#include <CTimeSeries.h>

Inheritance diagram for CTimeSeries:

Public Member Functions
void	allocate (const size_t &steps)

void	clear ()

virtual bool	compile (CObjectInterface::ContainerList listOfContainer)

	CTimeSeries ()

	CTimeSeries (const CTimeSeries &src)

virtual void	finish ()

C_FLOAT64	getConcentrationData (const size_t &step, const size_t &variable) const

const C_FLOAT64 &	getData (const size_t &step, const size_t &variable) const

const std::string &	getKey (const size_t &variable) const

const size_t &	getNumVariables () const

const size_t &	getRecordedSteps () const

std::string	getSBMLId (const size_t &variable, const CDataModel *pDataModel) const

const std::string &	getTitle (const size_t &variable) const

void	increaseAllocation ()

virtual void	output (const Activity &activity)

int	save (const std::string &fileName, bool writeParticleNumbers=false, const std::string &separator="\t") const

int	save (std::ostream &str, bool writeParticleNumbers=false, const std::string &separator="\t") const

virtual void	separate (const Activity &activity)

	~CTimeSeries ()

Public Member Functions inherited from COutputInterface
virtual void	close ()

	COutputInterface ()

	COutputInterface (const COutputInterface &src)

virtual const CObjectInterface::ObjectSet &	getObjects () const

virtual	~COutputInterface ()

Private Member Functions
CTimeSeries &	operator= (const CTimeSeries &)

Private Attributes
size_t	mAllocatedSteps

CVector< size_t >	mCompartment

CVectorCore< C_FLOAT64 >	mContainerValues

std::vector< std::string >	mKeys

C_FLOAT64	mNumberToQuantityFactor

size_t	mNumVariables

C_FLOAT64 *	mpEnd

C_FLOAT64 *	mpIt

CVector< size_t >	mPivot

size_t	mRecordedSteps

std::vector< std::string >	mTitles

Static Private Attributes
static C_FLOAT64	mDummyFloat

static std::string	mDummyString

Additional Inherited Members
Public Types inherited from COutputInterface
enum	Activity { BEFORE = 0x01 , DURING = 0x02 , AFTER = 0x04 , MONITORING = 0x08 }

Protected Types inherited from CMatrix< C_FLOAT64 >
typedef C_FLOAT64	elementType

Protected Member Functions inherited from CMatrix< C_FLOAT64 >
bool	applyPivot (const CVector< size_t > &pivot)

virtual C_FLOAT64 *	array ()

virtual const C_FLOAT64 *	array () const

	CMatrix (const CMatrix< C_FLOAT64 > &src)

	CMatrix (size_t rows=0, size_t cols=0)

virtual size_t	numCols () const

virtual size_t	numRows () const

virtual elementType &	operator() (const size_t &row, const size_t &col)

virtual const elementType &	operator() (const size_t &row, const size_t &col) const

virtual CMatrix< C_FLOAT64 > &	operator= (const C_FLOAT64 &value)

virtual CMatrix< C_FLOAT64 > &	operator= (const CMatrix< C_FLOAT64 > &rhs)

virtual C_FLOAT64 *	operator[] (size_t row)

virtual const C_FLOAT64 *	operator[] (size_t row) const

virtual void	resize (size_t rows, size_t cols, const bool &copy=false)

virtual size_t	size () const

virtual	~CMatrix ()

Protected Attributes inherited from COutputInterface
CObjectInterface::ObjectSet	mObjects

Protected Attributes inherited from CMatrix< C_FLOAT64 >
size_t	mCols

C_FLOAT64 *	mpBuffer

size_t	mRows

Constructor & Destructor Documentation

◆ CTimeSeries() [1/2]

CTimeSeries::CTimeSeries ( )

Default constructor

◆ CTimeSeries() [2/2]

CTimeSeries::CTimeSeries ( const CTimeSeries & src )

Copy constructor

Parameters

const CTimeSeries & src

References CVectorCore< CType >::initialize(), and mContainerValues.

◆ ~CTimeSeries()

CTimeSeries::~CTimeSeries ( )

Destructor

Member Function Documentation

◆ allocate()

void CTimeSeries::allocate ( const size_t & steps )

The maximal number of recorded steps. This must be set before compiling

Parameters

const size_t & steps

References mAllocatedSteps.

Referenced by CTimeSensTask::initialize(), CTrajectoryTask::initialize(), and CTSSATask::initialize().

◆ clear()

void CTimeSeries::clear ( )

Clear the time series

References mAllocatedSteps, mCompartment, mKeys, mNumberToQuantityFactor, mNumVariables, COutputInterface::mObjects, CMatrix< C_FLOAT64 >::mpBuffer, mpEnd, mpIt, mPivot, mRecordedSteps, CMatrix< C_FLOAT64 >::mRows, mTitles, CMatrix< CType >::resize(), CVector< CType >::resize(), and CMatrix< C_FLOAT64 >::size().

Referenced by CTimeSensTask::initialize(), CTrajectoryTask::initialize(), and CTSSATask::initialize().

◆ compile()

bool CTimeSeries::compile ( CObjectInterface::ContainerList listOfContainer )

virtual

compile the object list from name vector

Parameters

CObjectInterface::ContainerList	listOfContainer
const	CDataModel* pDataModel

Returns: bool success

Implements COutputInterface.

◆ finish()

void CTimeSeries::finish ( )

virtual

Finish the output

Implements COutputInterface.

◆ getConcentrationData()

C_FLOAT64 CTimeSeries::getConcentrationData	(	const size_t &	step,
		const size_t &	variable
	)		const

Retrieve the data (concentration for species) for the indexed step and variable

Parameters

const	size_t & step
const	size_t & variable

Returns: const C_FLOAT64 & data

References C_INVALID_INDEX, CMatrix< C_FLOAT64 >::mCols, mCompartment, mDummyFloat, mNumberToQuantityFactor, mNumVariables, CMatrix< C_FLOAT64 >::mpBuffer, mPivot, and mRecordedSteps.

Referenced by save().

◆ getData()

const C_FLOAT64 & CTimeSeries::getData	(	const size_t &	step,
		const size_t &	variable
	)		const

Retrieve the data (particle number for species) for the indexed step and variable

Parameters

const	size_t & step
const	size_t & variable

Returns: const C_FLOAT64 & data

References CMatrix< C_FLOAT64 >::mCols, mDummyFloat, mNumVariables, CMatrix< C_FLOAT64 >::mpBuffer, mPivot, and mRecordedSteps.

Referenced by save().

◆ getKey()

const std::string & CTimeSeries::getKey ( const size_t & variable ) const

Retrieve the key of the model entity of the indexed variable (column)

Parameters

const size_t & variable

Returns: const std::string & key

References mDummyString, mKeys, mNumVariables, and mPivot.

Referenced by getSBMLId().

◆ getNumVariables()

const size_t & CTimeSeries::getNumVariables ( ) const

Retrieve the number of variables (columns)

Returns: size_t & numVariables

References mNumVariables.

Referenced by save().

◆ getRecordedSteps()

const size_t & CTimeSeries::getRecordedSteps ( ) const

Retrieve the number of time steps (rows)

Returns: const size_t & recordedSteps

References mRecordedSteps.

◆ getSBMLId()

std::string CTimeSeries::getSBMLId	(	const size_t &	variable,
		const CDataModel *	pDataModel
	)		const

get the id of the SBML object corresponding to column indexed by variable. If there is no corresponding SBML object (e.g. if the model comes from a COPASI file) the empty string is returned.

Parameters

const size_t & variable

Returns: const std::string SBMLId

References CKeyFactory::get(), CDataModel::getCopasi2SBMLMap(), getKey(), CRootContainer::getKeyFactory(), and mDummyString.

◆ getTitle()

const std::string & CTimeSeries::getTitle ( const size_t & variable ) const

Retrieve the title of the indexed variable (column)

Parameters

const size_t & variable

Returns: const std::string & title

References mDummyString, mNumVariables, mPivot, and mTitles.

Referenced by save().

◆ increaseAllocation()

void CTimeSeries::increaseAllocation ( )

Increase the allocated space for the time series.

References mAllocatedSteps, CMatrix< C_FLOAT64 >::mCols, CMatrix< C_FLOAT64 >::mpBuffer, mpEnd, mpIt, mRecordedSteps, CMatrix< CType >::resize(), and CMatrix< C_FLOAT64 >::size().

Referenced by output(), and separate().

◆ operator=()

CTimeSeries& CTimeSeries::operator= ( const CTimeSeries & )

private

◆ output()

void CTimeSeries::output ( const Activity & activity )

virtual

Perform an output event for the current activity

Parameters

const Activity & activity

Implements COutputInterface.

References CVectorCore< CType >::array(), C_FLOAT64, COutputInterface::DURING, increaseAllocation(), CMatrix< C_FLOAT64 >::mCols, mContainerValues, mpEnd, mpIt, and mRecordedSteps.

◆ save() [1/2]

int CTimeSeries::save	(	const std::string &	fileName,
		bool	writeParticleNumbers = `false`,
		const std::string &	separator = `"\t"`
	)		const

Save the time series to a file

Parameters

const	std::string & fileName
bool	writeParticleNumbers (default: false)
const	std::string& separator (default: "\t")

Returns: int retcode

References CLocaleString::fromUtf8().

Referenced by CTrajectoryProblem::printResult().

◆ save() [2/2]

int CTimeSeries::save	(	std::ostream &	str,
		bool	writeParticleNumbers = `false`,
		const std::string &	separator = `"\t"`
	)		const

Save the time series to the given stream

Parameters

str	the stream to write the series to
bool	writeParticleNumbers (default: false)
const	std::string& separator (default: "\t")

Returns: int retcode

References C_FLOAT64, getConcentrationData(), getData(), getNumVariables(), getTitle(), and mRecordedSteps.

◆ separate()

void CTimeSeries::separate ( const Activity & activity )

virtual

Introduce an additional separator into the output

Parameters

const Activity & activity

Implements COutputInterface.

References C_FLOAT64, increaseAllocation(), CMatrix< C_FLOAT64 >::mCols, mpEnd, mpIt, and mRecordedSteps.

Member Data Documentation

◆ mAllocatedSteps

size_t CTimeSeries::mAllocatedSteps

private

The number of allocated steps

Referenced by allocate(), clear(), compile(), and increaseAllocation().

◆ mCompartment

CVector< size_t > CTimeSeries::mCompartment

private

Vector of indexes pointing to the column storing the volume of the containing compartment for a species (C_INVALID_INDEX otherwise)

Referenced by clear(), compile(), and getConcentrationData().

◆ mContainerValues

CVectorCore< C_FLOAT64 > CTimeSeries::mContainerValues

private

A reference to the values of the math container

Referenced by compile(), CTimeSeries(), and output().

◆ mDummyFloat

C_FLOAT64 CTimeSeries::mDummyFloat

staticprivate

Static C_FLOAT64 0.0 for performance reasons

Referenced by getConcentrationData(), and getData().

◆ mDummyString

std::string CTimeSeries::mDummyString

staticprivate

Static empty string for performance reasons

Referenced by getKey(), getSBMLId(), and getTitle().

◆ mKeys

std::vector< std::string > CTimeSeries::mKeys

private

Vector storing the keys for the model entity represented by each column

Referenced by clear(), compile(), and getKey().

◆ mNumberToQuantityFactor

C_FLOAT64 CTimeSeries::mNumberToQuantityFactor

private

Conversion factor needed for computing concentration data

Referenced by clear(), compile(), and getConcentrationData().

◆ mNumVariables

size_t CTimeSeries::mNumVariables

private

The number of variables exposed

Referenced by clear(), compile(), getConcentrationData(), getData(), getKey(), getNumVariables(), and getTitle().

◆ mpEnd

C_FLOAT64* CTimeSeries::mpEnd

private

Iterator pointing beyond the last allocated step (row)

Referenced by clear(), compile(), increaseAllocation(), output(), and separate().

◆ mpIt

C_FLOAT64* CTimeSeries::mpIt

private

Iterator pointing the next step (row) to be recorded

Referenced by clear(), compile(), increaseAllocation(), output(), and separate().

◆ mPivot

CVector< size_t > CTimeSeries::mPivot

private

Pivot rearranging the columns to a more user friendly order

Referenced by clear(), compile(), getConcentrationData(), getData(), getKey(), and getTitle().

◆ mRecordedSteps

size_t CTimeSeries::mRecordedSteps

private

The number of actually recorded steps

Referenced by clear(), compile(), getConcentrationData(), getData(), getRecordedSteps(), increaseAllocation(), output(), save(), and separate().

◆ mTitles

std::vector< std::string > CTimeSeries::mTitles

private

Vector of column titles.

Referenced by clear(), compile(), and getTitle().

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

Public Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ CTimeSeries() [1/2]

◆ CTimeSeries() [2/2]

◆ ~CTimeSeries()

Member Function Documentation

◆ allocate()

◆ clear()

◆ compile()

◆ finish()

◆ getConcentrationData()

◆ getData()

◆ getKey()

◆ getNumVariables()

◆ getRecordedSteps()

◆ getSBMLId()

◆ getTitle()

◆ increaseAllocation()

◆ operator=()

◆ output()

◆ save() [1/2]

◆ save() [2/2]

◆ separate()

Member Data Documentation

◆ mAllocatedSteps

◆ mCompartment

◆ mContainerValues

◆ mDummyFloat

◆ mDummyString

◆ mKeys

◆ mNumberToQuantityFactor

◆ mNumVariables

◆ mpEnd

◆ mpIt

◆ mPivot

◆ mRecordedSteps

◆ mTitles