#include "njn_dynprogprob.hpp"
(Private to src/algo/blast/gumbel_params.)

Inheritance diagram for DynProgProb:

Collaboration diagram for DynProgProb:

Public Member Functions
	DynProgProb (ValueFct valueFct_=0, size_t dimInputProb_=0, const double inputProb_=0, Int4 valueLower_=0, Int4 valueUpper_=0, const double *prob_=0)

	DynProgProb (const DynProgProb &dynProgProb_)

virtual	~DynProgProb ()

virtual	operator bool () const

virtual DynProgProb &	operator= (const DynProgProb &dynProgProb_)

virtual void	copy (const DynProgProb &dynProgProb_)

virtual void	copy (size_t step_, const double const array_, size_t arrayCapacity_, Int4 valueBegin_=0, Int4 valueLower_=0, Int4 valueUpper_=0, ValueFct valueFct_=0, size_t dimInputProb_=0, const double inputProb_=0)

virtual void	clear (Int4 valueLower_, Int4 valueUpper_=0, const double *prob_=0)

virtual void	clear ()

virtual void	setValueFct (ValueFct *valueFct_)

virtual void	setInput (size_t dimInputProb_, const double *inputProb_)

virtual void	update ()

virtual double	getProb (Int4 value_) const

virtual size_t	getStep () const

virtual const double const	getArray () const

virtual size_t	getArrayCapacity () const

virtual Int4	getValueBegin () const

virtual Int4	getValueLower () const

virtual Int4	getValueUpper () const

virtual ValueFct *	getValueFct () const

virtual size_t	getDimInputProb () const

virtual const double *	getInputProb () const

Public Member Functions inherited from DynProgProbProto
virtual	~DynProgProbProto ()

Static Public Attributes
static const size_t	VALUE_BEGIN

static const size_t	ARRAY_CAPACITY = 256

Protected Member Functions
virtual void	clear (Int4 valueBegin_, size_t arrayCapacity_)

virtual Int4	getArrayPos (Int4 value_) const

virtual Int4	getValueEnd () const

void	reserve (size_t arrayCapacity_)

virtual void	setValueBegin (Int4 valueBegin_)

virtual size_t &	lgetStep ()

virtual double **	lgetArray ()

virtual size_t &	lgetArrayCapacity ()

virtual Int4 &	lgetValueBegin ()

virtual Int4 &	lgetValueLower ()

virtual Int4 &	lgetValueUpper ()

Private Member Functions
virtual void	initInput (size_t dimInputProb_)

virtual void	freeInput ()

virtual Int4	getValue (size_t arrayPos_) const

virtual void	init (size_t arrayCapacity_)

virtual void	free ()

Private Attributes
size_t	d_step

double *	d_array_p [2]

size_t	d_arrayCapacity

Int4	d_valueBegin

Int4	d_valueLower

Int4	d_valueUpper

ValueFct *	d_valueFct

size_t	d_dimInputProb

double *	d_inputProb_p

Additional Inherited Members
Public Types inherited from DynProgProbProto
typedef Int4	ValueFct(Int4 oldValue_, size_t input_)

Detailed Description

Definition at line 50 of file njn_dynprogprob.hpp.

Constructor & Destructor Documentation

◆ DynProgProb() [1/2]

DynProgProb::DynProgProb	(	ValueFct *	valueFct_ = `0`,
		size_t	dimInputProb_ = `0`,
		const double *	inputProb_ = `0`,
		Int4	valueLower_ = `0`,
		Int4	valueUpper_ = `0`,
		const double *	prob_ = `0`
	)

inline

Definition at line 73 of file njn_dynprogprob.hpp.

◆ DynProgProb() [2/2]

DynProgProb::DynProgProb ( const DynProgProb & dynProgProb_ )

inline

Definition at line 96 of file njn_dynprogprob.hpp.

References copy().

◆ ~DynProgProb()

virtual DynProgProb::~DynProgProb ( )

inlinevirtual

Definition at line 104 of file njn_dynprogprob.hpp.

References free().

Member Function Documentation

◆ clear() [1/3]

virtual void DynProgProb::clear ( void )

inlinevirtual

Implements DynProgProbProto.

Reimplemented in DynProgProbLim.

Definition at line 148 of file njn_dynprogprob.hpp.

References clear().

Referenced by clear(), and DynProgProbLim::clear().

◆ clear() [2/3]

void DynProgProb::clear	(	Int4	valueBegin_,
		size_t	arrayCapacity_
	)

protectedvirtual

Reimplemented in DynProgProbLim.

Definition at line 80 of file njn_dynprogprob.cpp.

References d_step, d_valueBegin, free(), and init().

◆ clear() [3/3]

void DynProgProb::clear	(	Int4	valueLower_,
		Int4	valueUpper_ = `0`,
		const double *	prob_ = `0`
	)

virtual

Reimplemented in DynProgProbLim.

Definition at line 91 of file njn_dynprogprob.cpp.

References ARRAY_CAPACITY, assert, clear(), d_array_p, d_valueLower, d_valueUpper, getArrayCapacity(), getArrayPos(), i, and memCpy().

◆ copy() [1/2]

virtual void DynProgProb::copy ( const DynProgProb & dynProgProb_ )

inlinevirtual

Reimplemented in DynProgProbLim.

Definition at line 122 of file njn_dynprogprob.hpp.

References copy(), getArray(), getArrayCapacity(), getDimInputProb(), getInputProb(), getStep(), getValueBegin(), getValueFct(), getValueLower(), and getValueUpper().

Referenced by DynProgProbLim::copy().

◆ copy() [2/2]

void DynProgProb::copy	(	size_t	step_,
		const double const	array_,
		size_t	arrayCapacity_,
		Int4	valueBegin_ = `0`,
		Int4	valueLower_ = `0`,
		Int4	valueUpper_ = `0`,
		ValueFct *	valueFct_ = `0`,
		size_t	dimInputProb_ = `0`,
		const double *	inputProb_ = `0`
	)

virtual

Reimplemented in DynProgProbLim.

Definition at line 131 of file njn_dynprogprob.cpp.

References d_array_p, d_step, d_valueBegin, free(), getArrayCapacity(), i, init(), and memCpy().

◆ free()

void DynProgProb::free ( )

privatevirtual

Definition at line 67 of file njn_dynprogprob.cpp.

References d_array_p, d_arrayCapacity, getArrayCapacity(), and i.

Referenced by clear(), and copy().

◆ freeInput()

void DynProgProb::freeInput ( )

privatevirtual

Definition at line 173 of file njn_dynprogprob.cpp.

References d_dimInputProb, d_inputProb_p, and getDimInputProb().

Referenced by setInput().

◆ getArray()

virtual const double* const* DynProgProb::getArray ( ) const

inlinevirtual

Definition at line 175 of file njn_dynprogprob.hpp.

Referenced by copy().

◆ getArrayCapacity()

virtual size_t DynProgProb::getArrayCapacity ( ) const

inlinevirtual

Definition at line 176 of file njn_dynprogprob.hpp.

Referenced by clear(), copy(), free(), reserve(), setValueBegin(), and update().

◆ getArrayPos()

virtual Int4 DynProgProb::getArrayPos ( Int4 value_ ) const

inlineprotectedvirtual

Definition at line 216 of file njn_dynprogprob.hpp.

Referenced by clear(), and update().

◆ getDimInputProb()

virtual size_t DynProgProb::getDimInputProb ( ) const

inlinevirtual

Definition at line 182 of file njn_dynprogprob.hpp.

Referenced by copy(), freeInput(), setInput(), and update().

◆ getInputProb()

virtual const double* DynProgProb::getInputProb ( ) const

inlinevirtual

Definition at line 183 of file njn_dynprogprob.hpp.

Referenced by copy(), and update().

◆ getProb()

virtual double DynProgProb::getProb ( Int4 value_ ) const

inlinevirtual

Implements DynProgProbProto.

Definition at line 164 of file njn_dynprogprob.hpp.

◆ getStep()

virtual size_t DynProgProb::getStep ( ) const

inlinevirtual

Implements DynProgProbProto.

Definition at line 173 of file njn_dynprogprob.hpp.

Referenced by copy().

◆ getValue()

virtual Int4 DynProgProb::getValue ( size_t arrayPos_ ) const

inlineprivatevirtual

Definition at line 203 of file njn_dynprogprob.hpp.

◆ getValueBegin()

virtual Int4 DynProgProb::getValueBegin ( ) const

inlinevirtual

Definition at line 177 of file njn_dynprogprob.hpp.

Referenced by copy(), setValueBegin(), and update().

◆ getValueEnd()

virtual Int4 DynProgProb::getValueEnd ( ) const

inlineprotectedvirtual

Definition at line 221 of file njn_dynprogprob.hpp.

Referenced by update().

◆ getValueFct()

virtual ValueFct* DynProgProb::getValueFct ( ) const

inlinevirtual

Definition at line 181 of file njn_dynprogprob.hpp.

Referenced by copy(), and update().

◆ getValueLower()

virtual Int4 DynProgProb::getValueLower ( ) const

inlinevirtual

Implements DynProgProbProto.

Definition at line 178 of file njn_dynprogprob.hpp.

Referenced by copy(), and update().

◆ getValueUpper()

virtual Int4 DynProgProb::getValueUpper ( ) const

inlinevirtual

Implements DynProgProbProto.

Definition at line 179 of file njn_dynprogprob.hpp.

Referenced by copy(), and update().

◆ init()

void DynProgProb::init ( size_t arrayCapacity_ )

privatevirtual

Definition at line 53 of file njn_dynprogprob.cpp.

References d_array_p, d_arrayCapacity, i, and memZero().

Referenced by clear(), and copy().

◆ initInput()

void DynProgProb::initInput ( size_t dimInputProb_ )

privatevirtual

Definition at line 162 of file njn_dynprogprob.cpp.

References d_dimInputProb, d_inputProb_p, and memZero().

Referenced by setInput().

◆ lgetArray()

virtual double** DynProgProb::lgetArray ( )

inlineprotectedvirtual

Definition at line 232 of file njn_dynprogprob.hpp.

Referenced by DynProgProbLim::reserve(), DynProgProbLim::setValueBegin(), and DynProgProbLim::update().

◆ lgetArrayCapacity()

virtual size_t& DynProgProb::lgetArrayCapacity ( )

inlineprotectedvirtual

Definition at line 233 of file njn_dynprogprob.hpp.

Referenced by DynProgProbLim::reserve().

◆ lgetStep()

virtual size_t& DynProgProb::lgetStep ( )

inlineprotectedvirtual

Definition at line 231 of file njn_dynprogprob.hpp.

Referenced by DynProgProbLim::update().

◆ lgetValueBegin()

virtual Int4& DynProgProb::lgetValueBegin ( )

inlineprotectedvirtual

Definition at line 234 of file njn_dynprogprob.hpp.

Referenced by DynProgProbLim::setValueBegin().

◆ lgetValueLower()

virtual Int4& DynProgProb::lgetValueLower ( )

inlineprotectedvirtual

Definition at line 235 of file njn_dynprogprob.hpp.

Referenced by DynProgProbLim::update().

◆ lgetValueUpper()

virtual Int4& DynProgProb::lgetValueUpper ( )

inlineprotectedvirtual

Definition at line 236 of file njn_dynprogprob.hpp.

Referenced by DynProgProbLim::update().

◆ operator bool()

virtual DynProgProb::operator bool ( void ) const

inlinevirtual

Implements DynProgProbProto.

Definition at line 110 of file njn_dynprogprob.hpp.

◆ operator=()

virtual DynProgProb& DynProgProb::operator= ( const DynProgProb & dynProgProb_ )

inlinevirtual

Reimplemented in DynProgProbLim.

Definition at line 116 of file njn_dynprogprob.hpp.

References copy().

◆ reserve()

void DynProgProb::reserve ( size_t arrayCapacity_ )

protected

Definition at line 256 of file njn_dynprogprob.cpp.

References assert, d_array_p, d_arrayCapacity, getArrayCapacity(), i, memCpy(), and memZero().

Referenced by DynProgProbLim::reserve(), and update().

◆ setInput()

void DynProgProb::setInput	(	size_t	dimInputProb_,
		const double *	inputProb_
	)

virtual

Definition at line 183 of file njn_dynprogprob.cpp.

References d_inputProb_p, freeInput(), getDimInputProb(), initInput(), and memCpy().

◆ setValueBegin()

void DynProgProb::setValueBegin ( Int4 valueBegin_ )

protectedvirtual

Reimplemented in DynProgProbLim.

Definition at line 277 of file njn_dynprogprob.cpp.

References assert, d_array_p, d_valueBegin, getArrayCapacity(), getValueBegin(), i, memCpy(), and memZero().

Referenced by DynProgProbLim::setValueBegin(), and update().

◆ setValueFct()

virtual void DynProgProb::setValueFct ( ValueFct * valueFct_ )

inlinevirtual

Definition at line 150 of file njn_dynprogprob.hpp.

◆ update()

void DynProgProb::update ( )

virtual

Implements DynProgProbProto.

Reimplemented in DynProgProbLim.

Definition at line 196 of file njn_dynprogprob.cpp.

References assert, d_array_p, d_step, d_valueLower, d_valueUpper, getArrayCapacity(), getArrayPos(), getDimInputProb(), getInputProb(), getValueBegin(), getValueEnd(), getValueFct(), getValueLower(), getValueUpper(), i, kMax_I4, kMin_I4, memZero(), reserve(), setValueBegin(), and rapidjson::value.

Member Data Documentation

◆ ARRAY_CAPACITY

const size_t DynProgProb::ARRAY_CAPACITY = 256

static

Definition at line 71 of file njn_dynprogprob.hpp.

Referenced by clear().

◆ d_array_p

double* DynProgProb::d_array_p[2]

private

Definition at line 188 of file njn_dynprogprob.hpp.

Referenced by clear(), copy(), free(), init(), reserve(), setValueBegin(), and update().

◆ d_arrayCapacity

size_t DynProgProb::d_arrayCapacity

private

Definition at line 190 of file njn_dynprogprob.hpp.

Referenced by free(), init(), and reserve().

◆ d_dimInputProb

size_t DynProgProb::d_dimInputProb

private

Definition at line 197 of file njn_dynprogprob.hpp.

Referenced by freeInput(), and initInput().

◆ d_inputProb_p

double* DynProgProb::d_inputProb_p

private

Definition at line 198 of file njn_dynprogprob.hpp.

Referenced by freeInput(), initInput(), and setInput().

◆ d_step

size_t DynProgProb::d_step

private

Definition at line 187 of file njn_dynprogprob.hpp.

Referenced by clear(), copy(), and update().

◆ d_valueBegin

Int4 DynProgProb::d_valueBegin

private

Definition at line 191 of file njn_dynprogprob.hpp.

Referenced by clear(), copy(), and setValueBegin().

◆ d_valueFct

ValueFct* DynProgProb::d_valueFct

private

Definition at line 196 of file njn_dynprogprob.hpp.

◆ d_valueLower

Int4 DynProgProb::d_valueLower

private

Definition at line 192 of file njn_dynprogprob.hpp.

Referenced by clear(), and update().

◆ d_valueUpper

Int4 DynProgProb::d_valueUpper

private

Definition at line 193 of file njn_dynprogprob.hpp.

Referenced by clear(), and update().

◆ VALUE_BEGIN

const size_t DynProgProb::VALUE_BEGIN

static

Definition at line 70 of file njn_dynprogprob.hpp.

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

src/algo/blast/gumbel_params/njn_dynprogprob.hpp
src/algo/blast/gumbel_params/njn_dynprogprob.cpp

Public Member Functions

Static Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ DynProgProb() [1/2]

◆ DynProgProb() [2/2]

◆ ~DynProgProb()

Member Function Documentation

◆ clear() [1/3]

◆ clear() [2/3]

◆ clear() [3/3]

◆ copy() [1/2]

◆ copy() [2/2]

◆ free()

◆ freeInput()

◆ getArray()

◆ getArrayCapacity()

◆ getArrayPos()

◆ getDimInputProb()

◆ getInputProb()

◆ getProb()

◆ getStep()

◆ getValue()

◆ getValueBegin()

◆ getValueEnd()

◆ getValueFct()

◆ getValueLower()

◆ getValueUpper()

◆ init()

◆ initInput()

◆ lgetArray()

◆ lgetArrayCapacity()

◆ lgetStep()

◆ lgetValueBegin()

◆ lgetValueLower()

◆ lgetValueUpper()

◆ operator bool()

◆ operator=()

◆ reserve()

◆ setInput()

◆ setValueBegin()

◆ setValueFct()

◆ update()

Member Data Documentation

◆ ARRAY_CAPACITY

◆ d_array_p

◆ d_arrayCapacity

◆ d_dimInputProb

◆ d_inputProb_p

◆ d_step

◆ d_valueBegin

◆ d_valueFct

◆ d_valueLower

◆ d_valueUpper

◆ VALUE_BEGIN