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