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
All Classes All Packages
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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