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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 InputHandlers.
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 InterleavedInputComponents.
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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