- s -

• sample() : bpp::AbstractHmmTransitionMatrix
• sampleMean_() : bpp::AdaptiveKernelDensityEstimation
• scalar() : bpp::VectorTools
• scale() : bpp::MatrixTools , bpp::PrincipalComponentAnalysis
• sd() : bpp::VectorTools
• SecondOrderDerivable() : bpp::SecondOrderDerivable
• secondOrderDerivableFunction() : bpp::NewtonOneDimension
• SecondOrderDerivableWrapper() : bpp::SecondOrderDerivableWrapper
• seq() : bpp::VectorTools
• seqFromString() : bpp::NumCalcApplicationTools
• set() : bpp::AbstractDiscreteDistribution , bpp::BracketPoint , bpp::DiscreteDistributionInterface
• setA() : bpp::Bracket
• setAllParameters() : bpp::ParameterList
• setAllParametersValues() : bpp::AbstractNumericalDerivative , bpp::AbstractParametrizable , bpp::FunctionWrapper , bpp::InfinityFunctionWrapper , bpp::ParameterList , bpp::Parametrizable , bpp::ParametrizableAdapter
• setB() : bpp::Bracket
• setBracketing() : bpp::BrentOneDimension
• setBreakPoints() : bpp::HmmLikelihood , bpp::LogsumHmmLikelihood , bpp::LowMemoryRescaledHmmLikelihood , bpp::RescaledHmmLikelihood
• setBurnin() : bpp::AbstractOptimizationStopCondition
• setC() : bpp::Bracket
• setColumn() : bpp::Table< T >
• setColumnNames() : bpp::DataTable , bpp::Table< T >
• setConstraint() : bpp::AbstractParametrizable , bpp::FunctionWrapper , bpp::Parameter , bpp::Parametrizable , bpp::ParametrizableAdapter
• setConstraintPolicy() : bpp::AbstractOptimizer , bpp::DirectionFunction , bpp::OptimizerInterface
• setCoord() : bpp::Point2D< T >
• setCurrentBackgroundColor() : bpp::AbstractGraphicDevice , bpp::GraphicDevice , bpp::PgfGraphicDevice , bpp::XFigGraphicDevice
• setCurrentFont() : bpp::AbstractGraphicDevice , bpp::GraphicDevice , bpp::PgfGraphicDevice , bpp::XFigGraphicDevice
• setCurrentForegroundColor() : bpp::AbstractGraphicDevice , bpp::GraphicDevice , bpp::PgfGraphicDevice , bpp::XFigGraphicDevice
• setCurrentLayer() : bpp::AbstractGraphicDevice , bpp::GraphicDevice , bpp::PgfGraphicDevice
• setCurrentLineType() : bpp::AbstractGraphicDevice , bpp::GraphicDevice , bpp::PgfGraphicDevice , bpp::XFigGraphicDevice
• setCurrentPointSize() : bpp::AbstractGraphicDevice , bpp::GraphicDevice , bpp::PgfGraphicDevice
• setData() : bpp::DualityDiagram
• setDefaultStopCondition_() : bpp::AbstractOptimizer
• setDirection() : bpp::BfgsMultiDimensions
• setEdgeIndex() : bpp::AssociationGraphImplObserver< N, E, GraphImpl > , bpp::AssociationGraphObserver< N, E >
• setEdgeLinking() : bpp::AssociationGraphImplObserver< N, E, GraphImpl > , bpp::AssociationGraphObserver< N, E >
• setFamily() : bpp::Font
• setFather() : bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > , bpp::AssociationTreeGraphObserver< N, E > , bpp::TreeGraph , bpp::TreeGraphImpl< GraphImpl >
• setFontFlag() : bpp::XFigGraphicDevice
• setFrequencies() : bpp::OrderedSimplex , bpp::Simplex
• setFunction() : bpp::AbstractOptimizer , bpp::MetaOptimizer , bpp::OptimizerInterface , bpp::SimpleMultiDimensions , bpp::SimpleNewtonMultiDimensions
• setHmmStateAlphabet() : bpp::AbstractHmmTransitionMatrix , bpp::HmmEmissionProbabilities , bpp::HmmTransitionMatrix
• setInitialInterval() : bpp::BrentOneDimension , bpp::GoldenSectionSearch
• setInterval() : bpp::AbstractNumericalDerivative , bpp::NumericalDerivativeInterface
• setLowerBound() : bpp::IntervalConstraint
• setMaximumNumberOfCorrections() : bpp::NewtonOneDimension
• setMaximumNumberOfEvaluations() : bpp::AbstractOptimizer , bpp::OptimizerInterface
• setMedian() : bpp::AbstractDiscreteDistribution , bpp::DiscreteDistributionInterface , bpp::InvariantMixedDiscreteDistribution , bpp::MixtureOfDiscreteDistributions
• setMessageHandler() : bpp::AbstractOptimizer , bpp::AutoParameter , bpp::DirectionFunction , bpp::OptimizerInterface
• setName() : bpp::Parameter
• setNamespace() : bpp::AbstractParameterAliasable , bpp::AbstractParametrizable , bpp::FunctionWrapper , bpp::InvariantMixedDiscreteDistribution , bpp::LogsumHmmLikelihood , bpp::LowMemoryRescaledHmmLikelihood , bpp::MixtureOfDiscreteDistributions , bpp::Parametrizable , bpp::ParametrizableAdapter , bpp::RescaledHmmLikelihood
• setNodeIndex() : bpp::AssociationGraphImplObserver< N, E, GraphImpl > , bpp::AssociationGraphObserver< N, E >
• setNumberOfCategories() : bpp::AbstractDiscreteDistribution , bpp::DiscreteDistributionInterface , bpp::InvariantMixedDiscreteDistribution , bpp::MixtureOfDiscreteDistributions
• setOptimizationProgressCharacter() : bpp::AbstractOptimizer
• setOptimizer() : bpp::AbstractOptimizationStopCondition , bpp::OptimizationStopCondition
• setOriginalValue() : bpp::IntervalTransformedParameter , bpp::PlaceboTransformedParameter , bpp::RTransformedParameter , bpp::TransformedParameter
• setOutGroup() : bpp::TreeGraph , bpp::TreeGraphImpl< GraphImpl >
• setParameter() : bpp::ParameterList
• setParameterList() : bpp::AliasParameterListener
• setParameters() : bpp::AbstractNumericalDerivative , bpp::DirectionFunction , bpp::FunctionInterface , bpp::FunctionWrapper , bpp::InfinityFunctionWrapper , bpp::LogsumHmmLikelihood , bpp::LowMemoryRescaledHmmLikelihood , bpp::ParameterList , bpp::ReparametrizationFunctionWrapper , bpp::RescaledHmmLikelihood , bpp::TestFunction
• setParametersToDerivate() : bpp::AbstractNumericalDerivative , bpp::NumericalDerivativeInterface
• setParametersValues() : bpp::AbstractNumericalDerivative , bpp::AbstractParametrizable , bpp::FunctionWrapper , bpp::InfinityFunctionWrapper , bpp::ParameterList , bpp::Parametrizable , bpp::ParametrizableAdapter
• setParameterValue() : bpp::AbstractNumericalDerivative , bpp::AbstractParametrizable , bpp::FunctionWrapper , bpp::InfinityFunctionWrapper , bpp::ParameterList , bpp::Parametrizable , bpp::ParametrizableAdapter
• setPrecision() : bpp::AbstractDiscreteDistribution::Order , bpp::AbstractOutputStream , bpp::OutputStream , bpp::Parameter
• setProfiler() : bpp::AbstractOptimizer , bpp::OptimizerInterface
• setRoot() : bpp::AssociationGraphImplObserver< N, E, GraphImpl > , bpp::GlobalGraph , bpp::Graph
• setRow() : bpp::DataTable
• setRowName() : bpp::DataTable
• setRowNames() : bpp::DataTable , bpp::Table< T >
• setSeed() : bpp::RandomTools
• setSeries() : bpp::Font
• setShape() : bpp::Font
• setSize() : bpp::Font
• setStopCondition() : bpp::AbstractOptimizer , bpp::OptimizerInterface
• setStyle() : bpp::Font
• setTolerance() : bpp::AbstractOptimizationStopCondition , bpp::OptimizationStopCondition
• setTransitionProbabilities() : bpp::FullHmmTransitionMatrix
• setUpperBound() : bpp::IntervalConstraint
• setValue() : bpp::AutoParameter , bpp::Parameter
• setVerbose() : bpp::AbstractOptimizer , bpp::OptimizerInterface
• setWeight() : bpp::Font
• setX() : bpp::Point2D< T >
• setXUnit() : bpp::AbstractGraphicDevice , bpp::GraphicDevice
• setY() : bpp::Point2D< T >
• setYUnit() : bpp::AbstractGraphicDevice , bpp::GraphicDevice
• shannon() : bpp::VectorTools
• shannonContinuous() : bpp::VectorTools
• shannonDiscrete() : bpp::VectorTools
• shareParameter() : bpp::ParameterList
• shareParameter_() : bpp::AbstractParameterAliasable , bpp::AbstractParametrizable
• shareParameters() : bpp::ParameterList
• shareParameters_() : bpp::AbstractParameterAliasable , bpp::AbstractParametrizable
• shareSubList() : bpp::ParameterList
• shift() : bpp::NumTools
• sign() : bpp::NumTools
• SimpleDiscreteDistribution() : bpp::SimpleDiscreteDistribution
• SimpleMultiDimensions() : bpp::SimpleMultiDimensions
• SimpleNewtonMultiDimensions() : bpp::SimpleNewtonMultiDimensions
• Simplex() : bpp::DownhillSimplexMethod::Simplex , bpp::Simplex
• sin() : bpp::VectorTools
• singleKeyval() : bpp::KeyvalTools
• size() : bpp::MultiRange< T > , bpp::ParameterList , bpp::RangeCollection< T > , bpp::RangeSet< T >
• sliceWith() : bpp::Range< T >
• SMALL() : bpp::NumConstants
• solve() : bpp::LUDecomposition< Real >
• sonsIterator() : bpp::AssociationDAGraphImplObserver< N, E, DAGraphImpl > , bpp::AssociationDAGraphObserver< N, E > , bpp::AssociationTreeGraphImplObserver< N, E, TreeGraphImpl > , bpp::AssociationTreeGraphObserver< N, E > , bpp::TreeGraph , bpp::TreeGraphImpl< GraphImpl >
• sqr() : bpp::NumTools , bpp::VectorTools
• start() : bpp::AssociationGraphImplObserver< N, E, GraphImpl >::EdgeIteratorClass< GraphIterator, is_const > , bpp::AssociationGraphImplObserver< N, E, GraphImpl >::NodeIteratorClass< GraphIterator, is_const > , bpp::AssociationGraphObserver< N, E >::EdgeIterator , bpp::AssociationGraphObserver< N, E >::NodeIterator , bpp::EdgesIteratorClass< Graph::ALLGRAPHITER, is_const > , bpp::EdgesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const > , bpp::EdgesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const > , bpp::Graph::EdgeIterator , bpp::Graph::NodeIterator , bpp::NeighborIteratorClass< is_const > , bpp::NodesIteratorClass< Graph::ALLGRAPHITER, is_const > , bpp::NodesIteratorClass< Graph::INCOMINGNEIGHBORITER, is_const > , bpp::NodesIteratorClass< Graph::OUTGOINGNEIGHBORITER, is_const >
• startTimer() : bpp::ApplicationTools , bpp::BppApplication
• stateChanged() : bpp::StateListener
• StateChangedEvent() : bpp::StateChangedEvent
• StateListener() : bpp::StateListener
• StatTest() : bpp::StatTest
• StdStr() : bpp::StdStr
• step() : bpp::AbstractOptimizer , bpp::OptimizerInterface
• StlOutputStream() : bpp::StlOutputStream
• StlOutputStreamWrapper() : bpp::StlOutputStreamWrapper
• str() : bpp::StdStr
• strictLowerBound() : bpp::AbstractDiscreteDistribution , bpp::DiscreteDistributionInterface , bpp::IntervalConstraint
• strictUpperBound() : bpp::AbstractDiscreteDistribution , bpp::DiscreteDistributionInterface , bpp::IntervalConstraint
• StringTokenizer() : bpp::StringTokenizer
• sum() : bpp::VectorTools
• sumElements() : bpp::MatrixTools
• sumExp() : bpp::VectorTools
• sumProd() : bpp::VectorTools
• SvgGraphicDevice() : bpp::SvgGraphicDevice
• swap() : bpp::NumTools
• switchNodes() : bpp::GlobalGraph