor EstimateSPrintVisitor FindWindowFrame GenusWordConditionalProb A GenusWordConditionalProb holds the index of the genus node, and the conditional probability that genus node contains the word.GenusWordProbFileParser A parser to parse a reader containing a list of the indices of genus nodes and the conditional probabilities that genus nodes contains the words.HierarchyTree A HierarchyTree holds the taxonomic information of a taxon.HierarchyTree HierarchyVersion A HierarchyVersion holds the training set number and version of the taxonomy.LeaveOneOutTester LeaveOneOutTesterMain LineageSequence A ParsedRawSequence holds the data for a raw sequence.LineageSequenceParser A parser to parse a reader containing the raw sequences.LogWordPriorFileParser A parser to parse a read containing a list of the indices of words and the log value of word prior probabilities.Main MainMovingWindow MCSample MCSamplePrintUtil MCSampleResult MCTaxon MergeTaxonCount MultiClassifier MultiClassifierResult NameRankDupException NBClassifier PairwiseSeqDistance PixelCalculatorBean ProbIndexFileParser A parser to parser a reader contains a list of indices of words, and start indices of the conditional probabilities.RankAssignment A RankAssignment holds the classification result of a sequence at one rank level.RawGenusWordConditionalProb A RawGenusWordConditionalProb contains the index of the genus node and the conditional probability of the node contains the word.RawHierarchyTree A RawHierarchyTree holds the raw taxon and sequences information.RdmSelectTaxon Reprocess Score SeqErrorBean SeqInfo ShortSequenceException Handles exception for a short sequence.SigCalculator SortedROCSet SortedROCSet.PredictionCount SortedROCSet.ResultComparator StatusCount StatusCountUtils TaxaSimilarityMain Taxon Taxonomy A Taxonomy holds the raw taxon information.Taxonomy TaxonTree TrainingDataException Handles the exception occurred when parsing training information.TrainingInfo The TrainingInfo holds all the training information and taxonomy hierarchy information.TreeFactory A TreeFactory reads the raw taxonomic information and creates the RawHierarchyTree nodes.TreeFactory TreeFileParser A parser to parse a reader containing taxonomic training information.UncNode Unifrac UnifracTaxon UnifracTree UnifracTree.UnifracResult UnifracTreeBuilder UnifracTreeBuilder.UnifracSample ValidationClassificationResult ValidClassificationResultFacade Window WindowTester Ztable