A B C D E F G H I L M N O P Q R S T U V W Z

## A

AbstractNode - Class in edu.msu.cme.rdp.classifier.comparison
AbstractNode() - Constructor for class edu.msu.cme.rdp.classifier.comparison.AbstractNode
  Creates a new instance of AbstractNode
addChild(AbstractNode) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
addChild(UnifracTaxon, int) - Method in class edu.msu.cme.rdp.taxatree.UnifracTree
addConfidence(HierarchyTree, HashMap) - Method in class edu.msu.cme.rdp.classifier.Classifier
  increase the count of the RankAssignment in the map if match that node or any ancestor of that node.
addParent(HierarchyTree) - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
  Adds the parent HierarchyTree, also adds this node to the parent treenode as a child.
addRankCount(ClassificationResult) - Method in class edu.msu.cme.rdp.multicompare.MCSample
addS1Score(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
addS2Score(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
addSample(MCSample) - Method in class edu.msu.cme.rdp.multicompare.MultiClassifierResult
addSampleCount(MCSample, double) - Method in class edu.msu.cme.rdp.unifrac.UnifracTaxon
addSampleList(List<MCSample>) - Method in class edu.msu.cme.rdp.multicompare.MultiClassifierResult
addSequence(LineageSequence) - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
  For the given sequence name, its ancestors, and the sequence, creates a HierarchyTree for each ancestor, If the root does not exist, creates the root with a null parent.
addSequence(LineageSequence, boolean) - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
addSequence(String) - Method in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
addTaxon(int, int, String, MCSample, float) - Method in class edu.msu.cme.rdp.taxatree.UnifracTree
appendClassification(ClassificationResult) - Method in class edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder
appendClassifications(List<ClassificationResult>) - Method in class edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder
assignClass() - Method in class edu.msu.cme.rdp.classifier.train.validation.NBClassifier
  for a array of subclasses, gets the probabilities of each subclass, returns the classification whose subclass has the highest probability.
assignClassRandomsample() - Method in class edu.msu.cme.rdp.classifier.train.validation.NBClassifier
  This method random select certain number of words and calculate the probability This can only be called after the assignClass() filled the querySeq_wordProbArr matrix

## B

bins - Variable in class edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment
BIOMFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
BIOMFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
BIOMFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
BOOTSTRAP_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
BOOTSTRAP_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
BOOTSTRAP_OUTFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
BOOTSTRAP_OUTFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
BOOTSTRAP_OUTFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
BOOTSTRAP_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
BoxPlotUtils - Class in edu.msu.cme.rdp.classifier.train.validation.distance
BoxPlotUtils() - Constructor for class edu.msu.cme.rdp.classifier.train.validation.distance.BoxPlotUtils
buildTaxon(int, String, String, float, boolean) - Method in interface edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder.ClassifierTaxonFactory
buildTree() - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
  build the taxonomic tree without sequences attached to it

## C

calAUC(String, ArrayList<HashMap<String, StatusCount>>) - Static method in class edu.msu.cme.rdp.classifier.train.validation.StatusCountUtils
  calculate Area under curve sensitivity = #TP / (#TP + #FN) specificity = #TN / (#TN + #FP)
calculateSig(int, int) - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
calculateWordPrior() - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
calErrorRate(ArrayList<HashMap>) - Method in class edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidate
  sensitivity = #TP / (#TP + #FN) specificity = #TN / (#TN + #FP)
calF1score() - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
  F1 score = 2#TP / (2#TP + #FP + #FN)
calFPR() - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
  false positive rate = #FP / (#TN + #FP)
calPairwiseSimilaritye(String, String, String) - Method in class edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
calROCMatrix(String, ArrayList<HashMap<String, StatusCount>>) - Static method in class edu.msu.cme.rdp.classifier.train.validation.StatusCountUtils
  return the ROC matrix, for each rank, each bootstrap value sensitivity = #TP / (#TP + #FN) specificity = #TN / (#TN + #FP)
calSabSimilarity(String, String, String) - Method in class edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
calSensitivity() - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
  sensitivity = #TP / (#TP + #FN)
calSpecificity() - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
  specificity = #TN / (#TN + #FP)
changeConfidence(SigCalculator) - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
changeConfidence(SigCalculator) - Method in interface edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserNode
changeConfidence(SigCalculator) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
  calculate the count of sequences assigned to the node, only count the sequence with score for that node greater or equal to confidence cutoff value
changeConfidence(SigCalculator) - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode
changeParentSeqCount(int) - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
changeRank(String) - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
ClassificationParser - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
ClassificationParser(String, ClassifierFactory) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationParser
ClassificationParser(File, ClassifierFactory) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationParser
ClassificationParser(InputStream, ClassifierFactory) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationParser
ClassificationParser(Reader) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationParser
ClassificationResult - Class in edu.msu.cme.rdp.classifier
  This class holds the classification results for a query sequence.
ClassificationResult(Sequence, boolean, List<RankAssignment>, HierarchyVersion) - Constructor for class edu.msu.cme.rdp.classifier.ClassificationResult
  Creates a new instance of ClassificationResult.
ClassificationResultFormatter - Class in edu.msu.cme.rdp.classifier.io
ClassificationResultFormatter() - Constructor for class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
ClassificationResultFormatter.FORMAT - Enum in edu.msu.cme.rdp.classifier.io
Classifier - Class in edu.msu.cme.rdp.classifier
  This is the class to do the classification.
ClassifierCmd - Class in edu.msu.cme.rdp.classifier
  This is the legacy command line class to do the classification.
ClassifierCmd() - Constructor for class edu.msu.cme.rdp.classifier.ClassifierCmd
ClassifierFactory - Class in edu.msu.cme.rdp.classifier.utils
  A factory to create a classifier with the training information defined by the property file.
ClassifierGridware - Class in edu.msu.cme.rdp.multicompare.gridware
ClassifierGridware() - Constructor for class edu.msu.cme.rdp.multicompare.gridware.ClassifierGridware
ClassifierMain - Class in edu.msu.cme.rdp.classifier.cli
ClassifierMain() - Constructor for class edu.msu.cme.rdp.classifier.cli.ClassifierMain
ClassifierSequence - Class in edu.msu.cme.rdp.classifier.utils
  A Sequence containing the sequence information.
ClassifierSequence(Sequence) - Constructor for class edu.msu.cme.rdp.classifier.utils.ClassifierSequence
  Creates new ParsedSequence.
ClassifierSequence(String, String, String) - Constructor for class edu.msu.cme.rdp.classifier.utils.ClassifierSequence
ClassifierTraineeMaker - Class in edu.msu.cme.rdp.classifier.train
  A command line class to create training information from the raw data.
ClassifierTraineeMaker(String, String, String, int, String, String, String) - Constructor for class edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker
  Creates a new ClassifierTraineeMaker
ClassifierTreeBuilder<E extends edu.msu.cme.rdp.taxatree.Taxon> - Class in edu.msu.cme.rdp.taxatree.utils
ClassifierTreeBuilder(E, List<ClassificationResult>, float, ClassifierTreeBuilder.ClassifierTaxonFactory<E>) - Constructor for class edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder
ClassifierTreeBuilder(ConcretRoot<E>, List<ClassificationResult>, float, ClassifierTreeBuilder.ClassifierTaxonFactory<E>) - Constructor for class edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder
ClassifierTreeBuilder(E, float, ClassifierTreeBuilder.ClassifierTaxonFactory<E>) - Constructor for class edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder
ClassifierTreeBuilder(ConcretRoot<E>, float, ClassifierTreeBuilder.ClassifierTaxonFactory<E>) - Constructor for class edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder
ClassifierTreeBuilder.ClassifierTaxonFactory<E extends edu.msu.cme.rdp.taxatree.Taxon> - Interface in edu.msu.cme.rdp.taxatree.utils
classify(Sequence) - Method in class edu.msu.cme.rdp.classifier.Classifier
  Takes a query sequence, returns the classification result.
classify(ClassifierSequence) - Method in class edu.msu.cme.rdp.classifier.Classifier
classify(ClassifierSequence, int) - Method in class edu.msu.cme.rdp.classifier.Classifier
  Takes a query sequence, returns the classification result.
classify(TreeFactory, LineageSequenceParser, boolean, int, boolean) - Method in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTester
  perform leave-one-out test.
classify(TreeFactory, ArrayList, Window, int, int) - Method in class edu.msu.cme.rdp.classifier.train.validation.movingwindow.WindowTester
  classify each sequence from a parser
close() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationParser
close() - Method in class edu.msu.cme.rdp.classifier.train.LineageSequenceParser
  Closes the reader.
CmdOptions - Class in edu.msu.cme.rdp.classifier.cli
CmdOptions() - Constructor for class edu.msu.cme.rdp.classifier.cli.CmdOptions
compare(Object, Object) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonResultTreeSet.ComparisonResultComparator
compare(String, String) - Method in class edu.msu.cme.rdp.classifier.train.validation.distance.CompareTrainingSets
compare(SortedROCSet.PredictionCount, SortedROCSet.PredictionCount) - Method in class edu.msu.cme.rdp.classifier.train.validation.SortedROCSet.ResultComparator
COMPARE_OUTFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
COMPARE_OUTFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
COMPARE_OUTFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
CompareMisclassified - Class in edu.msu.cme.rdp.classifier.train.validation.leaveoneout
CompareMisclassified(String, String) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.CompareMisclassified
CompareTrainingSets - Class in edu.msu.cme.rdp.classifier.train.validation.distance
CompareTrainingSets(String, String[]) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.distance.CompareTrainingSets
CompareTrainingSets.HierarchyTreeExtend - Class in edu.msu.cme.rdp.classifier.train.validation.distance
ComparisonBrowserBean - Class in edu.msu.cme.rdp.classifier.comparison
ComparisonBrowserBean(String, String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
ComparisonBrowserNode - Interface in edu.msu.cme.rdp.classifier.comparison
ComparisonCmd - Class in edu.msu.cme.rdp.classifier.comparison
ComparisonCmd(String, String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
  Creates a new Manager
ComparisonResultComparator() - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonResultTreeSet.ComparisonResultComparator
ComparisonResultTreeSet - Class in edu.msu.cme.rdp.classifier.comparison
ComparisonResultTreeSet() - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonResultTreeSet
ComparisonResultTreeSet.ComparisonResultComparator - Class in edu.msu.cme.rdp.classifier.comparison
computeUnifrac() - Method in class edu.msu.cme.rdp.taxatree.UnifracTree
computeUnifracSig(int, boolean) - Method in class edu.msu.cme.rdp.taxatree.UnifracTree
computeWeightedUnifrac() - Method in class edu.msu.cme.rdp.taxatree.UnifracTree
containsSample(MCSample) - Method in class edu.msu.cme.rdp.unifrac.UnifracTaxon
CopyNumberParser - Class in edu.msu.cme.rdp.classifier.train
CopyNumberParser() - Constructor for class edu.msu.cme.rdp.classifier.train.CopyNumberParser
CopyNumberParser.TaxonCopyNumber - Class in edu.msu.cme.rdp.classifier.train
CorrectAssignment - Class in edu.msu.cme.rdp.classifier.train.validation
CorrectAssignment() - Constructor for class edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment
  Creates a new instance of CorrectAssignment
count - Variable in class edu.msu.cme.rdp.unifrac.UnifracTreeBuilder.UnifracSample
Count_Array_size - Static variable in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
createBoxplot(DefaultBoxAndWhiskerCategoryDataset, PrintStream, String, String, String, Font) - Static method in class edu.msu.cme.rdp.classifier.train.validation.distance.BoxPlotUtils
createClassifier() - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Creates a new Classifier if all the train information have been completed, throws exception if not.
createClassifier() - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
  Creates a new classifier.
createGenusWordProbList(Reader, List<GenusWordConditionalProb>, HierarchyVersion) - Static method in class edu.msu.cme.rdp.classifier.io.GenusWordProbFileParser
  Reads a file and saves GenusWordConditionalProb objects in a list.
createGenusWordProbList(Reader) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Reads in the index of the genus treenode and conditional probability that genus contains a word.
createLogWordPriorArr(Reader, float[], HierarchyVersion) - Static method in class edu.msu.cme.rdp.classifier.io.LogWordPriorFileParser
  Reads a file and saves the log word priors in an array.
createLogWordPriorArr(Reader) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Reads in the log value of the word prior probability and saves to an array LogWordPriorArr.
createPlot(String, File) - Method in class edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
createProbIndexArr(Reader, int[], HierarchyVersion) - Static method in class edu.msu.cme.rdp.classifier.io.ProbIndexFileParser
  Reads a file and saves the start index of conditional probability of the genera containing the word to an array.
createProbIndexArr(Reader) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Reads in start index of the conditional probability of each genus, saves to an array wordConditionalProbIndexArr.
createTree(Reader, HierarchyVersion) - Method in class edu.msu.cme.rdp.classifier.io.TreeFileParser
  Reads from a reader that contains the information for each treenode.
createTree(Reader) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Reads in the tree information from a reader and create all the HierarchyTrees.
createWordOccurrenceFromSubclasses() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  creates the word occurrence array from its children if the word occurrence for this node does not exist
CrossValidate - Class in edu.msu.cme.rdp.classifier.train.validation.crossvalidate
CrossValidate() - Constructor for class edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidate
CrossValidateMain - Class in edu.msu.cme.rdp.classifier.train.validation.crossvalidate
CrossValidateMain() - Constructor for class edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidateMain

## D

DecisionMaker - Class in edu.msu.cme.rdp.classifier.train.validation
DecisionMaker(TreeFactory) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.DecisionMaker
  Creates new DecisionMaker
DEFAULT_CONF - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
DEFAULT_FORMAT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
DEFAULT_GENE - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
DefaultPrintVisitor - Class in edu.msu.cme.rdp.multicompare.visitors
DefaultPrintVisitor(PrintStream, List<MCSample>) - Constructor for class edu.msu.cme.rdp.multicompare.visitors.DefaultPrintVisitor
DefaultPrintVisitor(PrintStream, List<MCSample>, boolean) - Constructor for class edu.msu.cme.rdp.multicompare.visitors.DefaultPrintVisitor
DefaultPrintVisitor(PrintStream, List<MCSample>, boolean, boolean) - Constructor for class edu.msu.cme.rdp.multicompare.visitors.DefaultPrintVisitor
delimiter - Static variable in class edu.msu.cme.rdp.classifier.train.LineageSequenceParser
displayTreeErrorRate(HierarchyTree, int) - Method in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTester
displayTreeErrorRate(HierarchyTree, int) - Method in class edu.msu.cme.rdp.classifier.train.validation.movingwindow.WindowTester
  search the tree node that the current test getSequence() belongs to
displayTreePhylo(HierarchyTree, String, int) - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
  display the phylogenetic tree for each node, display the index and the name for each sequence, diaplay the name and the description
doClassify(String, String, String, ClassificationResultFormatter.FORMAT, String, int) - Method in class edu.msu.cme.rdp.classifier.ClassifierCmd
  It classifies query sequences from the input file.
doClassify(String, String, String, String, ClassificationResultFormatter.FORMAT) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
  given the parser and root, calls the tester to do the classification

## E

edu.msu.cme.rdp.classifier - package edu.msu.cme.rdp.classifier
edu.msu.cme.rdp.classifier.cli - package edu.msu.cme.rdp.classifier.cli
edu.msu.cme.rdp.classifier.comparison - package edu.msu.cme.rdp.classifier.comparison
edu.msu.cme.rdp.classifier.io - package edu.msu.cme.rdp.classifier.io
edu.msu.cme.rdp.classifier.rrnaclassifier - package edu.msu.cme.rdp.classifier.rrnaclassifier
edu.msu.cme.rdp.classifier.train - package edu.msu.cme.rdp.classifier.train
edu.msu.cme.rdp.classifier.train.validation - package edu.msu.cme.rdp.classifier.train.validation
edu.msu.cme.rdp.classifier.train.validation.crossvalidate - package edu.msu.cme.rdp.classifier.train.validation.crossvalidate
edu.msu.cme.rdp.classifier.train.validation.distance - package edu.msu.cme.rdp.classifier.train.validation.distance
edu.msu.cme.rdp.classifier.train.validation.leaveoneout - package edu.msu.cme.rdp.classifier.train.validation.leaveoneout
edu.msu.cme.rdp.classifier.train.validation.movingwindow - package edu.msu.cme.rdp.classifier.train.validation.movingwindow
edu.msu.cme.rdp.classifier.utils - package edu.msu.cme.rdp.classifier.utils
edu.msu.cme.rdp.multicompare - package edu.msu.cme.rdp.multicompare
edu.msu.cme.rdp.multicompare.gridware - package edu.msu.cme.rdp.multicompare.gridware
edu.msu.cme.rdp.multicompare.taxon - package edu.msu.cme.rdp.multicompare.taxon
edu.msu.cme.rdp.multicompare.visitors - package edu.msu.cme.rdp.multicompare.visitors
edu.msu.cme.rdp.taxatree - package edu.msu.cme.rdp.taxatree
edu.msu.cme.rdp.taxatree.utils - package edu.msu.cme.rdp.taxatree.utils
edu.msu.cme.rdp.unifrac - package edu.msu.cme.rdp.unifrac
endElement(String, String, String) - Method in class edu.msu.cme.rdp.classifier.io.TreeFileParser
error(SAXParseException) - Method in class edu.msu.cme.rdp.classifier.io.TreeFileParser
EstimateSPrintVisitor - Class in edu.msu.cme.rdp.multicompare.visitors
EstimateSPrintVisitor(PrintStream, List<MCSample>, String, int) - Constructor for class edu.msu.cme.rdp.multicompare.visitors.EstimateSPrintVisitor

## F

fileFormats - Static variable in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
find(String) - Method in class edu.msu.cme.rdp.classifier.train.validation.movingwindow.FindWindowFrame
  Given the aligned E.coli seqstring, find the corresponding model position for each window.
findNode(int) - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
findNode(int) - Method in interface edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserNode
findNode(int) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
  returns a node with the given taxid if found.
findNode(int) - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode
FindWindowFrame - Class in edu.msu.cme.rdp.classifier.train.validation.movingwindow
FindWindowFrame() - Constructor for class edu.msu.cme.rdp.classifier.train.validation.movingwindow.FindWindowFrame
FORMAT_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
FORMAT_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
FORMAT_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
FUNGALITS_unite_GENE - Static variable in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
FUNGALITS_warcup_GENE - Static variable in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
FUNGALLSU_GENE - Static variable in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory

## G

GENE_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
GENE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
GENE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
generateWordPairDiffArr(int[], int) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  For a given word w1 and the reverse complement word w2, calculates the difference between the log word prior of w1 and w2 and saves to an array.
GENUS - Static variable in class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
GenusWordConditionalProb - Class in edu.msu.cme.rdp.classifier
  A GenusWordConditionalProb holds the index of the genus node, and the conditional probability that genus node contains the word.
GenusWordConditionalProb(int, float) - Constructor for class edu.msu.cme.rdp.classifier.GenusWordConditionalProb
  Creates a new instance of GenusWordConditionalProb For a word indexed in wordConditionalProbIndexArr, it holds the index of the genus node, and the conditional probability that genus node contains the word.
GenusWordProbFileParser - Class in edu.msu.cme.rdp.classifier.io
  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.
GenusWordProbFileParser() - Constructor for class edu.msu.cme.rdp.classifier.io.GenusWordProbFileParser
getAllRankOutput(ClassificationResult) - Static method in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
getAllRankOutput(ClassificationResult, double) - Static method in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
getAncestorNodes(HierarchyTree, String, List<String>) - Method in class edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
getAncestors() - Method in class edu.msu.cme.rdp.classifier.train.LineageSequence
  Returns the list of the ancestor taxa, with the highest ranked taxon first.
getAncestors() - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidClassificationResultFacade
getAssignments() - Method in class edu.msu.cme.rdp.classifier.ClassificationResult
  Returns a list of RankAssignments.
getBadSequences() - Method in class edu.msu.cme.rdp.multicompare.MultiClassifierResult
getBeginIndex() - Static method in class edu.msu.cme.rdp.classifier.train.validation.movingwindow.MainMovingWindow
getBestClass() - Method in class edu.msu.cme.rdp.classifier.RankAssignment
  Returns the HierarchyTree which the query sequence is assigned to.
getBestClass() - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidationClassificationResult
getBestClasspath(GoodWordIterator, HashMap<String, HierarchyTree>, boolean, int) - Method in class edu.msu.cme.rdp.classifier.train.validation.DecisionMaker
  For each sequence, find the best class among the list of genera using all the overlapping words.
getBiomOutput(String[], ClassificationResult, float, char) - Static method in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
  Output the classification result suitable to load into biom format.
getBl() - Method in class edu.msu.cme.rdp.unifrac.UnifracTaxon
getBootstrapCountTable() - Method in class edu.msu.cme.rdp.multicompare.MCSample
getBootstrapIndex(double) - Static method in class edu.msu.cme.rdp.multicompare.MCSample
getChild(String) - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
getChildTaxonList() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getClassificationParser(ClassifierFactory) - Method in class edu.msu.cme.rdp.multicompare.MCSampleResult
getClassifierVersion() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getClassifierVersion() - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
  Returns the version of the classifier.
getConfidence() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getConfidence() - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
getConfidence() - Method in class edu.msu.cme.rdp.classifier.RankAssignment
  Returns the estimate of confidence of the assignment.
getCopyCorrectedCount(MCSample) - Method in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
getCopyNumber() - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
getCopyNumber() - Method in class edu.msu.cme.rdp.classifier.train.CopyNumberParser.TaxonCopyNumber
getCopyNumber() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
getCount(MCSample) - Method in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
getCurrentBrowserRoot() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getDBOutput(ClassificationResult, float) - Static method in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
getDefaultConfidence() - Static method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getDepth() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getDepth() - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
  Returns the depth of the current taxon from root taxon.
getDepth() - Method in class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
getDesc() - Method in class edu.msu.cme.rdp.classifier.train.LineageSequence
getDescription() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqErrorBean
getDetailIterator(float) - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getDetailIterator(float) - Method in interface edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserNode
getDetailIterator(float) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
getDetailIterator(float) - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode
getDetailList() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getDetailListSize() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getDoubleSignificance() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getDupCount(String) - Method in class edu.msu.cme.rdp.multicompare.MCSample
getFactory(String) - Static method in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
  Returns a factory with the training information.
getFilterByConfOutput(ClassificationResult, float) - Static method in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
getFilterByConfOutput(String[], ClassificationResult, float) - Static method in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
getFixRankOutput(ClassificationResult) - Static method in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
getFixRankOutput(String[], ClassificationResult) - Static method in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
getFloatConfidence() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getFPR() - Method in class edu.msu.cme.rdp.classifier.train.validation.SortedROCSet.PredictionCount
getGenusIndex() - Method in class edu.msu.cme.rdp.classifier.GenusWordConditionalProb
  Returns the index of the genus node
getGenusIndex() - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
  Gets the index of the genus treenode in the genusNodeList.
getGenusIndex() - Method in class edu.msu.cme.rdp.classifier.train.RawGenusWordConditionalProb
  Returns the index of the genus.
getGenusIndex() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Returns the genus index of this treenode.
getGenusNodebyIndex(int) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns a genus node from the genusNodeList at the specified position.
getGenusNodeCount() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
getGenusNodeListSize() - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns the number of the genus nodes.
getGoodWordCount() - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierSequence
  Returns the number of words with valid bases.
getHierarchyInfo() - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns the info of the taxonomy hierarchy from of the training file.
getHierarchyTaxonList() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getHierarchyTrainsetNo() - Method in class edu.msu.cme.rdp.classifier.ClassificationResult
  Returns the version of the taxonomy hierarchy from of the training file.
getHierarchyTrainsetNo() - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
  Returns the info of the taxonomy hierarchy from of the training file.
getHierarchyVersion() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getHierarchyVersion() - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns the version of the taxonomical hierarchy.
getHierarchyVersion() - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
  Returns the version of the taxonomical hierarchy.
getHierLevel() - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
  Returns the hierarchy rank level.
getHierLevel() - Method in class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
getIndent() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getIndent() - Method in interface edu.msu.cme.rdp.classifier.comparison.Taxon
getLabeledNode() - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidClassificationResultFacade
getLeaveCount() - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
  Gets the size of sequence leaves directly belong to this treenode.
getLeaveCount() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Counts the number of sequence leaves below this tree.
getLeaves() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Gets the array of Sequenceleaves if any
getLineage() - Method in class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
getLineage() - Method in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
getLineageIterator() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getLineageIterator() - Method in interface edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserNode
getLineageList() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getLogLeaveCount(int) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns the log value of (number of leaves + 1) of a genus
getLogWordPrior(int) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns the log value of the prior probability of a word.
getLowestRank() - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
getMessage() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqErrorBean
getMessage() - Method in exception edu.msu.cme.rdp.classifier.ShortSequenceException
  Returns the error message.
getMissCount() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
getName() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getName() - Method in class edu.msu.cme.rdp.classifier.comparison.Score
getName() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
getName() - Method in interface edu.msu.cme.rdp.classifier.comparison.Taxon
getName() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
getName() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode
getName() - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
  Gets the name of the treenode.
getName() - Method in class edu.msu.cme.rdp.classifier.RankAssignment
  Returns the name of the assigned HierarchyTree.
getName() - Method in class edu.msu.cme.rdp.classifier.train.CopyNumberParser.TaxonCopyNumber
getName() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Gets the name of the treenode.
getName() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Gets the name of the treenode
getName() - Method in class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
getNextSeq() - Method in class edu.msu.cme.rdp.multicompare.MCSample
getNodeList(String, List) - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  get all the lowest level nodes in given hierarchy level starting from the given root
getNodeMap(String, HashMap<String, RawHierarchyTree>) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  get all the lowest level nodes in given hierarchy level starting from the given root
getNodeMap(String, HashMap<String, HierarchyTree>) - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  get all the lowest level nodes in given hierarchy level starting from the given root
getNonSingletonLeaveCount() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Counts the number of non-singleton sequence leaves below this tree.
getNum_hierLevelMap() - Method in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTester
getNumberofUniqueWords() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
getNumFN() - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
getNumFP() - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
getNumOfChildren() - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
getNumOfLeaves() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Counts the number of sequence leaves below this tree
getNumOfVotes() - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidationClassificationResult
getNumTN() - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
getNumTotalTestedseq() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
getNumTP() - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
getOutput(ClassificationResult, ClassificationResultFormatter.FORMAT) - Static method in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
getOutput(ClassificationResult, ClassificationResultFormatter.FORMAT, float, String[]) - Static method in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
getParent() - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
  Gets the parent treenode.
getParent() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Gets the parent treenode.
getParent() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Gets the parent treenode
getParentID() - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
  Returns the taxID of the parent taxon.
getParentID() - Method in class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
getPartialSeqIteratorbyGoodBases(int) - Method in class edu.msu.cme.rdp.classifier.train.LineageSequence
getPath() - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidClassificationResultFacade
  print the labeled path and the assigned path Note: the true path is list of string of ancestors for a sequence, the assigned path is a list of ClassificationResult for a sequence.
getPosteriorProb() - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidationClassificationResult
getProbability() - Method in class edu.msu.cme.rdp.classifier.GenusWordConditionalProb
  Returns the conditional probability that the genus node contains the word.
getProbability() - Method in class edu.msu.cme.rdp.classifier.train.RawGenusWordConditionalProb
  Returns the word conditional probability of the genus.
getPvalue(double) - Method in class edu.msu.cme.rdp.classifier.comparison.Ztable
getRank() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getRank() - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
getRank() - Method in class edu.msu.cme.rdp.classifier.comparison.Score
getRank() - Method in interface edu.msu.cme.rdp.classifier.comparison.Taxon
getRank() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
getRank() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode
getRank() - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
  Gets the rank of the treenode.
getRank() - Method in class edu.msu.cme.rdp.classifier.RankAssignment
  Returns the rank of the assigned HiearchyTree.
getRank() - Method in class edu.msu.cme.rdp.classifier.train.CopyNumberParser.TaxonCopyNumber
getRankAssignment() - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidClassificationResultFacade
getRankSet() - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
getResult() - Method in class edu.msu.cme.rdp.multicompare.MergeTaxonCount
getReversedSeq() - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierSequence
  Returns a Sequence object whose sequence string is the reverse complement of the current rRNA sequence string.
getRoot() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationParser
getRoot() - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Gets the root of the tree
getRoot() - Method in class edu.msu.cme.rdp.classifier.train.validation.distance.CompareTrainingSets.HierarchyTreeExtend
getRoot() - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
  Gets the root of the tree
getRoot() - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
getRoot() - Method in class edu.msu.cme.rdp.multicompare.MultiClassifierResult
getRoot() - Method in class edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder
getRootTree() - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns the root of the trees.
getS1Count() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getS1Count() - Method in interface edu.msu.cme.rdp.classifier.comparison.Taxon
getS1Filename() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getS1GifPercent() - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
getS1PercentStr() - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
getS1Total() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getS1Total() - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
getS2Count() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getS2Count() - Method in interface edu.msu.cme.rdp.classifier.comparison.Taxon
getS2Filename() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getS2GifPercent() - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
getS2PercentStr() - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
getS2Total() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getS2Total() - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
getSample(String) - Method in class edu.msu.cme.rdp.multicompare.MultiClassifierResult
getSampleName() - Method in class edu.msu.cme.rdp.multicompare.MCSample
getSamples() - Method in class edu.msu.cme.rdp.multicompare.MultiClassifierResult
getSamples() - Method in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
getSamples() - Method in class edu.msu.cme.rdp.taxatree.UnifracTree.UnifracResult
getScore() - Method in class edu.msu.cme.rdp.classifier.comparison.Score
getScoreList() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
getSe() - Method in class edu.msu.cme.rdp.classifier.train.validation.SortedROCSet.PredictionCount
getSeqCountLimit() - Static method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getSeqCountMap() - Method in class edu.msu.cme.rdp.multicompare.MultiClassifierResult
getSeqDoc() - Method in exception edu.msu.cme.rdp.classifier.ShortSequenceException
  Returns the sequence identifier.
getSeqErrorCount() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getSeqErrorList() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getSeqName() - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidClassificationResultFacade
getSequence() - Method in class edu.msu.cme.rdp.classifier.ClassificationResult
  Returns the query sequence
getSequences() - Method in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
getSignificance() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getSignificance() - Method in interface edu.msu.cme.rdp.classifier.comparison.Taxon
getSizeofChildren() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Gets the size of the children, either taxon children or sequence leaves.
getSizeofChildren() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Gets the size of the children
getSizeofLeaves() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Gets the size of sequence leaves directly belong to this tree, not including the hidden leaves
getSizeofSubclasses() - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
  Gets the list of the child treenodes.
getSizeofSubclasses() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Gets the size of the child treenodes.
getSizeofSubclasses() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Gets the size of the subclasses
getStart() - Method in class edu.msu.cme.rdp.classifier.train.validation.movingwindow.Window
getStartIndex(int) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns the start index of GenusIndexWordConditionalProb in the array for the specified wordIndex.
getStop() - Method in class edu.msu.cme.rdp.classifier.train.validation.movingwindow.Window
getStopIndex(int) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns the stop index of GenusIndexWordConditionalProb in the array for the specified wordIndex.
getSubclassbyName(String) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Gets the child treenode with the given name.
getSubclassbyName(String) - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Gets the subclass with the given name
getSubclasses() - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
  Gets the name of the treenode.
getSubclasses() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Gets the array of the subclasses if any.
getSubclasses() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Gets the array of the subclasses if any
getSubmitDate() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getTabularTaxonList() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getTaxid() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getTaxid() - Method in class edu.msu.cme.rdp.classifier.comparison.Score
getTaxid() - Method in interface edu.msu.cme.rdp.classifier.comparison.Taxon
getTaxid() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
getTaxid() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode
getTaxid() - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
  Gets the taxon id of the treenode.
getTaxid() - Method in class edu.msu.cme.rdp.classifier.RankAssignment
  Returns the taxid of the assigned HierachyTree
getTaxID() - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
  Returns the taxID.
getTaxID() - Method in class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
getTaxName() - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
  Returns the taxon name.
getTaxonIterator(int) - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getTaxonIterator(int) - Method in interface edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserNode
getTaxonomy() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Returns the taxon object of this treenode.
getTaxonomy() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
getTaxonomy(String, String, int, int) - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
getTitle() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
getTotalSeqs() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
getTrainRank() - Method in class edu.msu.cme.rdp.classifier.Classifier
getTrainRank() - Method in class edu.msu.cme.rdp.classifier.io.TreeFileParser
getTrainRank() - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
getTrainRank() - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
getTrainsetName() - Method in class edu.msu.cme.rdp.classifier.train.validation.distance.CompareTrainingSets.HierarchyTreeExtend
getTrainsetNo() - Method in class edu.msu.cme.rdp.classifier.ClassificationResult
  Returns the training set number of the taxonomy hierarchy from of the training file.
getTrainsetNo() - Method in class edu.msu.cme.rdp.classifier.utils.HierarchyVersion
  Returns the training set number of the taxonomy hierarchy from the header of the training file.
getUnifracMatrix() - Method in class edu.msu.cme.rdp.taxatree.UnifracTree.UnifracResult
getUnifracTree() - Method in class edu.msu.cme.rdp.unifrac.UnifracTreeBuilder
getVersion() - Method in class edu.msu.cme.rdp.classifier.utils.HierarchyVersion
  Returns the version of the taxonomy hierarchy from the header of the training file.
getWindowFrame(String) - Method in class edu.msu.cme.rdp.classifier.train.validation.movingwindow.MainMovingWindow
getWordConditionalProbObject(int) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns a GenusIndexWordConditionalProb from the genusIndex_wordConditionalProbList at the specified postion in the list.
getWordIndexArr() - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierSequence
getWordOccurrence(int) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Gets the word occurrence for the given word index.
getWordOccurrence(int) - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Gets the word occurrence for the given word index
getWordOccurrenceSize() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Returns the size of the array wordOccurrence.
getWordOccurrenceSize() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
getWordPairPriorDiff(int) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns the difference between given word and its reverse complement word.
getWordPrior(int) - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory

## H

hasCopyNumber() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
hasCopyNumber() - Method in class edu.msu.cme.rdp.multicompare.MultiClassifier
hasCopyNumberInfo() - Method in class edu.msu.cme.rdp.classifier.HierarchyTree
hasNext() - Method in class edu.msu.cme.rdp.classifier.train.LineageSequenceParser
  Returns true if there is a parsed sequence available.
hideSeq(GoodWordIterator) - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  This method hides a sequence by removing the words of that sequence from the total wordOccurrence
HIDETAXON_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
HIER_OUTFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
HIER_OUTFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
HIER_OUTFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
HierarchyTree - Class in edu.msu.cme.rdp.classifier
  A HierarchyTree holds the taxonomic information of a taxon.
HierarchyTree(String, int, String, int, int, double) - Constructor for class edu.msu.cme.rdp.classifier.HierarchyTree
  Creates new HierarchyTree given the taxonomic information.
HierarchyTree(String, int, String, int, int) - Constructor for class edu.msu.cme.rdp.classifier.HierarchyTree
HierarchyTree - Class in edu.msu.cme.rdp.classifier.train.validation
HierarchyTree(String, HierarchyTree, Taxonomy) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  Creates new HierarchyTree given the name and its parent
HierarchyTreeExtend(HierarchyTree, String) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.distance.CompareTrainingSets.HierarchyTreeExtend
HierarchyVersion - Class in edu.msu.cme.rdp.classifier.utils
  A HierarchyVersion holds the training set number and version of the taxonomy.
HierarchyVersion(String) - Constructor for class edu.msu.cme.rdp.classifier.utils.HierarchyVersion
  Creates a new instance of HierarchyVersion,

## I

incCount(MCSample, double) - Method in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
incCount(MCSample, double, double) - Method in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
incMissCount() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
incNumFN(int) - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
incNumFP(int) - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
incNumTN(int) - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
incNumTotalTestedseq() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
incNumTP(int) - Method in class edu.msu.cme.rdp.classifier.train.validation.StatusCount
increTotalSeqs() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
initWordOccurrence(LineageSequence, float[]) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  This method initiates the word occurrences from a sequence for the lowest level of the hierarchy tree.
initWordOccurrence(LineageSequence, float[], boolean) - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  This method initiate the word occurrence from the sequences for the lowest level of the hierarchy tree
isDoubleInt(double) - Method in class edu.msu.cme.rdp.multicompare.visitors.DefaultPrintVisitor
isMissed() - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidClassificationResultFacade
isReverse() - Method in class edu.msu.cme.rdp.classifier.ClassificationResult
isReverse() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
isReverse() - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierSequence
  Returns true if the sequence string is a minus strand.
isSeqReversed(ClassifierSequence) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
  Returns true if the sequence is in reverse orientation.
isSeqReversed(int[], int) - Method in class edu.msu.cme.rdp.classifier.TrainingInfo
isSignificant() - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
isSingleton() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
isSingleton() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
isWordOccurDone() - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree

## L

LeaveOneOutTester - Class in edu.msu.cme.rdp.classifier.train.validation.leaveoneout
LeaveOneOutTester(Writer, int) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTester
LeaveOneOutTesterMain - Class in edu.msu.cme.rdp.classifier.train.validation.leaveoneout
LeaveOneOutTesterMain(String, String, String, String, int, int, boolean) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
  Creates a new Classification
LENGTH_DESC - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
LENGTH_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
LENGTH_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
LineageSequence - Class in edu.msu.cme.rdp.classifier.train
  A ParsedRawSequence holds the data for a raw sequence.
LineageSequence(String, List<String>, String) - Constructor for class edu.msu.cme.rdp.classifier.train.LineageSequence
  Creates new ParsedRawSequence.
LineageSequenceParser - Class in edu.msu.cme.rdp.classifier.train
  A parser to parse a reader containing the raw sequences.
LineageSequenceParser(File) - Constructor for class edu.msu.cme.rdp.classifier.train.LineageSequenceParser
  Creates new RawSequenceParser to parse the input fasta file.
LineageSequenceParser(InputStream) - Constructor for class edu.msu.cme.rdp.classifier.train.LineageSequenceParser
  Creates new RawSequenceParser to parse the input fasta file.
LogWordPriorFileParser - Class in edu.msu.cme.rdp.classifier.io
  A parser to parse a read containing a list of the indices of words and the log value of word prior probabilities.
LogWordPriorFileParser() - Constructor for class edu.msu.cme.rdp.classifier.io.LogWordPriorFileParser

## M

main(String[]) - Static method in class edu.msu.cme.rdp.classifier.ClassifierCmd
  This is the main method to do classification.
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.cli.ClassifierMain
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker
  This is the main method to create training files from raw taxonomic information.
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidateMain
  This is the main method for cross validation test.
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.validation.crossvalidate.RdmSelectTaxon
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.validation.distance.BoxPlotUtils
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.validation.distance.CompareTrainingSets
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.validation.distance.PairwiseSeqDistance
  This program does the pairwise alignment between each pair of sequences, reports a summary of the average distances and the stdev at each rank.
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
  This calculates the average similarity (Sab score or pairwise alignment) between taxa at given ranks and plot the box and whisker plot and accumulation curve.
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.CompareMisclassified
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.validation.movingwindow.MainMovingWindow
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.utils.HierarchyVersion
Main - Class in edu.msu.cme.rdp.multicompare
Main() - Constructor for class edu.msu.cme.rdp.multicompare.Main
main(String[]) - Static method in class edu.msu.cme.rdp.multicompare.Main
main(String[]) - Static method in class edu.msu.cme.rdp.multicompare.MergeTaxonCount
main(String[]) - Static method in class edu.msu.cme.rdp.multicompare.Reprocess
  This class reprocesses the classification results (allrank output) and print out hierarchy output file, based on the confidence cutoff; and print out only the detail classification results with assignment at certain rank with confidence above the cutoff or/and matching a given taxon.
main(String[]) - Static method in class edu.msu.cme.rdp.unifrac.Unifrac
MainMovingWindow - Class in edu.msu.cme.rdp.classifier.train.validation.movingwindow
MainMovingWindow(String, String, String, String, String, int, int, int) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.movingwindow.MainMovingWindow
  Creates a new instance of MainMovingWindow
MAX_SEQ_LEN - Static variable in class edu.msu.cme.rdp.classifier.Classifier
MCSample - Class in edu.msu.cme.rdp.multicompare
MCSample(SeqReader, String) - Constructor for class edu.msu.cme.rdp.multicompare.MCSample
MCSample(File) - Constructor for class edu.msu.cme.rdp.multicompare.MCSample
MCSample(String) - Constructor for class edu.msu.cme.rdp.multicompare.MCSample
MCSample(String, File) - Constructor for class edu.msu.cme.rdp.multicompare.MCSample
MCSample(List<ClassifierSequence>, String) - Constructor for class edu.msu.cme.rdp.multicompare.MCSample
MCSample(List<ClassifierSequence>, String, File) - Constructor for class edu.msu.cme.rdp.multicompare.MCSample
MCSample(File, String) - Constructor for class edu.msu.cme.rdp.multicompare.MCSample
MCSample(File, File) - Constructor for class edu.msu.cme.rdp.multicompare.MCSample
MCSamplePrintUtil - Class in edu.msu.cme.rdp.multicompare
MCSamplePrintUtil() - Constructor for class edu.msu.cme.rdp.multicompare.MCSamplePrintUtil
MCSampleResult - Class in edu.msu.cme.rdp.multicompare
MCSampleResult(String) - Constructor for class edu.msu.cme.rdp.multicompare.MCSampleResult
MCSampleResult(String, File) - Constructor for class edu.msu.cme.rdp.multicompare.MCSampleResult
MCTaxon - Class in edu.msu.cme.rdp.multicompare.taxon
MCTaxon(int, String, String) - Constructor for class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
MCTaxon(int, String, String, boolean) - Constructor for class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
MCTaxon(Taxon) - Constructor for class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
MergeTaxonCount - Class in edu.msu.cme.rdp.multicompare
MergeTaxonCount() - Constructor for class edu.msu.cme.rdp.multicompare.MergeTaxonCount
METADATA_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
METADATA_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
METADATA_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
MIN_BOOTSTRAP_WORDS_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
MIN_BOOTSTRAP_WORDS_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
MIN_BOOTSTRSP_WORDS - Static variable in class edu.msu.cme.rdp.classifier.Classifier
MIN_BOOTSTRSP_WORDS - Static variable in class edu.msu.cme.rdp.classifier.train.validation.NBClassifier
MIN_GOOD_WORDS - Static variable in class edu.msu.cme.rdp.classifier.Classifier
MIN_SEQ_LEN - Static variable in class edu.msu.cme.rdp.classifier.Classifier
  The minimum number of bases per sequence.
MIN_WORDS_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
multiClassificationParser(List<MCSample>, float, PrintWriter, ClassificationResultFormatter.FORMAT, String, HashSet<String>) - Method in class edu.msu.cme.rdp.multicompare.MultiClassifier
  Input files are the classification results printRank indicates which rank to filter by the confidence for the detail assignment output taxonFilter indicates which taxon to match for the detail assignment output
MultiClassifier - Class in edu.msu.cme.rdp.multicompare
MultiClassifier(String, String) - Constructor for class edu.msu.cme.rdp.multicompare.MultiClassifier
MultiClassifier(String, String, File, File) - Constructor for class edu.msu.cme.rdp.multicompare.MultiClassifier
MultiClassifierResult - Class in edu.msu.cme.rdp.multicompare
MultiClassifierResult(ConcretRoot) - Constructor for class edu.msu.cme.rdp.multicompare.MultiClassifierResult
MultiClassifierResult(ConcretRoot, List<MCSample>, List<String>, Map<String, Long>) - Constructor for class edu.msu.cme.rdp.multicompare.MultiClassifierResult
multiCompare(List<MCSample>) - Method in class edu.msu.cme.rdp.multicompare.MultiClassifier
multiCompare(List<MCSample>, int) - Method in class edu.msu.cme.rdp.multicompare.MultiClassifier
multiCompare(List<MCSample>, float, int) - Method in class edu.msu.cme.rdp.multicompare.MultiClassifier
multiCompare(List<MCSample>, PrintWriter, int) - Method in class edu.msu.cme.rdp.multicompare.MultiClassifier
multiCompare(List<MCSample>, float, PrintWriter, ClassificationResultFormatter.FORMAT, int) - Method in class edu.msu.cme.rdp.multicompare.MultiClassifier
  Input files are sequence files

## N

NameRankDupException - Exception in edu.msu.cme.rdp.classifier.train
NameRankDupException(String) - Constructor for exception edu.msu.cme.rdp.classifier.train.NameRankDupException
NBClassifier - Class in edu.msu.cme.rdp.classifier.train.validation
NBClassifier(TreeFactory, int[], ArrayList<HierarchyTree>, boolean, int) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.NBClassifier
next() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationParser
next() - Method in class edu.msu.cme.rdp.classifier.train.LineageSequenceParser
  Returns the next parsed sequence.
NUM_OF_RUNS - Static variable in class edu.msu.cme.rdp.classifier.train.validation.DecisionMaker
numCorrect - Variable in class edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment
numTotal - Variable in class edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment

## O

OUTFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
OUTFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
OUTFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
OUTFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
OUTFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
OUTFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain

## P

PairwiseSeqDistance - Class in edu.msu.cme.rdp.classifier.train.validation.distance
PairwiseSeqDistance(String, String, AlignmentMode, boolean) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.distance.PairwiseSeqDistance
parse(String) - Method in class edu.msu.cme.rdp.classifier.train.CopyNumberParser
parseCopyNumberFile(String) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  parse the copy number file first step, take the copy number info from the lowest rank taxa, then calculate the copy number of the parent taxa based on the immediate children second step, for any taxon without copy number info, uses the
parseSequenceFile(LineageSequenceParser) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
PixelCalculatorBean - Class in edu.msu.cme.rdp.classifier.comparison
PixelCalculatorBean() - Constructor for class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
PredictionCount(double, double) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.SortedROCSet.PredictionCount
printBootstrapCountTable(PrintStream, MCSample) - Static method in class edu.msu.cme.rdp.multicompare.MCSamplePrintUtil
printLeaves() - Method in class edu.msu.cme.rdp.taxatree.UnifracTree
printLicense() - Static method in class edu.msu.cme.rdp.classifier.ClassifierCmd
  Prints the license information to std err.
printLicense() - Static method in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
  Prints the license information to std err.
printLicense() - Static method in class edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker
  Prints the license information to std err.
printResults(ConcretRoot<MCTaxon>, List<MCSample>, PrintStream, PrintStream) - Static method in class edu.msu.cme.rdp.multicompare.Main
printResults(PrintStream, UnifracTree.UnifracResult, String) - Static method in class edu.msu.cme.rdp.unifrac.Unifrac
printSummary(PrintStream) - Method in class edu.msu.cme.rdp.classifier.train.validation.distance.PairwiseSeqDistance
printWordPriors() - Method in class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
ProbIndexFileParser - Class in edu.msu.cme.rdp.classifier.io
  A parser to parser a reader contains a list of indices of words, and start indices of the conditional probabilities.
ProbIndexFileParser() - Constructor for class edu.msu.cme.rdp.classifier.io.ProbIndexFileParser
processOneHierBlock(ArrayList<String[]>) - Method in class edu.msu.cme.rdp.multicompare.MergeTaxonCount
processOneHierFile(String) - Method in class edu.msu.cme.rdp.multicompare.MergeTaxonCount

## Q

QUERYFILE1_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
QUERYFILE1_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
QUERYFILE2_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
QUERYFILE2_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
QUERYFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
QUERYFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
QUERYFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
QUERYFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
QUERYFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
QUERYFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
QUERYFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain

## R

randomSelectTaxon(File, File, float, String) - Static method in class edu.msu.cme.rdp.classifier.train.validation.crossvalidate.RdmSelectTaxon
  Random select taxa at given rank, and return all the sequence IDs assigned to the selected taxa.
RANK_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
RANK_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
RankAssignment - Class in edu.msu.cme.rdp.classifier
  A RankAssignment holds the classification result of a sequence at one rank level.
RankAssignment(HierarchyTree, float) - Constructor for class edu.msu.cme.rdp.classifier.RankAssignment
  Creates new RankAssignment.
RANKS - Static variable in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
RANKS - Static variable in class edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
RANKS_WITHSPECIES - Static variable in class edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter
RawGenusWordConditionalProb - Class in edu.msu.cme.rdp.classifier.train
  A RawGenusWordConditionalProb contains the index of the genus node and the conditional probability of the node contains the word.
RawGenusWordConditionalProb(int, float) - Constructor for class edu.msu.cme.rdp.classifier.train.RawGenusWordConditionalProb
  Creates a new instance of RawGenusWordConditionalProb.
RawHierarchyTree - Class in edu.msu.cme.rdp.classifier.train
  A RawHierarchyTree holds the raw taxon and sequences information.
RawHierarchyTree(String, RawHierarchyTree, Taxonomy) - Constructor for class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Creates new RawHierarchyTree given the name and its parent.
RdmSelectTaxon - Class in edu.msu.cme.rdp.classifier.train.validation.crossvalidate
RdmSelectTaxon() - Constructor for class edu.msu.cme.rdp.classifier.train.validation.crossvalidate.RdmSelectTaxon
readData(String, File, String, String) - Static method in class edu.msu.cme.rdp.classifier.train.validation.distance.BoxPlotUtils
readRanks(String) - Static method in class edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
readReplicateMapping(String) - Static method in class edu.msu.cme.rdp.multicompare.Main
readSampleMapping(String) - Static method in class edu.msu.cme.rdp.multicompare.Main
readTaxonDistance(String) - Method in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.CompareMisclassified
readTaxonFilterFile(String) - Static method in class edu.msu.cme.rdp.multicompare.Reprocess
refreshInnerTaxa() - Method in class edu.msu.cme.rdp.taxatree.UnifracTree
releaseWordOccurrence() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Resets the array wordOccurrence to null.
Reprocess - Class in edu.msu.cme.rdp.multicompare
Reprocess() - Constructor for class edu.msu.cme.rdp.multicompare.Reprocess
resetDefaultDataProp() - Static method in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
  Resets the data property file to the default data property file.
resetSamples() - Method in class edu.msu.cme.rdp.unifrac.UnifracTaxon
resetSamples(List<UnifracTreeBuilder.UnifracSample>) - Method in class edu.msu.cme.rdp.unifrac.UnifracTaxon
ResultComparator() - Constructor for class edu.msu.cme.rdp.classifier.train.validation.SortedROCSet.ResultComparator
RRNA_16S_GENE - Static variable in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
runTest(File, File, File, String, float, Integer, boolean, int) - Method in class edu.msu.cme.rdp.classifier.train.validation.crossvalidate.CrossValidate
  The method randomly selects a fraction of sequences from the source file as test set, used the remaining sequences from the source file as training set.

## S

sample - Variable in class edu.msu.cme.rdp.unifrac.UnifracTreeBuilder.UnifracSample
SAMPLE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
sampleCountMap - Variable in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
Score - Class in edu.msu.cme.rdp.classifier.comparison
Score(float, SeqInfo, Taxon) - Constructor for class edu.msu.cme.rdp.classifier.comparison.Score
  Creates a new instance of Score
seed - Static variable in class edu.msu.cme.rdp.classifier.train.validation.NBClassifier
SeqErrorBean - Class in edu.msu.cme.rdp.classifier.comparison
SeqErrorBean(String, String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.SeqErrorBean
  Creates a new instance of SeqErrorBean
SeqInfo - Class in edu.msu.cme.rdp.classifier.comparison
SeqInfo(String, String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.SeqInfo
  Creates a new instance of SeqInfo
setConfidence(String) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setCopyNumber(float) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
setCurrentRoot(String) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setDataProp(String, boolean) - Static method in class edu.msu.cme.rdp.classifier.utils.ClassifierFactory
  Sets the property file which contains the mapping of the training files.
setDepth(String) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setDepth(int) - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
setDepth(int) - Method in class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
setGenusIndex(int) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Sets the genus index of this treenode.
setIncSeqNodes(boolean) - Method in class edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder
setLabeledNode(HierarchyTree) - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidClassificationResultFacade
setLineage(String) - Method in class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
setLineage(String) - Method in class edu.msu.cme.rdp.multicompare.taxon.MCTaxon
setMissedRank(String) - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidClassificationResultFacade
setNumOfVotes(float) - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidationClassificationResult
setParentID(int) - Method in class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
setPosteriorProb(double) - Method in class edu.msu.cme.rdp.classifier.train.validation.ValidationClassificationResult
setRoot(ComparisonBrowserNode) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setS1Total(int) - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
setS2Total(int) - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
setSampleCount(MCSample, double) - Method in class edu.msu.cme.rdp.unifrac.UnifracTaxon
setSeqErrorList(List) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setSeqString(String) - Method in class edu.msu.cme.rdp.classifier.utils.ClassifierSequence
  Sets the sequence string.
setSubmitDate(Date) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setTaxon(Taxon) - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
setTaxonFactory(ClassifierTreeBuilder.ClassifierTaxonFactory<E>) - Method in class edu.msu.cme.rdp.taxatree.utils.ClassifierTreeBuilder
setTaxonList(Iterator) - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
SHORTSEQ_OUTFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
SHORTSEQ_OUTFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
SHORTSEQ_OUTFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
ShortSequenceException - Exception in edu.msu.cme.rdp.classifier
  Handles exception for a short sequence.
ShortSequenceException(String, String) - Constructor for exception edu.msu.cme.rdp.classifier.ShortSequenceException
  Creates a new instance of ShortSequenceException to handle short sequence.
SigCalculator - Class in edu.msu.cme.rdp.classifier.comparison
SigCalculator(int, int, float) - Constructor for class edu.msu.cme.rdp.classifier.comparison.SigCalculator
  Creates a new instance of SigCalculater
SortedROCSet - Class in edu.msu.cme.rdp.classifier.train.validation
SortedROCSet() - Constructor for class edu.msu.cme.rdp.classifier.train.validation.SortedROCSet
SortedROCSet.PredictionCount - Class in edu.msu.cme.rdp.classifier.train.validation
SortedROCSet.ResultComparator - Class in edu.msu.cme.rdp.classifier.train.validation
standardError - Variable in class edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment
startElement(String, String, String, Attributes) - Method in class edu.msu.cme.rdp.classifier.io.TreeFileParser
StatusCount - Class in edu.msu.cme.rdp.classifier.train.validation
StatusCount() - Constructor for class edu.msu.cme.rdp.classifier.train.validation.StatusCount
StatusCountUtils - Class in edu.msu.cme.rdp.classifier.train.validation
StatusCountUtils() - Constructor for class edu.msu.cme.rdp.classifier.train.validation.StatusCountUtils
step - Static variable in class edu.msu.cme.rdp.classifier.train.validation.movingwindow.FindWindowFrame
sumOfVotes - Variable in class edu.msu.cme.rdp.classifier.train.validation.CorrectAssignment

## T

TaxaSimilarityMain - Class in edu.msu.cme.rdp.classifier.train.validation.distance
TaxaSimilarityMain(List<String>) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.distance.TaxaSimilarityMain
Taxon - Interface in edu.msu.cme.rdp.classifier.comparison
TAXON_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
TAXON_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
TaxonCopyNumber(String, String, float) - Constructor for class edu.msu.cme.rdp.classifier.train.CopyNumberParser.TaxonCopyNumber
Taxonomy - Class in edu.msu.cme.rdp.classifier.train
  A Taxonomy holds the raw taxon information.
Taxonomy(int, String, int, int, String) - Constructor for class edu.msu.cme.rdp.classifier.train.Taxonomy
  Creates a new instance of Taxonomy
Taxonomy - Class in edu.msu.cme.rdp.classifier.train.validation
Taxonomy(int, String, int, int, String) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.Taxonomy
  Creates a new instance of Taxonomy
TaxonTree - Class in edu.msu.cme.rdp.classifier.comparison
TaxonTree(int, String, String, AbstractNode) - Constructor for class edu.msu.cme.rdp.classifier.comparison.TaxonTree
  Creates a new instance of TaxonTree
toString() - Method in class edu.msu.cme.rdp.multicompare.MCSample
TRAIN_SEQFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
TRAIN_SEQFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
TRAIN_SEQFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
TRAIN_TAXONFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
TRAIN_TAXONFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
TRAIN_TAXONFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.train.validation.leaveoneout.LeaveOneOutTesterMain
TrainingDataException - Exception in edu.msu.cme.rdp.classifier
  Handles the exception occurred when parsing training information.
TrainingDataException() - Constructor for exception edu.msu.cme.rdp.classifier.TrainingDataException
  Creates a new instance of TrainingDataException without detail message.
TrainingDataException(String) - Constructor for exception edu.msu.cme.rdp.classifier.TrainingDataException
  Constructs an instance of TrainingDataException with the specified detail message.
TrainingDataException(Throwable) - Constructor for exception edu.msu.cme.rdp.classifier.TrainingDataException
  Constructs an instance of TrainingDataException with the specified root cause.
TrainingInfo - Class in edu.msu.cme.rdp.classifier
  The TrainingInfo holds all the training information and taxonomy hierarchy information.
TrainingInfo() - Constructor for class edu.msu.cme.rdp.classifier.TrainingInfo
  Creates new TrainingInfo.
TRAINPROPFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
TRAINPROPFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
TRAINPROPFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.cli.CmdOptions
TreeFactory - Class in edu.msu.cme.rdp.classifier.train
  A TreeFactory reads the raw taxonomic information and creates the RawHierarchyTree nodes.
TreeFactory(Reader, int, String, String) - Constructor for class edu.msu.cme.rdp.classifier.train.TreeFactory
  Creates new TreeFactory.
TreeFactory - Class in edu.msu.cme.rdp.classifier.train.validation
TreeFactory(Reader) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.TreeFactory
  Creates new TreeFactory
TreeFileParser - Class in edu.msu.cme.rdp.classifier.io
  A parser to parse a reader containing taxonomic training information.
TreeFileParser() - Constructor for class edu.msu.cme.rdp.classifier.io.TreeFileParser
  Creates a new instance of TreeFileParser.

## U

UncNode - Class in edu.msu.cme.rdp.classifier.comparison
unhideSeq(GoodWordIterator) - Method in class edu.msu.cme.rdp.classifier.train.validation.HierarchyTree
  This method initiate the word occurrence from the sequences for the lowest level of the hierarchy tree
Unifrac - Class in edu.msu.cme.rdp.unifrac
Unifrac() - Constructor for class edu.msu.cme.rdp.unifrac.Unifrac
UnifracResult(List<MCSample>, float[][]) - Constructor for class edu.msu.cme.rdp.taxatree.UnifracTree.UnifracResult
UnifracSample() - Constructor for class edu.msu.cme.rdp.unifrac.UnifracTreeBuilder.UnifracSample
UnifracTaxon - Class in edu.msu.cme.rdp.unifrac
UnifracTaxon(int, String, String, float) - Constructor for class edu.msu.cme.rdp.unifrac.UnifracTaxon
UnifracTaxon(int, String, String, float, boolean) - Constructor for class edu.msu.cme.rdp.unifrac.UnifracTaxon
UnifracTaxon(MCTaxon, float) - Constructor for class edu.msu.cme.rdp.unifrac.UnifracTaxon
UnifracTree - Class in edu.msu.cme.rdp.taxatree
UnifracTree() - Constructor for class edu.msu.cme.rdp.taxatree.UnifracTree
UnifracTree.UnifracResult - Class in edu.msu.cme.rdp.taxatree
UnifracTreeBuilder - Class in edu.msu.cme.rdp.unifrac
UnifracTreeBuilder(List<ClassificationResult>, Map<String, UnifracTreeBuilder.UnifracSample>) - Constructor for class edu.msu.cme.rdp.unifrac.UnifracTreeBuilder
UnifracTreeBuilder(List<ClassificationResult>, Map<String, UnifracTreeBuilder.UnifracSample>, float) - Constructor for class edu.msu.cme.rdp.unifrac.UnifracTreeBuilder
UnifracTreeBuilder.UnifracSample - Class in edu.msu.cme.rdp.unifrac

## V

ValidationClassificationResult - Class in edu.msu.cme.rdp.classifier.train.validation
ValidationClassificationResult(HierarchyTree, float, float) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.ValidationClassificationResult
  Creates new ClassificationResult
ValidationClassificationResult(HierarchyTree, float) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.ValidationClassificationResult
ValidClassificationResultFacade - Class in edu.msu.cme.rdp.classifier.train.validation
ValidClassificationResultFacade(LineageSequence, List<ValidationClassificationResult>) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.ValidClassificationResultFacade
  Creates a new instance of ClassificationResultFacade
valueOf(String) - Static method in enum edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter.FORMAT
  Returns the enum constant of this type with the specified name.
values() - Static method in enum edu.msu.cme.rdp.classifier.io.ClassificationResultFormatter.FORMAT
  Returns an array containing the constants of this enum type, in the order they are declared.
visitNode(VisitInfo<MCTaxon>) - Method in class edu.msu.cme.rdp.multicompare.visitors.DefaultPrintVisitor
visitNode(VisitInfo<MCTaxon>) - Method in class edu.msu.cme.rdp.multicompare.visitors.EstimateSPrintVisitor

## W

Window - Class in edu.msu.cme.rdp.classifier.train.validation.movingwindow
Window(int, int) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.movingwindow.Window
  Creates a new instance of Window
window_size - Static variable in class edu.msu.cme.rdp.classifier.train.validation.movingwindow.FindWindowFrame
WindowTester - Class in edu.msu.cme.rdp.classifier.train.validation.movingwindow
WindowTester(Writer) - Constructor for class edu.msu.cme.rdp.classifier.train.validation.movingwindow.WindowTester
  Creates new Tester

## Z

Ztable - Class in edu.msu.cme.rdp.classifier.comparison
Ztable() - Constructor for class edu.msu.cme.rdp.classifier.comparison.Ztable
  Creates a new instance of Ztable

A B C D E F G H I L M N O P Q R S T U V W Z