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

## A

a(boolean) - Static method in class calhoun.util.Assert
a(boolean, String) - Static method in class calhoun.util.Assert
a(boolean, Object, Object) - Static method in class calhoun.util.Assert
a(boolean, Object, Object, Object) - Static method in class calhoun.util.Assert
a(boolean, Object, Object, Object, Object) - Static method in class calhoun.util.Assert
a(boolean, Object, Object, Object, Object, Object) - Static method in class calhoun.util.Assert
a(boolean, Object, Object, Object, Object, Object, Object) - Static method in class calhoun.util.Assert
a(boolean, Object, Object, Object, Object, Object, Object, Object) - Static method in class calhoun.util.Assert
a(boolean, Object, Object, Object, Object, Object, Object, Object, Object) - Static method in class calhoun.util.Assert
a(boolean, Object, Object, Object, Object, Object, Object, Object, Object, Object) - Static method in class calhoun.util.Assert
a(boolean, Object, Object, Object, Object, Object, Object, Object, Object, Object, Object) - Static method in class calhoun.util.Assert
AbstractFeatureManager<InputType> - Class in calhoun.analysis.crf
  base class for feature implementations.
AbstractFeatureManager() - Constructor for class calhoun.analysis.crf.AbstractFeatureManager
AbstractTestCase - Class in calhoun.util
  Basic test case with file matching (XML and regular) added as well as improved logging for errors.
AbstractTestCase() - Constructor for class calhoun.util.AbstractTestCase
AbstractTestCase(String) - Constructor for class calhoun.util.AbstractTestCase
ACGTN - Static variable in class calhoun.seq.KmerHasher
  Character hash function to use with DNA bases which included the ambiguity code "N".
ACGTNcomp - Static variable in class calhoun.seq.KmerHasher
  Character hash function to use with DNA bases which included the ambiguity code "N".
ACGTother - Static variable in class calhoun.seq.KmerHasher
  Character hash function to use with DNA bases which included the ambiguity code "N".
ACGTotherRC - Static variable in class calhoun.seq.KmerHasher
  Character hash function to use with DNA bases which included the ambiguity code "N".
add(int, int, int, int, int) - Method in class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryCachingDetails
add(int, int, Object) - Method in class calhoun.util.RangeMap
  Adds the object o into the map with interval lo - high.
addAll(Collection<T>, Iterator<? extends T>) - Static method in class calhoun.util.Util
addComponent(String, InputSequence<?>) - Method in class calhoun.analysis.crf.io.InputSequenceComposite
  adds a new component input sequence to this composite.
addComponents(Map<String, InputSequence<?>>) - Method in class calhoun.analysis.crf.io.InputSequenceComposite
  adds all input sequences in the given map as components.
addFeature(int, double) - Method in interface calhoun.analysis.crf.FeatureList
  returns a feature value for this evaluation.
addFeatureManager(FeatureManager) - Method in class calhoun.analysis.crf.CompositeFeatureManager
addFeatureManager(String, String, FeatureManager) - Method in class calhoun.analysis.crf.CompositeFeatureManager
addFirst(T) - Method in class calhoun.analysis.crf.solver.RecyclingBuffer
addNextQuality(SimpleFastaSequence) - Method in class calhoun.seq.QualityIterator
  Adds the next sequence of qualities in the file to the given FastaSequence.
AlignmentTree - Class in calhoun.analysis.crf.io
AlignmentTree() - Constructor for class calhoun.analysis.crf.io.AlignmentTree
AllIntergenicHiddenStateReader - Class in calhoun.analysis.crf.io
AllIntergenicHiddenStateReader() - Constructor for class calhoun.analysis.crf.io.AllIntergenicHiddenStateReader
alphaFile - Variable in class calhoun.analysis.crf.solver.LogFiles
alphaLengthFile - Variable in class calhoun.analysis.crf.solver.LogFiles
alphaLengthWriter - Variable in class calhoun.analysis.crf.solver.LogFiles
alphaWriter - Variable in class calhoun.analysis.crf.solver.LogFiles
an() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
  Actual Negatives
ap() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
  Actual Positives
appendPath(String, String) - Static method in class calhoun.util.FileUtil
  Adds a file or directory name to an existing directory name.
appendSeparator(File) - Static method in class calhoun.util.FileUtil
apply(double[], double[]) - Method in interface calhoun.analysis.crf.CRFObjectiveFunctionGradient
  computes the objective function value and the gradient.
apply(double[], double[]) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodGradient
apply(double[], double[]) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
apply(double[], double[]) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
apply(double[], double[]) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
approximateCorrelation() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
  This is the approximate correlation.
argmax(double[]) - Static method in class calhoun.analysis.crf.statistics.BasicStats
array - Variable in class calhoun.analysis.crf.solver.RecyclingBuffer
Assert - Class in calhoun.util
  Assertion class.
assertArrayEquals(byte[], byte[]) - Method in class calhoun.util.AbstractTestCase
assertArrayEquals(double[], double[]) - Method in class calhoun.util.AbstractTestCase
assertArrayEquals(double[], double[], double) - Method in class calhoun.util.AbstractTestCase
assertArrayEquals(int[], int[]) - Method in class calhoun.util.AbstractTestCase
assertBeginsWith(byte[], byte[]) - Method in class calhoun.util.AbstractTestCase
assertEndsWith(byte[], byte[]) - Method in class calhoun.util.AbstractTestCase
assertEquals(byte[], byte[]) - Method in class calhoun.util.AbstractTestCase
assertFilesMatch(String, String) - Method in class calhoun.util.AbstractTestCase
assertFlatFileRecordsMatch(String, String) - Method in class calhoun.util.AbstractTestCase
ASSERTION_TOLERANCE - Static variable in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
assertStringEquals(String[], List) - Method in class calhoun.util.AbstractTestCase
assertStringEquals(String[], String[]) - Method in class calhoun.util.AbstractTestCase
assertXmlFilesMatch(String, String) - Method in class calhoun.util.AbstractTestCase
assign(boolean) - Method in class calhoun.util.DenseBooleanMatrix2D
assign(int) - Method in class calhoun.util.DenseIntMatrix2D
averageConditionalProbability() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
  This is the average conditional probability.
averageSensitivitySpecificity() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
  This is the average of sensitivity and specifity.

## B

BasicStats - Class in calhoun.analysis.crf.statistics
BasicStats() - Constructor for class calhoun.analysis.crf.statistics.BasicStats
BasicStatsTest - Class in calhoun.analysis.crf.test
BasicStatsTest() - Constructor for class calhoun.analysis.crf.test.BasicStatsTest
BeanModel - Class in calhoun.analysis.crf
  a useful base class for creating model beans.
BeanModel() - Constructor for class calhoun.analysis.crf.BeanModel
BeanModel.Edge - Class in calhoun.analysis.crf
  an edge in the hidden state diagram.
BeanModel.Edge() - Constructor for class calhoun.analysis.crf.BeanModel.Edge
BeanModel.Edge(BeanModel.Node, BeanModel.Node) - Constructor for class calhoun.analysis.crf.BeanModel.Edge
BeanModel.Node - Class in calhoun.analysis.crf
  a hidden state.
BeanModel.Node() - Constructor for class calhoun.analysis.crf.BeanModel.Node
BeanModel.Node(int, String) - Constructor for class calhoun.analysis.crf.BeanModel.Node
bestScores - Variable in class calhoun.analysis.crf.CRFInference.InferenceResult
beta - Variable in class calhoun.analysis.crf.solver.LookbackBuffer
betaLengthFile - Variable in class calhoun.analysis.crf.solver.LogFiles
betaLengthWriter - Variable in class calhoun.analysis.crf.solver.LogFiles
betaNorm - Variable in class calhoun.analysis.crf.solver.LookbackBuffer
bigTree() - Static method in class calhoun.analysis.crf.test.ExampleTrees
bigTreeForEncode() - Static method in class calhoun.analysis.crf.test.ExampleTrees
BinaryTreeNode - Class in calhoun.analysis.crf.features.supporting.phylogenetic
BlastInterval13 - Class in calhoun.analysis.crf.features.interval13
BlastInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.BlastInterval13
BooleanInput - Class in calhoun.analysis.crf.io
  reads in an input consisting of a string of 1's and 0's that correspond to binary values.
BooleanInput() - Constructor for class calhoun.analysis.crf.io.BooleanInput

## C

CacheProcessor - Interface in calhoun.analysis.crf.solver
  interface to implementations of feature caches.
CacheProcessor.FeatureEvaluation - Class in calhoun.analysis.crf.solver
  This class holds the feature evaluations for a given position, or position/length combination.
CacheProcessor.LengthFeatureEvaluation - Class in calhoun.analysis.crf.solver
CacheProcessor.LengthFeatureEvaluation(int) - Constructor for class calhoun.analysis.crf.solver.CacheProcessor.LengthFeatureEvaluation
CacheProcessor.SolverSetup - Class in calhoun.analysis.crf.solver
CacheProcessor.SolverSetup() - Constructor for class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
CacheProcessor.StatePotentials - Class in calhoun.analysis.crf.solver
CacheProcessor.StatePotentials() - Constructor for class calhoun.analysis.crf.solver.CacheProcessor.StatePotentials
CacheProcessorBasic - Class in calhoun.analysis.crf.solver
  basic functionality common to most cache processors.
CacheProcessorBasic() - Constructor for class calhoun.analysis.crf.solver.CacheProcessorBasic
CacheProcessorDeluxe - Class in calhoun.analysis.crf.solver
  A policy based cache processor.
CacheProcessorDeluxe() - Constructor for class calhoun.analysis.crf.solver.CacheProcessorDeluxe
CacheProcessorDeluxe(CacheStrategySpec.CacheStrategy) - Constructor for class calhoun.analysis.crf.solver.CacheProcessorDeluxe
CacheProcessorTest - Class in calhoun.analysis.crf.test
CacheProcessorTest() - Constructor for class calhoun.analysis.crf.test.CacheProcessorTest
CacheProcessorTestRealShort - Class in calhoun.analysis.crf.test
CacheProcessorTestRealShort() - Constructor for class calhoun.analysis.crf.test.CacheProcessorTestRealShort
CacheStrategySpec - Class in calhoun.analysis.crf
CacheStrategySpec(CacheStrategySpec.CacheStrategy, Object) - Constructor for class calhoun.analysis.crf.CacheStrategySpec
CacheStrategySpec(CacheStrategySpec.CacheStrategy) - Constructor for class calhoun.analysis.crf.CacheStrategySpec
CacheStrategySpec.CacheStrategy - Enum in calhoun.analysis.crf
CacheStrategySpec.DenseBoundaryCachingDetails - Class in calhoun.analysis.crf
CacheStrategySpec.DenseBoundaryCachingDetails(int) - Constructor for class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryCachingDetails
CacheStrategySpec.DenseBoundaryEntry - Class in calhoun.analysis.crf
CacheStrategySpec.DenseBoundaryEntry(int, int, int, int, int) - Constructor for class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryEntry
CacheStrategySpec.DenseCachingDetails - Class in calhoun.analysis.crf
  Used in cases where the feature will return a value at every edge and/or node.
CacheStrategySpec.DenseCachingDetails() - Constructor for class calhoun.analysis.crf.CacheStrategySpec.DenseCachingDetails
CacheTest - Class in calhoun.analysis.crf.test
CacheTest() - Constructor for class calhoun.analysis.crf.test.CacheTest
calc(String) - Static method in class calhoun.seq.RepeatedSubsequence
  Returns the largest repeated subsequence in a given string.
calcResultIncrement(TrainingSequence, int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
  calculates statstics and output for results on a given test sequence
calcResultIncrement(TrainingSequence, int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
  calculates statstics and output for results on a given test sequence
calhoun.analysis.crf - package calhoun.analysis.crf
  the interface, main `Conrad` class, and solver for the Conrad engine.
calhoun.analysis.crf.executables.viewer - package calhoun.analysis.crf.executables.viewer
  prototype of a viewing utility for examiining the results of inference.
calhoun.analysis.crf.features.generic - package calhoun.analysis.crf.features.generic
  features useful across different models
calhoun.analysis.crf.features.interval13 - package calhoun.analysis.crf.features.interval13
  mdoel definition and setup for the interval13 model
calhoun.analysis.crf.features.interval29 - package calhoun.analysis.crf.features.interval29
calhoun.analysis.crf.features.supporting - package calhoun.analysis.crf.features.supporting
  utility classes used by feature managers in gene calling models
calhoun.analysis.crf.features.supporting.phylogenetic - package calhoun.analysis.crf.features.supporting.phylogenetic
  utility classes for phylogenetic analysis
calhoun.analysis.crf.features.tricycle13 - package calhoun.analysis.crf.features.tricycle13
  basic features and model for the tricycle13 gene calling model
calhoun.analysis.crf.io - package calhoun.analysis.crf.io
  handles input and output of gene calling formats
calhoun.analysis.crf.scoring - package calhoun.analysis.crf.scoring
  local similarity functions used in gene calling models
calhoun.analysis.crf.solver - package calhoun.analysis.crf.solver
  training and inference algorithms used in the CRF engine
calhoun.analysis.crf.solver.semimarkov - package calhoun.analysis.crf.solver.semimarkov
calhoun.analysis.crf.statistics - package calhoun.analysis.crf.statistics
  math utilities used by features and to evaluate results
calhoun.analysis.crf.test - package calhoun.analysis.crf.test
calhoun.analysis.crf.test.slow - package calhoun.analysis.crf.test.slow
calhoun.seq - package calhoun.seq
calhoun.seq.test - package calhoun.seq.test
calhoun.util - package calhoun.util
characterInPaddedAlignment(int, int) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
check() - Method in class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryCachingDetails
check() - Method in class calhoun.analysis.crf.CacheStrategySpec.DenseCachingDetails
checkConstraintsInTrainingData() - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
CheckException - Exception in calhoun.util
  Exception type for consistency check errors.
CheckException() - Constructor for exception calhoun.util.CheckException
CheckException(String) - Constructor for exception calhoun.util.CheckException
CheckException(String, Throwable) - Constructor for exception calhoun.util.CheckException
CheckException(Throwable) - Constructor for exception calhoun.util.CheckException
checkRepeat(String, int, int) - Static method in class calhoun.seq.RepeatedSubsequence
  Checks to see if the given sequence begins with n repeats, each of length l.
checkValidTransitions(List) - Method in class calhoun.analysis.crf.features.interval29.Interval29Model
clean() - Method in interface calhoun.analysis.crf.CRFObjectiveFunctionGradient
  Frees resources allocated by setTrainingData
clean() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodGradient
clean() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
clean() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
CleanLocalScoreSemiMarkovGradient - Class in calhoun.analysis.crf.solver.semimarkov
  computes an objective function which is the expected value of a local path similarity score on a semi-Markov model.
CleanLocalScoreSemiMarkovGradient() - Constructor for class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
CleanMaximumLikelihoodSemiMarkovGradient - Class in calhoun.analysis.crf.solver.semimarkov
  computes the likelihood of the true path for a semi-Markov CRF.
CleanMaximumLikelihoodSemiMarkovGradient() - Constructor for class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
clear() - Method in class calhoun.analysis.crf.solver.LookbackBuffer
  mi and stableStates are cleared as new values are entered.
close() - Method in class calhoun.analysis.crf.solver.LogFiles
close() - Method in class calhoun.seq.FastaWriter
  Closes the file.
CodingStopFeature - Class in calhoun.analysis.crf.features.tricycle13
CodingStopFeature() - Constructor for class calhoun.analysis.crf.features.tricycle13.CodingStopFeature
CodingStopFeature(List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.CodingStopFeature
ColtUtil - Class in calhoun.util
ColtUtil() - Constructor for class calhoun.util.ColtUtil
ColumnConditionalLogProbability - Class in calhoun.analysis.crf.features.supporting.phylogenetic
ColumnConditionalLogProbability(List<int[]>, int) - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.ColumnConditionalLogProbability
compareFiles(String, String) - Static method in class calhoun.util.XmlDiff
  Compares two XML files.
compareTwoEquivalentModelsTrainTestSameData(String, String, String) - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
compareTwoEquivalentModelsTrainTestSameData(String, String, String, double) - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
compareTwoEquivalentModelsTrainTestSameData(String, String, String, double) - Method in class calhoun.analysis.crf.test.Interval29BaselineTest
compareTwoEquivalentModelsTrainTestSameDataJustFeatureSums(String, String, String, double) - Method in class calhoun.analysis.crf.test.Interval29BaselineTest
compareTwoEquivalentModelsTrainTestSameDataWithDifferentStates(String, String, String, double) - Method in class calhoun.analysis.crf.test.Interval29BaselineTest
completeCounts() - Method in class calhoun.analysis.crf.features.supporting.PWMLookup
CompositeFeatureManager - Class in calhoun.analysis.crf
  a feature manager that combines feature types together.
CompositeFeatureManager() - Constructor for class calhoun.analysis.crf.CompositeFeatureManager
CompositeInput - Class in calhoun.analysis.crf.io
  Deprecated.
CompositeInput() - Constructor for class calhoun.analysis.crf.io.CompositeInput
  Deprecated.
CompositeInput.InputComponent - Class in calhoun.analysis.crf.io
  Deprecated.
CompositeInput.InputComponent() - Constructor for class calhoun.analysis.crf.io.CompositeInput.InputComponent
  Deprecated.
CompositeInput.LegacyInputHandler - Class in calhoun.analysis.crf.io
  Deprecated. legacy `InputHandler` that mirrors the original XML config file behavior.
CompositeInput.LegacyInputHandler(Object) - Constructor for class calhoun.analysis.crf.io.CompositeInput.LegacyInputHandler
  Deprecated. special constructor used by `Conrad` to pass the old style input config to the legacy input handler.
con2refLeft(int) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
con2refRight(int) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
condLogProb(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>, int, int) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.ColumnConditionalLogProbability
ConfigException - Exception in calhoun.util
  Exception type for system configuration exceptions.
ConfigException(String) - Constructor for exception calhoun.util.ConfigException
ConfigException(String, Throwable) - Constructor for exception calhoun.util.ConfigException
ConfigException(Throwable) - Constructor for exception calhoun.util.ConfigException
Conrad - Class in calhoun.analysis.crf
  the central class for the Conrad engine.
Conrad() - Constructor for class calhoun.analysis.crf.Conrad
  creates a Conrad engine with no configuration.
Conrad(String) - Constructor for class calhoun.analysis.crf.Conrad
  creates a Conrad engine based on configuration information from an XML model file.
ConstrainedFeatureManager - Class in calhoun.analysis.crf
  a feature manager that combines it's composite feature types together into a single feature.
ConstrainedFeatureManager() - Constructor for class calhoun.analysis.crf.ConstrainedFeatureManager
ConstraintTest - Class in calhoun.analysis.crf.test
ConstraintTest() - Constructor for class calhoun.analysis.crf.test.ConstraintTest
ConstraintTest.FixedEdges - Class in calhoun.analysis.crf.test
  Edge class used for testing that favors changing states whenever possible.
ConstraintTest.FixedEdges() - Constructor for class calhoun.analysis.crf.test.ConstraintTest.FixedEdges
contains(Object) - Method in class calhoun.util.RangeMap
  Returns true if the object is in the RangeMap
convert() - Method in class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature.MarkovHistory
convertDoubleArray(double[]) - Static method in class calhoun.util.Util
convertFloatList(List<Float>) - Static method in class calhoun.util.Util
convertIntList(List<Integer>) - Static method in class calhoun.util.Util
convertSeqFrom13To39(TrainingSequence<Character>) - Static method in class calhoun.analysis.crf.io.SequenceConverter
convertSeqFrom39To13(TrainingSequence<Character>) - Static method in class calhoun.analysis.crf.io.SequenceConverter
convertSeqFrom39To13(int[]) - Static method in class calhoun.analysis.crf.io.SequenceConverter
convertSeqFromInterval13ToInterval29(int[]) - Static method in class calhoun.analysis.crf.io.SequenceConverter
convertSeqFromInterval13ToTricycle13(TrainingSequence<Character>) - Static method in class calhoun.analysis.crf.io.SequenceConverter
convertSeqFromInterval13ToTricycle13(String) - Static method in class calhoun.analysis.crf.io.SequenceConverter
convertSeqFromInterval29ToInterval13(int[]) - Static method in class calhoun.analysis.crf.io.SequenceConverter
convertSeqFromInterval29ToInterval13Wrong(int[]) - Static method in class calhoun.analysis.crf.io.SequenceConverter
convertSeqFromTricycle13ToInterval13(TrainingSequence<Character>) - Static method in class calhoun.analysis.crf.io.SequenceConverter
convertSeqFromTricycle13ToInterval13(String) - Static method in class calhoun.analysis.crf.io.SequenceConverter
copyFile(File, File, boolean) - Static method in class calhoun.util.FileUtil
copyFile(File, File) - Static method in class calhoun.util.FileUtil
correct - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results
correct - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results
correlationCoefficient() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
  This is the Pearson correlation of two 0-1 random variables X=prediction and Y=reality CC = Cov(X,Y)/(Stddev(X)*Stddev(Y)) If either RV has zero variance, the CC is underfined: assertion faliure If this contingency table is not tracking TN, then CC is undefined: assertion failure
create(int, int) - Static method in class calhoun.analysis.crf.solver.CacheProcessor.FeatureEvaluation
create(CacheProcessor.StatePotentials[], int, int) - Static method in class calhoun.analysis.crf.solver.CacheProcessor.LengthFeatureEvaluation
CRFInference - Interface in calhoun.analysis.crf
  an interface to inference algorithms for CRFs.
CRFInference.InferenceResult - Class in calhoun.analysis.crf
  holder which contains the results of an inference run.
CRFInference.InferenceResult() - Constructor for class calhoun.analysis.crf.CRFInference.InferenceResult
CRFIOTest - Class in calhoun.analysis.crf.test
CRFIOTest() - Constructor for class calhoun.analysis.crf.test.CRFIOTest
CRFObjectiveFunctionGradient - Interface in calhoun.analysis.crf
  an interface to algorithms that compute an objective function and its gradient for CRFs.
CRFTest - Class in calhoun.analysis.crf.test
CRFTest() - Constructor for class calhoun.analysis.crf.test.CRFTest
CRFTraining - Interface in calhoun.analysis.crf
  an interface to numerical solvers for optimizing the CRF objective function.
crypto4dan() - Static method in class calhoun.analysis.crf.test.ExampleTrees
crypto5() - Static method in class calhoun.analysis.crf.test.ExampleTrees
ctCodingNucleotide - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results
ctCodingNucleotide - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results
ctExons - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results
ctExons - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results
ctStates - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results
ctStates - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results
ctTransitions - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results
ctTransitions - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results
currentStart - Variable in class calhoun.analysis.crf.solver.RecyclingBuffer

## D

d - Variable in class calhoun.analysis.crf.features.supporting.phylogenetic.BinaryTreeNode
DataException - Exception in calhoun.util
  Exception type for data errors.
DataException(String) - Constructor for exception calhoun.util.DataException
DataException(String, Throwable) - Constructor for exception calhoun.util.DataException
DataException(Throwable) - Constructor for exception calhoun.util.DataException
debug - Static variable in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
deepClone(Object) - Static method in class calhoun.util.Util
  make a copy of any serializable object graph
DEFAULT_LINE_LENGTH - Static variable in class calhoun.seq.FastaWriter
DenseBooleanMatrix2D - Class in calhoun.util
DenseBooleanMatrix2D(int, int) - Constructor for class calhoun.util.DenseBooleanMatrix2D
DenseIntMatrix2D - Class in calhoun.util
DenseIntMatrix2D(int, int) - Constructor for class calhoun.util.DenseIntMatrix2D
details - Variable in class calhoun.analysis.crf.CacheStrategySpec
determineNewlineSize(File) - Static method in class calhoun.util.FileUtil
  Determines the size of a newline character in the given text file.
DNA - Static variable in class calhoun.seq.KmerHasher
  Character hash function to use with DNA bases.
doCache(String, String, int, int) - Method in class calhoun.analysis.crf.test.CacheTest
dotProduct(double[], double[]) - Static method in class calhoun.util.ColtUtil

## E

edgeEvals - Variable in class calhoun.analysis.crf.solver.CacheProcessor.LengthFeatureEvaluation
elements - Variable in class calhoun.util.RangeMap.Interval
EmissionMarkovFeature - Class in calhoun.analysis.crf.features.tricycle13
EmissionMarkovFeature() - Constructor for class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature
EmissionMarkovFeature(List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature
EmissionMarkovFeature(List<int[]>, List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature
EmissionMarkovFeature.MarkovHistory - Class in calhoun.analysis.crf.features.tricycle13
EmissionMarkovFeature.MarkovHistory() - Constructor for class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature.MarkovHistory
end - Variable in class calhoun.analysis.crf.io.IntervalInputSequence.IntervalRangeMapValue
EndFeatures - Class in calhoun.analysis.crf.features.generic
  indicator functions that evaluate to true for a selected set of start states at the first position in the sequence.
EndFeatures() - Constructor for class calhoun.analysis.crf.features.generic.EndFeatures
entries - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryCachingDetails
equals(Object) - Method in class calhoun.util.DenseBooleanMatrix2D
equals(Object) - Method in class calhoun.util.DenseIntMatrix2D
equals(Object) - Method in class calhoun.util.RangeMap.Interval
ErrorException - Exception in calhoun.util
  Exception type for general errors.
ErrorException(String) - Constructor for exception calhoun.util.ErrorException
ErrorException(String, Throwable) - Constructor for exception calhoun.util.ErrorException
ErrorException(Throwable) - Constructor for exception calhoun.util.ErrorException
ESTEdge - Class in calhoun.analysis.crf.features.tricycle13
ESTEdge() - Constructor for class calhoun.analysis.crf.features.tricycle13.ESTEdge
ESTExon - Class in calhoun.analysis.crf.features.tricycle13
ESTExon() - Constructor for class calhoun.analysis.crf.features.tricycle13.ESTExon
ESTInterval13 - Class in calhoun.analysis.crf.features.interval13
ESTInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.ESTInterval13
ESTInterval29 - Class in calhoun.analysis.crf.features.interval29
ESTInterval29() - Constructor for class calhoun.analysis.crf.features.interval29.ESTInterval29
ESTIntron - Class in calhoun.analysis.crf.features.tricycle13
ESTIntron() - Constructor for class calhoun.analysis.crf.features.tricycle13.ESTIntron
evaluate(int, int, TrainingSequence<?>, int) - Method in interface calhoun.analysis.crf.LocalPathSimilarityScore
  compute a real-valued score between a given path and the true path at a given position.
evaluate(int, int, TrainingSequence<?>, int) - Method in class calhoun.analysis.crf.scoring.SimScoreMaxStateAgreement
evaluate(int, int, TrainingSequence<?>, int) - Method in class calhoun.analysis.crf.scoring.SimScoreMinCodingMiscallsSV13
evaluate(int, int, TrainingSequence<?>, int) - Method in class calhoun.analysis.crf.scoring.SimScoreMinExonBoundaryMiscallsSV13
evaluate(int, int, TrainingSequence<?>, int) - Method in class calhoun.analysis.crf.scoring.SimScoreStateAndExonBoundariesInt13
evaluate(double) - Method in class calhoun.analysis.crf.statistics.MixtureOfGammas
evaluateEdge(InputSequence, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.CompositeFeatureManager
evaluateEdge(InputSequence<? extends InputType>, int, int, int, FeatureList) - Method in interface calhoun.analysis.crf.FeatureManagerEdge
  Evaluates the set of features managed by this object for the given arguments.
evaluateEdge(InputSequence, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.generic.IndicatorEdges
evaluateEdge(InputSequence<?>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.generic.WeightedEdges
evaluateEdge(InputSequence<?>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.generic.WeightedStateChanges
evaluateEdge(InputSequence<? extends CompositeInput>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.ESTInterval13
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.GeneConstraintsInterval13
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.PWMInterval13
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.StateTransitionsInterval13
evaluateEdge(InputSequence<? extends CompositeInput>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval29.ESTInterval29
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval29.GeneConstraintsInterval29
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval29.PWMInterval29
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval29.StateTransitionsInterval29
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.CodingStopFeature
evaluateEdge(InputSequence<? extends CompositeInput>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.ESTEdge
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.GeneConstraints
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.MaxentMotifFeatures
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
evaluateEdge(InputSequence<? extends CompositeInput>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.PWM_evolution
evaluateEdge(InputSequence, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.test.ConstraintTest.FixedEdges
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.test.GeneConstraintsToy
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.test.TestFeatures.ExplicitHalfExponentialLengthFeature
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.test.TestFeatures.ExponentialLengthFeature
evaluateEdge(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.test.TestFeatures.HalfExponentialLengthFeature
evaluateEdgeLength(InputSequence, int, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.CompositeFeatureManager
evaluateEdgeLength(InputSequence<? extends InputType>, int, int, int, int, FeatureList) - Method in interface calhoun.analysis.crf.FeatureManagerEdgeExplicitLength
evaluateNode(InputSequence, int, int, FeatureList) - Method in class calhoun.analysis.crf.CompositeFeatureManager
evaluateNode(InputSequence<? extends InputType>, int, int, FeatureList) - Method in interface calhoun.analysis.crf.FeatureManagerNode
  Evaluates the set of features managed by this object for the given arguments.
evaluateNode(InputSequence<?>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.generic.EndFeatures
evaluateNode(InputSequence<?>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.generic.StartFeatures
evaluateNode(InputSequence<? extends CompositeInput>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.BlastInterval13
evaluateNode(InputSequence<? extends CompositeInput>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.ESTInterval13
evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.FootprintsInterval13
evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.GapFeaturesInterval13
evaluateNode(InputSequence<? extends Character>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.GeneConstraintsInterval13
evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.PhylogeneticLogprobInterval13
evaluateNode(InputSequence<? extends Character>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13Base
evaluateNode(InputSequence<? extends CompositeInput>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval29.ESTInterval29
evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval29.FootprintsInterval29
evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval29.GapFeaturesInterval29
evaluateNode(InputSequence<? extends Character>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval29.GeneConstraintsInterval29
evaluateNode(InputSequence<? extends Character>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29Base
evaluateNode(InputSequence<? extends Character>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature
evaluateNode(InputSequence<? extends CompositeInput>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.ESTEdge
evaluateNode(InputSequence<? extends CompositeInput>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.ESTExon
evaluateNode(InputSequence<? extends CompositeInput>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.ESTIntron
evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures
evaluateNode(InputSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.GapConjunctionFeatures
evaluateNode(InputSequence<? extends IntervalInputSequence.IntervalPosition>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.IntervalPresenceFeatures
evaluateNode(InputSequence<? extends Character>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.KmerFeatures
evaluateNode(InputSequence<? extends CompositeInput>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.PfamGenic
evaluateNode(InputSequence<? extends CompositeInput>, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.PfamPhase
evaluateNode(InputSequence<? extends Character>, int, int, FeatureList) - Method in class calhoun.analysis.crf.test.TestFeatures.EmissionFeature
evaluateNodeLength(InputSequence, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.CompositeFeatureManager
evaluateNodeLength(InputSequence<? extends InputType>, int, int, int, FeatureList) - Method in interface calhoun.analysis.crf.FeatureManagerNodeExplicitLength
evaluateNodeLength(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
evaluateNodeLength(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
evaluateNodeLength(InputSequence, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.features.tricycle13.IntronLengthFeature
evaluateNodeLength(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.test.TestFeatures.ExplicitHalfExponentialLengthFeature
evaluateNodeLength(InputSequence<? extends Character>, int, int, int, FeatureList) - Method in class calhoun.analysis.crf.test.TestFeatures.GaussianLengthFeature
evaluatePosition(int, int) - Method in interface calhoun.analysis.crf.solver.CacheProcessor
evaluatePosition(int, int) - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
evaluatePosition(int, int) - Method in class calhoun.analysis.crf.solver.NoCachingCacheProcessor
evaluateSegmentsEndingAt(int, int) - Method in interface calhoun.analysis.crf.solver.CacheProcessor
evaluateSegmentsEndingAt(int, int) - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
  The job of this function is to update the table "LengthFeatureEvaluation[][] lengthEvals" The first dimension is index by those states which have at least one explicit length node feature, corresponding to the state of an interval which ends at position currently under consideration.
evaluateSegmentsEndingAt(int, int) - Method in class calhoun.analysis.crf.solver.NoCachingCacheProcessor
EvolutionaryModel - Class in calhoun.analysis.crf.features.supporting.phylogenetic
EvolutionaryModel(PhylogeneticTreeFelsensteinOrder, double[], NucleotideSubstitutionModel) - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.EvolutionaryModel
ExampleTrees - Class in calhoun.analysis.crf.test
ExampleTrees() - Constructor for class calhoun.analysis.crf.test.ExampleTrees
execute() - Method in class calhoun.util.FileDiff
exitTransitions - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
exp - Static variable in class calhoun.util.ColtUtil
expectedProductFile - Variable in class calhoun.analysis.crf.solver.LogFiles
expectedProductWriter - Variable in class calhoun.analysis.crf.solver.LogFiles
expectFile - Variable in class calhoun.analysis.crf.solver.LogFiles
expectLengthFile - Variable in class calhoun.analysis.crf.solver.LogFiles
expectLengthWriter - Variable in class calhoun.analysis.crf.solver.LogFiles
expectWriter - Variable in class calhoun.analysis.crf.solver.LogFiles
exponentiate_real_matrix(DoubleMatrix2D, DoubleMatrix2D, int) - Static method in class calhoun.util.ColtUtil
exponentiate_symmetric_matrix(DoubleMatrix2D, DoubleMatrix2D) - Static method in class calhoun.util.ColtUtil
ExtensionMapper - Class in calhoun.analysis.crf.io
  an implementation of `FilenameMapper` that changes file extensions or add a new file extension onto the source file.
ExtensionMapper() - Constructor for class calhoun.analysis.crf.io.ExtensionMapper

## F

FastaAlignmentInput - Class in calhoun.analysis.crf.io
FastaAlignmentInput() - Constructor for class calhoun.analysis.crf.io.FastaAlignmentInput
FastaInput - Class in calhoun.analysis.crf.io
FastaInput() - Constructor for class calhoun.analysis.crf.io.FastaInput
FastaIterator - Class in calhoun.seq
  This class implements iterator and allows a fasta file to be iterated through without having to read anything.
FastaIterator(String) - Constructor for class calhoun.seq.FastaIterator
FastaIterator(File) - Constructor for class calhoun.seq.FastaIterator
FastaIterator(String, String) - Constructor for class calhoun.seq.FastaIterator
FastaIterator(File, File) - Constructor for class calhoun.seq.FastaIterator
  Creates an iterator over a sequence file and also possibly a quality file
FastaIterator.ReaderSequence - Class in calhoun.seq
  A minimal sequence class that slurps its sequence in immediately.
FastaIterator.ReaderSequence(File, String) - Constructor for class calhoun.seq.FastaIterator.ReaderSequence
FastaSequence - Interface in calhoun.seq
  Represents a generic sequence in a fasta file.
FastaWriter - Class in calhoun.seq
  Used for writing fasta files.
FastaWriter(String, boolean) - Constructor for class calhoun.seq.FastaWriter
  Opens a fasta file for writing.
FastaWriter(String, boolean, int) - Constructor for class calhoun.seq.FastaWriter
  Opens a fasta file for writing.
FastaWriter(File, boolean) - Constructor for class calhoun.seq.FastaWriter
  Opens a fasta file for writing.
FastaWriter(File, boolean, int) - Constructor for class calhoun.seq.FastaWriter
  Opens a fasta file for writing.
FastaWriter(Writer, int) - Constructor for class calhoun.seq.FastaWriter
featureIndex - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryEntry
featureIndex - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseCachingDetails
FeatureList - Interface in calhoun.analysis.crf
  used to pass feature evaluations from a FeatureManager to the Conrad engine during an `evaluate` call.
FeatureManager<InputType> - Interface in calhoun.analysis.crf
  evaluates CRF feature functions on the model.
FeatureManagerEdge<InputType> - Interface in calhoun.analysis.crf
  holds features whose value depends on the current state and the previous state.
FeatureManagerEdgeExplicitLength<InputType> - Interface in calhoun.analysis.crf
  Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
FeatureManagerNode<InputType> - Interface in calhoun.analysis.crf
  holds features whose value only depends on the current state, and not the previous state.
FeatureManagerNodeBoundaries<InputType> - Interface in calhoun.analysis.crf
  An extension of FeatureManagerNode for situations where the nodes use in semi-markov models is non-standard.
FeatureManagerNodeExplicitLength<InputType> - Interface in calhoun.analysis.crf
  Since Features are computed as needed dynamically at runtime, a FeatureManager controls training and dynamic creation of the features.
FeatureTest - Class in calhoun.analysis.crf.test
FeatureTest() - Constructor for class calhoun.analysis.crf.test.FeatureTest
FelsensteinFeatures - Class in calhoun.analysis.crf.features.tricycle13
FelsensteinFeatures(List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures
FelsensteinFeatures() - Constructor for class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures
FelsensteinFeatures(List<int[]>, List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures
FelsensteinFeatures(List<int[]>, List<int[]>, List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures
FileDiff - Class in calhoun.util
  Computes the 'diff' difference between two files.
FileDiff(String, String) - Constructor for class calhoun.util.FileDiff
  Constructor takes 2 file names - opens the files using UTF-8 encoding.
FileDiff(File, File) - Constructor for class calhoun.util.FileDiff
  Constructor takes 2 Files - opens the files using UTF-8 encoding.
FileDiff(Reader, Reader) - Constructor for class calhoun.util.FileDiff
FileDiff(Reader, Reader, boolean) - Constructor for class calhoun.util.FileDiff
FileInputHandlerTest - Class in calhoun.analysis.crf.test
FileInputHandlerTest() - Constructor for class calhoun.analysis.crf.test.FileInputHandlerTest
FilenameMapper - Interface in calhoun.analysis.crf.io
  An interface used to map filenames.
fileRecordCompare(String, String, String) - Static method in class calhoun.util.FileUtil
  Compares records in two flat files.
fileRecordCompare(String, String) - Static method in class calhoun.util.FileUtil
  Convience form of fileRecordCompare which does no masking
filesMatch(String, String) - Static method in class calhoun.util.FileDiff
FileUtil - Class in calhoun.util
  Utility functions for file management
FilterIterator<A> - Class in calhoun.util
FilterIterator(Iterator<A>) - Constructor for class calhoun.util.FilterIterator
finalize() - Method in class calhoun.analysis.crf.features.supporting.LogProbLookup
find(int, int) - Method in class calhoun.util.RangeMap
  Returns objects in the range map that overlap this range.
findContained(int, int) - Method in class calhoun.util.RangeMap
  Returns objects in the range map that are fully contained by the range.
findContaining(int, int) - Method in class calhoun.util.RangeMap
  Returns objects in the range map that fully contain the range.
FixedWeightOptimizer - Class in calhoun.analysis.crf.solver
  a dummy optimizer that just fixed the weights at values specified in the configuration.
FixedWeightOptimizer() - Constructor for class calhoun.analysis.crf.solver.FixedWeightOptimizer
FootprintsInterval13 - Class in calhoun.analysis.crf.features.interval13
FootprintsInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.FootprintsInterval13
FootprintsInterval29 - Class in calhoun.analysis.crf.features.interval29
FootprintsInterval29() - Constructor for class calhoun.analysis.crf.features.interval29.FootprintsInterval29
forgetTN() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
format(double[]) - Static method in class calhoun.util.ColtUtil
format(DoubleMatrix2D) - Static method in class calhoun.util.ColtUtil
format(LogRecord) - Method in class calhoun.util.SimplerFormatter
  Just prints a time followed by message followed by class function line
freeze() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
FunctionEvalTest - Class in calhoun.analysis.crf.test
FunctionEvalTest() - Constructor for class calhoun.analysis.crf.test.FunctionEvalTest

## G

gamma(double, double, double) - Static method in class calhoun.analysis.crf.statistics.GammaDistribution
gamma(double) - Static method in class calhoun.analysis.crf.statistics.GammaDistribution
GammaDistribution - Class in calhoun.analysis.crf.statistics
GammaDistribution() - Constructor for class calhoun.analysis.crf.statistics.GammaDistribution
GammaDistributionsTest - Class in calhoun.analysis.crf.test
GammaDistributionsTest() - Constructor for class calhoun.analysis.crf.test.GammaDistributionsTest
GapConjunctionFeatures - Class in calhoun.analysis.crf.features.tricycle13
GapConjunctionFeatures() - Constructor for class calhoun.analysis.crf.features.tricycle13.GapConjunctionFeatures
GapConjunctionFeaturesTest - Class in calhoun.analysis.crf.test
GapConjunctionFeaturesTest() - Constructor for class calhoun.analysis.crf.test.GapConjunctionFeaturesTest
GapFeaturesInterval13 - Class in calhoun.analysis.crf.features.interval13
GapFeaturesInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.GapFeaturesInterval13
GapFeaturesInterval29 - Class in calhoun.analysis.crf.features.interval29
GapFeaturesInterval29() - Constructor for class calhoun.analysis.crf.features.interval29.GapFeaturesInterval29
GeneConstraints - Class in calhoun.analysis.crf.features.tricycle13
  lmplements basic constraints on gene calls.
GeneConstraints() - Constructor for class calhoun.analysis.crf.features.tricycle13.GeneConstraints
GeneConstraintsInterval13 - Class in calhoun.analysis.crf.features.interval13
  Implements basic constraints on gene calls. 1) Intergenic - start must occur at ATG 2) Splice sites must be canonical GT/AG or GC/AG 3) Exon-stop must be followed by a start codon
GeneConstraintsInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.GeneConstraintsInterval13
GeneConstraintsInterval13Test - Class in calhoun.analysis.crf.test
  Tests that CRF is working with valid probabilities - the sum of all possible labelings is 1.
GeneConstraintsInterval13Test() - Constructor for class calhoun.analysis.crf.test.GeneConstraintsInterval13Test
GeneConstraintsInterval29 - Class in calhoun.analysis.crf.features.interval29
  Implements basic constraints on gene calls. 1) Intergenic - start must occur at ATG 2) Splice sites must be canonical GT/AG or GC/AG 3) Exon-stop must be followed by a start codon
GeneConstraintsInterval29() - Constructor for class calhoun.analysis.crf.features.interval29.GeneConstraintsInterval29
GeneConstraintsToy - Class in calhoun.analysis.crf.test
  Implements basic constraints on gene calls. 1) Intergenic - start must occur at ATG 2) Splice sites must be canonical GT/AG or GC/AG 3) Exon-stop must be followed by a start codon
GeneConstraintsToy() - Constructor for class calhoun.analysis.crf.test.GeneConstraintsToy
get(int) - Method in class calhoun.analysis.crf.solver.RecyclingBuffer
getAccuracy() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
  returns the exact nucleotide accuracy of the result
getAccuracy() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
  returns the exact nucleotide accuracy of the result
getAlphaFile() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
getAlphaFile() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
getAlphaLengthFile() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
getAlphaLengthFile() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
getBackPointers() - Method in class calhoun.analysis.crf.solver.Viterbi
getBaseAndExtension(File) - Static method in class calhoun.util.FileUtil
getBestScore() - Method in class calhoun.analysis.crf.solver.Viterbi
getBetaLengthFile() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
getBetaLengthFile() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
getbleft() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder
getBooleanProperty(String, boolean) - Method in class calhoun.util.TypedProperties
getbright() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder
getCacheProcessor() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodGradient
  gets the cache processor used to access feature evaluations
getCacheProcessor() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
  gets the cache processor used to access feature evaluations
getCacheProcessor() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
  gets the cache processor used to access feature evaluations
getCacheProcessor() - Method in class calhoun.analysis.crf.solver.SemiMarkovViterbi
  gets the cache processor used to access feature evaluations
getCacheStrategy() - Method in class calhoun.analysis.crf.AbstractFeatureManager
getCacheStrategy() - Method in class calhoun.analysis.crf.CompositeFeatureManager
getCacheStrategy() - Method in interface calhoun.analysis.crf.FeatureManager
  caching strategy that the `CacheProcessor` should use to cache values for this feature.
getCacheStrategy() - Method in class calhoun.analysis.crf.features.generic.WeightedEdges
getCacheStrategy() - Method in class calhoun.analysis.crf.features.generic.WeightedStateChanges
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.BlastInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.ESTInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.FootprintsInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.GapFeaturesInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.GeneConstraintsInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.PhylogeneticLogprobInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.PWMInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorNodeOnlyInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorZeroPadInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval13.StateTransitionsInterval13
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval29.ESTInterval29
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval29.FootprintsInterval29
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval29.GapFeaturesInterval29
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval29.GeneConstraintsInterval29
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval29.PWMInterval29
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorNodeOnlyInterval29
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorZeroPadInterval29
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
getCacheStrategy() - Method in class calhoun.analysis.crf.features.interval29.StateTransitionsInterval29
getCacheStrategy() - Method in class calhoun.analysis.crf.features.tricycle13.CodingStopFeature
getCacheStrategy() - Method in class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature
getCacheStrategy() - Method in class calhoun.analysis.crf.features.tricycle13.ESTEdge
getCacheStrategy() - Method in class calhoun.analysis.crf.features.tricycle13.ESTIntron
getCacheStrategy() - Method in class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures
getCacheStrategy() - Method in class calhoun.analysis.crf.features.tricycle13.GapConjunctionFeatures
getCacheStrategy() - Method in class calhoun.analysis.crf.features.tricycle13.PfamGenic
getCacheStrategy() - Method in class calhoun.analysis.crf.features.tricycle13.PfamPhase
getCacheStrategy() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
getCacheStrategy() - Method in class calhoun.analysis.crf.test.ConstraintTest.FixedEdges
getCacheStrategy() - Method in class calhoun.analysis.crf.test.TestFeatures.EmissionFeature
getCacheStrategy() - Method in class calhoun.analysis.crf.test.TestFeatures.ExplicitHalfExponentialLengthFeature
getCacheStrategy() - Method in class calhoun.analysis.crf.test.TestFeatures.ExponentialLengthFeature
getCacheStrategy() - Method in class calhoun.analysis.crf.test.TestFeatures.GaussianLengthFeature
getCacheStrategy() - Method in class calhoun.analysis.crf.test.TestFeatures.HalfExponentialLengthFeature
getColumnClass(int) - Method in class calhoun.analysis.crf.executables.viewer.ViterbiTableModel
getColumnCount() - Method in class calhoun.analysis.crf.executables.viewer.ViterbiTableModel
getColumnName(int) - Method in class calhoun.analysis.crf.executables.viewer.ViterbiTableModel
getColumnUniqueHash(int) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
getCommentLineIndicator() - Method in class calhoun.util.FileDiff
  Gets the comment line indicator string.
getComponent() - Method in class calhoun.analysis.crf.io.AlignmentTree
getComponent() - Method in class calhoun.analysis.crf.io.FastaAlignmentInput
getComponent(String) - Method in interface calhoun.analysis.crf.io.InputSequence
  For input sequences that are a composite of several different input objects, returns a particular component of the input.
getComponent(String) - Method in class calhoun.analysis.crf.io.InputSequenceBoolean
getComponent(String) - Method in class calhoun.analysis.crf.io.InputSequenceCharacter
getComponent(String) - Method in class calhoun.analysis.crf.io.InputSequenceComposite
getComponent(String) - Method in class calhoun.analysis.crf.io.InputSequenceInt
getComponent(String) - Method in class calhoun.analysis.crf.io.InputSequenceObject
getComponent(String) - Method in class calhoun.analysis.crf.io.IntervalInputSequence
getComponent(String) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
getComponent(String) - Method in class calhoun.analysis.crf.io.NameInputSequence
getComponent(String) - Method in class calhoun.analysis.crf.io.TrainingSequence
getComponentFeatures() - Method in class calhoun.analysis.crf.CompositeFeatureManager
getComponentNames() - Method in class calhoun.analysis.crf.io.AlignmentTree
getComponentNames() - Method in class calhoun.analysis.crf.io.FastaAlignmentInput
getComponentNames() - Method in class calhoun.analysis.crf.io.FastaInput
getComponentNames() - Method in interface calhoun.analysis.crf.io.InputComponentIO
  A list of names of the components of the InputSequence created by this reader.
getComponentNames() - Method in class calhoun.analysis.crf.io.InterleavedInputComponentBase
  returns the name of this component
getComponents() - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
  gets the current set of input components configured for this input handler.
getComponents() - Method in class calhoun.analysis.crf.io.InputSequenceComposite
  returns all of components of this input sequence.
getConsensusLength() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
getConsensusSeqs() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
getCRF() - Static method in class calhoun.analysis.crf.test.ZeroOrderManager
getCurrent() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
getData() - Method in class calhoun.analysis.crf.io.InputSequenceBoolean
  gets the boolean array containing the data for this sequence.
getData() - Method in class calhoun.analysis.crf.io.InputSequenceInt
  gets the int array containing the data for this sequence.
getData() - Method in interface calhoun.analysis.crf.solver.CacheProcessor
getData() - Method in class calhoun.analysis.crf.solver.CacheProcessorBasic
getDebugLevel() - Method in class calhoun.analysis.crf.solver.StandardOptimizer
getDisjointRegions() - Method in class calhoun.util.RangeMap
getDoubleArrayProperty(String, double[]) - Method in class calhoun.util.TypedProperties
getDoubleProperty(String, double) - Method in class calhoun.util.TypedProperties
getEmptyIntervals(int, int) - Method in class calhoun.util.RangeMap
  Returns the empty intervals.
getEndProb() - Method in class calhoun.analysis.crf.features.interval13.StateTransitionsInterval13
getEndProb() - Method in class calhoun.analysis.crf.features.interval29.StateTransitionsInterval29
getEpsForConvergence() - Method in class calhoun.analysis.crf.solver.StandardOptimizer
getEvolutionaryModelName() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.HKY85Model
getEvolutionaryModelName() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.Kimura80Model
getEvolutionaryModelName() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel
getExpectedProductFile() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
getExpectFile() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
getExpectFile() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
getExpectLengthFile() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
getExpectLengthFile() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
getExtension() - Method in class calhoun.analysis.crf.io.ExtensionMapper
  the new extension to use in the mapped file.
getFeatureEvaluations() - Method in interface calhoun.analysis.crf.solver.CacheProcessor
getFeatureEvaluations() - Method in class calhoun.analysis.crf.solver.CacheProcessorBasic
getFeatureName(int) - Method in class calhoun.analysis.crf.CompositeFeatureManager
getFeatureName(int) - Method in class calhoun.analysis.crf.Conrad
  looks up a feature's name given it's index
getFeatureName(int) - Method in class calhoun.analysis.crf.ConstrainedFeatureManager
  Return a concatenated name
getFeatureName(int) - Method in interface calhoun.analysis.crf.FeatureManager
  Returns a human identifiable name for the feature referenced by a given index.
getFeatureName(int) - Method in class calhoun.analysis.crf.features.generic.EndFeatures
getFeatureName(int) - Method in class calhoun.analysis.crf.features.generic.IndicatorEdges
getFeatureName(int) - Method in class calhoun.analysis.crf.features.generic.StartFeatures
getFeatureName(int) - Method in class calhoun.analysis.crf.features.generic.WeightedEdges
getFeatureName(int) - Method in class calhoun.analysis.crf.features.generic.WeightedStateChanges
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval13.BlastInterval13
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval13.ESTInterval13
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval13.FootprintsInterval13
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval13.GapFeaturesInterval13
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval13.GeneConstraintsInterval13
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval13.PhylogeneticLogprobInterval13
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval13.PWMInterval13
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13Base
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval13.StateTransitionsInterval13
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval29.ESTInterval29
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval29.FootprintsInterval29
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval29.GapFeaturesInterval29
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval29.GeneConstraintsInterval29
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval29.PWMInterval29
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29Base
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
getFeatureName(int) - Method in class calhoun.analysis.crf.features.interval29.StateTransitionsInterval29
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.CodingStopFeature
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.ESTEdge
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.ESTExon
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.ESTIntron
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.GapConjunctionFeatures
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.GeneConstraints
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.IntervalPresenceFeatures
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.IntronLengthFeature
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.KmerFeatures
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.MaxentMotifFeatures
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.PfamGenic
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.PfamPhase
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
getFeatureName(int) - Method in class calhoun.analysis.crf.features.tricycle13.PWM_evolution
getFeatureName(int) - Method in class calhoun.analysis.crf.test.ConstraintTest.FixedEdges
getFeatureName(int) - Method in class calhoun.analysis.crf.test.GeneConstraintsToy
getFeatureName(int) - Method in class calhoun.analysis.crf.test.TestFeatures.TestFeature
getFeatureOffset(int) - Method in class calhoun.analysis.crf.CompositeFeatureManager
getFeatureSums() - Method in interface calhoun.analysis.crf.solver.CacheProcessor
getFeatureSums() - Method in class calhoun.analysis.crf.solver.CacheProcessorBasic
getFeatureSums() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodGradient
getFeatureSums() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
getFeatureSums() - Method in class calhoun.analysis.crf.solver.NoCachingCacheProcessor
getFelsensteinOrder(String[]) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree
  Given an ordering of species in a multiple alignment file, determine an order for computations by which Felsenstein's algorithm can be performed, and the branch lengths involved at each step.
getFelsensteinOrder() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
getFile() - Method in class calhoun.seq.FastaIterator.ReaderSequence
getFilename() - Method in class calhoun.analysis.crf.io.CompositeInput.InputComponent
  Deprecated.
getFilename() - Method in class calhoun.seq.FastaWriter
getFilenameMapper() - Method in class calhoun.analysis.crf.io.OutputHandlerWriter
  gets the mapper which will be used to generate the output filename based on the output location.
getFirstPass() - Method in class calhoun.analysis.crf.solver.TwoPassOptimizer
getFN() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
getFP() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
getFrom() - Method in class calhoun.analysis.crf.BeanModel.Edge
getHandlers() - Method in class calhoun.analysis.crf.io.OutputHandlerComposite
  retursn the configured list of output handler.
getHeader() - Method in class calhoun.analysis.crf.io.FastaInput
getHeader() - Method in interface calhoun.seq.FastaSequence
  Gets the fasta header (with leading and trailing spaces trimmed)
getHeader() - Method in class calhoun.seq.SimpleFastaSequence
getHiddenSequenceFile() - Method in class calhoun.analysis.crf.io.CompositeInput
  Deprecated.
getHiddenSequenceFile() - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
  gets the name of the hidden sequence file.
getHiddenSequenceReader() - Method in class calhoun.analysis.crf.io.CompositeInput
  Deprecated.
getHiddenStateReader() - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
  gets the reader used to read in results for training data.
getHiddenStateReader() - Method in class calhoun.analysis.crf.io.InputHandlerFile
  gets the reader used to read in results for training data.
getHiddenStateReader() - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
  gets the reader used to read in results for training data.
getIgnoreWhitespace() - Method in class calhoun.util.FileDiff
getileft() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder
getIndex() - Method in class calhoun.analysis.crf.BeanModel.Node
getInference() - Method in class calhoun.analysis.crf.Conrad
  returns the configured inference algorithm which will be used to predict hidden states for new inputs once the model is trained.
getInputComponent() - Method in class calhoun.analysis.crf.AbstractFeatureManager
getInputComponent() - Method in interface calhoun.analysis.crf.FeatureManager
  Specifies the particular component of the input which this feature manager uses, if the input data is a composite input which has multiple components.
getInputComponent() - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
getInputComponent() - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
getInputHandler() - Method in class calhoun.analysis.crf.Conrad
  returns the configured input handler.
getInputHandler() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
  retursn the input handler used to write out the input sequences
getInputHandler() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
  retursn the input handler used to write out the input sequences
getInputReader() - Method in class calhoun.analysis.crf.io.InputHandlerFile
  gets the reader used to read in input sequences.
getInputReaders() - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
  gets the readers used to read in input sequences.
getInputSequence() - Method in class calhoun.analysis.crf.io.CompositeInput.InputComponent
  Deprecated.
getInputSequence() - Method in class calhoun.analysis.crf.io.TrainingSequence
  gets the underlying input sequence
getIntArrayProperty(String, int[]) - Method in class calhoun.util.TypedProperties
getIntervals() - Method in class calhoun.util.RangeMap
  Returns the individual intervals in the rangeMap.
getIntervals(int, int) - Method in class calhoun.util.RangeMap
  Like getIntervals, but allows you to define a start and stop.
getIntProperty(String, int) - Method in class calhoun.util.TypedProperties
getIntronProb() - Method in class calhoun.analysis.crf.features.interval13.StateTransitionsInterval13
getIntronProb() - Method in class calhoun.analysis.crf.features.interval29.StateTransitionsInterval29
getInvalidTransitions() - Method in interface calhoun.analysis.crf.solver.CacheProcessor
getInvalidTransitions() - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
getInvalidTransitions() - Method in class calhoun.analysis.crf.solver.NoCachingCacheProcessor
getiright() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder
getKmer(InputSequence<? extends Character>, int, int[]) - Method in class calhoun.analysis.crf.features.tricycle13.KmerFeatures
getKmerProb(int, String, int) - Method in class calhoun.analysis.crf.features.tricycle13.KmerFeatures
  Returns an individual entry from the counts list.
getLabeled(int) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
getLabeled(int) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
getLegalTransitions() - Method in class calhoun.analysis.crf.BeanModel
getLegalTransitions() - Method in interface calhoun.analysis.crf.ModelManager
  returns a boolean matrix where each `(row, column)` entry contains true if the model has a legal transition between state `row` and state `column`.
getLength() - Method in interface calhoun.seq.FastaSequence
  The number of sequence characters
getLength() - Method in class calhoun.seq.SimpleFastaSequence
getLength() - Method in class calhoun.util.RangeMap.Interval
getLengthFeatureEvaluations() - Method in interface calhoun.analysis.crf.solver.CacheProcessor
getLengthFeatureEvaluations() - Method in class calhoun.analysis.crf.solver.CacheProcessorBasic
getLookbackArrayFeatureSize() - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
getLookbackArraySize() - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
getManager() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
  gets the model used to generate results
getManager() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
  gets the model used to generate results
getMap() - Method in class calhoun.util.RangeMap
getMapper() - Method in class calhoun.analysis.crf.io.InputHandlerFile
  the mapper used to generate the name of the hidden sequence file from the input sequence file.
getMarginalsFile() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
getMarkovHistory() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
getMaxIters() - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
getMaxIters() - Method in class calhoun.analysis.crf.solver.StandardOptimizer
getMaxLengths() - Method in class calhoun.analysis.crf.SemiMarkovSetup
  gets the maximum lengths for each state.
getMean() - Method in class calhoun.analysis.crf.statistics.MixtureOfGammas
getMessage() - Method in exception calhoun.util.CheckException
getMessage() - Method in exception calhoun.util.ErrorException
getMForHessian() - Method in class calhoun.analysis.crf.solver.StandardOptimizer
getMinLengths() - Method in class calhoun.analysis.crf.SemiMarkovSetup
  gets the minimum lengths for each state.
getMix() - Method in class calhoun.analysis.crf.statistics.MixtureOfGammas
getModel() - Method in class calhoun.analysis.crf.Conrad
  returns the configured ModelManager object.
getMultipleAlignment() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence.MultipleAlignmentColumn
  returns the multiple alignment input sequence that this column comes from.
getName() - Method in class calhoun.analysis.crf.BeanModel.Node
getName() - Method in class calhoun.analysis.crf.io.CompositeInput.InputComponent
  Deprecated.
getName() - Method in class calhoun.analysis.crf.io.InterleavedInputComponentBase
  the name of the input sequence read and written by this component
getName() - Method in class calhoun.analysis.crf.io.NameInputSequence
getNameComponent() - Method in class calhoun.analysis.crf.io.GTFInputInterval13
getNodeMarginalFile() - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
getNodeMarginalFile() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
getNumFeatures() - Method in class calhoun.analysis.crf.CompositeFeatureManager
getNumFeatures() - Method in class calhoun.analysis.crf.Conrad
  returns the number of individual features in the model.
getNumFeatures() - Method in class calhoun.analysis.crf.ConstrainedFeatureManager
  Composite feature managers only return 1 feature.
getNumFeatures() - Method in interface calhoun.analysis.crf.FeatureManager
  Returns the number of features maintained by this `FeatureManager`.
getNumFeatures() - Method in class calhoun.analysis.crf.features.generic.EndFeatures
getNumFeatures() - Method in class calhoun.analysis.crf.features.generic.IndicatorEdges
getNumFeatures() - Method in class calhoun.analysis.crf.features.generic.StartFeatures
getNumFeatures() - Method in class calhoun.analysis.crf.features.generic.WeightedEdges
getNumFeatures() - Method in class calhoun.analysis.crf.features.generic.WeightedStateChanges
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval13.BlastInterval13
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval13.ESTInterval13
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval13.FootprintsInterval13
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval13.GapFeaturesInterval13
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval13.GeneConstraintsInterval13
  This is a constraint class, so we don't return features
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval13.PhylogeneticLogprobInterval13
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval13.PWMInterval13
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13Base
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval13.StateTransitionsInterval13
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval29.ESTInterval29
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval29.FootprintsInterval29
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval29.GapFeaturesInterval29
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval29.GeneConstraintsInterval29
  This is a constraint class, so we don't return features
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval29.PWMInterval29
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29Base
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
getNumFeatures() - Method in class calhoun.analysis.crf.features.interval29.StateTransitionsInterval29
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.CodingStopFeature
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.ESTEdge
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.ESTExon
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.ESTIntron
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.GapConjunctionFeatures
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.GeneConstraints
  This is a constraint class, so we don't return features
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.IntervalPresenceFeatures
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.IntronLengthFeature
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.KmerFeatures
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.MaxentMotifFeatures
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.PfamGenic
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.PfamPhase
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
getNumFeatures() - Method in class calhoun.analysis.crf.features.tricycle13.PWM_evolution
getNumFeatures() - Method in class calhoun.analysis.crf.test.ConstraintTest.FixedEdges
getNumFeatures() - Method in class calhoun.analysis.crf.test.GeneConstraintsToy
  This is a constraint class, so we don't return features
getNumFeatures() - Method in class calhoun.analysis.crf.test.TestFeatures.TestFeature
getNumSeqCap() - Method in class calhoun.analysis.crf.io.FastaInput
getNumSpecies() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree
getNumSpecies() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
getNumStates() - Method in class calhoun.analysis.crf.BeanModel
getNumStates() - Method in class calhoun.analysis.crf.Conrad
  returns the number of hidden states in the model
getNumStates() - Method in interface calhoun.analysis.crf.ModelManager
  the number of hidden states.
getObjectiveFunction() - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
  returns the configured objective function gradient which will be used by the optimizer during the training process.
getObjectiveFunction() - Method in class calhoun.analysis.crf.solver.StandardOptimizer
  returns the configured objective function gradient which will be used by the optimizer during the training process.
getObjectList() - Method in class calhoun.util.RangeMap
getOptimizer() - Method in class calhoun.analysis.crf.Conrad
  returns the configured numerical optimizer which will be used to select the optimal feature weights during training.
getOutputHandler() - Method in class calhoun.analysis.crf.Conrad
  gets the configured output handler.
getOverlapCorrections() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
getPadExon3prime() - Static method in class calhoun.analysis.crf.features.interval13.Interval13Model
getPadExon3prime() - Static method in class calhoun.analysis.crf.features.interval29.Interval29Model
getPadExon5prime() - Static method in class calhoun.analysis.crf.features.interval13.Interval13Model
getPadExon5prime() - Static method in class calhoun.analysis.crf.features.interval29.Interval29Model
getPadIntergenic() - Static method in class calhoun.analysis.crf.features.interval13.Interval13Model
getPadIntergenic() - Static method in class calhoun.analysis.crf.features.interval29.Interval29Model
getPadIntron3prime() - Static method in class calhoun.analysis.crf.features.interval13.Interval13Model
getPadIntron3prime() - Static method in class calhoun.analysis.crf.features.interval29.Interval29Model
getPadIntron5prime() - Static method in class calhoun.analysis.crf.features.interval13.Interval13Model
getPadIntron5prime() - Static method in class calhoun.analysis.crf.features.interval29.Interval29Model
getParameters() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.HKY85Model
getParameters() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.Kimura80Model
getParameters() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel
getPlainMessage() - Method in exception calhoun.util.CheckException
  Gets the plain message unembellished with stack traces and causes.
getPrev() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
getPwmGeometry() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
getQuadraticRegularization() - Method in class calhoun.analysis.crf.solver.StandardOptimizer
getQuality() - Method in interface calhoun.seq.FastaSequence
  Returns the quality scores for this sequence.
getQuality() - Method in class calhoun.seq.SimpleFastaSequence
getQuick(int, int) - Method in class calhoun.util.DenseBooleanMatrix2D
getQuick(int, int) - Method in class calhoun.util.DenseIntMatrix2D
getRateMatrix() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel
getRegions() - Method in class calhoun.util.RangeMap
getRegions(boolean) - Method in class calhoun.util.RangeMap
  Returns a list of Interval objects that contain overlapping elements.
getResultHandler() - Method in class calhoun.analysis.crf.io.OutputHandlerWriter
  gets the result handler which will be used to handle the output sequence
getRowCount() - Method in class calhoun.analysis.crf.executables.viewer.ViterbiTableModel
getScore() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
  gets the local similarity score function used to score each position in every path.
getScoreAlphaFile() - Method in class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
getSecondPass() - Method in class calhoun.analysis.crf.solver.TwoPassOptimizer
getSeededOptimizer() - Method in class calhoun.analysis.crf.solver.SeededOptimizer
getSeedModel() - Method in class calhoun.analysis.crf.solver.SeededOptimizer
getSequence() - Method in class calhoun.analysis.crf.io.FastaInput
getSequence() - Method in interface calhoun.seq.FastaSequence
  Returns the entire sequence.
getSequence(int, int) - Method in interface calhoun.seq.FastaSequence
  Returns a portions of the sequence.
getSequence() - Method in class calhoun.seq.SimpleFastaSequence
getSequence(int, int) - Method in class calhoun.seq.SimpleFastaSequence
getSequenceFeatureSums() - Method in interface calhoun.analysis.crf.solver.CacheProcessor
getSequenceFeatureSums() - Method in class calhoun.analysis.crf.solver.CacheProcessorBasic
getShortArrayProperty(String, short[]) - Method in class calhoun.util.TypedProperties
getSize() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
getSize() - Method in interface calhoun.seq.KmerHasher.CharacterHash
getSolverSetup() - Method in interface calhoun.analysis.crf.solver.CacheProcessor
getSolverSetup() - Method in class calhoun.analysis.crf.solver.CacheProcessorBasic
getSpeciesNames() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
getSpeciesSet() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree
getStart() - Method in class calhoun.util.RangeMap
  Returns the start of the first non-empty interval.
getStarts() - Method in class calhoun.analysis.crf.solver.FixedWeightOptimizer
  gets the fixed weights that will be used in place of an optimization.
getStarts() - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
getStarts() - Method in class calhoun.analysis.crf.solver.StandardOptimizer
getStateIndex(String) - Method in class calhoun.analysis.crf.BeanModel
getStateIndex(String) - Method in interface calhoun.analysis.crf.ModelManager
  looks up a hidden state's index given it's human readable name.
getStateName(int) - Method in class calhoun.analysis.crf.BeanModel
getStateName(int) - Method in class calhoun.analysis.crf.Conrad
  looks up the name of a state given it's index.
getStateName(int) - Method in interface calhoun.analysis.crf.ModelManager
  looks up the human readable name of a hidden state given it's index.
getStates() - Method in class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature.MarkovHistory
getStepSize() - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
getStop() - Method in class calhoun.util.RangeMap
  Returns the end of the last interval
getString() - Method in class calhoun.analysis.crf.io.InputSequenceCharacter
  returns the input sequence as a string
getTableCellRendererComponent(JTable, Object, boolean, boolean, int, int) - Method in class calhoun.analysis.crf.executables.viewer.ViterbiTableModel.ViterbiCellRenderer
getTN() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
getTo() - Method in class calhoun.analysis.crf.BeanModel.Edge
getTotalSize() - Method in class calhoun.analysis.crf.solver.RecyclingBuffer
getTP() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
getTrainingComponent(String) - Method in class calhoun.analysis.crf.io.TrainingSequence
  returns a new TrainingSequence created by taking a single component of the input sequence and pairing it with the hidden states for this Training Sequence.
getTrainingFile() - Method in class calhoun.analysis.crf.solver.CacheProcessorBasic
getTrainingTime() - Method in class calhoun.analysis.crf.Conrad
  returns the the total number of seconds used in training.
getTransition() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
getTree() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
getTree() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence.MultipleAlignmentColumn
  returns the tree for this alignment
getUnchangedObjective() - Method in class calhoun.analysis.crf.solver.StandardOptimizer
getUniqueHash() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence.MultipleAlignmentColumn
  returns a hash value for the characters in this column
getValueAt(int, int) - Method in class calhoun.analysis.crf.executables.viewer.ViterbiTableModel
getViterbiScores() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
getViterbiScores() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
getWeights() - Method in class calhoun.analysis.crf.Conrad
  returns the feature weights.
getX(int) - Method in interface calhoun.analysis.crf.io.InputSequence
  retrieves the input value at a position in the input sequence.
getX(int) - Method in class calhoun.analysis.crf.io.InputSequenceBoolean
getX(int) - Method in class calhoun.analysis.crf.io.InputSequenceCharacter
getX(int) - Method in class calhoun.analysis.crf.io.InputSequenceComposite
getX(int) - Method in class calhoun.analysis.crf.io.InputSequenceInt
getX(int) - Method in class calhoun.analysis.crf.io.InputSequenceObject
getX(int) - Method in class calhoun.analysis.crf.io.IntervalInputSequence
getX(int) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
getX(int) - Method in class calhoun.analysis.crf.io.NameInputSequence
getX(int) - Method in class calhoun.analysis.crf.io.TrainingSequence
  gets the value of the underlying input sequence at a particular position
getY() - Method in class calhoun.analysis.crf.io.TrainingSequence
  gets the vector of hidden state indices
getY(int) - Method in class calhoun.analysis.crf.io.TrainingSequence
  gets the hidden state index at a particular position
GTFInputInterval13 - Class in calhoun.analysis.crf.io
GTFInputInterval13() - Constructor for class calhoun.analysis.crf.io.GTFInputInterval13
GTFInputInterval29 - Class in calhoun.analysis.crf.io
GTFInputInterval29() - Constructor for class calhoun.analysis.crf.io.GTFInputInterval29
GTFWriterTest - Class in calhoun.analysis.crf.test
GTFWriterTest() - Constructor for class calhoun.analysis.crf.test.GTFWriterTest

## H

hasEntry(int, int) - Method in class calhoun.util.RangeMap
  Returns true if the map has an entry in the specfied range.
hash(char) - Method in interface calhoun.seq.KmerHasher.CharacterHash
hash(String, int) - Method in class calhoun.seq.KmerHasher
  Computes hash given a 0-based position on the string.
hash(char[]) - Method in class calhoun.seq.KmerHasher
  Computes a hash given a character array.
hash(char[], int) - Method in class calhoun.seq.KmerHasher
  Computes a hash given a character array.
hash(char) - Method in class calhoun.seq.KmerHasher
hashable(char) - Method in class calhoun.seq.KmerHasher
hasNext() - Method in class calhoun.analysis.crf.io.IteratorAdapterInputComponent
hasNext() - Method in class calhoun.analysis.crf.io.IteratorAdapterTrainingSequenceInput
hasNext() - Method in class calhoun.seq.FastaIterator
hasNext() - Method in class calhoun.seq.QualityIterator
hasNext() - Method in class calhoun.util.FilterIterator
hasQuality() - Method in class calhoun.seq.SimpleFastaSequence
hasSequence() - Method in class calhoun.seq.SimpleFastaSequence
HEADER_START - Static variable in class calhoun.seq.FastaIterator
hiddenStates - Variable in class calhoun.analysis.crf.CRFInference.InferenceResult
HKY85Model - Class in calhoun.analysis.crf.features.supporting.phylogenetic
HKY85Model(double[]) - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.HKY85Model
HKY85Model() - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.HKY85Model

## I

imperfect - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results
imperfect - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results
incorrect - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results
incorrect - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results
increment(InputSequence<? extends Character>, int, boolean) - Method in class calhoun.analysis.crf.features.supporting.LogProbLookup
increment(InputSequence<? extends Character>, int, boolean) - Method in class calhoun.analysis.crf.features.supporting.PWMLookup
increment(boolean, boolean) - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
incrementFN() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
incrementFP() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
incrementTN() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
incrementTP() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
index - Variable in class calhoun.analysis.crf.solver.CacheProcessor.FeatureEvaluation
IndicatorEdges - Class in calhoun.analysis.crf.features.generic
  a set of indicator features for the valid transitions in the model.
IndicatorEdges() - Constructor for class calhoun.analysis.crf.features.generic.IndicatorEdges
init() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
initStatesWithLookback(short[]) - Method in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
  Creates an array of StatePotential objects given the maximum lookback for each state.
InputComponentIO - Interface in calhoun.analysis.crf.io
  interface to read or write `InputSequence` components to or from a file.
InputHandler - Interface in calhoun.analysis.crf.io
  interface to classes that handle reading and writing of input data for the CRF.
InputHandlerBase - Class in calhoun.analysis.crf.io
  Utility class to abstract out some of the common behavior for `InputHandler`s.
InputHandlerBase() - Constructor for class calhoun.analysis.crf.io.InputHandlerBase
InputHandlerDirectory - Class in calhoun.analysis.crf.io
  an `InputHandler` used when the input is in several files within a single directory.
InputHandlerDirectory() - Constructor for class calhoun.analysis.crf.io.InputHandlerDirectory
InputHandlerFile - Class in calhoun.analysis.crf.io
  an `InputHandler` used when all of the input is in a single file.
InputHandlerFile() - Constructor for class calhoun.analysis.crf.io.InputHandlerFile
InputHandlerInterleaved - Class in calhoun.analysis.crf.io
  an `InputHandler` for handling input files that consist of multiple different sequences interleaved together in a file.
InputHandlerInterleaved() - Constructor for class calhoun.analysis.crf.io.InputHandlerInterleaved
  creates a new input handler, usually to be configured from an XML file
InputHandlerInterleaved(InterleavedInputComponent) - Constructor for class calhoun.analysis.crf.io.InputHandlerInterleaved
  creates a new input handler, containing a single `InterleavedInputComponent`
InputHandlerInterleaved(InterleavedInputComponent, boolean) - Constructor for class calhoun.analysis.crf.io.InputHandlerInterleaved
  creates a new input handler, containing a single `InterleavedInputComponent`
InputSequence<A> - Interface in calhoun.analysis.crf.io
  represents the observed inputs.
InputSequenceBoolean - Class in calhoun.analysis.crf.io
  an input sequence where the elements of the sequence are boolean values.
InputSequenceBoolean() - Constructor for class calhoun.analysis.crf.io.InputSequenceBoolean
  default constructor
InputSequenceBoolean(boolean[]) - Constructor for class calhoun.analysis.crf.io.InputSequenceBoolean
  creates an input sequence using data from this boolean array
InputSequenceCharacter - Class in calhoun.analysis.crf.io
  an input sequence where the elements of the sequence are string characters.
InputSequenceCharacter() - Constructor for class calhoun.analysis.crf.io.InputSequenceCharacter
  default constructor
InputSequenceCharacter(String) - Constructor for class calhoun.analysis.crf.io.InputSequenceCharacter
  creates an input sequence using data from this string
InputSequenceComposite - Class in calhoun.analysis.crf.io
  a composite input sequence made up of individual components.
InputSequenceComposite() - Constructor for class calhoun.analysis.crf.io.InputSequenceComposite
  default constructor.
InputSequenceComposite(Map<String, InputSequence<?>>) - Constructor for class calhoun.analysis.crf.io.InputSequenceComposite
  constructor that initializes the sequence with a set of components.
InputSequenceInt - Class in calhoun.analysis.crf.io
  an input sequence where the elements of the sequence are integer values.
InputSequenceInt() - Constructor for class calhoun.analysis.crf.io.InputSequenceInt
  default constructor
InputSequenceInt(int[]) - Constructor for class calhoun.analysis.crf.io.InputSequenceInt
  creates an input sequence using data from this int array
InputSequenceObject<T> - Class in calhoun.analysis.crf.io
  an input sequence where the elements of the sequence are objects.
InputSequenceObject() - Constructor for class calhoun.analysis.crf.io.InputSequenceObject
  default constructor
InputSequenceObject(T[]) - Constructor for class calhoun.analysis.crf.io.InputSequenceObject
  creates an input sequence using data from this Object array
insertIntoRangeMap(RangeMap) - Method in class calhoun.analysis.crf.io.IntervalInputSequence.IntervalRangeMapValue
InterleavedInputComponent - Interface in calhoun.analysis.crf.io
  an input component that can be used with the `InputHandlerInterleaved`.
InterleavedInputComponentBase - Class in calhoun.analysis.crf.io
  base class for `InterleavedInputComponent`s.
InterleavedInputComponentBase() - Constructor for class calhoun.analysis.crf.io.InterleavedInputComponentBase
Interval13BaselineTest - Class in calhoun.analysis.crf.test
Interval13BaselineTest() - Constructor for class calhoun.analysis.crf.test.Interval13BaselineTest
Interval13FeatureTest - Class in calhoun.analysis.crf.test
Interval13FeatureTest() - Constructor for class calhoun.analysis.crf.test.Interval13FeatureTest
Interval13Model - Class in calhoun.analysis.crf.features.interval13
Interval13Model() - Constructor for class calhoun.analysis.crf.features.interval13.Interval13Model
Interval13Tools - Class in calhoun.analysis.crf.features.interval13
Interval13Tools() - Constructor for class calhoun.analysis.crf.features.interval13.Interval13Tools
Interval21HiddenSequenceTranslator - Class in calhoun.analysis.crf.io
Interval21HiddenSequenceTranslator() - Constructor for class calhoun.analysis.crf.io.Interval21HiddenSequenceTranslator
Interval29BaselineTest - Class in calhoun.analysis.crf.test
Interval29BaselineTest() - Constructor for class calhoun.analysis.crf.test.Interval29BaselineTest
Interval29FeatureTest - Class in calhoun.analysis.crf.test
Interval29FeatureTest() - Constructor for class calhoun.analysis.crf.test.Interval29FeatureTest
Interval29Model - Class in calhoun.analysis.crf.features.interval29
Interval29Model() - Constructor for class calhoun.analysis.crf.features.interval29.Interval29Model
Interval29Tools - Class in calhoun.analysis.crf.features.interval29
Interval29Tools() - Constructor for class calhoun.analysis.crf.features.interval29.Interval29Tools
IntervalInput - Class in calhoun.analysis.crf.io
  an input component used to read in values that are similar for long intervals.
IntervalInput() - Constructor for class calhoun.analysis.crf.io.IntervalInput
IntervalInputSequence - Class in calhoun.analysis.crf.io
  an input sequence made up of intervals of constant valued features.
IntervalInputSequence(RangeMap, RangeMap, String, int) - Constructor for class calhoun.analysis.crf.io.IntervalInputSequence
  constructs an input sequence from the necessary data
IntervalInputSequence.IntervalPosition - Class in calhoun.analysis.crf.io
  provides interval based queries for a particular position in the input sequence for an IntervalInputSequence.
IntervalInputSequence.IntervalPosition(int) - Constructor for class calhoun.analysis.crf.io.IntervalInputSequence.IntervalPosition
  creates an IntervalPosition object for this sequence at this position.
IntervalInputSequence.IntervalRangeMapValue - Class in calhoun.analysis.crf.io
IntervalInputSequence.IntervalRangeMapValue(int, int, double) - Constructor for class calhoun.analysis.crf.io.IntervalInputSequence.IntervalRangeMapValue
IntervalPresenceFeatures - Class in calhoun.analysis.crf.features.tricycle13
IntervalPresenceFeatures() - Constructor for class calhoun.analysis.crf.features.tricycle13.IntervalPresenceFeatures
IntInput - Class in calhoun.analysis.crf.io
  reads in an input consisting of a list of ints that correspond to binary values.
IntInput() - Constructor for class calhoun.analysis.crf.io.IntInput
IntInputInterval29 - Class in calhoun.analysis.crf.io
IntInputInterval29() - Constructor for class calhoun.analysis.crf.io.IntInputInterval29
IntronLengthFeature - Class in calhoun.analysis.crf.features.tricycle13
  Learns from data an explicit length distribution for introns, and also subtracts out what it would have gotten from just the exponential distribution given by DenseWeightedEdgeFeatures.
IntronLengthFeature() - Constructor for class calhoun.analysis.crf.features.tricycle13.IntronLengthFeature
invalidate() - Method in interface calhoun.analysis.crf.FeatureList
  specifies that node, edge, or segment specified in the `evaluate` call is invalid.
invalidTransitions - Variable in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
isAllPaths() - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
isAllPaths() - Method in class calhoun.analysis.crf.solver.NoCachingCacheProcessor
  true if all paths (valid and invalid) are to be evaluated during the viterbi search.
isAllPaths() - Method in class calhoun.analysis.crf.solver.SemiMarkovViterbiNoCache
  true if all paths (valid and invalid) are to be evaluated during the viterbi search.
isAllPaths() - Method in class calhoun.analysis.crf.solver.Viterbi
  true if all paths (valid and invalid) are to be evaluated during the viterbi search.
isAppend() - Method in class calhoun.analysis.crf.io.ExtensionMapper
  returns the value of the append property.
isCellEditable(int, int) - Method in class calhoun.analysis.crf.executables.viewer.ViterbiTableModel
isFixFirstWeight() - Method in class calhoun.analysis.crf.solver.StandardOptimizer
isGzipFile(File) - Static method in class calhoun.util.FileUtil
isGzipFile(String) - Static method in class calhoun.util.FileUtil
isGzipStream(InputStream) - Static method in class calhoun.util.FileUtil
  Checks to see if the stream is in GZIP format, assuming that it is open to the start of a file or other resource.
isIgnoreInvalidTrainingData() - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
isIgnoreSemiMarkovSelfTransitions() - Method in class calhoun.analysis.crf.SemiMarkovSetup
  gets the flag indicating that self-transition edges for the semi-Markov states should be ignored.
isLocationIsLiteral() - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
  gets the meaning of the input location string.
isMultipleFeatures() - Method in class calhoun.analysis.crf.features.interval13.PhylogeneticLogprobInterval13
isMultipleFeatures() - Method in class calhoun.analysis.crf.features.interval13.PWMInterval13
isMultipleFeatures() - Method in class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13Base
  if true, a separate feature index is used for each state, creating 13 weights instead of 1.
isMultipleFeatures() - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
isMultipleFeatures() - Method in class calhoun.analysis.crf.features.interval29.PWMInterval29
isMultipleFeatures() - Method in class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29Base
  if true, a separate feature index is used for each state, creating 21 weights instead of 1.
isMultipleFeatures() - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
isNoIntergenic() - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
isRequireConvergence() - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
isRequireConvergence() - Method in class calhoun.analysis.crf.solver.StandardOptimizer
isRollingMatch(String, String) - Static method in class calhoun.seq.RepeatedSubsequence
  Test if infinite repetitions of a and b can be aligned
isTieFlag() - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
isValid() - Method in interface calhoun.analysis.crf.FeatureList
  checks if the current node, edge, or segment is valid.
isWriteTrainingData() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
isWriteTrainingData() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
IteratorAdapterInputComponent - Class in calhoun.analysis.crf.io
  utility adapter class for creating an iterator of input components from an `InputSequenceComposite` iterator.
IteratorAdapterInputComponent(Iterator<? extends InputSequence<?>>) - Constructor for class calhoun.analysis.crf.io.IteratorAdapterInputComponent
  constructs an iterator that separates out the input components of the parent iterator
IteratorAdapterTrainingSequenceInput<T> - Class in calhoun.analysis.crf.io
  utility class to convert an iterator over training sequences into an iterator over the underlying input sequences
IteratorAdapterTrainingSequenceInput(Iterator<? extends TrainingSequence<T>>) - Constructor for class calhoun.analysis.crf.io.IteratorAdapterTrainingSequenceInput
  constructs a new iterator which will extract the input sequence from the training sequences

## K

Kimura80Model - Class in calhoun.analysis.crf.features.supporting.phylogenetic
Kimura80Model(double[]) - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.Kimura80Model
Kimura80Model() - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.Kimura80Model
KmerFeatures - Class in calhoun.analysis.crf.features.tricycle13
  trains on the data and then evaluates to P(state | label) for given Kmers.
KmerFeatures(KmerFeatures.Cardinality) - Constructor for class calhoun.analysis.crf.features.tricycle13.KmerFeatures
KmerFeatures() - Constructor for class calhoun.analysis.crf.features.tricycle13.KmerFeatures
KmerFeatures(List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.KmerFeatures
KmerFeatures(List<int[]>, KmerFeatures.Cardinality) - Constructor for class calhoun.analysis.crf.features.tricycle13.KmerFeatures
KmerFeatures.Cardinality - Enum in calhoun.analysis.crf.features.tricycle13
KmerHasher - Class in calhoun.seq
  Class for computing kmer hashes.
KmerHasher(KmerHasher.CharacterHash, int) - Constructor for class calhoun.seq.KmerHasher
  Creates a hash from a given character hash and length.
KmerHasher.CharacterHash - Interface in calhoun.seq
KmerHasherTest - Class in calhoun.seq.test
KmerHasherTest() - Constructor for class calhoun.seq.test.KmerHasherTest
kmerName(int) - Method in class calhoun.analysis.crf.features.tricycle13.KmerFeatures
  Returns a string representation of a given kmer definition

## L

l - Variable in class calhoun.analysis.crf.features.supporting.phylogenetic.BinaryTreeNode
L1Distance(double[], double[]) - Static method in class calhoun.analysis.crf.statistics.BasicStats
LBFGSTest - Class in calhoun.analysis.crf.test
LBFGSTest() - Constructor for class calhoun.analysis.crf.test.LBFGSTest
leftPad - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryEntry
length() - Method in interface calhoun.analysis.crf.io.InputSequence
  Returns the length of this sequence
length() - Method in class calhoun.analysis.crf.io.InputSequenceBoolean
length() - Method in class calhoun.analysis.crf.io.InputSequenceCharacter
length() - Method in class calhoun.analysis.crf.io.InputSequenceComposite
length() - Method in class calhoun.analysis.crf.io.InputSequenceInt
length() - Method in class calhoun.analysis.crf.io.InputSequenceObject
length() - Method in class calhoun.analysis.crf.io.IntervalInputSequence
length() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
length() - Method in class calhoun.analysis.crf.io.NameInputSequence
length() - Method in class calhoun.analysis.crf.io.TrainingSequence
  gets the length of the input and training sequences
length - Variable in class calhoun.analysis.crf.solver.RecyclingBuffer
LETTERS - Static variable in class calhoun.seq.KmerHasher
  Character hash function to use with any letters.
lgamma(double, double, double) - Static method in class calhoun.analysis.crf.statistics.GammaDistribution
listComponents() - Method in interface calhoun.analysis.crf.io.InputSequence
  For input sequences that are a composite of several different input objects, returns a list of the names of the components in this input sequence.
listComponents() - Method in class calhoun.analysis.crf.io.InputSequenceBoolean
listComponents() - Method in class calhoun.analysis.crf.io.InputSequenceCharacter
listComponents() - Method in class calhoun.analysis.crf.io.InputSequenceComposite
listComponents() - Method in class calhoun.analysis.crf.io.InputSequenceInt
listComponents() - Method in class calhoun.analysis.crf.io.InputSequenceObject
listComponents() - Method in class calhoun.analysis.crf.io.IntervalInputSequence
listComponents() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
listComponents() - Method in class calhoun.analysis.crf.io.NameInputSequence
listComponents() - Method in class calhoun.analysis.crf.io.TrainingSequence
lm - Variable in class calhoun.analysis.crf.features.supporting.phylogenetic.BinaryTreeNode
ln - Static variable in class calhoun.util.ColtUtil
loadSequence(BufferedReader) - Method in class calhoun.seq.FastaIterator.ReaderSequence
LocalPathSimilarityScore - Interface in calhoun.analysis.crf
  interface for local scoring functions used by the local score gradient functions.
lockFile(RandomAccessFile) - Static method in class calhoun.util.FileUtil
  Locks a file.
lockFile(FileOutputStream) - Static method in class calhoun.util.FileUtil
  Locks a file.
logEvaluate(double) - Method in class calhoun.analysis.crf.statistics.MixtureOfGammas
LogFiles - Class in calhoun.analysis.crf.solver
LogFiles() - Constructor for class calhoun.analysis.crf.solver.LogFiles
loglikelihoodIncrement(double, double) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
loglikelihoodIncrement(double, double) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
logprob(int, InputSequence<? extends Character>, int) - Method in class calhoun.analysis.crf.features.supporting.MarkovPredictorLogprob
logprob(MultipleAlignmentInputSequence.MultipleAlignmentColumn, boolean) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.EvolutionaryModel
LogProbLookup - Class in calhoun.analysis.crf.features.supporting
LogProbLookup(int, double) - Constructor for class calhoun.analysis.crf.features.supporting.LogProbLookup
LogprobLookupTest - Class in calhoun.analysis.crf.test
  Tests that CRF is working with valid probabilities - the sum of all possible labelings is 1.
LogprobLookupTest() - Constructor for class calhoun.analysis.crf.test.LogprobLookupTest
logprobRC(MultipleAlignmentInputSequence.MultipleAlignmentColumn, boolean) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.EvolutionaryModel
longest_branch_length() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree
longestSeq - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
lookback - Variable in class calhoun.analysis.crf.solver.CacheProcessor.LengthFeatureEvaluation
LookbackBuffer - Class in calhoun.analysis.crf.solver
  This object holds information about previous positions during the computation of betas and expectations.
LookbackBuffer(int, int) - Constructor for class calhoun.analysis.crf.solver.LookbackBuffer
lookup(InputSequence<? extends Character>, int, boolean) - Method in class calhoun.analysis.crf.features.supporting.LogProbLookup
lookup(InputSequence<? extends Character>, int, boolean) - Method in class calhoun.analysis.crf.features.supporting.PWMLookup

## M

main(String[]) - Static method in class calhoun.analysis.crf.Conrad
  Command line entry point for running CRFs.
main(String[]) - Static method in class calhoun.analysis.crf.executables.viewer.ViterbiViewerApp
main(String[]) - Static method in class calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModelTest
makeTempCopy(File) - Static method in class calhoun.util.FileUtil
mapFilename(File) - Method in class calhoun.analysis.crf.io.ExtensionMapper
  Maps the source file name to a new name by altering the file extension.
mapFilename(File) - Method in interface calhoun.analysis.crf.io.FilenameMapper
  maps a filename from the source to a destination.
marginalsFile - Variable in class calhoun.analysis.crf.solver.LogFiles
marginalsWriter - Variable in class calhoun.analysis.crf.solver.LogFiles
MarkovPredictorLogprob - Class in calhoun.analysis.crf.features.supporting
MarkovPredictorLogprob(List<int[]>) - Constructor for class calhoun.analysis.crf.features.supporting.MarkovPredictorLogprob
  History is a list that contains one entry for each state.
MatrixOperationsTest - Class in calhoun.analysis.crf.test
MatrixOperationsTest() - Constructor for class calhoun.analysis.crf.test.MatrixOperationsTest
max(double[]) - Static method in class calhoun.analysis.crf.statistics.BasicStats
MaxentMotifFeatures - Class in calhoun.analysis.crf.features.tricycle13
MaxentMotifFeatures(List<int[]>, List<int[]>, List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.MaxentMotifFeatures
MaxentMotifFeatures(List<int[]>, List<int[]>, List<int[]>, List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.MaxentMotifFeatures
MaxentMotifModel - Class in calhoun.analysis.crf.features.supporting
MaxentMotifModel() - Constructor for class calhoun.analysis.crf.features.supporting.MaxentMotifModel
MaxentMotifModelTest - Class in calhoun.analysis.crf.test
MaxentMotifModelTest() - Constructor for class calhoun.analysis.crf.test.MaxentMotifModelTest
MaximumExpectedAccuracySemiMarkovGradient - Class in calhoun.analysis.crf.solver
  computes an objective function which is the expected value of a local path similarity score on a semi-Markov model.
MaximumExpectedAccuracySemiMarkovGradient() - Constructor for class calhoun.analysis.crf.solver.MaximumExpectedAccuracySemiMarkovGradient
MaximumExpectedAccuracyTest - Class in calhoun.analysis.crf.test
MaximumExpectedAccuracyTest() - Constructor for class calhoun.analysis.crf.test.MaximumExpectedAccuracyTest
MaximumLikelihoodGradient - Class in calhoun.analysis.crf.solver
  computes the likelihood of the true path for a Markov CRF.
MaximumLikelihoodGradient() - Constructor for class calhoun.analysis.crf.solver.MaximumLikelihoodGradient
MaximumLikelihoodSemiMarkovGradient - Class in calhoun.analysis.crf.solver
  computes the likelihood of the true path for a semi-Markov CRF.
MaximumLikelihoodSemiMarkovGradient() - Constructor for class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
maxInColumn(DoubleMatrix2D, int) - Static method in class calhoun.util.ColtUtil
  Returns the row with the largest value in the given column
maxInColumn(double[], int, int) - Static method in class calhoun.util.ColtUtil
maxLookback - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
maxStateLengths - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
maxValueInColumn(double[], int, int) - Static method in class calhoun.util.ColtUtil
meanDoubleArray(double[]) - Static method in class calhoun.analysis.crf.statistics.BasicStats
medianDoubleArray(double[]) - Static method in class calhoun.analysis.crf.statistics.BasicStats
mi - Variable in class calhoun.analysis.crf.solver.LookbackBuffer
MixtureOfGammas - Class in calhoun.analysis.crf.statistics
MixtureOfGammas(double, double, double, double, double) - Constructor for class calhoun.analysis.crf.statistics.MixtureOfGammas
MixtureOfGammas(double[]) - Constructor for class calhoun.analysis.crf.statistics.MixtureOfGammas
MixtureOfGammas(double[], boolean) - Constructor for class calhoun.analysis.crf.statistics.MixtureOfGammas
mleg(double, double) - Static method in class calhoun.analysis.crf.statistics.GammaDistribution
ModelManager - Interface in calhoun.analysis.crf
  overall itnerface for an entire model.
MultipleAlignmentInput - Class in calhoun.analysis.crf.io
  an input component that reads in multiple alignment sequences.
MultipleAlignmentInput() - Constructor for class calhoun.analysis.crf.io.MultipleAlignmentInput
MultipleAlignmentInputSequence - Class in calhoun.analysis.crf.io
  an input sequence where each element represents one column of a multiple alignment.
MultipleAlignmentInputSequence(String, RootedBinaryPhylogeneticTree) - Constructor for class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
MultipleAlignmentInputSequence(List<String>, List<String>, String, RootedBinaryPhylogeneticTree) - Constructor for class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
  constructs a multiple alignment input sequence.
MultipleAlignmentInputSequence.MultipleAlignmentColumn - Class in calhoun.analysis.crf.io
  represents the column of the alignment at a given position on the reference sequence
MultipleAlignmentInputSequence.MultipleAlignmentColumn(int) - Constructor for class calhoun.analysis.crf.io.MultipleAlignmentInputSequence.MultipleAlignmentColumn
  constructs the column at this position
MultipleSequenceTest - Class in calhoun.analysis.crf.test
MultipleSequenceTest() - Constructor for class calhoun.analysis.crf.test.MultipleSequenceTest

## N

n - Variable in class calhoun.analysis.crf.features.supporting.phylogenetic.BinaryTreeNode
NameInput - Class in calhoun.analysis.crf.io
  an input component that reads in a name for each sequence.
NameInput() - Constructor for class calhoun.analysis.crf.io.NameInput
NameInputSequence - Class in calhoun.analysis.crf.io
  input sequence that captures the 'name' of a sequence.
NameInputSequence() - Constructor for class calhoun.analysis.crf.io.NameInputSequence
  default constructor
NameInputSequence(String) - Constructor for class calhoun.analysis.crf.io.NameInputSequence
  constructors an input sequence using this name
nEvals - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseCachingDetails
newDocument() - Static method in class calhoun.util.XmlUtil
newElement(String) - Static method in class calhoun.util.XmlUtil
newick() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree
NewickTreeManipulationTest - Class in calhoun.analysis.crf.test
NewickTreeManipulationTest() - Constructor for class calhoun.analysis.crf.test.NewickTreeManipulationTest
next() - Method in class calhoun.analysis.crf.io.IteratorAdapterInputComponent
next() - Method in class calhoun.analysis.crf.io.IteratorAdapterTrainingSequenceInput
next() - Method in class calhoun.seq.FastaIterator
next() - Method in class calhoun.seq.QualityIterator
  Returns the next set of qualities in this file.
next() - Method in class calhoun.util.FilterIterator
nextQuality() - Method in class calhoun.seq.QualityIterator
  Returns the next set of qualities in this file.
nFeatures - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
NoCachingCacheProcessor - Class in calhoun.analysis.crf.solver
  a dummy cache processor that fulfills the interface but doesn't cache.
NoCachingCacheProcessor() - Constructor for class calhoun.analysis.crf.solver.NoCachingCacheProcessor
nodeEval - Variable in class calhoun.analysis.crf.solver.CacheProcessor.LengthFeatureEvaluation
nodeMarginalFile - Variable in class calhoun.analysis.crf.solver.LogFiles
nodeMarginalWriter - Variable in class calhoun.analysis.crf.solver.LogFiles
NonGradientTest - Class in calhoun.analysis.crf.test
NonGradientTest() - Constructor for class calhoun.analysis.crf.test.NonGradientTest
norm(double[]) - Static method in class calhoun.util.ColtUtil
NORM_FACTOR - Static variable in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
NORM_MAX - Static variable in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
NORM_MIN - Static variable in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
normalizeWeights(float[]) - Static method in class calhoun.util.Util
nPotentials - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
nSeqs - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
nSpecies() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree
nStates - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
nTables - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryCachingDetails
nTables - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseCachingDetails
nTransitions - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
nucleotide(int) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence.MultipleAlignmentColumn
  returns the value of this position in the alignment for the given species
NucleotideSubstitutionModel - Class in calhoun.analysis.crf.features.supporting.phylogenetic
NucleotideSubstitutionModel() - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel
NucleotideSubstitutionModelTest - Class in calhoun.analysis.crf.features.supporting.phylogenetic
NucleotideSubstitutionModelTest() - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModelTest
numClusters() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.ColumnConditionalLogProbability
numNodes() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder
numSpecies() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder
numSpecies() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence.MultipleAlignmentColumn
  returns the number of species in the alignment
numSpecies() - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
numSteps() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder

## O

open() - Method in class calhoun.analysis.crf.solver.LogFiles
openInputStream(Class, String) - Static method in class calhoun.util.ResourceLoader
  Opens an InputStream by trying each of the defined ResourceFinders.
openResource(Class, String) - Method in interface calhoun.util.ResourceLoader.ResourceFinder
openTextResource(Class, String) - Static method in class calhoun.util.ResourceLoader
optimize(ModelManager, List<? extends TrainingSequence<?>>) - Method in interface calhoun.analysis.crf.CRFTraining
  find the set of weights which maximizes the value of the objective function.
optimize(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.FixedWeightOptimizer
optimize(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.SeededOptimizer
optimize(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
optimize(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
optimize(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.TwoPassOptimizer
orderedPotentials - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
outputComplete() - Method in interface calhoun.analysis.crf.io.OutputHandler
  indicates the writing of output is complete.
outputComplete() - Method in class calhoun.analysis.crf.io.OutputHandlerComposite
outputComplete() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
outputComplete() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
outputComplete() - Method in class calhoun.analysis.crf.io.OutputHandlerWriter
OutputHandler - Interface in calhoun.analysis.crf.io
  handles outputting of results from predictions.
OutputHandlerComposite - Class in calhoun.analysis.crf.io
  an output handler that allows multiple output handlers to be configured.
OutputHandlerComposite() - Constructor for class calhoun.analysis.crf.io.OutputHandlerComposite
OutputHandlerGeneCallPredict - Class in calhoun.analysis.crf.io
  A legacy output handler that computes basic stats, gene calling statsm and then writes out a GTF file.
OutputHandlerGeneCallPredict() - Constructor for class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
  default constructor.
OutputHandlerGeneCallPredict(ModelManager, InputHandler) - Constructor for class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
  creates an output handler using this model and input handler
OutputHandlerGeneCallPredict.Results - Class in calhoun.analysis.crf.io
OutputHandlerGeneCallPredict.Results() - Constructor for class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results
OutputHandlerGeneCallStats - Class in calhoun.analysis.crf.io
  A legacy output handler that computes basic stats, gene calling statsm and then writes out a GTF file.
OutputHandlerGeneCallStats() - Constructor for class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
  default constructor.
OutputHandlerGeneCallStats(ModelManager, InputHandler) - Constructor for class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
  creates an output handler using this model and input handler
OutputHandlerGeneCallStats.Results - Class in calhoun.analysis.crf.io
OutputHandlerGeneCallStats.Results() - Constructor for class calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results
OutputHandlerGeneCallStatsInterval29 - Class in calhoun.analysis.crf.io
OutputHandlerGeneCallStatsInterval29() - Constructor for class calhoun.analysis.crf.io.OutputHandlerGeneCallStatsInterval29
OutputHandlerWriter - Class in calhoun.analysis.crf.io
  writes output to a file using a `TrainingSequenceIO`.
OutputHandlerWriter() - Constructor for class calhoun.analysis.crf.io.OutputHandlerWriter

## P

p - Variable in class calhoun.analysis.crf.features.supporting.phylogenetic.BinaryTreeNode
parseFile(String) - Static method in class calhoun.util.XmlUtil
  Creates a dom4j Document from a file.
parseString(String) - Static method in class calhoun.util.XmlUtil
  Creates a dom4j Document from a text string.
perfect - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict.Results
perfect - Variable in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats.Results
PfamGenic - Class in calhoun.analysis.crf.features.tricycle13
PfamGenic() - Constructor for class calhoun.analysis.crf.features.tricycle13.PfamGenic
PfamPhase - Class in calhoun.analysis.crf.features.tricycle13
PfamPhase() - Constructor for class calhoun.analysis.crf.features.tricycle13.PfamPhase
PhylogeneticLogprobInterval13 - Class in calhoun.analysis.crf.features.interval13
PhylogeneticLogprobInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.PhylogeneticLogprobInterval13
PhylogeneticTreeFelsensteinOrder - Class in calhoun.analysis.crf.features.supporting.phylogenetic
PhylogeneticTreeFelsensteinOrder() - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder
PhylogeneticTreeFelsensteinOrder(int[], int[], double[], double[]) - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder
pn() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
  Predicted Negatives
pos - Variable in class calhoun.analysis.crf.solver.LookbackBuffer
PositionWeightMatrixFeatures - Class in calhoun.analysis.crf.features.tricycle13
PositionWeightMatrixFeatures() - Constructor for class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
PositionWeightMatrixFeatures(List<int[]>, List<int[]>, List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
PositionWeightMatrixFeatures(List<int[]>, List<int[]>, List<int[]>, List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
PositionWeightMatrixFeatures.Geometry - Class in calhoun.analysis.crf.features.tricycle13
PositionWeightMatrixFeatures.Geometry() - Constructor for class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
potential - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryEntry
potential - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseCachingDetails
potentials - Variable in class calhoun.analysis.crf.solver.CacheProcessor.StatePotentials
pp() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
  Predicted Positives
predict(InputSequence) - Method in class calhoun.analysis.crf.Conrad
  preforms inference on the input sequence and determines the best labeling for the sequence using the configured inference algorithm.
predict(ModelManager, InputSequence<?>, double[]) - Method in interface calhoun.analysis.crf.CRFInference
  Return the labelling that maximizes the conditional probability P(y|x).
predict(ModelManager, InputSequence<?>, double[]) - Method in class calhoun.analysis.crf.solver.SemiMarkovViterbi
predict(ModelManager, InputSequence<?>, double[]) - Method in class calhoun.analysis.crf.solver.SemiMarkovViterbiNoCache
predict(ModelManager, InputSequence<?>, double[]) - Method in class calhoun.analysis.crf.solver.Viterbi
PredictedActualBinaryContingencyTable - Class in calhoun.analysis.crf.statistics
PredictedActualBinaryContingencyTable() - Constructor for class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
PredictedActualBinaryContingencyTableTest - Class in calhoun.analysis.crf.test
PredictedActualBinaryContingencyTableTest() - Constructor for class calhoun.analysis.crf.test.PredictedActualBinaryContingencyTableTest
prepareData(String) - Static method in class calhoun.analysis.crf.io.IntInput
  Convenience function for creating training sequences in test data.
prepareData(String) - Static method in class calhoun.analysis.crf.io.StringInput
  Convenience function for creating training sequences in test data.
prettyPrint(Document) - Static method in class calhoun.util.XmlUtil
  Pretty prints a document and returns the result as a String
prettyPrint(Node) - Static method in class calhoun.util.XmlUtil
  Pretty prints a dom4j Node and returns the result as a String
prettyPrint(Document, OutputStream) - Static method in class calhoun.util.XmlUtil
  Pretty prints a document to a given OutputStream
prettyPrint(Document, String) - Static method in class calhoun.util.XmlUtil
  Pretty prints a document to a given filename
primes - Static variable in class calhoun.util.PrimeUtil
primesToAtLeastN(int) - Static method in class calhoun.util.PrimeUtil
  Returns an array of primes that includes all primes up to at least N.
PrimeUtil - Class in calhoun.util
PrimeUtil() - Constructor for class calhoun.util.PrimeUtil
print(double[], int, int) - Static method in class calhoun.util.ColtUtil
print(int[], int, int) - Static method in class calhoun.util.ColtUtil
printNorm(double, int) - Static method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
printNorm(double, int) - Static method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
printToFile(double[], int, int) - Static method in class calhoun.util.ColtUtil
printWeights() - Method in class calhoun.analysis.crf.Conrad
  Returns a formatted string listing the weights.
PWM_evolution - Class in calhoun.analysis.crf.features.tricycle13
PWM_evolution(List<int[]>, List<int[]>, List<int[]>, List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.PWM_evolution
PWM_evolution(List<int[]>, List<int[]>, List<int[]>, List<int[]>, List<int[]>) - Constructor for class calhoun.analysis.crf.features.tricycle13.PWM_evolution
PWMInterval13 - Class in calhoun.analysis.crf.features.interval13
PWMInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.PWMInterval13
PWMInterval29 - Class in calhoun.analysis.crf.features.interval29
PWMInterval29() - Constructor for class calhoun.analysis.crf.features.interval29.PWMInterval29
PWMLookup - Class in calhoun.analysis.crf.features.supporting
PWMLookup(int, int, double) - Constructor for class calhoun.analysis.crf.features.supporting.PWMLookup

## Q

QualityIterator - Class in calhoun.seq
QualityIterator(String, boolean) - Constructor for class calhoun.seq.QualityIterator
QualityIterator(String) - Constructor for class calhoun.seq.QualityIterator
QualityIterator(BufferedReader) - Constructor for class calhoun.seq.QualityIterator
QualityIterator(File, boolean) - Constructor for class calhoun.seq.QualityIterator
queryMinus() - Method in class calhoun.analysis.crf.io.IntervalInputSequence.IntervalPosition
  returns true if an input interval exists on the negative strand at this position.
queryPlus() - Method in class calhoun.analysis.crf.io.IntervalInputSequence.IntervalPosition
  returns true if an input interval exists on the positive strand at this position.

## R

r - Variable in class calhoun.analysis.crf.features.supporting.phylogenetic.BinaryTreeNode
range() - Method in class calhoun.seq.KmerHasher
RangeMap - Class in calhoun.util
  A rangeMap contains a set of intervals and maps each interval to a set of objects that exist in that interval.
RangeMap() - Constructor for class calhoun.util.RangeMap
RangeMap.Interval - Class in calhoun.util
  An interval is a convenient data structure used to return a section of a RangeMap.
RangeMap.Interval() - Constructor for class calhoun.util.RangeMap.Interval
RangeMap.Interval(int, int, Set) - Constructor for class calhoun.util.RangeMap.Interval
RangeMapExamples - Class in calhoun.analysis.crf.test
RangeMapExamples() - Constructor for class calhoun.analysis.crf.test.RangeMapExamples
read(String) - Static method in class calhoun.analysis.crf.Conrad
  read in a Conrad engine from a file.
read(BufferedReader, Map<String, InputSequence<?>>) - Method in class calhoun.analysis.crf.io.BooleanInput
read(BufferedReader, Map<String, InputSequence<?>>) - Method in interface calhoun.analysis.crf.io.InterleavedInputComponent
  Read the contents of the sequence in from a reader.
read(BufferedReader, Map<String, InputSequence<?>>) - Method in class calhoun.analysis.crf.io.IntervalInput
read(BufferedReader, Map<String, InputSequence<?>>) - Method in class calhoun.analysis.crf.io.IntInput
read(BufferedReader, Map<String, InputSequence<?>>) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInput
read(BufferedReader, Map<String, InputSequence<?>>) - Method in class calhoun.analysis.crf.io.NameInput
read(BufferedReader, Map<String, InputSequence<?>>) - Method in class calhoun.analysis.crf.io.StringInput
readDoublesFromSingleTabbedLine(String) - Static method in class calhoun.util.FileUtil
readFile(File) - Static method in class calhoun.util.FileUtil
readFile(String) - Static method in class calhoun.util.FileUtil
  Reads a files into a String.
readFileAsBytes(String) - Static method in class calhoun.util.FileUtil
readFlatFile(String) - Static method in class calhoun.util.FileUtil
readFlatFileWithComments(String) - Static method in class calhoun.util.FileUtil
readInputData(String) - Method in class calhoun.analysis.crf.io.CompositeInput.LegacyInputHandler
  Deprecated.
readInputData(String) - Method in interface calhoun.analysis.crf.io.InputHandler
  returns the input data read from the specified location.
readInputData(String) - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
readInputData(String) - Method in class calhoun.analysis.crf.io.InputHandlerFile
readInputData(String) - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
readInputSequences(String, List<Map<String, InputSequence<?>>>) - Method in class calhoun.analysis.crf.io.AlignmentTree
readInputSequences(String, List<Map<String, InputSequence<?>>>) - Method in class calhoun.analysis.crf.io.FastaAlignmentInput
readInputSequences(String, List<Map<String, InputSequence<?>>>) - Method in class calhoun.analysis.crf.io.FastaInput
readInputSequences(String, List<Map<String, InputSequence<?>>>) - Method in interface calhoun.analysis.crf.io.InputComponentIO
  reads input sequences from this location.
readInputSequences(String, List<Map<String, InputSequence<?>>>) - Method in class calhoun.analysis.crf.io.InterleavedInputComponentBase
readInputStream(InputStream) - Static method in class calhoun.util.FileUtil
readLines(String) - Static method in class calhoun.util.FileUtil
readObject(String) - Static method in class calhoun.util.FileUtil
  Read a serialized Java object from a file.
readReader(Reader) - Static method in class calhoun.util.FileUtil
readSequence(BufferedReader) - Method in class calhoun.analysis.crf.io.Interval21HiddenSequenceTranslator
readSequence(BufferedReader) - Method in class calhoun.analysis.crf.io.IntInput
readSequence(BufferedReader) - Method in class calhoun.analysis.crf.io.IntInputInterval29
readTrainingData(String) - Method in class calhoun.analysis.crf.io.CompositeInput.LegacyInputHandler
  Deprecated.
readTrainingData(String, boolean) - Method in class calhoun.analysis.crf.io.CompositeInput.LegacyInputHandler
  Deprecated.
readTrainingData(String, boolean) - Method in interface calhoun.analysis.crf.io.InputHandler
  returns the training data read from the specified location.
readTrainingData(String) - Method in interface calhoun.analysis.crf.io.InputHandler
readTrainingData(String) - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
readTrainingData(String, boolean) - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
readTrainingData(String) - Method in class calhoun.analysis.crf.io.InputHandlerFile
readTrainingData(String, boolean) - Method in class calhoun.analysis.crf.io.InputHandlerFile
readTrainingData(String) - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
readTrainingData(String, boolean) - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
readTrainingSequences(Object, List<TrainingSequence<Map<String, Object>>>) - Method in class calhoun.analysis.crf.io.AllIntergenicHiddenStateReader
readTrainingSequences(Object, List<TrainingSequence<Map<String, Object>>>) - Method in class calhoun.analysis.crf.io.GTFInputInterval13
readTrainingSequences(Object, List<TrainingSequence<Map<String, Object>>>) - Method in class calhoun.analysis.crf.io.GTFInputInterval29
readTrainingSequences(Object, List<TrainingSequence<Map<String, Object>>>) - Method in class calhoun.analysis.crf.io.IntInput
readTrainingSequences(Object, List<TrainingSequence<Map<String, Object>>>) - Method in interface calhoun.analysis.crf.io.TrainingSequenceIO
  reads training sequences from the specified location.
RealIOTest - Class in calhoun.analysis.crf.test
RealIOTest() - Constructor for class calhoun.analysis.crf.test.RealIOTest
RecyclingBuffer<T> - Class in calhoun.analysis.crf.solver
  Utility class that implements a FIFO buffer with constant time adds, removes, and accesses to any position using a circular buffer in an array.
RecyclingBuffer(T[]) - Constructor for class calhoun.analysis.crf.solver.RecyclingBuffer
RecyclingBufferTest - Class in calhoun.analysis.crf.test
RecyclingBufferTest() - Constructor for class calhoun.analysis.crf.test.RecyclingBufferTest
ref2con(int) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
ReferenceBasePredictorInterval13 - Class in calhoun.analysis.crf.features.interval13
ReferenceBasePredictorInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13
ReferenceBasePredictorInterval13Base - Class in calhoun.analysis.crf.features.interval13
ReferenceBasePredictorInterval13Base() - Constructor for class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13Base
ReferenceBasePredictorInterval29 - Class in calhoun.analysis.crf.features.interval29
ReferenceBasePredictorInterval29() - Constructor for class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29
ReferenceBasePredictorInterval29Base - Class in calhoun.analysis.crf.features.interval29
ReferenceBasePredictorInterval29Base() - Constructor for class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29Base
ReferenceBasePredictorNodeOnlyInterval13 - Class in calhoun.analysis.crf.features.interval13
ReferenceBasePredictorNodeOnlyInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorNodeOnlyInterval13
ReferenceBasePredictorNodeOnlyInterval29 - Class in calhoun.analysis.crf.features.interval29
ReferenceBasePredictorNodeOnlyInterval29() - Constructor for class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorNodeOnlyInterval29
ReferenceBasePredictorTest - Class in calhoun.analysis.crf.test
  Tests that CRF is working with valid probabilities - the sum of all possible labelings is 1.
ReferenceBasePredictorTest() - Constructor for class calhoun.analysis.crf.test.ReferenceBasePredictorTest
ReferenceBasePredictorZeroPadInterval13 - Class in calhoun.analysis.crf.features.interval13
ReferenceBasePredictorZeroPadInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorZeroPadInterval13
ReferenceBasePredictorZeroPadInterval29 - Class in calhoun.analysis.crf.features.interval29
ReferenceBasePredictorZeroPadInterval29() - Constructor for class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorZeroPadInterval29
remove() - Method in class calhoun.analysis.crf.io.IteratorAdapterInputComponent
remove() - Method in class calhoun.analysis.crf.io.IteratorAdapterTrainingSequenceInput
remove() - Method in class calhoun.seq.FastaIterator
  Throws an UnsupportedOperationException.
remove() - Method in class calhoun.seq.QualityIterator
remove() - Method in class calhoun.util.FilterIterator
remove(Object) - Method in class calhoun.util.RangeMap
  Removes the object o from the map.
renameFile(File, File) - Static method in class calhoun.util.FileUtil
RepeatedSubsequence - Class in calhoun.seq
RepeatedSubsequence() - Constructor for class calhoun.seq.RepeatedSubsequence
RepeatedSubsequenceTest - Class in calhoun.seq.test
RepeatedSubsequenceTest() - Constructor for class calhoun.seq.test.RepeatedSubsequenceTest
ResourceLoader - Class in calhoun.util
  The ResourceLoader loads for resources by trying each of the following mechanisms: Treating the resourceID as a file name and opening it in the file system Loading a class resource with the specified resourceID Loading a system resource with the specified resourceID
ResourceLoader() - Constructor for class calhoun.util.ResourceLoader
ResourceLoader.ResourceFinder - Interface in calhoun.util
reverse(int) - Method in interface calhoun.seq.KmerHasher.CharacterHash
reverseComplement(String) - Static method in class calhoun.seq.KmerHasher
reverseShiftHash(char, int) - Method in class calhoun.seq.KmerHasher
  Updates an existing hash.
rightPad - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryEntry
rm - Variable in class calhoun.analysis.crf.features.supporting.phylogenetic.BinaryTreeNode
RootedBinaryPhylogeneticTree - Class in calhoun.analysis.crf.features.supporting.phylogenetic
RootedBinaryPhylogeneticTree(String) - Constructor for class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree
runBare() - Method in class calhoun.util.AbstractTestCase
  Overrides the default runTest to provide error logging.

## S

safeClose(Writer) - Static method in class calhoun.util.FileUtil
safeClose(Reader) - Static method in class calhoun.util.FileUtil
safeClose(OutputStream) - Static method in class calhoun.util.FileUtil
safeClose(InputStream) - Static method in class calhoun.util.FileUtil
safeClose(RandomAccessFile) - Static method in class calhoun.util.FileUtil
safeEquals(Object, Object) - Static method in class calhoun.util.Util
safeOpen(String) - Static method in class calhoun.util.FileUtil
safeRelease(FileLock) - Static method in class calhoun.util.FileUtil
safeWrite(Writer, String) - Static method in class calhoun.util.FileUtil
scalarmultiply(DoubleMatrix2D, double) - Static method in class calhoun.util.ColtUtil
scoreAlphaFile - Variable in class calhoun.analysis.crf.solver.LogFiles
scoreAlphaWriter - Variable in class calhoun.analysis.crf.solver.LogFiles
SeededOptimizer - Class in calhoun.analysis.crf.solver
  an optimizer that uses the weights from another model as the seed for a new optimization.
SeededOptimizer() - Constructor for class calhoun.analysis.crf.solver.SeededOptimizer
selfTransitions - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
SemiMarkovSetup - Class in calhoun.analysis.crf
  holds additional configuration information used in semi-Markov CRFs.
SemiMarkovSetup() - Constructor for class calhoun.analysis.crf.SemiMarkovSetup
  default constructor used by Spring during automatic configuration
SemiMarkovSetup(short[]) - Constructor for class calhoun.analysis.crf.SemiMarkovSetup
  constructs using this set of maximum lengths.
SemiMarkovSetup(short[], boolean) - Constructor for class calhoun.analysis.crf.SemiMarkovSetup
  constructs using this set of maximum lengths and value for the ignore flag.
SemiMarkovSetup(short[], short[], boolean) - Constructor for class calhoun.analysis.crf.SemiMarkovSetup
  constructs will all parameters.
SemiMarkovTest - Class in calhoun.analysis.crf.test
SemiMarkovTest() - Constructor for class calhoun.analysis.crf.test.SemiMarkovTest
SemiMarkovViterbi - Class in calhoun.analysis.crf.solver
  viterbi algorithm for semi-Markov CRFs.
SemiMarkovViterbi() - Constructor for class calhoun.analysis.crf.solver.SemiMarkovViterbi
SemiMarkovViterbiNoCache - Class in calhoun.analysis.crf.solver
  viterbi algorithm for semi-Markov CRFs.
SemiMarkovViterbiNoCache() - Constructor for class calhoun.analysis.crf.solver.SemiMarkovViterbiNoCache
sensitivity() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
  Sensitivity is TP/(TP+FN) is the fraction of actual events that are predicted.
seqOffsets - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
SequenceConverter - Class in calhoun.analysis.crf.io
  used for converting between different encodings of gene structure in a hidden sequence.
SequenceConverter() - Constructor for class calhoun.analysis.crf.io.SequenceConverter
SequenceConverterTest - Class in calhoun.analysis.crf.test
SequenceConverterTest() - Constructor for class calhoun.analysis.crf.test.SequenceConverterTest
serialVersionUID - Static variable in class calhoun.util.RangeMap
set(int, T) - Method in class calhoun.analysis.crf.solver.RecyclingBuffer
set(int, int, int, int) - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
set(int, int, int) - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
setAllPaths(boolean) - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
setAllPaths(boolean) - Method in class calhoun.analysis.crf.solver.NoCachingCacheProcessor
  sets whether all paths (valid and invalid) are to be evaluated during the viterbi search.
setAllPaths(boolean) - Method in class calhoun.analysis.crf.solver.SemiMarkovViterbiNoCache
  sets whether all paths (valid and invalid) are to be evaluated during the viterbi search.
setAllPaths(boolean) - Method in class calhoun.analysis.crf.solver.Viterbi
  sets whether all paths (valid and invalid) are to be evaluated during the viterbi search.
setAlphaFile(String) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
setAlphaFile(String) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
setAlphaLengthFile(String) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
setAlphaLengthFile(String) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
setAppend(boolean) - Method in class calhoun.analysis.crf.io.ExtensionMapper
  set the value of the append property.
setBackPointers(int[]) - Method in class calhoun.analysis.crf.solver.Viterbi
setBestScore(double[]) - Method in class calhoun.analysis.crf.solver.Viterbi
setBetaLengthFile(String) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
setBetaLengthFile(String) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
setCacheProcessor(CacheProcessor) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodGradient
  sets the cache processor used to access feature evaluations
setCacheProcessor(CacheProcessor) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
  sets the cache processor used to access feature evaluations
setCacheProcessor(CacheProcessor) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
  sets the cache processor used to access feature evaluations
setCacheProcessor(CacheProcessor) - Method in class calhoun.analysis.crf.solver.SemiMarkovViterbi
  sets the cache processor used to access feature evaluations
setClusters(List<List<BeanModel.Node>>) - Method in class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures
setCommentLineIndicator(String) - Method in class calhoun.util.FileDiff
  Sets the comment line indicator string.
setComponent(String) - Method in class calhoun.analysis.crf.io.AlignmentTree
setComponent(String) - Method in class calhoun.analysis.crf.io.FastaAlignmentInput
setComponentFeatures(List<FeatureManager>) - Method in class calhoun.analysis.crf.CompositeFeatureManager
setComponents(List<CompositeInput.InputComponent>) - Method in class calhoun.analysis.crf.io.CompositeInput
  Deprecated.
setComponents(List<InterleavedInputComponent>) - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
  sets the current set of input components configured for this input handler.
setCurrent(BeanModel.Node) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
setDebugLevel(int) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
setEdges(List<BeanModel.Edge>) - Method in class calhoun.analysis.crf.BeanModel
  sets the list of legal state transitions in this model.
setEpsForConvergence(double) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
setExonExponential(boolean) - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
setExonExponential(boolean) - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
setExpectedProductFile(String) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
setExpectFile(String) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
setExpectFile(String) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
setExpectLengthFile(String) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
setExpectLengthFile(String) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
setExtension(String) - Method in class calhoun.analysis.crf.io.ExtensionMapper
  sets the extension.
setFilename(String) - Method in class calhoun.analysis.crf.io.CompositeInput.InputComponent
  Deprecated.
setFilenameMapper(FilenameMapper) - Method in class calhoun.analysis.crf.io.OutputHandlerWriter
  sets the mapper which will be used to generate the output filename based on the output location.
setFirstPass(CRFTraining) - Method in class calhoun.analysis.crf.solver.TwoPassOptimizer
setFixFirstWeight(boolean) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
setForceExponential(boolean) - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
setForceExponential(boolean) - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
setFrom(BeanModel.Node) - Method in class calhoun.analysis.crf.BeanModel.Edge
setHandlers(List<OutputHandler>) - Method in class calhoun.analysis.crf.io.OutputHandlerComposite
  sets the list of output handlers
setHeader(String) - Method in class calhoun.analysis.crf.io.FastaInput
setHeader(String) - Method in class calhoun.seq.SimpleFastaSequence
setHiddenSequenceFile(String) - Method in class calhoun.analysis.crf.io.CompositeInput
  Deprecated.
setHiddenSequenceFile(String) - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
  sets the name of the hidden sequence file.
setHiddenSequenceReader(TrainingSequenceIO) - Method in class calhoun.analysis.crf.io.CompositeInput
  Deprecated.
setHiddenStateReader(TrainingSequenceIO) - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
  sets the reader used to get hidden sequences.
setHiddenStateReader(TrainingSequenceIO) - Method in class calhoun.analysis.crf.io.InputHandlerFile
  sets the reader used to get hidden sequences.
setHiddenStateReader(IntInput) - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
  sets the reader used to get hidden sequences.
setHistory(EmissionMarkovFeature.MarkovHistory) - Method in class calhoun.analysis.crf.features.tricycle13.CodingStopFeature
setHistory(EmissionMarkovFeature.MarkovHistory) - Method in class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature
setIgnoreInvalidTrainingData(boolean) - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
setIgnoreSemiMarkovSelfTransitions(boolean) - Method in class calhoun.analysis.crf.SemiMarkovSetup
  sets the flag indicating that self-transition edges for the semi-Markov states should be ignored.
setIgnoreWhitespace(boolean) - Method in class calhoun.util.FileDiff
  Sets whether to ignore whitespace.
setIndex(int) - Method in class calhoun.analysis.crf.BeanModel.Node
setInference(CRFInference) - Method in class calhoun.analysis.crf.Conrad
  sets the inference algorithm.
setInputComponent(String) - Method in class calhoun.analysis.crf.AbstractFeatureManager
setInputComponent(String) - Method in interface calhoun.analysis.crf.FeatureManager
  Sets which particular component of a CompositeInput this FeatureManager has access to.
setInputComponent(String) - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
setInputComponent(String) - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
setInputData(ModelManager, InputSequence<?>) - Method in interface calhoun.analysis.crf.solver.CacheProcessor
setInputData(ModelManager, InputSequence<?>) - Method in class calhoun.analysis.crf.solver.CacheProcessorBasic
setInputHandler(InputHandler) - Method in class calhoun.analysis.crf.Conrad
  sets the configured input handler.
setInputHandler(InputHandler) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
  sets the inputHandler used to write out the input sequences
setInputHandler(InputHandler) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
  sets the inputHandler used to write out the input sequences
setInputReader(InputComponentIO) - Method in class calhoun.analysis.crf.io.InputHandlerFile
  gets the reader used to read in input sequences.
setInputReaders(Map<String, InputComponentIO>) - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
  sets the readers used to read in input sequences.
setInputSequence(InterleavedInputComponentBase) - Method in class calhoun.analysis.crf.io.CompositeInput.InputComponent
  Deprecated.
setIntronExponential(boolean) - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
setKmerDefinitions(List<List<Integer>>) - Method in class calhoun.analysis.crf.features.tricycle13.KmerFeatures
setLocationIsLiteral(boolean) - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
  sets the meaning of the input location string.
setLookbackArrayFeatureSize(int) - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
setLookbackArraySize(int) - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
setManager(ModelManager) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
  sets the model used to generate results
setManager(ModelManager) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
  sets the model used to generate results
setMapper(FilenameMapper) - Method in class calhoun.analysis.crf.io.InputHandlerFile
  the mapper used to generate the name of the hidden sequence file from the input sequence file.
setMarginalsFile(String) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
setMarkovHistory(EmissionMarkovFeature.MarkovHistory) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
setMaxIters(int) - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
setMaxIters(int) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
setMaxLengths(short[]) - Method in class calhoun.analysis.crf.SemiMarkovSetup
  sets the maximum lengths for each state.
setMForHessian(int) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
setMinLengths(short[]) - Method in class calhoun.analysis.crf.SemiMarkovSetup
  sets the minimum lengths for each state.
setModel(ModelManager) - Method in class calhoun.analysis.crf.Conrad
  sets the model.
setMultipleFeatures(boolean) - Method in class calhoun.analysis.crf.features.interval13.PhylogeneticLogprobInterval13
setMultipleFeatures(boolean) - Method in class calhoun.analysis.crf.features.interval13.PWMInterval13
setMultipleFeatures(boolean) - Method in class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13Base
setMultipleFeatures(boolean) - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
  set to true to indicate that intergenic, exonic, and intergenic lengths should each get a separate weight.
setMultipleFeatures(boolean) - Method in class calhoun.analysis.crf.features.interval29.PWMInterval29
setMultipleFeatures(boolean) - Method in class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29Base
setMultipleFeatures(boolean) - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
  set to true to indicate that intergenic, exonic, and intergenic lengths should each get a separate weight.
setName(String) - Method in class calhoun.analysis.crf.BeanModel.Node
setName(String) - Method in class calhoun.analysis.crf.io.CompositeInput.InputComponent
  Deprecated.
setName(String) - Method in class calhoun.analysis.crf.io.InterleavedInputComponentBase
  sets the name of the input sequence read and written by this component
setNameComponent(String) - Method in class calhoun.analysis.crf.io.GTFInputInterval13
setNarrowBoundaries(boolean) - Method in class calhoun.analysis.crf.features.interval13.Interval13Model
setNarrowBoundaries(boolean) - Method in class calhoun.analysis.crf.features.interval29.Interval29Model
setNodeMarginalFile(String) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
setNodeMarginalFile(String) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
setNodes(List<BeanModel.Node>) - Method in class calhoun.analysis.crf.BeanModel
  sets the list of hidden states in this model.
setNoIntergenic(boolean) - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
setNumSeqCap(Integer) - Method in class calhoun.analysis.crf.io.FastaInput
setObjectiveFunction(CRFObjectiveFunctionGradient) - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
  sets the objective function gradient.
setObjectiveFunction(CRFObjectiveFunctionGradient) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
  sets the objective function gradient.
setOptimizer(CRFTraining) - Method in class calhoun.analysis.crf.Conrad
  sets the numerical optimizer.
setOutputHandler(OutputHandler) - Method in class calhoun.analysis.crf.Conrad
  sets the configured output handler.
setOutputLocation(String) - Method in interface calhoun.analysis.crf.io.OutputHandler
  sets the output location to write to.
setOutputLocation(String) - Method in class calhoun.analysis.crf.io.OutputHandlerComposite
setOutputLocation(String) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
setOutputLocation(String) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
setOutputLocation(String) - Method in class calhoun.analysis.crf.io.OutputHandlerWriter
setOverlapCorrections(List<BeanModel.Node>) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
setParameters(double[]) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.HKY85Model
setParameters(double[]) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.Kimura80Model
setParameters(double[]) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel
setPrev(BeanModel.Node) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
setPwmGeometry(List<PositionWeightMatrixFeatures.Geometry>) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
setQuadraticRegularization(double) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
setQuality(byte[]) - Method in class calhoun.seq.SimpleFastaSequence
setQuick(int, int, boolean) - Method in class calhoun.util.DenseBooleanMatrix2D
setQuick(int, int, int) - Method in class calhoun.util.DenseIntMatrix2D
setRareThreshold(int) - Method in class calhoun.analysis.crf.features.tricycle13.KmerFeatures
setRequireConvergence(boolean) - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
setRequireConvergence(boolean) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
setResultHandler(TrainingSequenceIO) - Method in class calhoun.analysis.crf.io.OutputHandlerWriter
  sets the result handler which will be used to handle the output sequence
setScore(LocalPathSimilarityScore) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
  sets the local similarity score function used to score each position in every path.
setScoreAlphaFile(String) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
setSecondPass(CRFTraining) - Method in class calhoun.analysis.crf.solver.TwoPassOptimizer
setSeededOptimizer(CRFTraining) - Method in class calhoun.analysis.crf.solver.SeededOptimizer
setSeedModel(File) - Method in class calhoun.analysis.crf.solver.SeededOptimizer
setSemiMarkovSetup(SemiMarkovSetup) - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
setSemiMarkovSetup(SemiMarkovSetup) - Method in class calhoun.analysis.crf.solver.SemiMarkovViterbiNoCache
  sets up the semiMarkov parameters, such as maximum segment lengths.
setSequence(String) - Method in class calhoun.analysis.crf.io.FastaInput
setSequence(String) - Method in class calhoun.seq.SimpleFastaSequence
setSize(int) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
setStarts(double[]) - Method in interface calhoun.analysis.crf.CRFTraining
  Sets the starting weights for the optimization.
setStarts(double[]) - Method in class calhoun.analysis.crf.solver.FixedWeightOptimizer
  sets the values to use as feature weights.
setStarts(double[]) - Method in class calhoun.analysis.crf.solver.SeededOptimizer
  starting weights are ignored for a SeededOptimizer, since they are always taken from the seeded model.
setStarts(double[]) - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
setStarts(double[]) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
setStarts(double[]) - Method in class calhoun.analysis.crf.solver.TwoPassOptimizer
setStates(int[]) - Method in class calhoun.analysis.crf.features.generic.EndFeatures
setStates(int[]) - Method in class calhoun.analysis.crf.features.generic.StartFeatures
setStates(List<List<BeanModel.Node>>) - Method in class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature.MarkovHistory
setStepSize(double) - Method in class calhoun.analysis.crf.solver.SimplexOptimizer
setTieFlag(boolean) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
setTo(BeanModel.Node) - Method in class calhoun.analysis.crf.BeanModel.Edge
setTrainingData(ModelManager, List<? extends TrainingSequence<?>>) - Method in interface calhoun.analysis.crf.CRFObjectiveFunctionGradient
  sets the training data that will be used for evaluation of the objective function.
setTrainingData(ModelManager, List<? extends TrainingSequence<?>>) - Method in interface calhoun.analysis.crf.solver.CacheProcessor
setTrainingData(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.CacheProcessorBasic
setTrainingData(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.CacheProcessorDeluxe
setTrainingData(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodGradient
setTrainingData(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.MaximumLikelihoodSemiMarkovGradient
setTrainingData(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.NoCachingCacheProcessor
setTrainingData(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanLocalScoreSemiMarkovGradient
setTrainingData(ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.solver.semimarkov.CleanMaximumLikelihoodSemiMarkovGradient
setTrainingFile(String) - Method in class calhoun.analysis.crf.solver.CacheProcessorBasic
setTransition(int) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures.Geometry
setUnchangedObjective(int) - Method in class calhoun.analysis.crf.solver.StandardOptimizer
setup(ModelManager, List<? extends TrainingSequence<?>>, boolean, short[], boolean) - Method in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
setup(double[], boolean) - Method in class calhoun.analysis.crf.statistics.MixtureOfGammas
setValueAt(Object, int, int) - Method in class calhoun.analysis.crf.executables.viewer.ViterbiTableModel
setWeights(double[]) - Method in class calhoun.analysis.crf.Conrad
  sets feature weights.
setWriteTrainingData(boolean) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
setWriteTrainingData(boolean) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
setY(int[]) - Method in class calhoun.analysis.crf.io.TrainingSequence
  sets the vector of hidden state indices.
setY(int, int) - Method in class calhoun.analysis.crf.io.TrainingSequence
  sets the hidden state index at a particular position
shiftHash(char, int) - Method in class calhoun.seq.KmerHasher
  Updates an existing hash.
SimpleFastaSequence - Class in calhoun.seq
SimpleFastaSequence() - Constructor for class calhoun.seq.SimpleFastaSequence
SimpleFastaSequence(String, String) - Constructor for class calhoun.seq.SimpleFastaSequence
SimplerFormatter - Class in calhoun.util
  Simpler formatter than the default Java SimpleFormatter.
SimplerFormatter() - Constructor for class calhoun.util.SimplerFormatter
SimplexOptimizer - Class in calhoun.analysis.crf.solver
  uses a nelder-mead algorithm (the simplex method) to do a general function optimization objective function.
SimplexOptimizer() - Constructor for class calhoun.analysis.crf.solver.SimplexOptimizer
SimScoreMaxStateAgreement - Class in calhoun.analysis.crf.scoring
SimScoreMaxStateAgreement() - Constructor for class calhoun.analysis.crf.scoring.SimScoreMaxStateAgreement
SimScoreMinCodingMiscallsSV13 - Class in calhoun.analysis.crf.scoring
SimScoreMinCodingMiscallsSV13() - Constructor for class calhoun.analysis.crf.scoring.SimScoreMinCodingMiscallsSV13
SimScoreMinExonBoundaryMiscallsSV13 - Class in calhoun.analysis.crf.scoring
SimScoreMinExonBoundaryMiscallsSV13() - Constructor for class calhoun.analysis.crf.scoring.SimScoreMinExonBoundaryMiscallsSV13
SimScoreStateAndExonBoundariesInt13 - Class in calhoun.analysis.crf.scoring
SimScoreStateAndExonBoundariesInt13() - Constructor for class calhoun.analysis.crf.scoring.SimScoreStateAndExonBoundariesInt13
size() - Method in class calhoun.util.RangeMap
SlowTestMaxentMotifModel - Class in calhoun.analysis.crf.test.slow
SlowTestMaxentMotifModel() - Constructor for class calhoun.analysis.crf.test.slow.SlowTestMaxentMotifModel
specificity() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
  Specificity is the TP/(TP+FP) is the fraction of predicted events that are real.
stableState - Variable in class calhoun.analysis.crf.solver.LookbackBuffer
StandardOptimizer - Class in calhoun.analysis.crf.solver
  uses a L-BFGS algorithm to optimize the objective function.
StandardOptimizer() - Constructor for class calhoun.analysis.crf.solver.StandardOptimizer
start - Variable in class calhoun.analysis.crf.io.IntervalInputSequence.IntervalRangeMapValue
start - Variable in class calhoun.util.RangeMap.Interval
StartFeatures - Class in calhoun.analysis.crf.features.generic
  indicator functions that evaluate to true for a selected set of start states at the first position in the sequence.
StartFeatures() - Constructor for class calhoun.analysis.crf.features.generic.StartFeatures
state - Variable in class calhoun.analysis.crf.solver.CacheProcessor.StatePotentials
state2cluster(int) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.ColumnConditionalLogProbability
StateLengthLogprobInterval13 - Class in calhoun.analysis.crf.features.interval13
StateLengthLogprobInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
StateLengthLogprobInterval29 - Class in calhoun.analysis.crf.features.interval29
StateLengthLogprobInterval29() - Constructor for class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
statesWithLookback - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
statesWithoutLookback - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
StateTransitionsInterval13 - Class in calhoun.analysis.crf.features.interval13
StateTransitionsInterval13() - Constructor for class calhoun.analysis.crf.features.interval13.StateTransitionsInterval13
StateTransitionsInterval29 - Class in calhoun.analysis.crf.features.interval29
StateTransitionsInterval29() - Constructor for class calhoun.analysis.crf.features.interval29.StateTransitionsInterval29
stateVector2StateLengths(List<? extends TrainingSequence<?>>, int) - Static method in class calhoun.analysis.crf.io.SequenceConverter
stop - Variable in class calhoun.util.RangeMap.Interval
strategy - Variable in class calhoun.analysis.crf.CacheStrategySpec
StringInput - Class in calhoun.analysis.crf.io
  reads in an input consisting of a string.
StringInput() - Constructor for class calhoun.analysis.crf.io.StringInput
subSequence(int, int) - Method in interface calhoun.analysis.crf.io.InputSequence
  tTakes a subinterval of the input sequence with given start-end coordinates which are relative coordinates, 1-based, and inclusive.
subSequence(int, int) - Method in class calhoun.analysis.crf.io.InputSequenceBoolean
subSequence(int, int) - Method in class calhoun.analysis.crf.io.InputSequenceCharacter
subSequence(int, int) - Method in class calhoun.analysis.crf.io.InputSequenceComposite
subSequence(int, int) - Method in class calhoun.analysis.crf.io.InputSequenceInt
subSequence(int, int) - Method in class calhoun.analysis.crf.io.InputSequenceObject
subSequence(int, int) - Method in class calhoun.analysis.crf.io.IntervalInputSequence
subSequence(int, int) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInputSequence
subSequence(int, int) - Method in class calhoun.analysis.crf.io.NameInputSequence
subSequence(int, int) - Method in class calhoun.analysis.crf.io.TrainingSequence
subtree(String[]) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree
sumDoubleArray(double[]) - Static method in class calhoun.analysis.crf.statistics.BasicStats
summarize() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.EvolutionaryModel
summarize() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.HKY85Model
summarize() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.Kimura80Model
summarize() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel
summarize() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.PhylogeneticTreeFelsensteinOrder
summarize(PrintStream) - Method in class calhoun.analysis.crf.statistics.MixtureOfGammas
summarize() - Method in class calhoun.analysis.crf.statistics.PredictedActualBinaryContingencyTable
summarize_tree() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree

## T

T - Variable in class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree
tableNum - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseBoundaryEntry
tableNum - Variable in class calhoun.analysis.crf.CacheStrategySpec.DenseCachingDetails
test(String) - Method in class calhoun.analysis.crf.Conrad
  runs a trained model against a set of input data with known results and evaluates the performance.
test(String, String) - Method in class calhoun.analysis.crf.Conrad
test(List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.Conrad
test(List<? extends TrainingSequence<?>>, String) - Method in class calhoun.analysis.crf.Conrad
  runs a trained model against a set of input data with known results and evaluates the performance.
test(A) - Method in class calhoun.util.FilterIterator
test2() - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
test3() - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
testAllSparseRejectTrainingDataStatesTooShort() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testAlternateObjectiveFunction() - Method in class calhoun.analysis.crf.test.MaximumExpectedAccuracyTest
testArrayReaderInt() - Method in class calhoun.analysis.crf.test.CRFIOTest
testAspTree() - Method in class calhoun.analysis.crf.test.NewickTreeManipulationTest
testBigTree() - Method in class calhoun.analysis.crf.test.NewickTreeManipulationTest
testCache() - Method in class calhoun.analysis.crf.test.CacheTest
testCachedAOFGradient() - Method in class calhoun.analysis.crf.test.MaximumExpectedAccuracyTest
testCacheHarder() - Method in class calhoun.analysis.crf.test.CacheTest
testCacheProcessorsWithInvalidation() - Method in class calhoun.analysis.crf.test.CacheProcessorTestRealShort
testCallTypes() - Method in class calhoun.seq.test.KmerHasherTest
testColt() - Method in class calhoun.analysis.crf.test.SemiMarkovTest
testComponentFeatures() - Method in class calhoun.analysis.crf.test.FeatureTest
testConstraintsDifferentCaches() - Method in class calhoun.analysis.crf.test.ConstraintTest
testConvergence() - Method in class calhoun.analysis.crf.test.NonGradientTest
testCPDAllDiscardInvalid() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testCPDAllDiscardInvalidLocalScore() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testCPDAllSequencesInvalid() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testCPDRejectTrainingDataStatesTooLong() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testCPDRejectTrainingDataStatesTooShort() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testCPDRejectTrainingDataStatesTooShortEnd() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testCPDRejectTrainingDataStatesTooShortStart() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testCPDRejectTrainingDataStatesViolatesConstraints() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testCryptoTree() - Method in class calhoun.analysis.crf.test.NewickTreeManipulationTest
testDnaLengthOne() - Method in class calhoun.seq.test.KmerHasherTest
testDnaLengthTwo() - Method in class calhoun.seq.test.KmerHasherTest
testDummy() - Method in class calhoun.analysis.crf.test.Interval29BaselineTest
testEdgeShort() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testEdgeTrivial() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testEncodeSpeciesFromBigTree() - Method in class calhoun.analysis.crf.test.NewickTreeManipulationTest
testEquivalentResultsVariousCacheProcessors() - Method in class calhoun.analysis.crf.test.CacheProcessorTestRealShort
testFeatureNames() - Method in class calhoun.analysis.crf.test.FeatureTest
TestFeatures - Class in calhoun.analysis.crf.test
TestFeatures() - Constructor for class calhoun.analysis.crf.test.TestFeatures
TestFeatures.EmissionFeature - Class in calhoun.analysis.crf.test
TestFeatures.EmissionFeature() - Constructor for class calhoun.analysis.crf.test.TestFeatures.EmissionFeature
TestFeatures.ExplicitHalfExponentialLengthFeature - Class in calhoun.analysis.crf.test
TestFeatures.ExplicitHalfExponentialLengthFeature() - Constructor for class calhoun.analysis.crf.test.TestFeatures.ExplicitHalfExponentialLengthFeature
TestFeatures.ExponentialLengthFeature - Class in calhoun.analysis.crf.test
TestFeatures.ExponentialLengthFeature() - Constructor for class calhoun.analysis.crf.test.TestFeatures.ExponentialLengthFeature
TestFeatures.GaussianLengthFeature - Class in calhoun.analysis.crf.test
TestFeatures.GaussianLengthFeature() - Constructor for class calhoun.analysis.crf.test.TestFeatures.GaussianLengthFeature
TestFeatures.HalfExponentialLengthFeature - Class in calhoun.analysis.crf.test
TestFeatures.HalfExponentialLengthFeature() - Constructor for class calhoun.analysis.crf.test.TestFeatures.HalfExponentialLengthFeature
TestFeatures.TestFeature - Class in calhoun.analysis.crf.test
TestFeatures.TestFeature() - Constructor for class calhoun.analysis.crf.test.TestFeatures.TestFeature
testFilenameMapper() - Method in class calhoun.analysis.crf.test.FileInputHandlerTest
testFull() - Method in class calhoun.analysis.crf.test.PredictedActualBinaryContingencyTableTest
testFullCycle() - Method in class calhoun.analysis.crf.test.CRFTest
testGammaDistribution() - Method in class calhoun.analysis.crf.test.GammaDistributionsTest
testGammaFunction() - Method in class calhoun.analysis.crf.test.GammaDistributionsTest
testGapFeature() - Method in class calhoun.analysis.crf.test.GapConjunctionFeaturesTest
testGeneCallerLocalScore() - Method in class calhoun.analysis.crf.test.MaximumExpectedAccuracyTest
testGeneConstraintsEvaluation() - Method in class calhoun.analysis.crf.test.GeneConstraintsInterval13Test
testGeneConstraintsTraining() - Method in class calhoun.analysis.crf.test.GeneConstraintsInterval13Test
testGradEvals() - Method in class calhoun.analysis.crf.test.MaximumExpectedAccuracyTest
testGradientEdge() - Method in class calhoun.analysis.crf.test.NonGradientTest
testGradientEdgeShort() - Method in class calhoun.analysis.crf.test.FunctionEvalTest
testGradientEdgeTrivial() - Method in class calhoun.analysis.crf.test.FunctionEvalTest
testGradStateFunc() - Method in class calhoun.analysis.crf.test.FunctionEvalTest
testIncremental() - Method in class calhoun.analysis.crf.test.PredictedActualBinaryContingencyTableTest
testIncrementalPartial() - Method in class calhoun.analysis.crf.test.PredictedActualBinaryContingencyTableTest
testInference() - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
testInputSequenceFileReader() - Method in class calhoun.analysis.crf.test.CRFIOTest
testInputSequenceReader() - Method in class calhoun.analysis.crf.test.CRFIOTest
testInputSequenceSubsetterCommandLine() - Method in class calhoun.analysis.crf.test.CRFIOTest
testInputSequenceSubsetterCommandLineForcingGenic() - Method in class calhoun.analysis.crf.test.CRFIOTest
testInputSequenceSubsetterCommandLineSeparateFiles() - Method in class calhoun.analysis.crf.test.CRFIOTest
testKmerFeatures() - Method in class calhoun.analysis.crf.test.FeatureTest
testLBFGS() - Method in class calhoun.analysis.crf.test.LBFGSTest
testLengthCache() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testLengthCacheDummy() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testLetterLengthOne() - Method in class calhoun.seq.test.KmerHasherTest
testLettersLengthTwo() - Method in class calhoun.seq.test.KmerHasherTest
testLittle() - Method in class calhoun.analysis.crf.test.MaximumExpectedAccuracyTest
testLogProbLookupEasy() - Method in class calhoun.analysis.crf.test.ReferenceBasePredictorTest
testLogProbLookupHard() - Method in class calhoun.analysis.crf.test.ReferenceBasePredictorTest
testLogProbLookupRC() - Method in class calhoun.analysis.crf.test.LogprobLookupTest
testMainLBGFS() - Method in class calhoun.analysis.crf.test.LBFGSTest
testMainLBGFSCached() - Method in class calhoun.analysis.crf.test.LBFGSTest
testMainLBGFSCachedSemiMarkov() - Method in class calhoun.analysis.crf.test.LBFGSTest
testMarkov13VsMarkov29() - Method in class calhoun.analysis.crf.test.Interval29BaselineTest
testMarkov13VsSemiMarkov29() - Method in class calhoun.analysis.crf.test.Interval29BaselineTest
testMarkovModelWithMarkovTrainingTestingVsSemiMarkovCPDTrainingTesting() - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
testMatrixExponential() - Method in class calhoun.analysis.crf.test.MatrixOperationsTest
testMaxentDonorModel() - Method in class calhoun.analysis.crf.test.MaxentMotifModelTest
testMaxentModel() - Method in class calhoun.analysis.crf.test.MaxentMotifModelTest
testMean() - Method in class calhoun.analysis.crf.test.BasicStatsTest
testMedian() - Method in class calhoun.analysis.crf.test.BasicStatsTest
testMixtureGammaModel() - Method in class calhoun.analysis.crf.test.GammaDistributionsTest
testMixtureGammaModelForceExponential() - Method in class calhoun.analysis.crf.test.GammaDistributionsTest
testMixtureOfGammasClass() - Method in class calhoun.analysis.crf.test.GammaDistributionsTest
testModulo() - Method in class calhoun.analysis.crf.test.RealIOTest
testMultipleSequences() - Method in class calhoun.analysis.crf.test.MultipleSequenceTest
testNode() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testNoGradient() - Method in class calhoun.analysis.crf.test.NonGradientTest
testPartial() - Method in class calhoun.analysis.crf.test.PredictedActualBinaryContingencyTableTest
testRangeMapPositionQueryExample() - Method in class calhoun.analysis.crf.test.RangeMapExamples
testReadingBaselineXMLConfigFile() - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
testReadingSSBaselineCPDXMLConfigFile() - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
testRealFormats() - Method in class calhoun.analysis.crf.test.RealIOTest
testRealFormats2() - Method in class calhoun.analysis.crf.test.RealIOTest
testRealFormatsMulti() - Method in class calhoun.analysis.crf.test.RealIOTest
testRealFormatsNeg() - Method in class calhoun.analysis.crf.test.RealIOTest
testRecyclingBuffer() - Method in class calhoun.analysis.crf.test.RecyclingBufferTest
testRecyclingBufferWithArray() - Method in class calhoun.analysis.crf.test.RecyclingBufferTest
testReferenceBasePredictor() - Method in class calhoun.analysis.crf.test.ReferenceBasePredictorTest
testRejectInvalidTrainingPath() - Method in class calhoun.analysis.crf.test.ValidPathsTest
testRepeatedSubsequence() - Method in class calhoun.seq.test.RepeatedSubsequenceTest
testReverse() - Method in class calhoun.seq.test.KmerHasherTest
testRollingMatch() - Method in class calhoun.seq.test.RepeatedSubsequenceTest
testSemiCRFCompareWithBaseClass() - Method in class calhoun.analysis.crf.test.SemiMarkovTest
testSemiCRFViterbiCompareWithBaseClass() - Method in class calhoun.analysis.crf.test.SemiMarkovTest
testSemiCRFViterbiCompareWithBaseClassWithFeatures() - Method in class calhoun.analysis.crf.test.SemiMarkovTest
testSemiCRFViterbiCompareWithBaseClassWithLengths() - Method in class calhoun.analysis.crf.test.SemiMarkovTest
testSemiMarkovBadTraining() - Method in class calhoun.analysis.crf.test.SemiMarkovTest
testSemiMarkovCommandLine() - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
testSemiRealExample() - Method in class calhoun.analysis.crf.test.MaximumExpectedAccuracyTest
testSequenceConverter() - Method in class calhoun.analysis.crf.test.SequenceConverterTest
testSequenceConverter13models() - Method in class calhoun.analysis.crf.test.SequenceConverterTest
testShift() - Method in class calhoun.seq.test.KmerHasherTest
testSlowMaxentModel() - Method in class calhoun.analysis.crf.test.slow.SlowTestMaxentMotifModel
testSpringConfig() - Method in class calhoun.analysis.crf.test.CRFTest
testStateTransitions() - Method in class calhoun.analysis.crf.test.Interval13FeatureTest
testStateTransitions() - Method in class calhoun.analysis.crf.test.Interval29FeatureTest
testSumPaths() - Method in class calhoun.analysis.crf.test.ValidPathsTest
  Tests that the sum of the likelihoods of the valid paths is 1
testSumPathsAllPaths() - Method in class calhoun.analysis.crf.test.ValidPathsTest
  Tests all 2-state combinations with a restricted model and onlyValidTransitions = false
testSumPathsAllPathsCached() - Method in class calhoun.analysis.crf.test.ValidPathsTest
  Tests all 2-state combinations with a restricted model and onlyValidTransitions = false
testSumPathsMoreComplicated() - Method in class calhoun.analysis.crf.test.ValidPathsTest
  Tests that the sum of the likelihoods of the valid paths is 1, uses a model that allows 0-0
testToolkitMainSeparateTraining() - Method in class calhoun.analysis.crf.test.CRFTest
testTrainingAndInferenceCacheProcessorCompare() - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
testTrainingAndInferenceMarkovVsSemiMarkov() - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
testTrainTestSplitCommandLine() - Method in class calhoun.analysis.crf.test.CRFIOTest
testTricycle13Interval13Conversion() - Method in class calhoun.analysis.crf.test.SequenceConverterTest
testTwoFeaturesNonTrivial() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testTwoFeaturesNonTrivial() - Method in class calhoun.analysis.crf.test.FunctionEvalTest
testTwoFeaturesTrivial() - Method in class calhoun.analysis.crf.test.CacheProcessorTest
testTwoFeaturesTrivial() - Method in class calhoun.analysis.crf.test.FunctionEvalTest
testUntiedModel() - Method in class calhoun.analysis.crf.test.Interval13BaselineTest
testViterbi() - Method in class calhoun.analysis.crf.test.NonGradientTest
testViterbiConstraints() - Method in class calhoun.analysis.crf.test.ConstraintTest
testWithoutAnswers(String, String) - Method in class calhoun.analysis.crf.Conrad
testWriteFeatures() - Method in class calhoun.analysis.crf.test.FeatureTest
testWriteGTF() - Method in class calhoun.analysis.crf.test.GTFWriterTest
toString() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.BinaryTreeNode
toString() - Method in class calhoun.analysis.crf.io.InputSequenceCharacter
toString() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
toString() - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
toString() - Method in class calhoun.analysis.crf.io.TrainingSequence
toString() - Method in class calhoun.util.DenseBooleanMatrix2D
toString() - Method in class calhoun.util.DenseIntMatrix2D
toString() - Method in class calhoun.util.FileDiff
toString() - Method in class calhoun.util.RangeMap.Interval
toString() - Method in class calhoun.util.RangeMap
toStringStrand(String) - Method in class calhoun.analysis.crf.io.IntervalInputSequence.IntervalRangeMapValue
total_branch_length() - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.RootedBinaryPhylogeneticTree
totalPositions - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
train(int, ModelManager, List) - Method in class calhoun.analysis.crf.CompositeFeatureManager
train(String) - Method in class calhoun.analysis.crf.Conrad
  fully trains this Conrad engine with this training data.
train(List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.Conrad
  fully trains this Conrad engine with this training data.
train(int, ModelManager, List) - Method in class calhoun.analysis.crf.ConstrainedFeatureManager
train(int, ModelManager, List<? extends TrainingSequence<? extends InputType>>) - Method in interface calhoun.analysis.crf.FeatureManager
  Provides access to the entire training set so that FeatureManager can compute global properties and assign feature indices.
train(int, ModelManager, List) - Method in class calhoun.analysis.crf.features.generic.EndFeatures
  Edge features don't train based on the data.
train(int, ModelManager, List) - Method in class calhoun.analysis.crf.features.generic.IndicatorEdges
  Edge features don't train based on the data.
train(int, ModelManager, List) - Method in class calhoun.analysis.crf.features.generic.StartFeatures
  Start features don't train based on the data.
train(int, ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.features.generic.WeightedEdges
train(int, ModelManager, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.features.generic.WeightedStateChanges
train(int, ModelManager, List<? extends TrainingSequence<? extends CompositeInput>>) - Method in class calhoun.analysis.crf.features.interval13.BlastInterval13
train(int, ModelManager, List<? extends TrainingSequence<? extends CompositeInput>>) - Method in class calhoun.analysis.crf.features.interval13.ESTInterval13
train(int, ModelManager, List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>>) - Method in class calhoun.analysis.crf.features.interval13.FootprintsInterval13
train(int, ModelManager, List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>>) - Method in class calhoun.analysis.crf.features.interval13.GapFeaturesInterval13
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.interval13.GeneConstraintsInterval13
train(int, ModelManager, List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>>) - Method in class calhoun.analysis.crf.features.interval13.PhylogeneticLogprobInterval13
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.interval13.PWMInterval13
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.interval13.ReferenceBasePredictorInterval13Base
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.interval13.StateLengthLogprobInterval13
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.interval13.StateTransitionsInterval13
train(int, ModelManager, List<? extends TrainingSequence<? extends CompositeInput>>) - Method in class calhoun.analysis.crf.features.interval29.ESTInterval29
train(int, ModelManager, List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>>) - Method in class calhoun.analysis.crf.features.interval29.FootprintsInterval29
train(int, ModelManager, List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>>) - Method in class calhoun.analysis.crf.features.interval29.GapFeaturesInterval29
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.interval29.GeneConstraintsInterval29
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.interval29.PWMInterval29
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.interval29.ReferenceBasePredictorInterval29Base
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.interval29.StateLengthLogprobInterval29
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.interval29.StateTransitionsInterval29
train(List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.supporting.MarkovPredictorLogprob
train(ModelManager, List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>>) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.ColumnConditionalLogProbability
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.tricycle13.CodingStopFeature
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.tricycle13.EmissionMarkovFeature
train(int, ModelManager, List<? extends TrainingSequence<? extends CompositeInput>>) - Method in class calhoun.analysis.crf.features.tricycle13.ESTEdge
train(int, ModelManager, List<? extends TrainingSequence<? extends CompositeInput>>) - Method in class calhoun.analysis.crf.features.tricycle13.ESTExon
train(int, ModelManager, List<? extends TrainingSequence<? extends CompositeInput>>) - Method in class calhoun.analysis.crf.features.tricycle13.ESTIntron
train(int, ModelManager, List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>>) - Method in class calhoun.analysis.crf.features.tricycle13.FelsensteinFeatures
train(int, ModelManager, List<? extends TrainingSequence<? extends MultipleAlignmentInputSequence.MultipleAlignmentColumn>>) - Method in class calhoun.analysis.crf.features.tricycle13.GapConjunctionFeatures
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.tricycle13.GeneConstraints
  Set up the matrix Depends on states starting with the words 'intergenic, intron, and exon'.
train(int, ModelManager, List<? extends TrainingSequence<? extends IntervalInputSequence.IntervalPosition>>) - Method in class calhoun.analysis.crf.features.tricycle13.IntervalPresenceFeatures
train(int, ModelManager, List) - Method in class calhoun.analysis.crf.features.tricycle13.IntronLengthFeature
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.tricycle13.KmerFeatures
  Computes the P(label | kmer) for each kmer across all of the training data.
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.tricycle13.MaxentMotifFeatures
train(int, ModelManager, List<? extends TrainingSequence<? extends CompositeInput>>) - Method in class calhoun.analysis.crf.features.tricycle13.PfamGenic
train(int, ModelManager, List<? extends TrainingSequence<? extends CompositeInput>>) - Method in class calhoun.analysis.crf.features.tricycle13.PfamPhase
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.features.tricycle13.PositionWeightMatrixFeatures
train(int, ModelManager, List<? extends TrainingSequence<? extends CompositeInput>>) - Method in class calhoun.analysis.crf.features.tricycle13.PWM_evolution
train(int, ModelManager, List) - Method in class calhoun.analysis.crf.test.ConstraintTest.FixedEdges
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.test.GeneConstraintsToy
  Set up the matrix Depends on states starting with the words 'intergenic, intron, and exon'.
train(int, ModelManager, List<? extends TrainingSequence<? extends Character>>) - Method in class calhoun.analysis.crf.test.TestFeatures.TestFeature
trainFeatures(String) - Method in class calhoun.analysis.crf.Conrad
  trains only the features in the current model with this training data.
trainFeatures(List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.Conrad
  trains only the features in the current model with this training data.
TrainingSequence<A> - Class in calhoun.analysis.crf.io
  represents an input sequence that also contains a sequence of hidden states.
TrainingSequence(InputSequence<? extends A>) - Constructor for class calhoun.analysis.crf.io.TrainingSequence
  constructs a training sequence using just the input sequence.
TrainingSequence(InputSequence<? extends A>, int[]) - Constructor for class calhoun.analysis.crf.io.TrainingSequence
  constructs a training sequence using these input and hidden sequences
TrainingSequenceIO - Interface in calhoun.analysis.crf.io
  Interface for reading a training sequence from the specified location.
trainMaxentDistributionUsingAllPairwiseConstraints(List<int[]>, int, int, double) - Static method in class calhoun.analysis.crf.features.supporting.MaxentMotifModel
trainWeights(String) - Method in class calhoun.analysis.crf.Conrad
  optimizes the feature weights for the current model with this training data.
trainWeights(List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.Conrad
  optimizes the feature weights for the current model with this training data.
transform(String, String, String) - Static method in class calhoun.util.XmlUtil
transitionFrom - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
transitionIndex - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
transitionMatrix(double) - Method in class calhoun.analysis.crf.features.supporting.phylogenetic.NucleotideSubstitutionModel
transitionProb - Variable in class calhoun.analysis.crf.solver.LookbackBuffer
transitionTo - Variable in class calhoun.analysis.crf.solver.CacheProcessor.SolverSetup
TwoPassOptimizer - Class in calhoun.analysis.crf.solver
  a two pass optimizer that does an initial optimization and then uses the weights generated from that as the start of a second optimization.
TwoPassOptimizer() - Constructor for class calhoun.analysis.crf.solver.TwoPassOptimizer
TypedProperties - Class in calhoun.util
TypedProperties() - Constructor for class calhoun.util.TypedProperties
TypedProperties(Properties) - Constructor for class calhoun.util.TypedProperties

## U

unzipFile(File, File) - Static method in class calhoun.util.FileUtil
Util - Class in calhoun.util

## V

ValidPathsTest - Class in calhoun.analysis.crf.test
  Tests that CRF is working with valid probabilities - the sum of all possible labelings is 1.
ValidPathsTest() - Constructor for class calhoun.analysis.crf.test.ValidPathsTest
value - Variable in class calhoun.analysis.crf.io.IntervalInputSequence.IntervalRangeMapValue
value - Variable in class calhoun.analysis.crf.solver.CacheProcessor.FeatureEvaluation
valueOf(String) - Static method in enum calhoun.analysis.crf.CacheStrategySpec.CacheStrategy
  Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum calhoun.analysis.crf.features.tricycle13.KmerFeatures.Cardinality
  Returns the enum constant of this type with the specified name.
values() - Static method in enum calhoun.analysis.crf.CacheStrategySpec.CacheStrategy
  Returns an array containing the constants of this enum type, in the order they're declared.
values() - Static method in enum calhoun.analysis.crf.features.tricycle13.KmerFeatures.Cardinality
  Returns an array containing the constants of this enum type, in the order they're declared.
values() - Method in class calhoun.util.RangeMap
Viterbi - Class in calhoun.analysis.crf.solver
Viterbi() - Constructor for class calhoun.analysis.crf.solver.Viterbi
ViterbiTableModel - Class in calhoun.analysis.crf.executables.viewer
ViterbiTableModel(Conrad, TrainingSequence) - Constructor for class calhoun.analysis.crf.executables.viewer.ViterbiTableModel
ViterbiTableModel.ViterbiCellRenderer - Class in calhoun.analysis.crf.executables.viewer
ViterbiTableModel.ViterbiCellRenderer() - Constructor for class calhoun.analysis.crf.executables.viewer.ViterbiTableModel.ViterbiCellRenderer
ViterbiViewerApp - Class in calhoun.analysis.crf.executables.viewer
ViterbiViewerApp(String, String) - Constructor for class calhoun.analysis.crf.executables.viewer.ViterbiViewerApp

## W

WeightedEdges - Class in calhoun.analysis.crf.features.generic
  learns transition probabilities from the data and then creates a single feature for all edge transitions.
WeightedEdges() - Constructor for class calhoun.analysis.crf.features.generic.WeightedEdges
WeightedStateChanges - Class in calhoun.analysis.crf.features.generic
  learns transition probabilities from the data and then creates a single feature for all edge transitions out of a given state.
WeightedStateChanges() - Constructor for class calhoun.analysis.crf.features.generic.WeightedStateChanges
write(String) - Method in class calhoun.analysis.crf.Conrad
  writes this Conrad engine to a file.
write(Writer, Map<String, ? extends InputSequence<?>>) - Method in class calhoun.analysis.crf.io.BooleanInput
write(Writer, Map<String, ? extends InputSequence<?>>) - Method in interface calhoun.analysis.crf.io.InterleavedInputComponent
  Output this sequence to the given writer.
write(Writer, Map<String, ? extends InputSequence<?>>) - Method in class calhoun.analysis.crf.io.IntervalInput
write(Writer, Map<String, ? extends InputSequence<?>>) - Method in class calhoun.analysis.crf.io.IntInput
write(Writer, Map<String, ? extends InputSequence<?>>) - Method in class calhoun.analysis.crf.io.MultipleAlignmentInput
write(Writer, Map<String, ? extends InputSequence<?>>) - Method in class calhoun.analysis.crf.io.NameInput
write(Writer, Map<String, ? extends InputSequence<?>>) - Method in class calhoun.analysis.crf.io.StringInput
writeFeatures(Conrad, String, InputSequence) - Method in class calhoun.analysis.crf.test.FeatureTest
writeFile(File, String) - Static method in class calhoun.util.FileUtil
  Writes a string out to a file.
writeFile(String, String) - Static method in class calhoun.util.FileUtil
  Writes a string out to a file.
writeGTF(List<? extends TrainingSequence<?>>, String) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
writeGTF(List<? extends TrainingSequence<?>>, String) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
writeHiddenSequence39GFF(TrainingSequence<Character>, String) - Method in class calhoun.analysis.crf.io.SequenceConverter
writeHiddenSequenceGFF(TrainingSequence<Character>, String) - Static method in class calhoun.analysis.crf.io.SequenceConverter
writeInputData(String, Iterator) - Method in class calhoun.analysis.crf.io.CompositeInput.LegacyInputHandler
  Deprecated.
writeInputData(String, Iterator<? extends InputSequence<?>>) - Method in interface calhoun.analysis.crf.io.InputHandler
  writes input data to the specified location.
writeInputData(String, Iterator<? extends InputSequence<?>>) - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
writeInputData(String, Iterator<? extends InputSequence<?>>) - Method in class calhoun.analysis.crf.io.InputHandlerFile
writeInputData(String, Iterator<? extends InputSequence<?>>) - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
writeInputSequences(String, List<? extends Map<String, ? extends InputSequence<?>>>) - Method in class calhoun.analysis.crf.io.AlignmentTree
writeInputSequences(String, List<? extends Map<String, ? extends InputSequence<?>>>) - Method in class calhoun.analysis.crf.io.FastaAlignmentInput
writeInputSequences(String, List<? extends Map<String, ? extends InputSequence<?>>>) - Method in class calhoun.analysis.crf.io.FastaInput
writeInputSequences(String, List<? extends Map<String, ? extends InputSequence<?>>>) - Method in interface calhoun.analysis.crf.io.InputComponentIO
  writes input sequences to this location.
writeInputSequences(String, List<? extends Map<String, ? extends InputSequence<?>>>) - Method in class calhoun.analysis.crf.io.InterleavedInputComponentBase
writeObject(String, Object) - Static method in class calhoun.util.FileUtil
  Serializes a Java object out to a file.
writeOutput(InputSequence<?>, int[]) - Method in interface calhoun.analysis.crf.io.OutputHandler
  Writes out a set of predicted hidden states.
writeOutput(InputSequence<?>, int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerComposite
writeOutput(InputSequence<?>, int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
writeOutput(InputSequence<?>, int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
writeOutput(InputSequence<?>, int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerWriter
writeSeq(String, String) - Method in class calhoun.seq.FastaWriter
  Writes a sequence to the file.
writeSeq(String, String, Integer, Integer) - Method in class calhoun.seq.FastaWriter
  Writes a portion of the sequence to the file.
writeSeq(FastaSequence) - Method in class calhoun.seq.FastaWriter
  Writes a sequence to the file, which may have been previously read from a different file.
writeSequence(Writer, int[]) - Method in class calhoun.analysis.crf.io.IntInput
writeTestOutput(InputSequence<?>, int[], int[]) - Method in interface calhoun.analysis.crf.io.OutputHandler
  Writes out a set of hidden states compared with a known true path.
writeTestOutput(InputSequence<?>, int[], int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerComposite
writeTestOutput(InputSequence<?>, int[], int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallPredict
writeTestOutput(InputSequence<?>, int[], int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStats
writeTestOutput(InputSequence<?>, int[], int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerGeneCallStatsInterval29
writeTestOutput(InputSequence<?>, int[], int[]) - Method in class calhoun.analysis.crf.io.OutputHandlerWriter
writeTrainingData(String, List) - Method in class calhoun.analysis.crf.io.CompositeInput.LegacyInputHandler
  Deprecated.
writeTrainingData(String, List<? extends TrainingSequence<?>>) - Method in interface calhoun.analysis.crf.io.InputHandler
  writes training data to the specified location.
writeTrainingData(String, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.io.InputHandlerDirectory
writeTrainingData(String, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.io.InputHandlerFile
writeTrainingData(String, List<? extends TrainingSequence<?>>) - Method in class calhoun.analysis.crf.io.InputHandlerInterleaved
writeTrainingSequences(Object, Iterator<int[]>) - Method in class calhoun.analysis.crf.io.AllIntergenicHiddenStateReader
writeTrainingSequences(Object, Iterator<int[]>) - Method in class calhoun.analysis.crf.io.GTFInputInterval13
writeTrainingSequences(Object, Iterator<int[]>) - Method in class calhoun.analysis.crf.io.IntInput
writeTrainingSequences(Object, Iterator<int[]>) - Method in interface calhoun.analysis.crf.io.TrainingSequenceIO
  writes training sequences to the specified location.

## X

XmlDiff - Class in calhoun.util
  Utility class for diffing XML
XmlUtil - Class in calhoun.util
  Utility functions to simplify XML.

## Z

ZeroOrderManager - Class in calhoun.analysis.crf.test
ZeroOrderManager() - Constructor for class calhoun.analysis.crf.test.ZeroOrderManager
ZeroOrderModel - Class in calhoun.analysis.crf.test
ZeroOrderModel() - Constructor for class calhoun.analysis.crf.test.ZeroOrderModel

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