bpp::Node_DF Class Reference

Base dataflow Node class. More...

#include <Bpp/Phyl/Likelihood/DataFlow/DataFlow.h>

Inheritance diagram for bpp::Node_DF:

Collaboration diagram for bpp::Node_DF:

Public Member Functions
	Node_DF ()=default
	Node_DF (const Node_DF &)=delete
	Node_DF (Node_DF &&)=delete
Node_DF &	operator= (const Node_DF &)=delete
Node_DF &	operator= (Node_DF &&)=delete
virtual	~Node_DF ()
	Node_DF (const NodeRefVec &dependenciesArg)
	Node_DF (NodeRefVec &&dependenciesArg)
bool	isValid () const noexcept
std::size_t	nbDependentNodes () const noexcept
	Number of dependent nodes (ie nodes that depend on this) More...
const std::vector< Node_DF * > &	dependentNodes () const noexcept
std::size_t	nbDependencies () const noexcept
	Number of dependencies (ie nodes we depend on) More...
const NodeRefVec &	dependencies () const noexcept
const NodeRef &	dependency (std::size_t i) const noexcept
virtual std::string	description () const
	Node pretty name (default = type name). More...
virtual std::string	color () const
virtual std::string	shape () const
virtual std::string	debugInfo () const
	Node debug info (default = ""): user defined detailed info for DF graph debug. More...
virtual bool	hasNumericalProperty (NumericalProperty prop) const
	Test if the node has the given numerical property. More...
virtual bool	compareAdditionalArguments (const Node_DF &other) const
	Compare node-specific configuration to another. More...
virtual std::size_t	hashAdditionalArguments () const
	Return the hash of node-specific configuration. More...
virtual NodeRef	derive (Context &c, const Node_DF &node)
	Returns a node computing d(this_node_expression)/d(node_expression). More...
virtual NodeRef	recreate (Context &c, NodeRefVec &&deps)
	Recreate the node with different dependencies. More...
void	computeRecursively ()
	Compute this node value, recomputing dependencies (transitively) as needed. More...

Protected Member Functions
virtual void	compute ()=0
	Computation implementation. More...
void	invalidateRecursively () noexcept
	Invalidate (transitively) dependent nodes from this one. More...
void	makeInvalid () noexcept
void	makeValid () noexcept
void	resetDependencies_ (NodeRefVec &&dependenciesArg)

Private Member Functions
void	registerNode (Node_DF *n)
void	unregisterNode (const Node_DF *n)

Private Attributes
NodeRefVec	dependencyNodes_ {}
std::vector< Node_DF * >	dependentNodes_ {}
bool	isValid_ {false}

Friends
class	Context

Detailed Description

Base dataflow Node class.

All data flow nodes inherit from this class. Instances of this class must be used through std::shared_ptr<T>.

A base node represents something that can be computed from its dependencies. The computation is defined by the compute() method in derived classes.

The base class stores a boolean indicating if the current value is valid. This boolean is used to cache intermediate results in the graph, and avoid recomputings. When data flow graph leaves change, they invalidate (transitively) dependent nodes. This means setting the valid flag to false, to trigger a recomputation at next access.

Each node has dependencies: other nodes providing data it needs to compute. These dependencies are stored as NodeRef (shared_ptr<Node>). Thus, multiple nodes can depend on the same value, to shared intermediate results. The list of dependencies is FIXED at creation, and cannot be changed. Changing the meaning of a node (dependencies, config) is done by creating a different node.

Nodes also store pointers to dependent nodes. Dependent nodes are nodes which have a direct dependency to the current node. This is used to propagate invalidations to all transitive dependent nodes of a leaf. Dependent nodes are stored as raw pointers (no ownership).

Base nodes thus store the data flow graph topology, in terms of pointer to base Node. This is useful for code reuse: no templates in topology walks code. It is useful for debugging: can print the whole graph structure. Accessing the derived classes (for compute) can be done efficiently with static_cast.

Two main invariants are maintained at all times by this class. 1: If a node is valid, all its transitive dependencies are valid. 2: If a node is invalid, all transitively dependent nodes are invalid.

In addition, two properties are implemented for performance: 1: During computation of a node dependencies, do not recompute valid nodes. 2: Only invalidate transitively dependent node, not others (still valid).

Specific features are present in the base class as virtual functions. This include derivation (numerical values), debug, etc. These features have no-op or failure defaults which can be overridden in derived classes.

Definition at line 151 of file DataFlow.h.

Constructor & Destructor Documentation

Node_DF() [1/5]

bpp::Node_DF::Node_DF ( )

default

Node_DF() [2/5]

bpp::Node_DF::Node_DF ( const Node_DF &  )

delete

Node_DF() [3/5]

bpp::Node_DF::Node_DF ( Node_DF &&  )

delete

~Node_DF()

bpp::Node_DF::~Node_DF ( )

virtual

Definition at line 142 of file DataFlow.cpp.

References dependencyNodes_.

Node_DF() [4/5]

bpp::Node_DF::Node_DF

(

const NodeRefVec &

dependenciesArg

)

Definition at line 123 of file DataFlow.cpp.

References dependencyNodes_.

Node_DF() [5/5]

bpp::Node_DF::Node_DF

(

NodeRefVec &&

dependenciesArg

)

Definition at line 132 of file DataFlow.cpp.

References dependencyNodes_.

Member Function Documentation

color()

virtual std::string bpp::Node_DF::color ( ) const

inlinevirtual

Reimplemented in bpp::Sequence_DF, bpp::ShiftParameter, bpp::ConfiguredParameter, bpp::NumericConstant< T >, bpp::MatrixProduct< R, T0, T1 >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::TransitionMatrixFromTransitionMatrix, bpp::EquilibriumFrequenciesFromTransitionMatrix, bpp::ConfiguredTransitionMatrix, bpp::FrequenciesFromSimplex, bpp::ConfiguredSimplex, bpp::ProbabilityFromMixedModel, bpp::ProbabilitiesFromMixedModel, bpp::TransitionFunctionFromModel, bpp::TransitionMatrixFromModel, bpp::EquilibriumFrequenciesFromModel, bpp::ConfiguredModel, bpp::FrequenciesFromFrequencySet, bpp::ConfiguredFrequencySet, bpp::CategoryFromDiscreteDistribution, bpp::ProbabilityFromDiscreteDistribution, bpp::ProbabilitiesFromDiscreteDistribution, bpp::ConfiguredDistribution, and bpp::ValueFromConfiguredParameter.

Definition at line 190 of file DataFlow.h.

Referenced by bpp::writeDotEdge(), and bpp::writeDotNode().

compareAdditionalArguments()

bool bpp::Node_DF::compareAdditionalArguments ( const Node_DF &  other ) const

virtual

Compare node-specific configuration to another.

Required by Context for merging. It must compare everything in the node configuration except its type and dependencies. See DataFlowNumeric for examples. The default returns false, so nodes are considered different and not merged.

Reimplemented in bpp::Sequence_DF, bpp::ConfiguredParameter, bpp::ConfiguredModel, bpp::NumericConstant< T >, bpp::BackwardHmmLikelihood_DF, bpp::ForwardHmmD2Likelihood_DF, bpp::ForwardHmmDLikelihood_DF, bpp::ForwardHmmLikelihood_DF, bpp::CondLikelihood, bpp::FrequenciesFromSimplex, bpp::ValueFromConfiguredParameter, bpp::ShiftParameter, bpp::ProbabilityFromMixedModel, bpp::ProbabilitiesFromMixedModel, bpp::FrequenciesFromFrequencySet, bpp::CategoryFromDiscreteDistribution, bpp::ProbabilityFromDiscreteDistribution, bpp::ProbabilitiesFromDiscreteDistribution, bpp::Identity< R >, bpp::Convert< R, F >, bpp::ConstantOne< T >, bpp::ConstantZero< T >, bpp::CombineDeltaShifted< T >, bpp::ShiftDelta< T >, bpp::MatrixProduct< R, T0, T1 >, bpp::LogSumExp< R, T0, T1 >, bpp::SumOfLogarithms< F >, bpp::ScalarProduct< R, T0, T1 >, bpp::CWiseConstantPow< T >, bpp::CWiseExp< T >, bpp::CWiseLog< T >, bpp::CWiseInverse< T >, bpp::CWiseNegate< T >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, ReductionOf< T > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >, bpp::CWiseAdd< R, T >, bpp::CWiseAdd< R, ReductionOf< T > >, bpp::CWiseSub< R, std::tuple< T0, T1 > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::CWiseCompound< R, ReductionOf< T > >, bpp::CWiseMatching< R, ReductionOf< T > >, bpp::CWisePattern< R >, bpp::CWiseFill< R, T >, bpp::TransitionMatrixFromTransitionMatrix, bpp::EquilibriumFrequenciesFromTransitionMatrix, bpp::ConfiguredTransitionMatrix, bpp::ConfiguredSimplex, bpp::TransitionFunctionFromModel, bpp::TransitionMatrixFromModel, bpp::EquilibriumFrequenciesFromModel, bpp::ConfiguredFrequencySet, and bpp::ConfiguredDistribution.

Definition at line 170 of file DataFlow.cpp.

compute()

virtual void bpp::Node_DF::compute ( )

protectedpure virtual

Computation implementation.

This functions is defined by derived classes. It should compute the new node value from dependency node values. When called, dependency node are guaranteed to have valid values.

This function is private to prevent use for invalid dependencies. Higher level functions like computeRecursively call it while ensuring dependency validity.

Compute has access to dependencies as a NodeRefVec (base Node_DF classes only). The recommended usage is to check dependency types at Node construction. Then use static_cast to access derived classes efficiently from the NodeRefVec. See DataFlowNumeric.h for examples.

Implemented in bpp::BackwardHmmLikelihood_DF, bpp::ForwardHmmD2Likelihood_DF, bpp::ForwardHmmDLikelihood_DF, bpp::ForwardHmmLikelihood_DF, bpp::CondLikelihood, bpp::ConfiguredParameter, bpp::ConfiguredModel, bpp::CombineDeltaShifted< T >, bpp::SumOfLogarithms< F >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseAdd< R, T >, bpp::CWiseAdd< R, ReductionOf< T > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::CWiseCompound< R, ReductionOf< T > >, bpp::CWiseMatching< R, ReductionOf< T > >, bpp::CWisePattern< R >, bpp::CWiseFill< R, T >, bpp::TransitionMatrixFromTransitionMatrix, bpp::EquilibriumFrequenciesFromTransitionMatrix, bpp::FrequenciesFromSimplex, bpp::Sequence_DF, bpp::ValueFromConfiguredParameter, bpp::ShiftParameter, bpp::ProbabilityFromMixedModel, bpp::ProbabilitiesFromMixedModel, bpp::TransitionFunctionFromModel, bpp::TransitionMatrixFromModel, bpp::EquilibriumFrequenciesFromModel, bpp::FrequenciesFromFrequencySet, bpp::CategoryFromDiscreteDistribution, bpp::ProbabilityFromDiscreteDistribution, bpp::ProbabilitiesFromDiscreteDistribution, bpp::Identity< R >, bpp::Convert< R, F >, bpp::NumericMutable< T >, bpp::NumericConstant< T >, bpp::ConstantOne< T >, bpp::ConstantZero< T >, bpp::ShiftDelta< T >, bpp::MatrixProduct< R, T0, T1 >, bpp::LogSumExp< R, T0, T1 >, bpp::ScalarProduct< R, T0, T1 >, bpp::CWiseConstantPow< T >, bpp::CWiseExp< T >, bpp::CWiseLog< T >, bpp::CWiseInverse< T >, bpp::CWiseNegate< T >, bpp::CWiseMul< R, ReductionOf< T > >, bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >, bpp::CWiseSub< R, std::tuple< T0, T1 > >, bpp::ConfiguredTransitionMatrix, bpp::ConfiguredSimplex, bpp::ConfiguredFrequencySet, bpp::ConfiguredDistribution, bpp::CombineDeltaShifted< T >, bpp::CombineDeltaShifted< T >, bpp::SumOfLogarithms< F >, bpp::SumOfLogarithms< F >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseAdd< R, T >, bpp::CWiseAdd< R, T >, bpp::CWiseAdd< R, T >, bpp::CWiseAdd< R, ReductionOf< T > >, bpp::CWiseAdd< R, ReductionOf< T > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::CWiseFill< R, T >, bpp::CWiseFill< R, T >, and bpp::CWiseFill< R, T >.

computeRecursively()

void bpp::Node_DF::computeRecursively

(

)

Compute this node value, recomputing dependencies (transitively) as needed.

Not thread safe !

Definition at line 183 of file DataFlow.cpp.

References isValid().

Referenced by bpp::Value< T >::targetValue().

debugInfo()

std::string bpp::Node_DF::debugInfo ( ) const

virtual

Node debug info (default = ""): user defined detailed info for DF graph debug.

Reimplemented in bpp::BackwardHmmLikelihood_DF, bpp::ForwardHmmD2Likelihood_DF, bpp::ForwardHmmDLikelihood_DF, bpp::ForwardHmmLikelihood_DF, bpp::CondLikelihood, bpp::ShiftParameter, bpp::ConfiguredParameter, bpp::Identity< R >, bpp::Convert< R, F >, bpp::NumericMutable< T >, bpp::NumericConstant< T >, bpp::ConstantOne< T >, bpp::ConstantZero< T >, bpp::CombineDeltaShifted< T >, bpp::ShiftDelta< T >, bpp::MatrixProduct< R, T0, T1 >, bpp::LogSumExp< R, T0, T1 >, bpp::SumOfLogarithms< F >, bpp::ScalarProduct< R, T0, T1 >, bpp::CWiseConstantPow< T >, bpp::CWiseExp< T >, bpp::CWiseLog< T >, bpp::CWiseInverse< T >, bpp::CWiseNegate< T >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, ReductionOf< T > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >, bpp::CWiseAdd< R, T >, bpp::CWiseAdd< R, ReductionOf< T > >, bpp::CWiseSub< R, std::tuple< T0, T1 > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::CWiseCompound< R, ReductionOf< T > >, bpp::CWiseMatching< R, ReductionOf< T > >, bpp::CWisePattern< R >, bpp::CWiseFill< R, T >, bpp::TransitionMatrixFromTransitionMatrix, bpp::EquilibriumFrequenciesFromTransitionMatrix, bpp::ConfiguredTransitionMatrix, bpp::FrequenciesFromSimplex, bpp::ConfiguredSimplex, bpp::Sequence_DF, bpp::ValueFromConfiguredParameter, bpp::ProbabilityFromMixedModel, bpp::ProbabilitiesFromMixedModel, bpp::TransitionFunctionFromModel, bpp::TransitionMatrixFromModel, bpp::EquilibriumFrequenciesFromModel, bpp::ConfiguredModel, bpp::FrequenciesFromFrequencySet, bpp::ConfiguredFrequencySet, bpp::CategoryFromDiscreteDistribution, bpp::ProbabilityFromDiscreteDistribution, bpp::ProbabilitiesFromDiscreteDistribution, and bpp::ConfiguredDistribution.

Definition at line 166 of file DataFlow.cpp.

Referenced by bpp::writeDotNode().

dependencies()

const NodeRefVec& bpp::Node_DF::dependencies ( ) const

inlinenoexcept

Definition at line 183 of file DataFlow.h.

References dependencyNodes_.

Referenced by bpp::CWiseAdd< R, ReductionOf< T > >::compute(), bpp::CombineDeltaShifted< T >::compute(), bpp::CWiseMul< R, ReductionOf< T > >::compute(), bpp::ConfiguredDistribution::ConfiguredDistribution(), bpp::ConfiguredFrequencySet::ConfiguredFrequencySet(), bpp::ConfiguredModel::ConfiguredModel(), bpp::ConfiguredSimplex::ConfiguredSimplex(), bpp::ConfiguredTransitionMatrix::ConfiguredTransitionMatrix(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::derive(), and bpp::CWiseMul< R, ReductionOf< T > >::derive().

dependency()

const NodeRef& bpp::Node_DF::dependency ( std::size_t  i ) const

inlinenoexcept

Definition at line 185 of file DataFlow.h.

References dependencyNodes_.

Referenced by bpp::BackwardHmmLikelihood_DF::BackwardHmmLikelihood_DF(), bpp::ForwardHmmLikelihood_DF::build(), bpp::ValueFromConfiguredParameter::color(), bpp::CWiseFill< R, T >::compute(), bpp::CWiseApply< R, T, F >::compute(), bpp::CWiseAdd< R, std::tuple< T0, T1 > >::compute(), bpp::CWiseAdd< R, T >::compute(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::compute(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::compute(), bpp::SumOfLogarithms< F >::compute(), bpp::CombineDeltaShifted< T >::compute(), bpp::CWiseSub< R, std::tuple< T0, T1 > >::compute(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::compute(), bpp::CWiseMean< R, ReductionOf< T >, P >::compute(), bpp::CWiseNegate< T >::compute(), bpp::CWiseInverse< T >::compute(), bpp::CWiseLog< T >::compute(), bpp::CWiseExp< T >::compute(), bpp::CWiseConstantPow< T >::compute(), bpp::ScalarProduct< R, T0, T1 >::compute(), bpp::LogSumExp< R, T0, T1 >::compute(), bpp::MatrixProduct< R, T0, T1 >::compute(), bpp::ShiftDelta< T >::compute(), bpp::Convert< R, F >::compute(), bpp::Identity< R >::compute(), bpp::ProbabilitiesFromDiscreteDistribution::compute(), bpp::ProbabilityFromDiscreteDistribution::compute(), bpp::CategoryFromDiscreteDistribution::compute(), bpp::FrequenciesFromFrequencySet::compute(), bpp::EquilibriumFrequenciesFromModel::compute(), bpp::TransitionMatrixFromModel::compute(), bpp::TransitionFunctionFromModel::compute(), bpp::ProbabilitiesFromMixedModel::compute(), bpp::ProbabilityFromMixedModel::compute(), bpp::ShiftParameter::compute(), bpp::ValueFromConfiguredParameter::compute(), bpp::FrequenciesFromSimplex::compute(), bpp::EquilibriumFrequenciesFromTransitionMatrix::compute(), bpp::TransitionMatrixFromTransitionMatrix::compute(), bpp::CWisePattern< R >::compute(), bpp::CWiseMatching< R, ReductionOf< T > >::compute(), bpp::CWiseCompound< R, ReductionOf< T > >::compute(), bpp::ConfiguredParameter::compute(), bpp::CombineDeltaShifted< T >::create(), bpp::TransitionMatrixFromModel::debugInfo(), bpp::TransitionFunctionFromModel::debugInfo(), bpp::ValueFromConfiguredParameter::debugInfo(), bpp::CondLikelihood::debugInfo(), bpp::CWiseFill< R, T >::derive(), bpp::CWisePattern< R >::derive(), bpp::CWiseMatching< R, ReductionOf< T > >::derive(), bpp::CWiseCompound< R, ReductionOf< T > >::derive(), bpp::CWiseApply< R, T, F >::derive(), bpp::CWiseAdd< R, std::tuple< T0, T1 > >::derive(), bpp::CWiseSub< R, std::tuple< T0, T1 > >::derive(), bpp::CWiseAdd< R, ReductionOf< T > >::derive(), bpp::CWiseAdd< R, T >::derive(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::derive(), bpp::CWiseMean< R, ReductionOf< T >, P >::derive(), bpp::CWiseMul< R, std::tuple< T0, T1 > >::derive(), bpp::CWiseMul< R, ReductionOf< T > >::derive(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::derive(), bpp::CWiseNegate< T >::derive(), bpp::CWiseInverse< T >::derive(), bpp::CWiseLog< T >::derive(), bpp::CWiseExp< T >::derive(), bpp::CWiseConstantPow< T >::derive(), bpp::ScalarProduct< R, T0, T1 >::derive(), bpp::SumOfLogarithms< F >::derive(), bpp::LogSumExp< R, T0, T1 >::derive(), bpp::MatrixProduct< R, T0, T1 >::derive(), bpp::ShiftDelta< T >::derive(), bpp::CombineDeltaShifted< T >::derive(), bpp::Convert< R, F >::derive(), bpp::Identity< R >::derive(), bpp::ProbabilitiesFromDiscreteDistribution::derive(), bpp::ProbabilityFromDiscreteDistribution::derive(), bpp::CategoryFromDiscreteDistribution::derive(), bpp::FrequenciesFromFrequencySet::derive(), bpp::EquilibriumFrequenciesFromModel::derive(), bpp::TransitionMatrixFromModel::derive(), bpp::TransitionFunctionFromModel::derive(), bpp::ProbabilitiesFromMixedModel::derive(), bpp::ProbabilityFromMixedModel::derive(), bpp::ShiftParameter::derive(), bpp::ValueFromConfiguredParameter::derive(), bpp::FrequenciesFromSimplex::derive(), bpp::EquilibriumFrequenciesFromTransitionMatrix::derive(), bpp::TransitionMatrixFromTransitionMatrix::derive(), bpp::BackwardHmmLikelihood_DF::derive(), bpp::ConfiguredParameter::derive(), bpp::ValueFromConfiguredParameter::description(), bpp::ConfiguredParameter::getValue(), bpp::ConfiguredParameter::recreate(), bpp::ConfiguredParameter::setValue(), and bpp::writeDotEdge().

dependentNodes()

const std::vector<Node_DF*>& bpp::Node_DF::dependentNodes ( ) const

inlinenoexcept

Definition at line 175 of file DataFlow.h.

References dependentNodes_.

derive()

NodeRef bpp::Node_DF::derive ( Context &  c, const Node_DF &  node  )

virtual

Returns a node computing d(this_node_expression)/d(node_expression).

The expression represented by 'node' is considered as a variable. Event if 'node' is a constant value node, d(node)/d(node) == 1. The derivative of a matrix is the matrix of the derivatives. Derivation is undefined by default, and this function will throw an exception. Implementations will usually recursively derive sub-expressions and combine them.

Reimplemented in bpp::ConfiguredParameter, bpp::BackwardHmmLikelihood_DF, bpp::ForwardHmmD2Likelihood_DF, bpp::ForwardHmmDLikelihood_DF, bpp::ForwardHmmLikelihood_DF, bpp::CondLikelihood, bpp::TransitionMatrixFromTransitionMatrix, bpp::EquilibriumFrequenciesFromTransitionMatrix, bpp::FrequenciesFromSimplex, bpp::Sequence_DF, bpp::ValueFromConfiguredParameter, bpp::ShiftParameter, bpp::ProbabilityFromMixedModel, bpp::ProbabilitiesFromMixedModel, bpp::TransitionFunctionFromModel, bpp::TransitionMatrixFromModel, bpp::EquilibriumFrequenciesFromModel, bpp::FrequenciesFromFrequencySet, bpp::CategoryFromDiscreteDistribution, bpp::ProbabilityFromDiscreteDistribution, bpp::ProbabilitiesFromDiscreteDistribution, bpp::Identity< R >, bpp::Convert< R, F >, bpp::NumericMutable< T >, bpp::NumericConstant< T >, bpp::ConstantOne< T >, bpp::ConstantZero< T >, bpp::CombineDeltaShifted< T >, bpp::ShiftDelta< T >, bpp::MatrixProduct< R, T0, T1 >, bpp::LogSumExp< R, T0, T1 >, bpp::SumOfLogarithms< F >, bpp::ScalarProduct< R, T0, T1 >, bpp::CWiseConstantPow< T >, bpp::CWiseExp< T >, bpp::CWiseLog< T >, bpp::CWiseInverse< T >, bpp::CWiseNegate< T >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, ReductionOf< T > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >, bpp::CWiseAdd< R, T >, bpp::CWiseAdd< R, ReductionOf< T > >, bpp::CWiseSub< R, std::tuple< T0, T1 > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::CWiseCompound< R, ReductionOf< T > >, bpp::CWiseMatching< R, ReductionOf< T > >, bpp::CWisePattern< R >, and bpp::CWiseFill< R, T >.

Definition at line 173 of file DataFlow.cpp.

References description().

Referenced by bpp::Value< T >::deriveAsValue().

description()

std::string bpp::Node_DF::description ( ) const

virtual

Node pretty name (default = type name).

Reimplemented in bpp::ShiftParameter, bpp::ConfiguredParameter, bpp::NumericMutable< T >, bpp::NumericConstant< T >, bpp::CombineDeltaShifted< T >, bpp::MatrixProduct< R, T0, T1 >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::TransitionMatrixFromTransitionMatrix, bpp::ConfiguredTransitionMatrix, bpp::ConfiguredSimplex, bpp::Sequence_DF, bpp::TransitionFunctionFromModel, bpp::TransitionMatrixFromModel, bpp::ConfiguredModel, bpp::ConfiguredFrequencySet, bpp::ConfiguredDistribution, and bpp::ValueFromConfiguredParameter.

Definition at line 151 of file DataFlow.cpp.

References bpp::prettyTypeName().

Referenced by derive(), bpp::Sequence_DF::description(), bpp::NumericConstant< T >::description(), bpp::NumericMutable< T >::description(), recreate(), and bpp::writeDotNode().

hashAdditionalArguments()

std::size_t bpp::Node_DF::hashAdditionalArguments ( ) const

virtual

Return the hash of node-specific configuration.

Compute a hash from additional arguments of the node. The hashed values must the same as the ones compared by compareAdditionalArguments. The default returns 0, which is ok if there are no additional arguments.

Reimplemented in bpp::Sequence_DF, bpp::ConfiguredParameter, bpp::ConfiguredModel, bpp::NumericConstant< T >, bpp::ShiftParameter, bpp::ConstantOne< T >, bpp::ConstantZero< T >, bpp::CombineDeltaShifted< T >, bpp::ShiftDelta< T >, bpp::CWiseConstantPow< T >, bpp::ConfiguredTransitionMatrix, bpp::ConfiguredSimplex, bpp::ConfiguredFrequencySet, and bpp::ConfiguredDistribution.

Definition at line 171 of file DataFlow.cpp.

hasNumericalProperty()

bool bpp::Node_DF::hasNumericalProperty ( NumericalProperty  prop ) const

virtual

Test if the node has the given numerical property.

This is an optional indication only, used for optimisations. If unsure, leave it to always false (the default implementation). This should be non recursive, to ensure a constant time check.

Reimplemented in bpp::NumericConstant< T >, bpp::ConstantOne< T >, and bpp::ConstantZero< T >.

Definition at line 168 of file DataFlow.cpp.

Referenced by bpp::ScalarProduct< R, T0, T1 >::create(), bpp::CWisePattern< R >::create(), bpp::CWiseAdd< R, T >::create(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::create(), bpp::CWiseDiv< R, std::tuple< T0, T1 > >::create(), bpp::CWiseNegate< T >::create(), bpp::CWiseInverse< T >::create(), bpp::CWiseLog< T >::create(), bpp::CWiseExp< T >::create(), bpp::CWiseConstantPow< T >::create(), and bpp::CombineDeltaShifted< T >::create().

invalidateRecursively()

void bpp::Node_DF::invalidateRecursively ( )

protectednoexcept

Invalidate (transitively) dependent nodes from this one.

Not thread safe !

Definition at line 219 of file DataFlow.cpp.

References isValid().

Referenced by bpp::Value< T >::modify(), and resetDependencies_().

isValid()

bool bpp::Node_DF::isValid ( ) const

inlinenoexcept

Definition at line 166 of file DataFlow.h.

References isValid_.

Referenced by computeRecursively(), invalidateRecursively(), and bpp::writeDotNode().

makeInvalid()

void bpp::Node_DF::makeInvalid ( )

inlineprotectednoexcept

Definition at line 270 of file DataFlow.h.

References isValid_.

Referenced by resetDependencies_().

makeValid()

void bpp::Node_DF::makeValid ( )

inlineprotectednoexcept

Definition at line 271 of file DataFlow.h.

References isValid_.

Referenced by bpp::Value< T >::modify(), bpp::NumericConstant< T >::NumericConstant(), bpp::NumericMutable< T >::NumericMutable(), and bpp::Sequence_DF::Sequence_DF().

nbDependencies()

std::size_t bpp::Node_DF::nbDependencies ( ) const

inlinenoexcept

Number of dependencies (ie nodes we depend on)

Definition at line 181 of file DataFlow.h.

References dependencyNodes_.

Referenced by bpp::SumOfLogarithms< F >::compute(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::compute(), bpp::CWiseMean< R, ReductionOf< T >, P >::compute(), bpp::EquilibriumFrequenciesFromModel::compute(), bpp::TransitionMatrixFromModel::compute(), bpp::CWiseMatching< R, ReductionOf< T > >::compute(), bpp::CWiseCompound< R, ReductionOf< T > >::compute(), bpp::CWiseMatching< R, ReductionOf< T > >::derive(), bpp::CWiseCompound< R, ReductionOf< T > >::derive(), bpp::CWiseAdd< R, ReductionOf< T > >::derive(), bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >::derive(), bpp::CWiseMean< R, ReductionOf< T >, P >::derive(), bpp::CWiseMul< R, ReductionOf< T > >::derive(), bpp::SumOfLogarithms< F >::derive(), bpp::CombineDeltaShifted< T >::derive(), bpp::EquilibriumFrequenciesFromModel::derive(), and bpp::TransitionMatrixFromModel::derive().

nbDependentNodes()

std::size_t bpp::Node_DF::nbDependentNodes ( ) const

inlinenoexcept

Number of dependent nodes (ie nodes that depend on this)

Definition at line 172 of file DataFlow.h.

References dependentNodes_.

operator=() [1/2]

Node_DF& bpp::Node_DF::operator= ( const Node_DF &  )

delete

operator=() [2/2]

Node_DF& bpp::Node_DF::operator= ( Node_DF &&  )

delete

recreate()

NodeRef bpp::Node_DF::recreate ( Context &  c, NodeRefVec &&  deps  )

virtual

Recreate the node with different dependencies.

Reimplemented in bpp::ConfiguredParameter, bpp::BackwardHmmLikelihood_DF, bpp::ForwardHmmD2Likelihood_DF, bpp::ForwardHmmDLikelihood_DF, bpp::ForwardHmmLikelihood_DF, bpp::CondLikelihood, bpp::TransitionMatrixFromTransitionMatrix, bpp::EquilibriumFrequenciesFromTransitionMatrix, bpp::ConfiguredTransitionMatrix, bpp::FrequenciesFromSimplex, bpp::ConfiguredSimplex, bpp::Sequence_DF, bpp::ValueFromConfiguredParameter, bpp::ShiftParameter, bpp::ProbabilityFromMixedModel, bpp::ProbabilitiesFromMixedModel, bpp::TransitionFunctionFromModel, bpp::TransitionMatrixFromModel, bpp::EquilibriumFrequenciesFromModel, bpp::ConfiguredModel, bpp::FrequenciesFromFrequencySet, bpp::ConfiguredFrequencySet, bpp::CategoryFromDiscreteDistribution, bpp::ProbabilityFromDiscreteDistribution, bpp::ProbabilitiesFromDiscreteDistribution, bpp::ConfiguredDistribution, bpp::Identity< R >, bpp::Convert< R, F >, bpp::CombineDeltaShifted< T >, bpp::ShiftDelta< T >, bpp::MatrixProduct< R, T0, T1 >, bpp::LogSumExp< R, T0, T1 >, bpp::SumOfLogarithms< F >, bpp::ScalarProduct< R, T0, T1 >, bpp::CWiseConstantPow< T >, bpp::CWiseExp< T >, bpp::CWiseLog< T >, bpp::CWiseInverse< T >, bpp::CWiseNegate< T >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, ReductionOf< T > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >, bpp::CWiseAdd< R, T >, bpp::CWiseAdd< R, ReductionOf< T > >, bpp::CWiseSub< R, std::tuple< T0, T1 > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::CWiseCompound< R, ReductionOf< T > >, bpp::CWiseMatching< R, ReductionOf< T > >, bpp::CWisePattern< R >, bpp::CWiseFill< R, T >, bpp::NumericConstant< T >, bpp::NumericMutable< T >, bpp::ConstantOne< T >, and bpp::ConstantZero< T >.

Definition at line 178 of file DataFlow.cpp.

References description().

registerNode()

void bpp::Node_DF::registerNode ( Node_DF *  n )

private

Definition at line 240 of file DataFlow.cpp.

References dependentNodes_.

resetDependencies_()

void bpp::Node_DF::resetDependencies_ ( NodeRefVec &&  dependenciesArg )

inlineprotected

Definition at line 288 of file DataFlow.h.

References dependencyNodes_, invalidateRecursively(), and makeInvalid().

shape()

virtual std::string bpp::Node_DF::shape ( ) const

inlinevirtual

Reimplemented in bpp::MatrixProduct< R, T0, T1 >, bpp::CWiseDiv< R, std::tuple< T0, T1 > >, bpp::CWiseMul< R, std::tuple< T0, T1 > >, bpp::CWiseMean< R, ReductionOf< T >, P >, bpp::CWiseMean< R, ReductionOf< T >, ReductionOf< P > >, bpp::CWiseAdd< R, std::tuple< T0, T1 > >, bpp::CWiseApply< R, T, F >, bpp::TransitionMatrixFromTransitionMatrix, bpp::TransitionFunctionFromModel, and bpp::TransitionMatrixFromModel.

Definition at line 195 of file DataFlow.h.

Referenced by bpp::writeDotNode().

unregisterNode()

void bpp::Node_DF::unregisterNode ( const Node_DF *  n )

private

Definition at line 245 of file DataFlow.cpp.

References dependentNodes_.

Friends And Related Function Documentation

Context

friend class Context

friend

Definition at line 316 of file DataFlow.h.

Member Data Documentation

dependencyNodes_

NodeRefVec bpp::Node_DF::dependencyNodes_ {}

private

Definition at line 312 of file DataFlow.h.

Referenced by dependencies(), dependency(), nbDependencies(), Node_DF(), resetDependencies_(), and ~Node_DF().

dependentNodes_

std::vector<Node_DF*> bpp::Node_DF::dependentNodes_ {}

private

Definition at line 313 of file DataFlow.h.

Referenced by dependentNodes(), nbDependentNodes(), registerNode(), and unregisterNode().

isValid_

bool bpp::Node_DF::isValid_ {false}

private

Definition at line 314 of file DataFlow.h.

Referenced by isValid(), makeInvalid(), and makeValid().

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The documentation for this class was generated from the following files:

• Bpp/Phyl/Likelihood/DataFlow/DataFlow.h
• Bpp/Phyl/Likelihood/DataFlow/DataFlow.cpp