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

## A

ABORTED - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
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
AbstractNode.LineageIterator - Class in edu.msu.cme.rdp.classifier.comparison
  An Iterator of the ancestor nodes of the current node(not included) returns the most recent ancestor last.
AbstractNode.LineageIterator() - Constructor for class edu.msu.cme.rdp.classifier.comparison.AbstractNode.LineageIterator
AbstractNode.TaxonIterator - Class in edu.msu.cme.rdp.classifier.comparison
  An Iterator of the BrowserNode.
AbstractNode.TaxonIterator(int) - Constructor for class edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator
accumulateProbArr - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
addBestGenusNode(HierarchyTree, List) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
  Adds a single RankAssignment to the list of the classification results if a treenode is already included in the list, simply increases the confidence for that RankAssignment by 1, for easy calculation.
addChild(AbstractNode) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
addConfidence(HierarchyTree, HashMap) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.rrnaclassifier.HierarchyTree
  Adds the parent HierarchyTree, also adds this node to the parent treenode as a child.
addParent(RawHierarchyTree) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Adds the parent HierarchyTree, also adds this node to the parent tree as a child.
addS1Score(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
addS2Score(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
addScore(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
addSequence(ParsedRawSequence) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
addSequencewithLineage(ParsedRawSequence) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  For the given sequence name, its ancestors, and the sequence string, creates a HierarchyTree for each ancestor, If the root does not exist, creates the root with a null parent.
addSequencewithTaxid(ParsedRawSequence) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  For the given sequence name, its assigned taxid, and the sequence string, creates a HierarchyTree for each ancestor, If the root does not exist, creates the root with a null parent.
addSibling(AbstractNode) - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
addSubclass(HierarchyTree) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
  Adds a child treenode to subclass.
addSubclass(RawHierarchyTree) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Adds a child treenode.
ancestors - Variable in class edu.msu.cme.rdp.classifier.train.ParsedRawSequence
assignments - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResult

## B

bestClass - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.RankAssignment
browserBean - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager

## C

calculateSig(int, int) - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
calFactorial(int, int) - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
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
changeRank(String) - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
charIntegerLookup - Static variable in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
charIntegerLookup - Static variable in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
charLookup - Static variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
CLASS_OUTFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
CLASS_OUTFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
CLASS_OUTFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
ClassificationResult - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  This class holds the classification results for a query sequence.
ClassificationResult(Sequence, List, HierarchyVersion) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResult
  Creates a new instance of ClassificationResult.
ClassificationResultFormatter - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
ClassificationResultFormatter() - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResultFormatter
ClassificationResultFormatter.FORMAT - Enum in edu.msu.cme.rdp.classifier.rrnaclassifier
ClassificationResultFormatter.FORMAT() - Constructor for enum edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResultFormatter.FORMAT
Classifier - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  This is the class to do the classification.
Classifier(TrainingInfo) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
  Creates new Classifier.
ClassifierCmd - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  This is the command line class to do the classification.
ClassifierCmd() - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
classifierFactory - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
ClassifierFactory - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  A factory to create a classifier with the training information defined by the property file.
ClassifierFactory() - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
  Creates a new instance of ClassifierFactory.
ClassifierTest - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  A test class for Classifier.
ClassifierTest(String) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierTest
ClassifierTraineeMaker - Class in edu.msu.cme.rdp.classifier.train
  A command line class to create training information from the raw data.
ClassifierTraineeMaker(String, String, int, String, String, String) - Constructor for class edu.msu.cme.rdp.classifier.train.ClassifierTraineeMaker
  Creates a new ClassifierTraineeMaker
classifierVer - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
classifierVersion - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
classify(Sequence) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
  Takes a query sequence, returns the classification result.
close() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
  Closes the reader.
close() - Method in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
  Closes the reader.
combinedTotal - Variable in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
compare(Object, Object) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonResultTreeSet.ComparisonResultComparator
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
ComparisonBrowserBean - Class in edu.msu.cme.rdp.classifier.comparison
ComparisonBrowserBean(String, String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
ComparisonBrowserBeanTest - Class in edu.msu.cme.rdp.classifier.comparison
ComparisonBrowserBeanTest(String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBeanTest
ComparisonBrowserNode - Interface in edu.msu.cme.rdp.classifier.comparison
ComparisonCmd - Class in edu.msu.cme.rdp.classifier.comparison
ComparisonCmd(String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
  Creates a new Manager
ComparisonManager - Class in edu.msu.cme.rdp.classifier.comparison
ComparisonManager(InputStream, String, InputStream, String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
ComparisonManager.Timer - Class in edu.msu.cme.rdp.classifier.comparison
  The timer will wake up and check the time set by jsp, if the time expired, which indicates the jsp page has been refreshed for a long time, abort the current seqmatch thread.
ComparisonManager.Timer() - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonManager.Timer
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
ComparisonResultTreeSet.ComparisonResultComparator() - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonResultTreeSet.ComparisonResultComparator
ComparisonSuite - Class in edu.msu.cme.rdp.classifier.comparison
ComparisonSuite(String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.ComparisonSuite
complementLookup - Static variable in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
COMPLETED - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
CONF_DESC - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
CONF_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
CONF_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
confCutoff - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.SampleDetailIterator
confCutoff - Variable in class edu.msu.cme.rdp.classifier.comparison.UncNode.SampleDetailIterator
confidence - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
confidence - Variable in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
confidence - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.RankAssignment
confidenceCutoff - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
confidenceValue - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
convert(String) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
  Retrieves appropriate value from the property file.
createClassifier() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
  Creates a new classifier.
createClassifier() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Creates a new Classifier if all the train information have been completed, throws exception if not.
createGenusNodeList(HierarchyTree) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Returns a list of all the genus rank nodes.
createGenusWordConditionalProb() - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  This method does all the setup work for wordPrior and word conditional probability.
createGenusWordProbList(Reader, List, HierarchyVersion) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.GenusWordProbFileParser
  Reads a file and saves GenusWordConditionalProb objects in a list.
createGenusWordProbList(Reader) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Reads in the index of the genus treenode and conditional probability that genus contains a word.
createLogWordPriorArr(Reader, float[], HierarchyVersion) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.LogWordPriorFileParser
  Reads a file and saves the log word priors in an array.
createLogWordPriorArr(Reader) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Reads in the log value of the word prior probability and saves to an array LogWordPriorArr.
createNodeList(RawHierarchyTree, String, List) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Gets all the lowest level nodes in given hierarchy level starting from the given root.
createProbIndexArr(Reader, int[], HierarchyVersion) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.rrnaclassifier.TrainingInfo
  Reads in start index of the conditional probability of each genus, saves to an array wordConditionalProbIndexArr.
createTree(Reader) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Reads in the tree information from a reader and create all the HierarchyTrees.
createTree(Reader, HierarchyVersion) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParser
  Reads from a reader that contains the information for each treenode.
createWordIndex(String) - Method in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
  Fetches every overlapping word, change the string to integer and saves in an array.
createWordIndexArr() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Fetches every overlapping word from the sequence string, changes each word to integer format and saves in an array.
createWordIndexArr() - Method in interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
  Fetches every overlapping word from the sequence string, changes each word to integer format and saves in an array.
creatTaxidMap(Reader) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  It reads in a file containing the taxonomy information for all the nodes.
curIndex - Variable in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
currentRoot - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
curScore - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.SampleDetailIterator
curScore - Variable in class edu.msu.cme.rdp.classifier.comparison.UncNode.SampleDetailIterator
curSeq - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
curSeq - Variable in class edu.msu.cme.rdp.classifier.train.RawSequenceParser

## D

dataDir - Static variable in class edu.msu.cme.rdp.classifier.comparison.Ztable
  The default data directory, relative to the classpath.
dataDir - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
  The default data directory, relative to the classpath.
dataProp - Static variable in class edu.msu.cme.rdp.classifier.comparison.Ztable
dataProp - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
decomposeHeader(String) - Method in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
  Takes two different formats: the old format is a string of sequence header( ancestors seperated by delimiter, such as ";" in our case).
DEFAULT_CON_CUTOFF - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
DEFAULT_CONF - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
DEFAULT_DEPTH - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
DEFAULT_FORMAT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
defaultDataProp - Static variable in class edu.msu.cme.rdp.classifier.comparison.Ztable
  The default data property file name, inside the default data directory
defaultDataProp - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
  The default data property file name, inside the default data directory
defaultFormat - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
delimiter - Static variable in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
DELIMITER_Z - Static variable in class edu.msu.cme.rdp.classifier.comparison.Ztable
depth - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator
depth - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
depth - Variable in class edu.msu.cme.rdp.classifier.train.Taxonomy
depthValue - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
description - Variable in class edu.msu.cme.rdp.classifier.comparison.SeqErrorBean
df - Static variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
df - Static variable in class edu.msu.cme.rdp.classifier.comparison.Ztable
DISPLAY_LIMIT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
displayResult(ClassificationResult) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
displayTrainingTree(HierarchyTree) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParserTest
displayTrainingTree(RawHierarchyTree) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Writes the phylogenetic taxonmic information of the given root and all the descendant nodes to a 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
doClassify(String, String, String, ClassificationResultFormatter.FORMAT) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
  It classifies query sequences from the input file.
docText - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence

## E

edu.msu.cme.rdp.classifier.comparison - package edu.msu.cme.rdp.classifier.comparison
edu.msu.cme.rdp.classifier.readseqwrapper - package edu.msu.cme.rdp.classifier.readseqwrapper
edu.msu.cme.rdp.classifier.rrnaclassifier - package edu.msu.cme.rdp.classifier.rrnaclassifier
  Provides classes for reading training information and classifying sequence.
edu.msu.cme.rdp.classifier.train - package edu.msu.cme.rdp.classifier.train
  Provides classes for creating the training files from the raw training data.
emblErrorMsg - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
endElement(String, String, String) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParser
error(SAXParseException) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParser
errorList - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
exceedLimit - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager

## F

faction - Variable in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
factory - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
factory - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
FAILED - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
fastaErrorMsg - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
findAncestor(HierarchyTree, RankAssignment, List) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
  Finds the ancestors of the given node up to the root.
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
firstChild - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
firstS1Score - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
firstS2Score - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
firstScore - Variable in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
format - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
FORMAT_DESC - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
FORMAT_DESC - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
FORMAT_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
FORMAT_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
FORMAT_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
FORMAT_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
formatError - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
FREQ_LIMIT - Static variable in class edu.msu.cme.rdp.classifier.comparison.SigCalculator

## G

genbankErrorMsg - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
generateWordPairDiffArr(int[], int) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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_wordConditionalProbList - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
genus_wordConditionalProbList - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
genusIndex - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.GenusWordConditionalProb
genusIndex - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
  -1 means not a genus node.
genusIndex - Variable in class edu.msu.cme.rdp.classifier.train.RawGenusWordConditionalProb
genusIndex - Variable in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
genusNodeList - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
genusNodeList - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
GenusWordConditionalProb - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  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.rrnaclassifier.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.rrnaclassifier
  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.rrnaclassifier.GenusWordProbFileParser
  Creates a new instance of GenusWordProbFileParser
getAllRankOutput(ClassificationResult) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResultFormatter
getAncestors() - Method in class edu.msu.cme.rdp.classifier.train.ParsedRawSequence
  Returns the list of the ancestor taxa, with the highest ranked taxon first.
getAssignments() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResult
  Returns a list of RankAssignments.
getBestClass() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.RankAssignment
  Returns the HierarchyTree which the query sequence is assigned to.
getBrowserBean() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
getChildbyTaxid(int, String, String) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
  Given a assignment, first search the asigned node among the children, if the child does not exist, create a new child node.
getChildTaxonList() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getClassifierVersion() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getClassifierVersion() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.rrnaclassifier.RankAssignment
  Returns the estimate of confidence of the assignment.
getCurrentBrowserRoot() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getDBOutput(ClassificationResult) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.
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
getDocumentText() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Returns the whole documentation in text.
getDoubleSignificance() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getFactory() - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
  Returns a factory with the training information.
getFinalResultList(HashMap, HierarchyTree) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
getFirstChild() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getFirstChild() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
getFirstChild() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode
getFirstS1Score() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
getFirstS2Score() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
getFirstScore() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
getFixRankOutput(ClassificationResult) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResultFormatter
getFixRankOutput(String[], ClassificationResult) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResultFormatter
getFloatConfidence() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getGenusIndex() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.GenusWordConditionalProb
  Returns the index of the genus node
getGenusIndex() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.rrnaclassifier.TrainingInfo
  Returns a genus node from the genusNodeList at the specified position.
getGenusNodeList() - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Return the list of geneus nodes.
getGenusNodeListSize() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Returns the number of the genus nodes.
getGoodWordCount() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Returns the number of words with valid bases.
getGoodWordCount() - Method in interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
  Returns the number of words without invalid base(s).
getGreedyPath(HierarchyTree, List) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
  Returns a list of RankAssignment in which root is the first item.
getHierarchyInfo() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.rrnaclassifier.ClassificationResult
  Returns the version of the taxonomy hierarchy from of the training file.
getHierarchyTrainsetNo() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.rrnaclassifier.ClassifierFactory
  Returns the version of the taxonomical hierarchy.
getHierarchyVersion() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Returns the version of the taxonomical hierarchy.
getHierLevel() - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
  Returns the hierarchy rank level.
getIndent() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getIndent() - Method in interface edu.msu.cme.rdp.classifier.comparison.Taxon
getLastCheckTime() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
getLastS1Score() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
getLastS2Score() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
getLeaveCount() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.
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.rrnaclassifier.TrainingInfo
  Returns the log value of (number of leaves + 1) of a genus
getLogLeaveCount(int) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Returns the log value of ( number of leaves plus 1 ).
getLogWordPrior(int) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Returns the log value of the prior probability of a word.
getLogWordPrior(int) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Returns the log value for word prior probability for the given word index.
getMask() - Method in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
  Returns the mask.
getMessage() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqErrorBean
getMessage() - Method in exception edu.msu.cme.rdp.classifier.rrnaclassifier.ShortSequenceException
  Returns the error message.
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.readseqwrapper.ParsedSequence
  Returns the name of the sequence record.
getName() - Method in interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
  Returns the name of the sequence record.
getName() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
  Gets the name of the treenode.
getName() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.RankAssignment
  Returns the name of the assigned HierarchyTree.
getName() - Method in class edu.msu.cme.rdp.classifier.train.ParsedRawSequence
  Returns the name of the sequence.
getName() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Gets the name of the treenode.
getNextAssignScore() - Method in class edu.msu.cme.rdp.classifier.comparison.Score
getNextElement() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator
getNextElement() - Method in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
  Reads from the input stream and returns a parsed sequence.
getNextSeqScore() - Method in class edu.msu.cme.rdp.classifier.comparison.Score
getNextSequence() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
  Returns the next available ParsedSequence from input.
getNextSibling() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
getNonDefaultFactory() - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
  Returns a factory with the training information for the non-default training data files.
getNonSingletonLeaveCount() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Counts the number of non-singleton sequence leaves below this tree.
getNumOfChildren() - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
getNumofWords() - Method in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
  Returns the number of unique words.
getOutput(ClassificationResult, ClassificationResultFormatter.FORMAT) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResultFormatter
getParent() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
  the parent of the root is null
getParent() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
  Gets the parent treenode.
getParent() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Gets the parent treenode.
getParentID() - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
  Returns the taxID of the parent taxon.
getProbability() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.
getProgress() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
getPvalue(double) - Method in class edu.msu.cme.rdp.classifier.comparison.Ztable
getRandomIndex(int) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
  Generates a random integer in the range of 0 to the specified maximum integer.
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.rrnaclassifier.HierarchyTree
  Gets the rank of the treenode.
getRank() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.RankAssignment
  Returns the rank of the assigned HiearchyTree.
getReversedSeq() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Returns a Sequence object whose sequence string is the reverse complement of the current rRNA sequence string.
getReversedSeq() - Method in interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
  Returns a Sequence object whose sequence string is the reverse complement of the current sequence string.
getReversedSeqString(String) - Static method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Returns the reverse complement string of the given rRNA sequence string .
getReversedWord(int[]) - Static method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Returns the reverse complement of the word in an integer array format.
getRoot() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
getRoot() - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Gets the root of the tree
getRootTree() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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
getS1Filename() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
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
getS2Filename() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
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
getScore() - Method in class edu.msu.cme.rdp.classifier.comparison.Score
getScoreList() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
getSeqCountLimit() - Static method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
getSeqDoc() - Method in exception edu.msu.cme.rdp.classifier.rrnaclassifier.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
getSeqInfo() - Method in class edu.msu.cme.rdp.classifier.comparison.Score
getSeqString() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Returns the sequence string.
getSeqString() - Method in interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
  Returns the sequence string of the sequence record.
getSequence() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResult
  Returns the query sequence
getSequence() - Method in class edu.msu.cme.rdp.classifier.train.ParsedRawSequence
  Returns the sequence string.
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.
getSizeofSubclasses() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.
getStartIndex(int) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Returns the start index of GenusIndexWordConditionalProb in the array for the specified wordIndex.
getStartIndex(int) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Returns the start index of RawGenusWordConditionalProb in the array for the given wordIndex.
getStatus() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
getStopIndex(int) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Returns the stop index of GenusIndexWordConditionalProb in the array for the specified wordIndex.
getStopIndex(int) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Returns the stop index of RawGenusWordConditionalProb in the array for the given wordIndex.
getSubclassbyName(String) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Gets the child treenode with the given name.
getSubclasses() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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.
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.rrnaclassifier.HierarchyTree
  Gets the taxon id of the treenode.
getTaxid() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.RankAssignment
  Returns the taxid of the assigned HierachyTree
getTaxID() - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
  Returns the taxID.
getTaxName() - Method in class edu.msu.cme.rdp.classifier.train.Taxonomy
  Returns the taxon name.
getTaxon() - Method in class edu.msu.cme.rdp.classifier.comparison.Score
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(ParsedRawSequence, int, int) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Gets the Taxonomy for the tree node in the ancestor list.
getTitle() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
getTitle() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Returns the title of the documentation of the sequcence record.
getTitle() - Method in interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
  Returns the title of the sequence record.
getTrainsetNo() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResult
  Returns the training set number of the taxonomy hierarchy from of the training file.
getTrainsetNo() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion
  Returns the training set number of the taxonomy hierarchy from the header of the training file.
getVersion() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion
  Returns the version of the taxonomy hierarchy from the header of the training file.
getWordConditionalProb(int) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Returns a GenusWordConditionalProb from the array given the postion.
getWordConditionalProbObject(int) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Returns a GenusIndexWordConditionalProb from the genusIndex_wordConditionalProbList at the specified postion in the list.
getWordIndex(int[]) - Static method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Returns an integer representation of a single word.
getWordOccurrence(int) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  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.
getWordPairPriorDiff(int) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Returns the difference between given word and its reverse complement word.
getWordsize() - Method in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
  Returns the size of word.
goodWordCount - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
GoodWordIterator - Class in edu.msu.cme.rdp.classifier.train
  A GoodWordIterator creates a list of valid words from the input string.
GoodWordIterator(String) - Constructor for class edu.msu.cme.rdp.classifier.train.GoodWordIterator
  Creates a new instance of GoodWordIterator
GoodWordIteratorTest - Class in edu.msu.cme.rdp.classifier.train
  A test class for GoodWordIterator.
GoodWordIteratorTest(String) - Constructor for class edu.msu.cme.rdp.classifier.train.GoodWordIteratorTest

## H

hasNext() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.LineageIterator
hasNext() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator
hasNext() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo.ScoreIterator
hasNext() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.DetailIterator
hasNext() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.SampleDetailIterator
hasNext() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode.DetailIterator
hasNext() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode.SampleDetailIterator
hasNext() - Method in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
  Returns true if the iteration has more good element on deck.
hasNext() - Method in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
  Returns true if there is a parsed sequence available.
HierarchyTree - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  A HierarchyTree holds the taxonomic information of a taxon.
HierarchyTree(String, int, String, int, int) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
  Creates new HierarchyTree given the taxonomic information.
HierarchyTreeTest - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  A test class for HierarchyTree.
HierarchyTreeTest(String) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTreeTest
hierarchyVer - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
HierarchyVersion - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  A HierarchyVersion holds the training set number and version of the taxonomy.
HierarchyVersion(String) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion
  Creates a new instance of HierarchyVersion,
hierarchyVersion - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
hierLevel - Variable in class edu.msu.cme.rdp.classifier.train.Taxonomy
hVersion - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResult

## I

incS1Count(int) - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
incS2Count(int) - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
indent - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
index - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.LineageIterator
init() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
  Checks the format of the input.
initWordOccurrence(ParsedRawSequence, 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.
intComplementLookup - Static variable in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
isAborted() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
isCompleted() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
isGenusWordProbListDone - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
isProbIndexArrDone - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
isReverse() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
isReverse() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Returns true if the sequence string is a minus strand.
isReverse() - Method in interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
  Returns true if the sequence string is a minus strand.
isRunning() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
isSeqReversed(Sequence) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Returns true if the sequence is in reverse orientation.
isSignificant() - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
isSingleton() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
isTreeDone - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
isWordExist(int[], int) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Checks if this word already been added to the wordOccurrence.
isWordPriorArrDone - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo

## L

largeProportionTest(int, int) - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
lastCheckTime - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
lastS1Score - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
lastS2Score - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
leaveCount - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
leaveCount - Variable in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
lineage - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.LineageIterator
load(String) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParser
logArr - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
logLeaveCountArr - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
logWordPriorArr - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
LogWordPriorFileParser - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  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.rrnaclassifier.LogWordPriorFileParser
  Creates a new instance of LogWordPriorFileParser.

## M

main(String[]) - Static method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBeanTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.comparison.ComparisonSuite
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.comparison.SigCalculatorTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.comparison.TaxonTreeTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.comparison.UncNodeTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.comparison.ZtableTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequenceTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParserTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
  This is the main method to do classification.
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTreeTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParserTest
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.GoodWordIteratorTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTreeTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.RawSequenceParserTest
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.TrainSuite
main(String[]) - Static method in class edu.msu.cme.rdp.classifier.train.TreeFactoryTest
MASK - Static variable in interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
  The mask for converting a string to integer
MASK - Static variable in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
matcher - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
matcher - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion
matcher - Variable in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
MAX_ASCII - Static variable in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
MAX_ASCII - Static variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
MAX_ASCII - Static variable in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
MAX_CONF - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
MAX_DEPTH - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
MAX_NUM_OF_WORDS - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
  The assumed maximum number of words per sequence.
MAX_SEQUENCE - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
MAX_Z - Static variable in class edu.msu.cme.rdp.classifier.comparison.Ztable
maxPercent - Variable in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
message - Variable in class edu.msu.cme.rdp.classifier.comparison.SeqErrorBean
message - Variable in exception edu.msu.cme.rdp.classifier.rrnaclassifier.ShortSequenceException
MIN_CONF - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
MIN_DEPTH - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
MIN_GOOD_WORDS - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
MIN_SEQ_LEN - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
  The minimum number of bases per sequence.
modifySequence(String) - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
  Modifies the sequence string.
modifySequence(String) - Method in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
  Modifies the sequence.

## N

name - Variable in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
name - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
name - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
name - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
name - Variable in class edu.msu.cme.rdp.classifier.train.ParsedRawSequence
name - Variable in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
next() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.LineageIterator
next() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator
next() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo.ScoreIterator
next() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.DetailIterator
next() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.SampleDetailIterator
next() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode.DetailIterator
next() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode.SampleDetailIterator
next() - Method in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
  Returns the next good element in the iteration.
next() - Method in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
  Returns the next parsed sequence.
nextAssignScore - Variable in class edu.msu.cme.rdp.classifier.comparison.Score
nextSeqScore - Variable in class edu.msu.cme.rdp.classifier.comparison.Score
nextSibling - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
node - Variable in class edu.msu.cme.rdp.classifier.comparison.Score
NOT_STARTED - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
NUM_OF_RUNS - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
  The number of bootstrap trials.
NUM_OF_WORDS - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
numOfChildren - Variable in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
numOfDone - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
numOfWords - Variable in class edu.msu.cme.rdp.classifier.train.GoodWordIterator

## O

onDeck - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.LineageIterator
onDeck - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator
onDeck - Variable in class edu.msu.cme.rdp.classifier.comparison.SeqInfo.ScoreIterator
onDeck - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.DetailIterator
onDeck - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.SampleDetailIterator
onDeck - Variable in class edu.msu.cme.rdp.classifier.comparison.UncNode.DetailIterator
onDeck - Variable in class edu.msu.cme.rdp.classifier.comparison.UncNode.SampleDetailIterator
onDeck - Variable in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
options - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
options - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
OUTFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
OUTFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
OUTFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd

## P

parent - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
parent - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
parent - Variable in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
parentID - Variable in class edu.msu.cme.rdp.classifier.train.Taxonomy
parentPath - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
ParsedRawSequence - Class in edu.msu.cme.rdp.classifier.train
  A ParsedRawSequence holds the data for a raw sequence.
ParsedRawSequence(String, List, String) - Constructor for class edu.msu.cme.rdp.classifier.train.ParsedRawSequence
  Creates new ParsedRawSequence.
ParsedSequence - Class in edu.msu.cme.rdp.classifier.readseqwrapper
  A Sequence containing the sequence information.
ParsedSequence(String, String) - Constructor for class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Creates new ParsedSequence.
ParsedSequence(String, String, String, String) - Constructor for class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Creates new ParsedSequence.
ParsedSequenceTest - Class in edu.msu.cme.rdp.classifier.readseqwrapper
  A test class for ParsedSequence.
ParsedSequenceTest(String) - Constructor for class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequenceTest
pattern - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
pattern - Variable in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
PixelCalculatorBean - Class in edu.msu.cme.rdp.classifier.comparison
PixelCalculatorBean() - Constructor for class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
printGenusIndex_WordProbArr(String) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Writes the indices of genus nodes and the conditional probabilities of words occurred in these genus nodes to a file.
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.rrnaclassifier.ClassifierCmd
  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.
printSignificance(TaxonTree, BufferedWriter) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
printTrainingFiles(String) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Writes the entire phylogenetic taxonmic information to a file.
printWordConditionalProbIndexArr(String) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Writes the indices of words and the start indices of conditional probability of the genera containing these words to a file.
printWordPriors(String) - Method in class edu.msu.cme.rdp.classifier.train.TreeFactory
  Writes the log values of the word prior probabilities to a file.
ProbIndexFileParser - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  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.rrnaclassifier.ProbIndexFileParser
  Creates a new instance of ProbFileParser.
pSeq - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResult

## 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.comparison.ComparisonCmd
QUERYFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
QUERYFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
QUERYFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
querySeq_wordProbArr - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier

## R

rank - Variable in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
rank - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
rank - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
RankAssignment - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  A RankAssignment holds the classification result of a sequence at one rank level.
RankAssignment(HierarchyTree, float) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.RankAssignment
  Creates new RankAssignment.
RANKS - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResultFormatter
ratio_1 - Variable in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
ratio_2 - Variable in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
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.
RawHierarchyTreeTest - Class in edu.msu.cme.rdp.classifier.train
  A test class for RawHierarchyTree.
RawHierarchyTreeTest(String) - Constructor for class edu.msu.cme.rdp.classifier.train.RawHierarchyTreeTest
RawSequenceParser - Class in edu.msu.cme.rdp.classifier.train
  A parser to parse a reader containing the raw sequences.
RawSequenceParser(Reader) - Constructor for class edu.msu.cme.rdp.classifier.train.RawSequenceParser
  Creates new RawSequenceParser to parse the input fasta file.
RawSequenceParserTest - Class in edu.msu.cme.rdp.classifier.train
  A test class for RawSequenceParser.
RawSequenceParserTest(String) - Constructor for class edu.msu.cme.rdp.classifier.train.RawSequenceParserTest
reader - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
reader - Variable in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
readZtable(InputStreamReader) - Method in class edu.msu.cme.rdp.classifier.comparison.Ztable
reconstructTree(ClassificationResult, TaxonTree, String) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
  reconstruct the hierarchical tree based on the ClassificationResult we assume that the first assignment is always the root and the only root
reconstructTree(ClassificationResult, TaxonTree, String) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
regex - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion
regexEmbl - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
regexFasta - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
regexFasta - Variable in class edu.msu.cme.rdp.classifier.train.RawSequenceParser
regexGenbank - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
relativePath - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
releaseWordOccurrence() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Resets the array wordOccurrence to null.
remove() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.LineageIterator
remove() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator
remove() - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo.ScoreIterator
remove() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.DetailIterator
remove() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.SampleDetailIterator
remove() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode.DetailIterator
remove() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode.SampleDetailIterator
resetCount() - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
resetCurIndex() - Method in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
  Reset the current index to 0.
resetDefaultDataProp() - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
  Resets the data property file to the default data property file.
reverse - Variable in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
reverse - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
RNA_BASES - Static variable in interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
  The number of rna bases (ATGC).
root - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator
root - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
root - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParser
ROOT_DEPTH - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
  The depth of root of the RawHierarchyTree is set to 0
ROOT_INDENT - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode.TaxonIterator
rootTree - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
rootTree - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
run() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
run() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager.Timer
RUNNING - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager

## S

s1Count - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
s1DetailIterator - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.DetailIterator
s1DetailIterator - Variable in class edu.msu.cme.rdp.classifier.comparison.UncNode.DetailIterator
s1Filename - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
s1Filename - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
s1SeqList - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
s1Total - Variable in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
s1Total - Variable in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
s2Count - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
s2DetailIterator - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.DetailIterator
s2DetailIterator - Variable in class edu.msu.cme.rdp.classifier.comparison.UncNode.DetailIterator
s2Filename - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
s2Filename - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
s2SeqList - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
s2Total - Variable in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
s2Total - Variable in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
SAMPLE1 - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
SAMPLE1 - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
SAMPLE2 - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
SAMPLE2 - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
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
score - Variable in class edu.msu.cme.rdp.classifier.comparison.Score
seq - Variable in class edu.msu.cme.rdp.classifier.train.GoodWordIteratorTest
seqDoc - Variable in exception edu.msu.cme.rdp.classifier.rrnaclassifier.ShortSequenceException
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 - Variable in class edu.msu.cme.rdp.classifier.comparison.Score
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
SeqInfo.ScoreIterator - Class in edu.msu.cme.rdp.classifier.comparison
  An Iterator of scores of assignments sequence
SeqInfo.ScoreIterator() - Constructor for class edu.msu.cme.rdp.classifier.comparison.SeqInfo.ScoreIterator
seqString - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
Sequence - Interface in edu.msu.cme.rdp.classifier.readseqwrapper
  An abstract class, providing an interface for accessing a sequence.
sequence - Variable in class edu.msu.cme.rdp.classifier.train.ParsedRawSequence
SequenceParser - Class in edu.msu.cme.rdp.classifier.readseqwrapper
  A class whick parses the input sequences and creates Sequence objects.
SequenceParser(InputStream) - Constructor for class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
  Creates new SequenceParser to parse the sequences from an InputStream.
SequenceParser(Reader) - Constructor for class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
  Creates new SequenceParser to parse the sequences from a Reader.
SequenceParserException - Exception in edu.msu.cme.rdp.classifier.readseqwrapper
  A class to handle the exception during sequence parsing.
SequenceParserException(String) - Constructor for exception edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParserException
  Creates a new instance of SequenceParserException with detail message.
SequenceParserTest - Class in edu.msu.cme.rdp.classifier.readseqwrapper
  A test class for SequenceParser.
SequenceParserTest(String) - Constructor for class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParserTest
setAbort(boolean) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
setCheckTime(int) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
setConfidence(String) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setConfidence(float) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.RankAssignment
  Set the confidence of the assignment.
setConfidenceCutoff(float) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
setCurrentRoot(String) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setDataProp(String, boolean) - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.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
setFirstS1Score(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
setFirstS2Score(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
setGenusIndex(int) - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
  Sets the genus index of this treenode.
setIndent(int) - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
setLastCheckTime(Date) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
setNextAssignScore(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.Score
setNextElement(Iterator, Iterator) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.DetailIterator
setNextElement(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTree.SampleDetailIterator
setNextElement(Iterator, Iterator) - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode.DetailIterator
setNextElement(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.UncNode.SampleDetailIterator
setNextSeqScore(Score) - Method in class edu.msu.cme.rdp.classifier.comparison.Score
setParent(AbstractNode) - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
setReverse(boolean) - Method in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
setRoot(ComparisonBrowserNode) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setS1Filename(String) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setS1Total(int) - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
setS2Filename(String) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setS2Total(int) - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
setSeqErrorList(List) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setSeqString(String) - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
  Sets the sequence string.
setSequenceFormat() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
  Checks the format of the first input sequence.
setSignificance(double) - Method in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
setStatus(String) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
setSubmitDate(Date) - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
setTaxon(Taxon) - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
setTaxonList(Iterator) - Method in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
ShortSequenceException - Exception in edu.msu.cme.rdp.classifier.rrnaclassifier
  Handles exception for a short sequence.
ShortSequenceException(String, String) - Constructor for exception edu.msu.cme.rdp.classifier.rrnaclassifier.ShortSequenceException
  Creates a new instance of ShortSequenceException to handle short sequence.
sig99 - Variable in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
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
SigCalculatorTest - Class in edu.msu.cme.rdp.classifier.comparison
SigCalculatorTest(String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.SigCalculatorTest
significance - Variable in class edu.msu.cme.rdp.classifier.comparison.AbstractNode
smallProportionTest(int, int) - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
  This test works good for small propotion <5% Calculates the probability for y occurrences in sample2 when x occurrences is observed in sample1.
start() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
startElement(String, String, String, Attributes) - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParser
status - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
subclasses - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
subclasses - Variable in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
submitDate - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBean
suite() - Static method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBeanTest
suite() - Static method in class edu.msu.cme.rdp.classifier.comparison.ComparisonSuite
suite() - Static method in class edu.msu.cme.rdp.classifier.comparison.SigCalculatorTest
suite() - Static method in class edu.msu.cme.rdp.classifier.comparison.TaxonTreeTest
suite() - Static method in class edu.msu.cme.rdp.classifier.comparison.UncNodeTest
suite() - Static method in class edu.msu.cme.rdp.classifier.comparison.ZtableTest
suite() - Static method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequenceTest
suite() - Static method in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParserTest
suite() - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierTest
suite() - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTreeTest
suite() - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
suite() - Static method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParserTest
suite() - Static method in class edu.msu.cme.rdp.classifier.train.GoodWordIteratorTest
suite() - Static method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTreeTest
suite() - Static method in class edu.msu.cme.rdp.classifier.train.RawSequenceParserTest
suite() - Static method in class edu.msu.cme.rdp.classifier.train.TrainSuite
  Test suite of the package edu.msu.cme.rdp.classifier.train.
suite() - Static method in class edu.msu.cme.rdp.classifier.train.TreeFactoryTest

## T

taxid - Variable in class edu.msu.cme.rdp.classifier.comparison.TaxonTree
taxid - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTree
taxID - Variable in class edu.msu.cme.rdp.classifier.train.Taxonomy
taxidMap - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
taxName - Variable in class edu.msu.cme.rdp.classifier.train.Taxonomy
taxnameMap - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
taxon - Variable in class edu.msu.cme.rdp.classifier.comparison.PixelCalculatorBean
Taxon - Interface in edu.msu.cme.rdp.classifier.comparison
taxon - Variable in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
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
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
TaxonTree.DetailIterator - Class in edu.msu.cme.rdp.classifier.comparison
  An Iterator of the sequences assigned to the node
TaxonTree.DetailIterator(float) - Constructor for class edu.msu.cme.rdp.classifier.comparison.TaxonTree.DetailIterator
TaxonTree.SampleDetailIterator - Class in edu.msu.cme.rdp.classifier.comparison
TaxonTree.SampleDetailIterator(Score, float) - Constructor for class edu.msu.cme.rdp.classifier.comparison.TaxonTree.SampleDetailIterator
TaxonTreeTest - Class in edu.msu.cme.rdp.classifier.comparison
TaxonTreeTest(String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.TaxonTreeTest
testAddSequence() - Method in class edu.msu.cme.rdp.classifier.train.TreeFactoryTest
  Test of addSequence method, of class edu.msu.cme.rdp.classifier.train.TreeFactory.
testCalculateSig() - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculatorTest
testCalFactorial() - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculatorTest
testChangeConfidence() - Method in class edu.msu.cme.rdp.classifier.comparison.TaxonTreeTest
  Test of changeConfidence method
testChangeConfidence() - Method in class edu.msu.cme.rdp.classifier.comparison.UncNodeTest
  Test of changeConfidence method
testClassify() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierTest
testCreateClassifier() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
  Test of getRootTree method, of class classification.TrainingInfo.
testCreateGenusWordProbList() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
  Test of createGenusWordProbLis method, of class classification.TrainingInfo.
testCreateLogWordPriorArr() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
  Test of createLogWordPriorArr method, of class classification.TrainingInfo.
testCreateProbIndexArr() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
  Test of makeProbIndexArr method, of class classification.TrainingInfo.
testCreateTree() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
  Test of createTree method, of class classification.TrainingInfo.
testCreateWordIndexArr() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequenceTest
  Test of createWordIndexArr method, of class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence.
testGetName() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyTreeTest
testGetNextSequence() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParserTest
  Test of getNextSequence method, of class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser.
testGetPvalue() - Method in class edu.msu.cme.rdp.classifier.comparison.ZtableTest
testGetReversedSeq() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequenceTest
  Test of getReversedSeq method, of class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence.
testGetReversedWord() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequenceTest
  Test of getReversedWord method, of class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence.
testGetTabularTaxonList() - Method in class edu.msu.cme.rdp.classifier.comparison.ComparisonBrowserBeanTest
testGetWordIndex() - Method in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequenceTest
  Test of getWordIndex method, of class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence.
testInitWordOccurrence() - Method in class edu.msu.cme.rdp.classifier.train.RawHierarchyTreeTest
  Tests the RawHierarchyTree initWordOccurrence() methods.
testNext() - Method in class edu.msu.cme.rdp.classifier.train.GoodWordIteratorTest
  Test of next() method, of class GoodWordIterator.
testNext() - Method in class edu.msu.cme.rdp.classifier.train.RawSequenceParserTest
  Tests RawSequenceParser next() method.
testParseTreeFile() - Method in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParserTest
  Test of parseTreeFile method, of class classification.TrainingFileParser.
testSimulation() - Method in class edu.msu.cme.rdp.classifier.comparison.SigCalculatorTest
TEXT_FORMAT - Static variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
timer - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
title - Variable in class edu.msu.cme.rdp.classifier.comparison.SeqInfo
title - Variable in class edu.msu.cme.rdp.classifier.readseqwrapper.ParsedSequence
totalNumOfSequence - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager
totalSequences - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
TrainingDataException - Exception in edu.msu.cme.rdp.classifier.rrnaclassifier
  Handles the exception occurred when parsing training information.
TrainingDataException() - Constructor for exception edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingDataException
  Creates a new instance of TrainingDataException without detail message.
TrainingDataException(String) - Constructor for exception edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingDataException
  Constructs an instance of TrainingDataException with the specified detail message.
TrainingDataException(Throwable) - Constructor for exception edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingDataException
  Constructs an instance of TrainingDataException with the specified root cause.
trainingInfo - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.Classifier
trainingInfo - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory
TrainingInfo - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  The TrainingInfo holds all the training information and taxonomy hierarchy information.
TrainingInfo() - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
  Creates new TrainingInfo.
TrainingInfoTest - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  A test class for TrainingInfo.
TrainingInfoTest(String) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfoTest
trainingVersion - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
TRAINPROPFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
TRAINPROPFILE_DESC - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
TRAINPROPFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
TRAINPROPFILE_LONG_OPT - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
TRAINPROPFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonCmd
TRAINPROPFILE_SHORT_OPT - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierCmd
trainsetNo - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion
TrainSuite - Class in edu.msu.cme.rdp.classifier.train
  A test suite for package edu.msu.cme.rdp.classifier.train.
TrainSuite(String) - Constructor for class edu.msu.cme.rdp.classifier.train.TrainSuite
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.
TreeFactoryTest - Class in edu.msu.cme.rdp.classifier.train
  A test class for TreeFactory.
TreeFactoryTest(String) - Constructor for class edu.msu.cme.rdp.classifier.train.TreeFactoryTest
treeFile - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
TreeFileParser - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  A parser to parse a reader containing taxonomic training information.
TreeFileParser() - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParser
  Creates a new instance of TreeFileParser.
TreeFileParserTest - Class in edu.msu.cme.rdp.classifier.rrnaclassifier
  A test class for TreeFileParser.
TreeFileParserTest(String) - Constructor for class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParserTest
treeNodeStack - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TreeFileParser

## U

UncNode - Class in edu.msu.cme.rdp.classifier.comparison
UncNode(AbstractNode) - Constructor for class edu.msu.cme.rdp.classifier.comparison.UncNode
  Creates a new instance of UncNode
UncNode.DetailIterator - Class in edu.msu.cme.rdp.classifier.comparison
  An Iterator of the sequences assigned to the node
UncNode.DetailIterator(float) - Constructor for class edu.msu.cme.rdp.classifier.comparison.UncNode.DetailIterator
UncNode.SampleDetailIterator - Class in edu.msu.cme.rdp.classifier.comparison
UncNode.SampleDetailIterator(Score, float) - Constructor for class edu.msu.cme.rdp.classifier.comparison.UncNode.SampleDetailIterator
UncNodeTest - Class in edu.msu.cme.rdp.classifier.comparison
UncNodeTest(String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.UncNodeTest
UNKNOWN_SEQ - Static variable in class edu.msu.cme.rdp.classifier.readseqwrapper.SequenceParser
urlProperties - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.ClassifierFactory

## V

valueOf(String) - Static method in enum edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResultFormatter.FORMAT
  Returns the enum constant of this type with the specified name.
values() - Static method in enum edu.msu.cme.rdp.classifier.rrnaclassifier.ClassificationResultFormatter.FORMAT
  Returns an array containing the constants of this enum type, in the order they are declared.
version - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion
versionPattern - Static variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.HierarchyVersion

## W

waitTime - Variable in class edu.msu.cme.rdp.classifier.comparison.ComparisonManager.Timer
WF1 - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
  A factor for probability correction
WF2 - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
  A factor for probability correction
wordConditionalProb - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.GenusWordConditionalProb
wordConditionalProb - Variable in class edu.msu.cme.rdp.classifier.train.RawGenusWordConditionalProb
wordConditionalProbIndexArr - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
wordIndexArr - Variable in class edu.msu.cme.rdp.classifier.train.GoodWordIterator
wordIt - Variable in class edu.msu.cme.rdp.classifier.train.GoodWordIteratorTest
wordOccurrence - Variable in class edu.msu.cme.rdp.classifier.train.RawHierarchyTree
wordPairPriorDiffArr - Variable in class edu.msu.cme.rdp.classifier.rrnaclassifier.TrainingInfo
wordPriorArr - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
wordProbPointerArr - Variable in class edu.msu.cme.rdp.classifier.train.TreeFactory
WORDSIZE - Static variable in interface edu.msu.cme.rdp.classifier.readseqwrapper.Sequence
  The size of a word.
WORDSIZE - Static variable in class edu.msu.cme.rdp.classifier.train.GoodWordIterator

## Z

zHash - Variable in class edu.msu.cme.rdp.classifier.comparison.Ztable
ztable - Variable in class edu.msu.cme.rdp.classifier.comparison.SigCalculator
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
ZtableTest - Class in edu.msu.cme.rdp.classifier.comparison
ZtableTest(String) - Constructor for class edu.msu.cme.rdp.classifier.comparison.ZtableTest

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