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

I

INITIALHASHSIZE - Static variable in class edu.duke.cs.banjo.utility.BANJO
 
InfluenceScorer - class edu.duke.cs.banjo.utility.InfluenceScorer.
Computes the influence score for all the edges in a network, based on the work of Jing Yu and Alexander Hartemink, as published in Yu, et al., Bioinformatics (2004).
InfluenceScorer(BayesNetStructureI, Settings) - Constructor for class edu.duke.cs.banjo.utility.InfluenceScorer
 
i - Variable in class edu.duke.cs.banjo.data.observations.Counter
 
ignorableWhitespace(char[], int, int) - Method in class edu.duke.cs.banjo.utility.XMLProcessor.TextExtractor
 
initLogGammaTable() - Method in class edu.duke.cs.banjo.learner.components.EvaluatorBDe.LogGammaArray
 
initMatrix() - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
initMatrix(int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
initMatrix() - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
initMatrix(int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
initMatrix() - Method in interface edu.duke.cs.banjo.bayesnet.EdgesWithCachedStatisticsI
 
initMatrix(int) - Method in interface edu.duke.cs.banjo.bayesnet.EdgesWithCachedStatisticsI
 
initialParents - Variable in class edu.duke.cs.banjo.bayesnet.BayesNetManager
 
initialProcessParametersAsLoaded - Variable in class edu.duke.cs.banjo.data.settings.Settings
 
initialProcessParametersLowercase - Variable in class edu.duke.cs.banjo.data.settings.Settings
 
initializeBayesNet() - Method in class edu.duke.cs.banjo.bayesnet.BayesNetManager
 
initializeBayesNet(EdgesWithCachedStatisticsI) - Method in class edu.duke.cs.banjo.bayesnet.BayesNetManager
 
initializeBayesNet() - Method in interface edu.duke.cs.banjo.bayesnet.BayesNetManagerI
 
initializeBayesNet(EdgesWithCachedStatisticsI) - Method in interface edu.duke.cs.banjo.bayesnet.BayesNetManagerI
 
innerLoopStart - Variable in class edu.duke.cs.banjo.learner.SearcherGreedy
 
innerLoopStart - Variable in class edu.duke.cs.banjo.learner.SearcherSimAnneal
 
intermediateTime - Variable in class edu.duke.cs.banjo.learner.Searcher
 
intervals - Variable in class edu.duke.cs.banjo.data.observations.DataPreparerBasic
 
intervals - Variable in class edu.duke.cs.banjo.data.observations.Discretizer
 
isChangeAccepted(double, BayesNetChangeI) - Method in class edu.duke.cs.banjo.learner.components.Decider
 
isChangeAccepted(double, BayesNetChangeI) - Method in class edu.duke.cs.banjo.learner.components.DeciderGreedy
 
isChangeAccepted(double, BayesNetChangeI) - Method in interface edu.duke.cs.banjo.learner.components.DeciderI
 
isChangeAccepted(double, BayesNetChangeI) - Method in class edu.duke.cs.banjo.learner.components.DeciderMetropolis
 
isChangeValid(BayesNetManagerI, BayesNetChangeI) - Method in class edu.duke.cs.banjo.learner.components.CycleChecker
 
isChangeValid(BayesNetManagerI, BayesNetChangeI) - Method in class edu.duke.cs.banjo.learner.components.CycleCheckerApplyThenCheck
 
isChangeValid(BayesNetManagerI, BayesNetChangeI) - Method in class edu.duke.cs.banjo.learner.components.CycleCheckerCheckThenApply
 
isChangeValid(BayesNetManagerI, BayesNetChangeI) - Method in interface edu.duke.cs.banjo.learner.components.CycleCheckerI
Checks whether the proposed bayesNetChange results in a cycle in the network described by the bayesNetManager.
isCyclic(int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.CycleFinder
 
isCyclic(int, int[]) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.CycleFinder
 
isCyclic(int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.CycleFinderDFS
 
isCyclic(int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.CycleFinderDFSorig
 
isCyclic(int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.CycleFinderDFSwithShmueli
 
isCyclic(BayesNetChangeI) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
isCyclic() - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
isCyclic(int, int[]) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
isCyclic(BayesNetChangeI) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
isCyclic() - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
isCyclic(int, int[]) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
isCyclic(BayesNetChangeI) - Method in interface edu.duke.cs.banjo.bayesnet.EdgesWithCachedStatisticsI
 
isCyclic() - Method in interface edu.duke.cs.banjo.bayesnet.EdgesWithCachedStatisticsI
 
isCyclic() - Method in class edu.duke.cs.banjo.learner.components.CycleCheckerApplyThenCheck
 
isCyclic() - Method in class edu.duke.cs.banjo.learner.components.CycleCheckerCheckThenApply
 
isCyclicBFS(BayesNetChangeI) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
isCyclicDFSorig(BayesNetChangeI) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
isCyclic__TEST_ENTIRE_STRUC() - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.CycleFinder
 
isCyclic__TEST_ENTIRE_STRUC() - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.CycleFinderDFS
 
isCyclic__TEST_ENTIRE_STRUC() - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.CycleFinderDFSorig
 
isCyclic__TEST_ENTIRE_STRUC() - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics.CycleFinderDFSwithShmueli
 
isDefaultValueUsed - Variable in class edu.duke.cs.banjo.data.settings.SettingItem
 
isDefaultValueUsed() - Method in class edu.duke.cs.banjo.data.settings.SettingItem
 
isEquivalent - Variable in class edu.duke.cs.banjo.learner.Searcher
 
isEquivalent(Set, BayesNetStructureI) - Method in class edu.duke.cs.banjo.learner.components.EquivalenceChecker
 
isEquivalent(Set, BayesNetStructureI) - Method in class edu.duke.cs.banjo.learner.components.EquivalenceCheckerBasic
 
isEquivalent(BayesNetStructureI, BayesNetStructureI) - Method in class edu.duke.cs.banjo.learner.components.EquivalenceCheckerBasic
 
isEquivalent(EdgesAsMatrixWithCachedStatistics, EdgesAsMatrixWithCachedStatistics) - Method in class edu.duke.cs.banjo.learner.components.EquivalenceCheckerBasic
 
isEquivalent(EdgesAsArrayWithCachedStatistics, EdgesAsArrayWithCachedStatistics) - Method in class edu.duke.cs.banjo.learner.components.EquivalenceCheckerBasic
 
isEquivalent(EdgesWithCachedStatisticsI, EdgesWithCachedStatisticsI) - Method in class edu.duke.cs.banjo.learner.components.EquivalenceCheckerBasic
 
isEquivalent(Set, BayesNetStructureI) - Method in interface edu.duke.cs.banjo.learner.components.EquivalenceCheckerI
 
isEquivalent(Set, BayesNetStructureI) - Method in class edu.duke.cs.banjo.learner.components.EquivalenceCheckerSkip
 
isEquivalent(BayesNetStructureI, BayesNetStructureI) - Method in class edu.duke.cs.banjo.learner.components.EquivalenceCheckerSkip
 
isEquivalent(EdgesWithCachedStatisticsI, EdgesWithCachedStatisticsI) - Method in class edu.duke.cs.banjo.learner.components.EquivalenceCheckerSkip
 
isParent(int, int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsArrayWithCachedStatistics
 
isParent(int, int, int) - Method in class edu.duke.cs.banjo.bayesnet.EdgesAsMatrixWithCachedStatistics
 
isParent(int, int, int) - Method in interface edu.duke.cs.banjo.bayesnet.EdgesWithCachedStatisticsI
 
isSettingValueValid(String) - Method in class edu.duke.cs.banjo.data.settings.Settings
 
isValidSetting - Variable in class edu.duke.cs.banjo.data.settings.SettingItem
 
isValidSetting() - Method in class edu.duke.cs.banjo.data.settings.SettingItem
 
itemNameCanonical - Variable in class edu.duke.cs.banjo.data.settings.SettingItem
 
itemNameDescriptive - Variable in class edu.duke.cs.banjo.data.settings.SettingItem
 
itemNameForComparison - Variable in class edu.duke.cs.banjo.data.settings.SettingItem
 
itemNameForDisplay - Variable in class edu.duke.cs.banjo.data.settings.SettingItem
 
itemNameFormattedForDisplay - Variable in class edu.duke.cs.banjo.data.settings.SettingItem
 
itemValueAsLoaded - Variable in class edu.duke.cs.banjo.data.settings.SettingItem
 
itemValueValidated - Variable in class edu.duke.cs.banjo.data.settings.SettingItem
 
iterationsPerTemperature - Variable in class edu.duke.cs.banjo.learner.SearcherSimAnneal
 

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