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

A

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

B

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

C

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

D

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

E

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

F

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

G

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

H

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

I

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

L

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

M

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

N

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

O

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

P

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

Q

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

R

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

S

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

T

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

U

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

V

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

W

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

Z

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