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

A

AbstractSvmProblem<L extends Comparable,P,R extends SvmProblem<L,P,R>> - Class in edu.berkeley.compbio.jlibsvm

AbstractSvmProblem() - Constructor for class edu.berkeley.compbio.jlibsvm.AbstractSvmProblem

accuracy() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionCrossValidationResults

accuracyGivenClassified() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionCrossValidationResults

active - Variable in class edu.berkeley.compbio.jlibsvm.Solver

addExample(P, L) - Method in class edu.berkeley.compbio.jlibsvm.binary.MutableBinaryClassificationProblemImpl

addExample(P, L) - Method in class edu.berkeley.compbio.jlibsvm.multi.MutableMultiClassProblemImpl

addExample(P, L) - Method in interface edu.berkeley.compbio.jlibsvm.MutableSvmProblem

addExample(P, Float) - Method in class edu.berkeley.compbio.jlibsvm.oneclass.MutableOneClassProblemImpl

addExample(P, Float) - Method in class edu.berkeley.compbio.jlibsvm.regression.MutableRegressionProblemImpl

addExampleFloat(P, Float) - Method in class edu.berkeley.compbio.jlibsvm.binary.MutableBinaryClassificationProblemImpl

addExampleFloat(P, Float) - Method in class edu.berkeley.compbio.jlibsvm.multi.MutableMultiClassProblemImpl

addExampleFloat(P, Float) - Method in interface edu.berkeley.compbio.jlibsvm.MutableSvmProblem

addExampleFloat(P, Float) - Method in class edu.berkeley.compbio.jlibsvm.oneclass.MutableOneClassProblemImpl

addExampleFloat(P, Float) - Method in class edu.berkeley.compbio.jlibsvm.regression.MutableRegressionProblemImpl

allExamples - Variable in class edu.berkeley.compbio.jlibsvm.Solver

allVsAllMode - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

allVsAllMode - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

alpha - Variable in class edu.berkeley.compbio.jlibsvm.SolutionVector

AlphaModel<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

AlphaModel() - Constructor for class edu.berkeley.compbio.jlibsvm.binary.AlphaModel

alphas - Variable in class edu.berkeley.compbio.jlibsvm.binary.AlphaModel

ArrayParsers - Class in edu.berkeley.compbio.jlibsvm.util

ArrayParsers() - Constructor for class edu.berkeley.compbio.jlibsvm.util.ArrayParsers

asBuilder() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

asBuilder() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterGrid

asBuilder(ImmutableSvmParameter.Builder) - Static method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint

asBuilder() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint

B

BasicKernelQMatrix<P> - Class in edu.berkeley.compbio.jlibsvm.qmatrix

BasicKernelQMatrix(KernelFunction<P>, int, int) - Constructor for class edu.berkeley.compbio.jlibsvm.qmatrix.BasicKernelQMatrix

basicTest() - Method in class edu.berkeley.compbio.jlibsvm.binary.C_SVCTest

BatchClusterLabelInverter<T extends edu.berkeley.compbio.ml.cluster.Clusterable<T>> - Class in edu.berkeley.compbio.jlibsvm.multi

BatchClusterLabelInverter() - Constructor for class edu.berkeley.compbio.jlibsvm.multi.BatchClusterLabelInverter

bestClusterMove(T) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVMAdapter

bestProbabilityLabel(Map<L, Float>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

BinaryClassificationProblem<L extends Comparable,P> - Interface in edu.berkeley.compbio.jlibsvm.binary

BinaryClassificationProblemImpl<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

BinaryClassificationProblemImpl(Class, Map<P, L>, Map<P, Integer>) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

BinaryClassificationProblemImpl(Class, Map<P, L>, Map<P, Integer>, ScalingModel<P>, L, L) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

BinaryClassificationProblemImpl(BinaryClassificationProblemImpl<L, P>, Set<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

BinaryClassificationSVM<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

BinaryClassificationSVM() - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationSVM

BinaryModel<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

BinaryModel() - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

BinaryModel(Properties, LabelParser<L>) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

BinaryModel(ImmutableSvmParameterPoint<L, P>) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

BinarySolver<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

BinarySolver(List<SolutionVector<P>>, QMatrix<P>, float, float, float, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BinarySolver

BinarySolverNu<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

BinarySolverNu(List<SolutionVector<P>>, QMatrix<P>, float, float, float, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BinarySolverNu

BooleanClassificationProblemImpl<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

BooleanClassificationProblemImpl(Class, L, Set<P>, L, Set<P>, Map<P, Integer>) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BooleanClassificationProblemImpl

BooleanClassificationProblemImpl(BooleanClassificationProblemImpl<L, P>, Set<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.BooleanClassificationProblemImpl

BooleanInvertingKernelQMatrix<P> - Class in edu.berkeley.compbio.jlibsvm.qmatrix

BooleanInvertingKernelQMatrix(KernelFunction<P>, int, int) - Constructor for class edu.berkeley.compbio.jlibsvm.qmatrix.BooleanInvertingKernelQMatrix

build() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

build() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterGrid.Builder

build() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint.Builder

builder() - Static method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterGrid

ByteLabelInverter - Class in edu.berkeley.compbio.jlibsvm.labelinverter

ByteLabelInverter() - Constructor for class edu.berkeley.compbio.jlibsvm.labelinverter.ByteLabelInverter

C

C - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint.Builder

C - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint

C_SVC<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

C_SVC() - Constructor for class edu.berkeley.compbio.jlibsvm.binary.C_SVC

C_SVCTest - Class in edu.berkeley.compbio.jlibsvm.binary

C_SVCTest() - Constructor for class edu.berkeley.compbio.jlibsvm.binary.C_SVCTest

cache_size - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

cache_size - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

calculate_rho(AlphaModel<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.Solver

calculate_rho(AlphaModel<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.Solver_NU

Cn - Variable in class edu.berkeley.compbio.jlibsvm.Solver

coef0 - Variable in class edu.berkeley.compbio.jlibsvm.kernel.PolynomialKernel

coef0 - Variable in class edu.berkeley.compbio.jlibsvm.kernel.SigmoidKernel

compact() - Method in class edu.berkeley.compbio.jlibsvm.binary.AlphaModel

Remove vectors whose alpha is zero, leaving only support vectors

compareTo(SolutionVector) - Method in class edu.berkeley.compbio.jlibsvm.SolutionVector

CompositeGaussianRBFKernel<T> - Class in edu.berkeley.compbio.jlibsvm.kernel

CompositeGaussianRBFKernel(double, KernelFunction<T>) - Constructor for class edu.berkeley.compbio.jlibsvm.kernel.CompositeGaussianRBFKernel

computeOneVsAllProbabilities(Map<KernelFunction<P>, float[]>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

computeQ(SolutionVector<P>, SolutionVector<P>) - Method in class edu.berkeley.compbio.jlibsvm.qmatrix.BasicKernelQMatrix

computeQ(SolutionVector<P>, SolutionVector<P>) - Method in class edu.berkeley.compbio.jlibsvm.qmatrix.BooleanInvertingKernelQMatrix

computeQ(SolutionVector<P>, SolutionVector<P>) - Method in class edu.berkeley.compbio.jlibsvm.qmatrix.KernelQMatrix

continuousCrossValidation(SvmProblem<L, P, R>, ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.SVM

ContinuousModel<P> - Interface in edu.berkeley.compbio.jlibsvm

An SVM solution which assigns a floating-point value to unknown points.

Cp - Variable in class edu.berkeley.compbio.jlibsvm.Solver

createClusters() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVMAdapter

createScaledCopy(Map<P, L>, Map<P, Integer>, ScalingModel<P>) - Method in class edu.berkeley.compbio.jlibsvm.AbstractSvmProblem

createScaledCopy(Map<P, L>, Map<P, Integer>, ScalingModel<P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

createScaledCopy(Map<P, L>, Map<P, Integer>, ScalingModel<P>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassProblemImpl

createScaledCopy(Map<P, Float>, Map<P, Integer>, ScalingModel<P>) - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassProblemImpl

createScaledCopy(Map<P, Float>, Map<P, Integer>, ScalingModel<P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionProblemImpl

crossValidationFolds - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

When learning scaling, only bother with this many examples, assuming they're in random order.

crossValidationFolds - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

crossValidationResults - Variable in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

crossValidationResults - Variable in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

Cset - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterGrid.Builder

D

degree - Variable in class edu.berkeley.compbio.jlibsvm.kernel.PolynomialKernel

discreteCrossValidation(SvmProblem<L, P, R>, ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.SVM

DiscreteModel<L,P> - Interface in edu.berkeley.compbio.jlibsvm

An SVM solution which can classify unknown points using a set of discrete labels.

dot(SparseVector, SparseVector) - Static method in class edu.berkeley.compbio.jlibsvm.util.MathSupport

E

edu.berkeley.compbio.jlibsvm - package edu.berkeley.compbio.jlibsvm

edu.berkeley.compbio.jlibsvm.binary - package edu.berkeley.compbio.jlibsvm.binary

edu.berkeley.compbio.jlibsvm.kernel - package edu.berkeley.compbio.jlibsvm.kernel

edu.berkeley.compbio.jlibsvm.labelinverter - package edu.berkeley.compbio.jlibsvm.labelinverter

edu.berkeley.compbio.jlibsvm.legacyexec - package edu.berkeley.compbio.jlibsvm.legacyexec

edu.berkeley.compbio.jlibsvm.multi - package edu.berkeley.compbio.jlibsvm.multi

edu.berkeley.compbio.jlibsvm.oneclass - package edu.berkeley.compbio.jlibsvm.oneclass

edu.berkeley.compbio.jlibsvm.qmatrix - package edu.berkeley.compbio.jlibsvm.qmatrix

edu.berkeley.compbio.jlibsvm.regression - package edu.berkeley.compbio.jlibsvm.regression

edu.berkeley.compbio.jlibsvm.scaler - package edu.berkeley.compbio.jlibsvm.scaler

edu.berkeley.compbio.jlibsvm.util - package edu.berkeley.compbio.jlibsvm.util

EMPTY_SV_ARRAY - Static variable in class edu.berkeley.compbio.jlibsvm.Solver

entrySet() - Method in class edu.berkeley.compbio.jlibsvm.util.SubtractionMap

eps - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

eps - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

EpsilonSVR<P,R extends RegressionProblem<P,R>> - Class in edu.berkeley.compbio.jlibsvm.regression

EpsilonSVR() - Constructor for class edu.berkeley.compbio.jlibsvm.regression.EpsilonSVR

equals(Object) - Method in class edu.berkeley.compbio.jlibsvm.SolutionVector

evaluate(T, T) - Method in class edu.berkeley.compbio.jlibsvm.kernel.CompositeGaussianRBFKernel

evaluate(SparseVector, SparseVector) - Method in class edu.berkeley.compbio.jlibsvm.kernel.GaussianRBFKernel

evaluate(P, P) - Method in interface edu.berkeley.compbio.jlibsvm.kernel.KernelFunction

evaluate(SparseVector, SparseVector) - Method in class edu.berkeley.compbio.jlibsvm.kernel.LinearKernel

evaluate(SparseVector, SparseVector) - Method in class edu.berkeley.compbio.jlibsvm.kernel.PolynomialKernel

evaluate(SparseVector, SparseVector) - Method in class edu.berkeley.compbio.jlibsvm.kernel.PrecomputedKernel

evaluate(SparseVector, SparseVector) - Method in class edu.berkeley.compbio.jlibsvm.kernel.SigmoidKernel

evaluate(SolutionVector<P>, SolutionVector<P>) - Method in class edu.berkeley.compbio.jlibsvm.qmatrix.KernelQMatrix

evaluateDiagonal(SolutionVector<P>) - Method in class edu.berkeley.compbio.jlibsvm.qmatrix.KernelQMatrix

evaluateDiagonal(SolutionVector<P>) - Method in interface edu.berkeley.compbio.jlibsvm.qmatrix.QMatrix

evaluateF(SparseVector, SparseVector) - Method in class edu.berkeley.compbio.jlibsvm.kernel.PrecomputedKernel

exampleCounts - Variable in class edu.berkeley.compbio.jlibsvm.AbstractSvmProblem

exampleIds - Variable in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

examples - Variable in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

ExplicitSvmProblem<L extends Comparable,P,R extends SvmProblem<L,P,R>> - Interface in edu.berkeley.compbio.jlibsvm

Deprecated.

ExplicitSvmProblemImpl<L extends Comparable,P,R extends SvmProblem<L,P,R>> - Class in edu.berkeley.compbio.jlibsvm

ExplicitSvmProblemImpl(Map<P, L>, Map<P, Integer>) - Constructor for class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

ExplicitSvmProblemImpl(Map<P, L>, Map<P, Integer>, ScalingModel<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

ExplicitSvmProblemImpl(Map<P, L>, Map<P, Integer>, ScalingModel<P>, Set<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

F

falseClassSVlimit - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

falseClassSVlimit - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

G

G - Variable in class edu.berkeley.compbio.jlibsvm.SolutionVector

gamma - Variable in class edu.berkeley.compbio.jlibsvm.kernel.GammaKernel

GammaKernel<T> - Class in edu.berkeley.compbio.jlibsvm.kernel

GammaKernel(double) - Constructor for class edu.berkeley.compbio.jlibsvm.kernel.GammaKernel

GaussianRBFKernel - Class in edu.berkeley.compbio.jlibsvm.kernel

GaussianRBFKernel(Properties) - Constructor for class edu.berkeley.compbio.jlibsvm.kernel.GaussianRBFKernel

GaussianRBFKernel(float) - Constructor for class edu.berkeley.compbio.jlibsvm.kernel.GaussianRBFKernel

get(int) - Method in class edu.berkeley.compbio.jlibsvm.util.SparseVector

getBestLabel() - Method in class edu.berkeley.compbio.jlibsvm.multi.VotingResult

getBestOneClassProbability() - Method in class edu.berkeley.compbio.jlibsvm.multi.VotingResult

getBestOneVsAllProbability() - Method in class edu.berkeley.compbio.jlibsvm.multi.VotingResult

getBestVoteProportion() - Method in class edu.berkeley.compbio.jlibsvm.multi.VotingResult

getBooleanExamples() - Method in interface edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblem

getBooleanExamples() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

getBooleanExamples() - Method in class edu.berkeley.compbio.jlibsvm.binary.BooleanClassificationProblemImpl

getCacheRows() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

getCrossValidationResults() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

getCrossValidationResults() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

getCrossValidationResults() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

getCrossValidationResults() - Method in class edu.berkeley.compbio.jlibsvm.SolutionModel

getExampleCounts() - Method in class edu.berkeley.compbio.jlibsvm.AbstractSvmProblem

getExampleCounts() - Method in interface edu.berkeley.compbio.jlibsvm.SvmProblem

getExampleIds() - Method in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

getExampleIds() - Method in interface edu.berkeley.compbio.jlibsvm.SvmProblem

getExamples() - Method in interface edu.berkeley.compbio.jlibsvm.ExplicitSvmProblem

Deprecated.

getExamples() - Method in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

getExamples() - Method in interface edu.berkeley.compbio.jlibsvm.SvmProblem

getExamplesByLabel() - Method in interface edu.berkeley.compbio.jlibsvm.multi.MultiClassProblem

getExamplesByLabel() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassProblemImpl

getFalseLabel() - Method in interface edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblem

getFalseLabel() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

getFalseLabel() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

getGamma() - Method in class edu.berkeley.compbio.jlibsvm.kernel.GammaKernel

getGridParams() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterGrid

getHeldOutPoints() - Method in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

getHeldOutPoints() - Method in interface edu.berkeley.compbio.jlibsvm.SvmProblem

getId(P) - Method in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

getId(P) - Method in interface edu.berkeley.compbio.jlibsvm.SvmProblem

getInfo() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

getInfo() - Method in class edu.berkeley.compbio.jlibsvm.multi.SvmMultiClassCrossValidationResults

getKernelName() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

getKernelName() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

getKernelName() - Method in class edu.berkeley.compbio.jlibsvm.SolutionModel

getLabel() - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassModel

getLabel() - Method in interface edu.berkeley.compbio.jlibsvm.oneclass.OneClassProblem

getLabel() - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassProblemImpl

getLabelClass() - Method in interface edu.berkeley.compbio.jlibsvm.multi.MultiClassProblem

getLabelClass() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassProblemImpl

getLabelInverter() - Method in interface edu.berkeley.compbio.jlibsvm.multi.MultiClassProblem

getLabelInverter() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassProblemImpl

getLabels() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

getLabels() - Method in interface edu.berkeley.compbio.jlibsvm.ExplicitSvmProblem

Deprecated.

getLabels() - Method in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

getLabels() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

getLabels() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

getLabels() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

getLabels() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionProblemImpl

getLabels() - Method in class edu.berkeley.compbio.jlibsvm.SolutionModel

getLabels() - Method in interface edu.berkeley.compbio.jlibsvm.SvmProblem

getLaplaceParameter() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

getNumExamples() - Method in class edu.berkeley.compbio.jlibsvm.binary.BooleanClassificationProblemImpl

getNumExamples() - Method in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

getNumExamples() - Method in interface edu.berkeley.compbio.jlibsvm.SvmProblem

getPreferredSize() - Method in class edu.berkeley.compbio.jlibsvm.legacyexec.svm_toy

getProbability(P, L) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

getProbability(P) - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassModel

HACK guess at a probability of being in the one class by logistic function.

getQ(SolutionVector<P>, SolutionVector<P>[], float[]) - Method in class edu.berkeley.compbio.jlibsvm.qmatrix.KernelQMatrix

getQ(SolutionVector<P>, SolutionVector<P>[], SolutionVector<P>[], float[]) - Method in class edu.berkeley.compbio.jlibsvm.qmatrix.KernelQMatrix

getQ(SolutionVector<P>, SolutionVector<P>[], float[]) - Method in interface edu.berkeley.compbio.jlibsvm.qmatrix.QMatrix

getQ(SolutionVector<P>, SolutionVector<P>[], SolutionVector<P>[], float[]) - Method in interface edu.berkeley.compbio.jlibsvm.qmatrix.QMatrix

getScaledCopy(ScalingModelLearner<P>) - Method in interface edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblem

getScaledCopy(ScalingModelLearner<P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

getScaledCopy(ScalingModelLearner<P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.BooleanClassificationProblemImpl

There's no sense in scaling Boolean values, so this is a noop.

getScaledCopy(ScalingModelLearner<P>) - Method in interface edu.berkeley.compbio.jlibsvm.multi.MultiClassProblem

getScaledCopy(ScalingModelLearner<P>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassProblemImpl

getScaledCopy(ScalingModelLearner<P>) - Method in interface edu.berkeley.compbio.jlibsvm.oneclass.OneClassProblem

getScaledCopy(ScalingModelLearner<P>) - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassProblemImpl

getScaledCopy(ScalingModelLearner<P>) - Method in interface edu.berkeley.compbio.jlibsvm.regression.RegressionProblem

getScaledCopy(ScalingModelLearner<P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionProblemImpl

getScalingModel() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

getScalingModel() - Method in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

getScalingModel() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

getScalingModel() - Method in interface edu.berkeley.compbio.jlibsvm.SvmProblem

getSecondBestOneClassProbability() - Method in class edu.berkeley.compbio.jlibsvm.multi.VotingResult

getSecondBestOneVsAllProbability() - Method in class edu.berkeley.compbio.jlibsvm.multi.VotingResult

getSecondBestVoteProportion() - Method in class edu.berkeley.compbio.jlibsvm.multi.VotingResult

getSigmoid() - Method in class edu.berkeley.compbio.jlibsvm.binary.SvmBinaryCrossValidationResults

getSumAlpha() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

getSvmType() - Method in class edu.berkeley.compbio.jlibsvm.binary.C_SVC

getSvmType() - Method in class edu.berkeley.compbio.jlibsvm.binary.Nu_SVC

getSvmType() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVM

getSvmType() - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassSVC

getSvmType() - Method in class edu.berkeley.compbio.jlibsvm.regression.EpsilonSVR

getSvmType() - Method in class edu.berkeley.compbio.jlibsvm.regression.Nu_SVR

getSvmType() - Method in class edu.berkeley.compbio.jlibsvm.SVM

getTargetValue(P) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

getTargetValue(P) - Method in class edu.berkeley.compbio.jlibsvm.binary.BooleanClassificationProblemImpl

getTargetValue(P) - Method in interface edu.berkeley.compbio.jlibsvm.ExplicitSvmProblem

Deprecated.

getTargetValue(P) - Method in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

getTargetValue(P) - Method in interface edu.berkeley.compbio.jlibsvm.SvmProblem

getTrueLabel() - Method in interface edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblem

getTrueLabel() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

getTrueLabel() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

getTrueProbability(P) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

getTrueProbability(float[], int[]) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

getWeight(L) - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

gridsearchBinaryMachinesIndependently - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

gridsearchBinaryMachinesIndependently - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

H

hashCode() - Method in class edu.berkeley.compbio.jlibsvm.SolutionVector

heldOutPoints - Variable in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

I

id - Variable in class edu.berkeley.compbio.jlibsvm.SolutionVector

keep track of the sample id for mapping to ranks

identifyTypeAndLoad(String) - Static method in class edu.berkeley.compbio.jlibsvm.SolutionModel

ImmutableSvmParameter<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm

I do not like it

ImmutableSvmParameter(ImmutableSvmParameter.Builder<L, P>) - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

ImmutableSvmParameter.Builder<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm

ImmutableSvmParameter.Builder() - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

ImmutableSvmParameter.Builder(ImmutableSvmParameter<L, P>) - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

ImmutableSvmParameter.Builder(ImmutableSvmParameter.Builder<L, P>) - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

ImmutableSvmParameterGrid<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm

For now this supports sweeping over C and different kernels (which may have e.g.

ImmutableSvmParameterGrid(ImmutableSvmParameterGrid.Builder<L, P>) - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterGrid

ImmutableSvmParameterGrid.Builder<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm

ImmutableSvmParameterGrid.Builder(ImmutableSvmParameter.Builder) - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterGrid.Builder

ImmutableSvmParameterGrid.Builder(ImmutableSvmParameterGrid<L, P>) - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterGrid.Builder

ImmutableSvmParameterGrid.Builder() - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterGrid.Builder

ImmutableSvmParameterPoint<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm

ImmutableSvmParameterPoint(ImmutableSvmParameterPoint.Builder<L, P>) - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint

ImmutableSvmParameterPoint.Builder<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm

ImmutableSvmParameterPoint.Builder(ImmutableSvmParameter.Builder) - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint.Builder

ImmutableSvmParameterPoint.Builder(ImmutableSvmParameterPoint) - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint.Builder

ImmutableSvmParameterPoint.Builder() - Constructor for class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint.Builder

inactive - Variable in class edu.berkeley.compbio.jlibsvm.Solver

indexes - Variable in class edu.berkeley.compbio.jlibsvm.util.SparseVector

init() - Method in class edu.berkeley.compbio.jlibsvm.legacyexec.svm_toy

initActiveSet() - Method in class edu.berkeley.compbio.jlibsvm.Solver

initializeWithSamples(ClusterableIterator<T>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVMAdapter

initRanks(Collection<SolutionVector<P>>) - Method in class edu.berkeley.compbio.jlibsvm.qmatrix.KernelQMatrix

initRanks(Collection<SolutionVector<P>>) - Method in interface edu.berkeley.compbio.jlibsvm.qmatrix.QMatrix

invert(Byte) - Method in class edu.berkeley.compbio.jlibsvm.labelinverter.ByteLabelInverter

invert(L) - Method in interface edu.berkeley.compbio.jlibsvm.labelinverter.LabelInverter

invert(String) - Method in class edu.berkeley.compbio.jlibsvm.labelinverter.StringLabelInverter

invert(BasicBatchCluster<T>) - Method in class edu.berkeley.compbio.jlibsvm.multi.BatchClusterLabelInverter

isFeasible(BinaryClassificationProblem, ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.Nu_SVC

isShrinkable(double, double) - Method in class edu.berkeley.compbio.jlibsvm.SolutionVector

isShrinkable(double, double, double, double) - Method in class edu.berkeley.compbio.jlibsvm.SolutionVector

isUpperBound() - Method in class edu.berkeley.compbio.jlibsvm.SolutionVector

isWeightsEmpty() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

K

kernel - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint.Builder

kernel - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint

kernel - Variable in class edu.berkeley.compbio.jlibsvm.qmatrix.KernelQMatrix

KernelFunction<P> - Interface in edu.berkeley.compbio.jlibsvm.kernel

KernelQMatrix<P> - Class in edu.berkeley.compbio.jlibsvm.qmatrix

kernelSet - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterGrid.Builder

L

LabelInverter<L> - Interface in edu.berkeley.compbio.jlibsvm.labelinverter

LabelParser<L> - Interface in edu.berkeley.compbio.jlibsvm

An object that can map strings to classification labels of the generic type L.

labels - Variable in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

the unique set of targetvalues, in a defined order avoid populating for regression! OK, regression should never call getLabels(), then.

laplaceParameter - Variable in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

laplaceParameter(RegressionProblem<P, R>, ImmutableSvmParameter<Float, P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionSVM

learnScaling(ScalingModelLearner<P>) - Method in class edu.berkeley.compbio.jlibsvm.AbstractSvmProblem

learnScaling(Iterable<SparseVector>) - Method in class edu.berkeley.compbio.jlibsvm.scaler.LinearScalingModelLearner

learnScaling(Iterable<P>) - Method in class edu.berkeley.compbio.jlibsvm.scaler.NoopScalingModelLearner

default implementation returns the identity ScalingModel; override for interesting behavior

learnScaling(Iterable<P>) - Method in interface edu.berkeley.compbio.jlibsvm.scaler.ScalingModelLearner

learnScaling(Iterable<SparseVector>) - Method in class edu.berkeley.compbio.jlibsvm.scaler.ZscoreScalingModelLearner

LIBSVM_VERSION - Static variable in class edu.berkeley.compbio.jlibsvm.SVM

LinearKernel - Class in edu.berkeley.compbio.jlibsvm.kernel

LinearKernel() - Constructor for class edu.berkeley.compbio.jlibsvm.kernel.LinearKernel

LinearScalingModelLearner - Class in edu.berkeley.compbio.jlibsvm.scaler

Learn the minima and maxima of each dimension from the training data, so as to transform points into the [-1, 1] interval.

LinearScalingModelLearner(int, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.scaler.LinearScalingModelLearner

LinearScalingModelLearner.LinearScalingModel - Class in edu.berkeley.compbio.jlibsvm.scaler

LinearScalingModelLearner.LinearScalingModel(Map<Integer, Float>, Map<Integer, Float>) - Constructor for class edu.berkeley.compbio.jlibsvm.scaler.LinearScalingModelLearner.LinearScalingModel

linearTerm - Variable in class edu.berkeley.compbio.jlibsvm.SolutionVector

M

main(String[]) - Static method in class edu.berkeley.compbio.jlibsvm.legacyexec.svm_predict

main(String[]) - Static method in class edu.berkeley.compbio.jlibsvm.legacyexec.svm_scale

main(String[]) - Static method in class edu.berkeley.compbio.jlibsvm.legacyexec.svm_toy

main(String[]) - Static method in class edu.berkeley.compbio.jlibsvm.legacyexec.svm_train

maintainCache(SolutionVector<P>[], SolutionVector<P>[]) - Method in class edu.berkeley.compbio.jlibsvm.qmatrix.KernelQMatrix

maintainCache(SolutionVector<P>[], SolutionVector<P>[]) - Method in interface edu.berkeley.compbio.jlibsvm.qmatrix.QMatrix

makeFold(Set<P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

makeFold(Set<P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.BooleanClassificationProblemImpl

makeFold(Set<P>) - Method in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

makeFold(Set<P>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassProblemImpl

makeFold(Set<P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionProblemImpl

makeFolds(int) - Method in class edu.berkeley.compbio.jlibsvm.binary.BooleanClassificationProblemImpl

makeFolds(int) - Method in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

makeFolds(int) - Method in interface edu.berkeley.compbio.jlibsvm.SvmProblem

MathSupport - Class in edu.berkeley.compbio.jlibsvm.util

MathSupport() - Constructor for class edu.berkeley.compbio.jlibsvm.util.MathSupport

maxIndex() - Method in class edu.berkeley.compbio.jlibsvm.util.SparseVector

minVoteProportion - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

minVoteProportion - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

MultiClassificationSVM<L extends Comparable<L>,P> - Class in edu.berkeley.compbio.jlibsvm.multi

MultiClassificationSVM(BinaryClassificationSVM<L, P>) - Constructor for class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVM

MultiClassificationSVMAdapter<T extends edu.berkeley.compbio.ml.cluster.Clusterable<T>> - Class in edu.berkeley.compbio.jlibsvm.multi

MultiClassificationSVMAdapter(Set<String>, Map<String, Set<String>>, ProhibitionModel<T>, Set<String>, ImmutableSvmParameter<BasicBatchCluster<T>, T>) - Constructor for class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVMAdapter

MultiClassModel<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.multi

MultiClassModel(MultiClassModel<L, P>, Collection<L>) - Constructor for class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

Make a derived copy for leave-one-out testing

MultiClassModel(ImmutableSvmParameter, int) - Constructor for class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

MultiClassModel.AllVsAllMode - Enum in edu.berkeley.compbio.jlibsvm.multi

MultiClassModel.OneVsAllMode - Enum in edu.berkeley.compbio.jlibsvm.multi

MultiClassProblem<L extends Comparable,P> - Interface in edu.berkeley.compbio.jlibsvm.multi

MultiClassProblemImpl<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.multi

MultiClassProblemImpl(Class, LabelInverter<L>, Map<P, L>, Map<P, Integer>, ScalingModel<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.multi.MultiClassProblemImpl

For now, pending further cleanup, we need to create arrays of the label type.

MultiClassProblemImpl(MultiClassProblemImpl<L, P>, Set<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.multi.MultiClassProblemImpl

MutableBinaryClassificationProblemImpl<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

MutableBinaryClassificationProblemImpl(Class, int) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.MutableBinaryClassificationProblemImpl

MutableMultiClassProblemImpl<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.multi

MutableMultiClassProblemImpl(Class, LabelInverter<L>, int, ScalingModel<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.multi.MutableMultiClassProblemImpl

For now, pending further cleanup, we need to create arrays of the label type.

MutableOneClassProblemImpl<L,P> - Class in edu.berkeley.compbio.jlibsvm.oneclass

MutableOneClassProblemImpl(int, L) - Constructor for class edu.berkeley.compbio.jlibsvm.oneclass.MutableOneClassProblemImpl

MutableRegressionProblemImpl<P> - Class in edu.berkeley.compbio.jlibsvm.regression

MutableRegressionProblemImpl(int) - Constructor for class edu.berkeley.compbio.jlibsvm.regression.MutableRegressionProblemImpl

MutableSvmProblem<L extends Comparable,P,R extends SvmProblem<L,P,R>> - Interface in edu.berkeley.compbio.jlibsvm

An SVM problem to which training examples may be added.

N

NO_LAPLACE_PARAMETER - Static variable in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

NoopScalingModel<P> - Class in edu.berkeley.compbio.jlibsvm.scaler

NoopScalingModel() - Constructor for class edu.berkeley.compbio.jlibsvm.scaler.NoopScalingModel

NoopScalingModelLearner<P> - Class in edu.berkeley.compbio.jlibsvm.scaler

NoopScalingModelLearner() - Constructor for class edu.berkeley.compbio.jlibsvm.scaler.NoopScalingModelLearner

noProbabilityCopy() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

normalizeL2 - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

normalizeL2 - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

normalizeL2() - Method in class edu.berkeley.compbio.jlibsvm.util.SparseVector

nu - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

nu - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

Nu_SVC<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

Nu_SVC() - Constructor for class edu.berkeley.compbio.jlibsvm.binary.Nu_SVC

Nu_SVR<P,R extends RegressionProblem<P,R>> - Class in edu.berkeley.compbio.jlibsvm.regression

Nu_SVR() - Constructor for class edu.berkeley.compbio.jlibsvm.regression.Nu_SVR

numExamples - Variable in class edu.berkeley.compbio.jlibsvm.Solver

numSVs - Variable in class edu.berkeley.compbio.jlibsvm.binary.AlphaModel

O

obj - Variable in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

OneClassModel<L,P> - Class in edu.berkeley.compbio.jlibsvm.oneclass

OneClassModel() - Constructor for class edu.berkeley.compbio.jlibsvm.oneclass.OneClassModel

OneClassProblem<L,P> - Interface in edu.berkeley.compbio.jlibsvm.oneclass

OneClassProblemImpl<L,P> - Class in edu.berkeley.compbio.jlibsvm.oneclass

OneClassProblemImpl(Map<P, Float>, Map<P, Integer>, L) - Constructor for class edu.berkeley.compbio.jlibsvm.oneclass.OneClassProblemImpl

OneClassProblemImpl(Map<P, Float>, Map<P, Integer>, L, ScalingModel<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.oneclass.OneClassProblemImpl

OneClassSolver<L,P> - Class in edu.berkeley.compbio.jlibsvm.oneclass

OneClassSolver(List<SolutionVector<P>>, QMatrix<P>, float, float, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.oneclass.OneClassSolver

OneClassSVC<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.oneclass

OneClassSVC() - Constructor for class edu.berkeley.compbio.jlibsvm.oneclass.OneClassSVC

oneVsAllMode - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

oneVsAllMode - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

oneVsAllThreshold - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

oneVsAllThreshold - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

optimize() - Method in class edu.berkeley.compbio.jlibsvm.Solver

P

p - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

p - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

paint(Graphics) - Method in class edu.berkeley.compbio.jlibsvm.legacyexec.svm_toy

param - Variable in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

a thing that is confusing here: if a grid search was done, then the specific point that was the optimum should be recorded here.

param - Variable in class edu.berkeley.compbio.jlibsvm.multi.SvmMultiClassCrossValidationResults

if we did a grid search, keep track of which parameter set was used for these results

param - Variable in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

parse(String) - Method in interface edu.berkeley.compbio.jlibsvm.LabelParser

parseFloatArray(String) - Static method in class edu.berkeley.compbio.jlibsvm.util.ArrayParsers

parseIntArray(String) - Static method in class edu.berkeley.compbio.jlibsvm.util.ArrayParsers

performCrossValidation(BinaryClassificationProblem<L, P>, ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationSVM

Cross-validation decision values for probability estimates

performCrossValidation(MultiClassProblem<L, P>, ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVM

performCrossValidation(R, ImmutableSvmParameter<Float, P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionSVM

performCrossValidation(R, ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.SVM

perfString() - Method in class edu.berkeley.compbio.jlibsvm.qmatrix.KernelQMatrix

perfString() - Method in interface edu.berkeley.compbio.jlibsvm.qmatrix.QMatrix

point - Variable in class edu.berkeley.compbio.jlibsvm.SolutionVector

PolynomialKernel - Class in edu.berkeley.compbio.jlibsvm.kernel

PolynomialKernel(int, float, float) - Constructor for class edu.berkeley.compbio.jlibsvm.kernel.PolynomialKernel

powi(double, int) - Static method in class edu.berkeley.compbio.jlibsvm.util.MathSupport

PrecomputedKernel - Class in edu.berkeley.compbio.jlibsvm.kernel

PrecomputedKernel() - Constructor for class edu.berkeley.compbio.jlibsvm.kernel.PrecomputedKernel

PrecomputedKernel(Properties) - Constructor for class edu.berkeley.compbio.jlibsvm.kernel.PrecomputedKernel

predict(float) - Method in class edu.berkeley.compbio.jlibsvm.SigmoidProbabilityModel

predictLabel(P) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

predictLabel(float[], int[]) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

predictLabel(P) - Method in interface edu.berkeley.compbio.jlibsvm.DiscreteModel

predictLabel(P) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

predictLabel(P) - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassModel

predictLabelWithQuality(P) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

predictProbability(P) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

predictValue(P) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

predictValue(float[], int[]) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

predictValue(P) - Method in interface edu.berkeley.compbio.jlibsvm.ContinuousModel

predictValue(P) - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassModel

predictValue(P) - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

prepareModelSvMaps() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

printSolutionInfo(BinaryClassificationProblem<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

probability - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

probability - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

processMouseEvent(MouseEvent) - Method in class edu.berkeley.compbio.jlibsvm.legacyexec.svm_toy

putOneVsAllModel(L, BinaryModel<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

putOneVsOneModel(L, L, BinaryModel<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

putResults(HierarchicalTypedPropertyNode<String, Serializable, ?>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVMAdapter

putWeight(L, Float) - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

Q

QMatrix<P> - Interface in edu.berkeley.compbio.jlibsvm.qmatrix

Kernel evaluation

the static method k_function is for doing single kernel evaluation

the constructor of Kernel prepares to calculate the l*l kernel matrix

the member function get_Q is for getting one column from the Q Matrix

R

r - Variable in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

r - Variable in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

rank - Variable in class edu.berkeley.compbio.jlibsvm.SolutionVector

Used by the cacheing mechanism to keep track of which SVs are the most active.

readSupportVectors(BufferedReader) - Method in class edu.berkeley.compbio.jlibsvm.binary.AlphaModel

readSupportVectors(BufferedReader) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

readSupportVectors(BufferedReader) - Method in class edu.berkeley.compbio.jlibsvm.SolutionModel

redistributeUnbalancedC - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

For unbalanced data, redistribute the misclassification cost C according to the numbers of examples in each class, so that each class has the same total misclassification weight assigned to it and the average is param.C

redistributeUnbalancedC - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

For unbalanced data, redistribute the misclassification cost C according to the numbers of examples in each class, so that each class has the same total misclassification weight assigned to it and the average is param.C

RegressionCrossValidationResults<P,R extends RegressionProblem<P,R>> - Class in edu.berkeley.compbio.jlibsvm.regression

RegressionCrossValidationResults(RegressionProblem<P, R>, Map<P, Float>) - Constructor for class edu.berkeley.compbio.jlibsvm.regression.RegressionCrossValidationResults

RegressionModel<P> - Class in edu.berkeley.compbio.jlibsvm.regression

RegressionModel() - Constructor for class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

RegressionProblem<P,R> - Interface in edu.berkeley.compbio.jlibsvm.regression

RegressionProblemImpl<P,R extends RegressionProblem<P,R>> - Class in edu.berkeley.compbio.jlibsvm.regression

RegressionProblemImpl(Map<P, Float>, Map<P, Integer>, ScalingModel<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.regression.RegressionProblemImpl

RegressionProblemImpl(Map<P, Float>, Map<P, Integer>, ScalingModel<P>, Set<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.regression.RegressionProblemImpl

RegressionProblemImpl(RegressionProblemImpl<P, R>, Set<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.regression.RegressionProblemImpl

RegressionProblemImpl(Map<P, Float>, Map<P, Integer>) - Constructor for class edu.berkeley.compbio.jlibsvm.regression.RegressionProblemImpl

RegressionSolver<P> - Class in edu.berkeley.compbio.jlibsvm.regression

RegressionSolver(List<SolutionVector<P>>, QMatrix<P>, float, float, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.regression.RegressionSolver

RegressionSolverNu<P> - Class in edu.berkeley.compbio.jlibsvm.regression

RegressionSolverNu(List<SolutionVector<P>>, QMatrix<P>, float, float, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.regression.RegressionSolverNu

RegressionSVM<P,R extends RegressionProblem<P,R>> - Class in edu.berkeley.compbio.jlibsvm.regression

RegressionSVM() - Constructor for class edu.berkeley.compbio.jlibsvm.regression.RegressionSVM

resetActiveSet() - Method in class edu.berkeley.compbio.jlibsvm.Solver

rho - Variable in class edu.berkeley.compbio.jlibsvm.binary.AlphaModel

runningMean(int, float, float) - Static method in class edu.berkeley.compbio.jlibsvm.scaler.ZscoreScalingModelLearner

runningStddevQ(int, float, float, float) - Static method in class edu.berkeley.compbio.jlibsvm.scaler.ZscoreScalingModelLearner

runningStddevQtoStddevInPlace(Map<Integer, Float>, int) - Static method in class edu.berkeley.compbio.jlibsvm.scaler.ZscoreScalingModelLearner

S

save(String) - Method in class edu.berkeley.compbio.jlibsvm.SolutionModel

scaleBinaryMachinesIndependently - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

scaleBinaryMachinesIndependently - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

scaledCopy(SparseVector) - Method in class edu.berkeley.compbio.jlibsvm.scaler.LinearScalingModelLearner.LinearScalingModel

scaledCopy(P) - Method in class edu.berkeley.compbio.jlibsvm.scaler.NoopScalingModel

default implementation just returns the original object, but an overriding implementation that actually changes something should return a copy

scaledCopy(P) - Method in interface edu.berkeley.compbio.jlibsvm.scaler.ScalingModel

scaledCopy(SparseVector) - Method in class edu.berkeley.compbio.jlibsvm.scaler.ZscoreScalingModelLearner.ZscoreScalingModel

scalingModel - Variable in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

scalingModel - Variable in class edu.berkeley.compbio.jlibsvm.ExplicitSvmProblemImpl

ScalingModel<P> - Interface in edu.berkeley.compbio.jlibsvm.scaler

scalingModelLearner - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

scalingModelLearner - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

When learning scaling, only bother with this many examples, assuming they're in random order.

ScalingModelLearner<P> - Interface in edu.berkeley.compbio.jlibsvm.scaler

selectWorkingPair() - Method in class edu.berkeley.compbio.jlibsvm.Solver

selectWorkingPair() - Method in class edu.berkeley.compbio.jlibsvm.Solver_NU

setBinarySvm(BinaryClassificationSVM<BasicBatchCluster<T>, T>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVMAdapter

setGamma(double) - Method in class edu.berkeley.compbio.jlibsvm.kernel.GammaKernel

setScalingModel(ScalingModel<P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

setScalingModel(ScalingModel<P>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

setSize(Dimension) - Method in class edu.berkeley.compbio.jlibsvm.legacyexec.svm_toy

setSize(int, int) - Method in class edu.berkeley.compbio.jlibsvm.legacyexec.svm_toy

setSvmType(String) - Method in class edu.berkeley.compbio.jlibsvm.SolutionModel

setupLabels() - Method in interface edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblem

setupLabels() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationProblemImpl

setupLabels() - Method in class edu.berkeley.compbio.jlibsvm.binary.BooleanClassificationProblemImpl

shrinking - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

shrinking - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

SigmoidKernel - Class in edu.berkeley.compbio.jlibsvm.kernel

SigmoidKernel(Properties) - Constructor for class edu.berkeley.compbio.jlibsvm.kernel.SigmoidKernel

SigmoidKernel(float, float) - Constructor for class edu.berkeley.compbio.jlibsvm.kernel.SigmoidKernel

SigmoidProbabilityModel - Class in edu.berkeley.compbio.jlibsvm

SigmoidProbabilityModel(float[], boolean[]) - Constructor for class edu.berkeley.compbio.jlibsvm.SigmoidProbabilityModel

size() - Method in class edu.berkeley.compbio.jlibsvm.util.SubtractionMap

SolutionModel<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm

SolutionModel() - Constructor for class edu.berkeley.compbio.jlibsvm.SolutionModel

SolutionVector<P> - Class in edu.berkeley.compbio.jlibsvm

SolutionVector(int, P, Boolean, float) - Constructor for class edu.berkeley.compbio.jlibsvm.SolutionVector

SolutionVector(int, P, Boolean, float, float) - Constructor for class edu.berkeley.compbio.jlibsvm.SolutionVector

SolutionVector.Status - Enum in edu.berkeley.compbio.jlibsvm

solve() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinarySolver

solve() - Method in class edu.berkeley.compbio.jlibsvm.binary.BinarySolverNu

solve() - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassSolver

solve() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionSolver

solve() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionSolverNu

Solver<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm

An SMO algorithm in Fan et al., JMLR 6(2005), p.

Solver(List<SolutionVector<P>>, QMatrix<P>, float, float, float, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.Solver

Solver.SolutionVectorPair - Class in edu.berkeley.compbio.jlibsvm

Solver.SolutionVectorPair(SolutionVector, SolutionVector, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.Solver.SolutionVectorPair

Solver_NU<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm

Solver for nu-svm classification and regression

additional constraint: e^T \alpha = constant

Solver_NU(List<SolutionVector<P>>, QMatrix<P>, float, float, float, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.Solver_NU

SparseVector - Class in edu.berkeley.compbio.jlibsvm.util

This acts something like a Map from int to float

SparseVector(int) - Constructor for class edu.berkeley.compbio.jlibsvm.util.SparseVector

SparseVector(int, float, float) - Constructor for class edu.berkeley.compbio.jlibsvm.util.SparseVector

Create randomized vectors for testing

SparseVector(SparseVector, float, SparseVector, float) - Constructor for class edu.berkeley.compbio.jlibsvm.util.SparseVector

StringLabelInverter - Class in edu.berkeley.compbio.jlibsvm.labelinverter

StringLabelInverter() - Constructor for class edu.berkeley.compbio.jlibsvm.labelinverter.StringLabelInverter

SubtractionMap<P,L> - Class in edu.berkeley.compbio.jlibsvm.util

SubtractionMap(Map<P, L>, Set<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.util.SubtractionMap

SubtractionMap(Collection<Map.Entry<P, L>>, Set<P>) - Constructor for class edu.berkeley.compbio.jlibsvm.util.SubtractionMap

SubtractionMap(Map<P, L>, Set<P>, int) - Constructor for class edu.berkeley.compbio.jlibsvm.util.SubtractionMap

SubtractionMap(Collection<Map.Entry<P, L>>, Set<P>, int) - Constructor for class edu.berkeley.compbio.jlibsvm.util.SubtractionMap

supportsLaplace() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

supportsOneVsOneProbability() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

supportVectors - Variable in class edu.berkeley.compbio.jlibsvm.binary.AlphaModel

SVM<L extends Comparable,P,R extends SvmProblem<L,P,R>> - Class in edu.berkeley.compbio.jlibsvm

SVM() - Constructor for class edu.berkeley.compbio.jlibsvm.SVM

svm_predict - Class in edu.berkeley.compbio.jlibsvm.legacyexec

svm_predict() - Constructor for class edu.berkeley.compbio.jlibsvm.legacyexec.svm_predict

svm_scale - Class in edu.berkeley.compbio.jlibsvm.legacyexec

svm_scale() - Constructor for class edu.berkeley.compbio.jlibsvm.legacyexec.svm_scale

svm_toy - Class in edu.berkeley.compbio.jlibsvm.legacyexec

svm_toy() - Constructor for class edu.berkeley.compbio.jlibsvm.legacyexec.svm_toy

svm_train - Class in edu.berkeley.compbio.jlibsvm.legacyexec

svm_train() - Constructor for class edu.berkeley.compbio.jlibsvm.legacyexec.svm_train

SvmBinaryCrossValidationResults<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.binary

SvmBinaryCrossValidationResults(BinaryClassificationProblem<L, P>, Map<P, Float>, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.binary.SvmBinaryCrossValidationResults

SvmContext<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm

SvmContext() - Constructor for class edu.berkeley.compbio.jlibsvm.SvmContext

SvmException - Exception in edu.berkeley.compbio.jlibsvm

SvmException() - Constructor for exception edu.berkeley.compbio.jlibsvm.SvmException

SvmException(String) - Constructor for exception edu.berkeley.compbio.jlibsvm.SvmException

SvmException(Throwable) - Constructor for exception edu.berkeley.compbio.jlibsvm.SvmException

SvmException(String, Throwable) - Constructor for exception edu.berkeley.compbio.jlibsvm.SvmException

SvmMultiClassCrossValidationResults<L extends Comparable,P> - Class in edu.berkeley.compbio.jlibsvm.multi

SvmMultiClassCrossValidationResults(MultiClassProblem<L, P>, Map<P, L>) - Constructor for class edu.berkeley.compbio.jlibsvm.multi.SvmMultiClassCrossValidationResults

SvmProblem<L extends Comparable,P,R> - Interface in edu.berkeley.compbio.jlibsvm

An SVM problem consisting of a mapping of training examples to labels.

svmType - Variable in class edu.berkeley.compbio.jlibsvm.SolutionModel

names the SVM that was used to produce this model; used only for writeToStream

SVs - Variable in class edu.berkeley.compbio.jlibsvm.binary.AlphaModel

T

targetValue - Variable in class edu.berkeley.compbio.jlibsvm.SolutionVector

test(ClusterableIterator<T>, DissimilarityMeasure<String>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVMAdapter

toFileOutputString() - Method in class edu.berkeley.compbio.jlibsvm.kernel.GaussianRBFKernel

toPrimitive(Boolean[]) - Static method in class edu.berkeley.compbio.jlibsvm.util.MathSupport

This is provided by apache commons, but let's avoid the dependency

toString() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameterPoint

toString() - Method in class edu.berkeley.compbio.jlibsvm.kernel.GaussianRBFKernel

toString() - Method in class edu.berkeley.compbio.jlibsvm.kernel.LinearKernel

toString() - Method in class edu.berkeley.compbio.jlibsvm.kernel.PolynomialKernel

toString() - Method in class edu.berkeley.compbio.jlibsvm.kernel.PrecomputedKernel

toString() - Method in class edu.berkeley.compbio.jlibsvm.kernel.SigmoidKernel

toString() - Method in class edu.berkeley.compbio.jlibsvm.SolutionVector

toString() - Method in class edu.berkeley.compbio.jlibsvm.util.SparseVector

train(BinaryClassificationProblem<L, P>, ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationSVM

train(MultiClassProblem<L, P>, ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVM

train() - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVMAdapter

train(OneClassProblem<L, P>, ImmutableSvmParameter<Float, P>) - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassSVC

train(R, ImmutableSvmParameter<Float, P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.EpsilonSVR

train(R, ImmutableSvmParameter<Float, P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.Nu_SVR

train(R, ImmutableSvmParameter<Float, P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionSVM

train(R, ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.SVM

trainGrid(MultiClassProblem<L, P>, ImmutableSvmParameterGrid<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVM

trainOne(BinaryClassificationProblem<L, P>, float, float, ImmutableSvmParameterPoint<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryClassificationSVM

Normal training on the entire problem, with no scaling and no cross-validation-based probability measure.

trainOne(BinaryClassificationProblem<L, P>, float, float, ImmutableSvmParameterPoint<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.C_SVC

trainOne(BinaryClassificationProblem<L, P>, float, float, ImmutableSvmParameterPoint<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.Nu_SVC

trainScaled(MultiClassProblem<L, P>, ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassificationSVM

Train the classifier, and also prepare the probability sigmoid thing if requested.

U

unknown() - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionCrossValidationResults

updateAlphaStatus(float, float) - Method in class edu.berkeley.compbio.jlibsvm.SolutionVector

upperBoundNegative - Variable in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

upperBoundPositive - Variable in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

V

validateParam(ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.C_SVC

validateParam(ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.binary.Nu_SVC

validateParam(ImmutableSvmParameterPoint<Float, P>) - Method in class edu.berkeley.compbio.jlibsvm.oneclass.OneClassSVC

validateParam(ImmutableSvmParameter<Float, P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.EpsilonSVR

validateParam(ImmutableSvmParameterPoint<Float, P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.Nu_SVR

validateParam(ImmutableSvmParameter<Float, P>) - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionSVM

validateParam(ImmutableSvmParameter<L, P>) - Method in class edu.berkeley.compbio.jlibsvm.SVM

valueOf(String) - Static method in enum edu.berkeley.compbio.jlibsvm.multi.MultiClassModel.AllVsAllMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.berkeley.compbio.jlibsvm.multi.MultiClassModel.OneVsAllMode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum edu.berkeley.compbio.jlibsvm.SolutionVector.Status

Returns the enum constant of this type with the specified name.

values() - Static method in enum edu.berkeley.compbio.jlibsvm.multi.MultiClassModel.AllVsAllMode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.berkeley.compbio.jlibsvm.multi.MultiClassModel.OneVsAllMode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum edu.berkeley.compbio.jlibsvm.SolutionVector.Status

Returns an array containing the constants of this enum type, in the order they are declared.

values - Variable in class edu.berkeley.compbio.jlibsvm.util.SparseVector

VotingResult<L> - Class in edu.berkeley.compbio.jlibsvm.multi

VotingResult() - Constructor for class edu.berkeley.compbio.jlibsvm.multi.VotingResult

VotingResult(L, float, float, float, float, float, float) - Constructor for class edu.berkeley.compbio.jlibsvm.multi.VotingResult

W

weights - Variable in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter.Builder

withProbabilityCopy() - Method in class edu.berkeley.compbio.jlibsvm.ImmutableSvmParameter

writeSupportVectors(DataOutputStream) - Method in class edu.berkeley.compbio.jlibsvm.binary.AlphaModel

writeSupportVectors(DataOutputStream) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

writeToStream(DataOutputStream) - Method in class edu.berkeley.compbio.jlibsvm.binary.AlphaModel

writeToStream(DataOutputStream) - Method in class edu.berkeley.compbio.jlibsvm.binary.BinaryModel

writeToStream(DataOutputStream) - Method in class edu.berkeley.compbio.jlibsvm.multi.MultiClassModel

writeToStream(DataOutputStream) - Method in class edu.berkeley.compbio.jlibsvm.regression.RegressionModel

writeToStream(DataOutputStream) - Method in class edu.berkeley.compbio.jlibsvm.SolutionModel

This really should be addToProps, for symmetry

Z

ZscoreScalingModelLearner - Class in edu.berkeley.compbio.jlibsvm.scaler

ZscoreScalingModelLearner(int, boolean) - Constructor for class edu.berkeley.compbio.jlibsvm.scaler.ZscoreScalingModelLearner

ZscoreScalingModelLearner.ZscoreScalingModel - Class in edu.berkeley.compbio.jlibsvm.scaler

ZscoreScalingModelLearner.ZscoreScalingModel(Map<Integer, Float>, Map<Integer, Float>) - Constructor for class edu.berkeley.compbio.jlibsvm.scaler.ZscoreScalingModelLearner.ZscoreScalingModel

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