CVectorCore< CType > Class Template Reference

#include <CVector.h>

Inheritance diagram for CVectorCore< CType >:

Collaboration diagram for CVectorCore< CType >:

Public Types
typedef CType	elementType

Public Member Functions
bool	applyPivot (const CVectorCore< size_t > &pivot)
CType *	array ()
const CType *	array () const
	CVectorCore (const size_t &size=0, CType *vector=NULL)
	CVectorCore (const CVectorCore< CType > &src)
CType &	operator() (const size_t &row)
const CType &	operator() (const size_t &row) const
CVectorCore< CType > &	operator= (const CType &value)
CType &	operator[] (const size_t &row)
const CType &	operator[] (const size_t &row) const
size_t	size () const
	~CVectorCore ()

Protected Attributes
size_t	mSize
CType *	mVector

Friends
std::ostream &	operator<< (std::ostream &os, const CVectorCore< CType > &A)

Detailed Description

template<typename CType>
class CVectorCore< CType >

Definition at line 29 of file CVector.h.

Member Typedef Documentation

template<typename CType>

typedef CType CVectorCore< CType >::elementType

Definition at line 37 of file CVector.h.

Constructor & Destructor Documentation

template<typename CType>

CVectorCore< CType >::CVectorCore ( const size_t &  size = 0, CType *  vector = NULL  )

inline

Specific constructor

Parameters

const	size_t & size (default: 0)
CType	* vector (default: NULL)

Definition at line 58 of file CVector.h.

                                    :
    mSize(size),
    mVector(vector)
  {}

template<typename CType>

CVectorCore< CType >::CVectorCore ( const CVectorCore< CType > &  src )

inline

Copy constructor

Parameters

const

CVectorCore< CType > & src

Definition at line 68 of file CVector.h.

                                               :
    mSize(src.mSize),
    mVector(src.mVector)
  {}

template<typename CType>

CVectorCore< CType >::~CVectorCore ( )

inline

Destructor.

Definition at line 76 of file CVector.h.

  {}

Member Function Documentation

template<typename CType>

bool CVectorCore< CType >::applyPivot ( const CVectorCore< size_t > &  pivot )

inline

Reorder the elements according to the provided pivots

Parameters

const

CVectorCore<size_t> & pivot

Returns

bool success

Definition at line 172 of file CVector.h.

Referenced by CExperiment::read(), and CEigen::stabilityAnalysis().

  {
    if (pivot.size() != mSize) return false;

    bool * pApplied = new bool[mSize];
    CVectorCore < bool > Applied(mSize, pApplied);

    Applied = false;
    CType tmp;

    size_t i;
    size_t to;
    size_t from;

    for (i = 0; i < mSize; i++)
      if (!Applied[i])
        {
          to = i;
          from = pivot[i];

          if (to != from)
            {
              tmp = mVector[i];

              while (from != i)
                {
                  mVector[to] = mVector[from];
                  Applied[to] = true;

                  to = from;
                  from = pivot[to];
                }

              mVector[to] = tmp;
            }

          Applied[to] = true;
        }

    delete [] pApplied;

    return true;
  }

template<typename CType>

CType* CVectorCore< CType >::array ( )

inline

Retrieve the array of the vector elements. This is suitable for interfacing with clapack routines.

Returns

CType * array

Definition at line 139 of file CVector.h.

Referenced by CMathContainer::allocate(), CLinkMatrix::applyColumnPivot(), CMathContainer::applyInitialValues(), CHistoCurveData::boundingRect(), CLinkMatrix::build(), CSSAMethod::buildExtremeCurrents(), CBitPatternTreeMethod::buildFluxModes(), CBitPatternMethod::buildFluxModes(), CModel::buildRedStoi(), CModel::buildUserOrder(), CEigen::calcEigenValues(), CLyapWolfMethod::calculate(), CFitProblem::calculate(), CStochDirectMethod::calculateAmu(), CTrajAdaptiveSA::calculateAmu(), CTauLeapMethod::calculateAmu(), CTrajectoryMethodDsaLsodar::calculateAmu(), CLNAMethod::calculateCovarianceMatrixReduced(), CFitProblem::calculateCrossValidation(), CModel::calculateDerivatives(), CNewtonMethod::calculateDerivativesX(), CModel::calculateDerivativesX(), CModel::calculateJacobian(), CModel::calculateJacobianX(), CBitPatternMethod::CalculateKernel(), CBitPatternTreeMethod::CalculateKernel(), CTrajectoryMethodDsaLsodar::calculatePropensities(), CMathModel::calculateRootDerivatives(), CMathModel::calculateRootJacobian(), CExperimentSet::calculateStatistics(), CFitProblem::calculateStatistics(), CMCAMethod::calculateUnscaledConcentrationCC(), CMCAMethod::calculateUnscaledElasticities(), CExperiment::calculateWeights(), CExperiment::CExperiment(), CFluxScore::CFluxScore(), CMCAMethod::checkSummationTheorems(), CLinkMatrix::clearPivoting(), CMathContainer::CMathContainer(), CMathModel::compile(), CTimeSeries::compile(), CExperimentSet::compile(), CopasiPlot::compile(), CMathContainer::compileEvents(), CMathContainer::compileObjects(), CLinkMatrix::completePivotInformation(), CMathReaction::copy(), CVector< CProcessReportItem * >::copy(), CPermutation::CPermutation(), COptMethodPS::create(), CMathContainer::createApplyInitialValuesSequence(), CMathContainer::createDependencyGraphs(), CLsodaMethod::createRootMask(), CMathContainer::createSynchronizeInitialValuesSequence(), CMathContainer::createUpdateSimulationValuesSequence(), COptMethodSRES::creation(), CStepMatrix::CStepMatrix(), CMathModel::determineInitialRoots(), CTrajectoryMethodDsaLsodar::CPartition::determineStochasticSpecies(), CILDMMethod::deuflhard(), CILDMModifiedMethod::deuflhard_metab(), CHybridMethodODE45::doInverseInterpolation(), CNewtonMethod::doNewtonStep(), CTrajAdaptiveSA::doSingleSSAStep(), CStochDirectMethod::doSingleStep(), CTauLeapMethod::doSingleStep(), CTrajectoryMethodDsaLsodar::doSingleStep(), CTrajAdaptiveSA::doSingleTauLeapStep(), CLyapWolfMethod::evalF(), CTrajectoryMethodDsaLsodar::evalF(), CMathModel::evaluateRoots(), CMathContainer::fetchInitialState(), CMathContainer::fetchState(), CProgressBar::finish(), CMathReaction::fire(), CTrajectoryMethodDsaLsodar::fireReaction(), CStepMatrixColumn::getAllUnsetBitIndexes(), CStepMatrix::getAllUnsetBitIndexes(), CBitPatternMethod::getAllUnsetBitIndexes(), CMathContainer::getInitialValuePointer(), CMathContainer::getMathObject(), CStepMatrix::getUnsetBitIndexes(), CBitPatternTreeMethod::getUnsetBitIndexes(), CBitPatternMethod::getUnsetBitIndexes(), CKeyFactory::HashTable::HashTable(), COptMethodLevenbergMarquardt::hessian(), CPermutation::init(), CMathContainer::init(), CExperiment::initExtendedTimeSeries(), CopasiPlot::initFromSpec(), CMathReaction::initialize(), CLyapTask::initialize(), CSteadyStateTask::initialize(), CTSSAMethod::initializeAtol(), CModel::initializeAtolVector(), CMathContainer::initializeDiscontinuousCreationPointer(), CMathContainer::initializeEvents(), CMathContainer::initializePointers(), CExperiment::initializeScalingMatrix(), CLyapTask::initObjects(), CHybridMethodLSODA::integrateDeterministicPart(), CHybridMethodODE45::integrateDeterministicPart(), CTSSAMethod::integrationStep(), CLsodaMethod::maskRoots(), COptMethodPS::move(), COptMethodSRES::mutate(), CILDMMethod::newton(), CILDMModifiedMethod::newton_for_timestep(), CILDMModifiedMethod::newton_new(), CZeroSet::operator&=(), CFluxScore::operator<(), operator<<(), CZeroSet::operator==(), CZeroSet::operator>=(), CZeroSet::operator|=(), COptMethodPS::optimise(), COptMethodLevenbergMarquardt::optimise(), COptMethodPraxis::optimise(), COptMethodTruncatedNewton::optimise(), COptMethodHGASA::optimise(), CLyapWolfMethod::orthonormalize(), partialSortWithPivot(), CLsodaMethod::peekAhead(), CBitPatternMethod::performRankTest(), CPermutation::pick(), CMathModel::processRoots(), CMathContainer::pushInitialState(), CMathContainer::pushState(), COptMethodPS::reachedStdDeviation(), CExperiment::read(), C2DCurveData::reallocated(), CBandedGraphData::reallocated(), CHistoCurveData::reallocated(), CStateTemplate::reorder(), CopasiPlot::resizeCurveData(), COptProblem::restoreModel(), CProcessQueue::rootsFound(), CopasiPlot::saveData(), CTSSAMethod::schur(), CTSSAMethod::schur_desc(), COptMethodEP::select(), COptMethodGA::select(), CMathContainer::setInitialState(), CMathContainer::setState(), CMathContainer::setStateReduced(), CMathEvent::setTargetValues(), CStateTemplate::setUserOrder(), CModelParameterCompartment::setValue(), CPermutation::shuffle(), CNewtonMethod::solveJacobianXeqB(), sortWithPivot(), CEigen::stabilityAnalysis(), CLyapWolfMethod::start(), CTrajAdaptiveSA::start(), CLsodaMethod::start(), CLsodaMethod::stateChanged(), CILDMModifiedMethod::step(), CCSPMethod::step(), CLyapWolfMethod::step(), CLsodaMethod::step(), CExperiment::storeExtendedTimeSeriesData(), CExperiment::sumOfSquares(), CExperiment::sumOfSquaresStore(), CTSSAMethod::sylvester(), CNewtonMethod::targetFunction(), CopasiPlot::updateCurves(), CSteadyStateTask::updateMatrices(), CModel::updateSimulatedValues(), and CTauLeapMethod::updateSystem().

{return mVector;}

template<typename CType>

const CType* CVectorCore< CType >::array ( ) const

inline

Retrieve the array of the vector elements. This is suitable for interfacing with clapack routines.

Returns

const CType * array

Definition at line 146 of file CVector.h.

{return mVector;}

template<typename CType>

CType& CVectorCore< CType >::operator() ( const size_t &  row )

inline

Retrieve a vector element using Fortan style indexing.

Parameters

const

size_t & row

Returns

const CType & element

Definition at line 123 of file CVector.h.

  {return *(mVector + (row - 1));}

template<typename CType>

const CType& CVectorCore< CType >::operator() ( const size_t &  row ) const

inline

Retrieve a vector element using Fortan style indexing.

Parameters

const

size_t & row

Returns

const CType & element

Definition at line 131 of file CVector.h.

  {return *(mVector + (row - 1));}

template<typename CType>

CVectorCore< CType>& CVectorCore< CType >::operator= ( const CType &  value )

inline

Assignment operator

Parameters

const

CType & value

Definition at line 83 of file CVector.h.

  {
    size_t i;
    CType * tmp = mVector;

    for (i = 0; i < mSize; i++, tmp++)
      {
        *tmp = value;
      }

    return *this;
  }

template<typename CType>

CType& CVectorCore< CType >::operator[] ( const size_t &  row )

inline

Retrieve an element of the vector

Parameters

const

size_t & row

Returns

CType & element

Definition at line 107 of file CVector.h.

  {return *(mVector + row);}

template<typename CType>

const CType& CVectorCore< CType >::operator[] ( const size_t &  row ) const

inline

Retrieve an element of the vector

Parameters

const

size_t & row

Returns

const CType & element

Definition at line 115 of file CVector.h.

  {return *(mVector + row);}

template<typename CType>

size_t CVectorCore< CType >::size ( ) const

inline

The number of elements stored in the vector.

Returns

size_t size

Definition at line 100 of file CVector.h.

Referenced by CProcessReport::addItem(), CMathContainer::allocate(), CLinkMatrix::applyColumnPivot(), applyPartialPivot(), CVectorCore< CProcessReportItem * >::applyPivot(), applyPivot(), CMatrix< CFitConstraint * >::applyPivot(), CLinkMatrix::applyRowPivot(), CSSAMethod::buildExtremeCurrents(), CBitPatternTreeMethod::buildFluxModes(), CBitPatternMethod::buildFluxModes(), CModel::buildUserOrder(), CLyapWolfMethod::calculate(), CFitProblem::calculate(), CStochDirectMethod::calculateAmu(), CTrajAdaptiveSA::calculateAmu(), CTauLeapMethod::calculateAmu(), CTrajectoryMethodDsaLsodar::calculateAmu(), CFitProblem::calculateCrossValidation(), CMathModel::calculateRootDerivatives(), CMathModel::calculateRootJacobian(), CExperimentSet::calculateStatistics(), CFitProblem::calculateStatistics(), COptProblem::calculateStatistics(), CExperiment::calculateWeights(), CBandedGraphData::CBandedGraphData(), CQTSSATimeScaleWidget::changedInterval(), CLinkMatrix::clearPivoting(), CMathContainer::CMathContainer(), CTimeSeries::compile(), CExperimentSet::compile(), CopasiPlot::compile(), CMathContainer::compileObjects(), CLinkMatrix::completePivotInformation(), CMathReaction::copy(), CVector< CProcessReportItem * >::copy(), CPermutation::CPermutation(), CMathContainer::createApplyInitialValuesSequence(), CMathContainer::createDependencyGraphs(), CLsodaMethod::createRootMask(), CVector< CProcessReportItem * >::CVector(), CMathModel::determineInitialRoots(), CSSAMethod::diag(), CNewtonMethod::doNewtonStep(), CTrajAdaptiveSA::doSingleSSAStep(), CStochDirectMethod::doSingleStep(), CTrajAdaptiveSA::doSingleTauLeapStep(), CQFittingResult::enterProtected(), CTrajectoryMethodDsaLsodar::evalF(), CLsodaMethod::evalR(), CMathModel::evaluateRoots(), CMathContainer::fetchInitialState(), CMathContainer::fetchState(), CProgressBar::finish(), CProcessReport::finish(), CMathReaction::fire(), CTrajectoryMethodDsaLsodar::fireReaction(), CStepMatrix::getAllUnsetBitIndexes(), CBitPatternMethod::getAllUnsetBitIndexes(), CMathContainer::getInitialValuePointer(), CMathContainer::getMathObject(), CZeroSet::getNumberOfBits(), CZeroSet::getNumberOfUnsetBits(), CMathModel::getNumRoots(), CStepMatrix::getUnsetBitIndexes(), CBitPatternTreeMethod::getUnsetBitIndexes(), CBitPatternMethod::getUnsetBitIndexes(), COptMethodLevenbergMarquardt::hessian(), CPermutation::init(), CMathContainer::init(), CMathReaction::initialize(), COptMethodLevenbergMarquardt::initialize(), CFitProblem::initialize(), CSteadyStateTask::initialize(), CTSSAMethod::initializeAtol(), CModel::initializeAtolVector(), CMathContainer::initializeDiscontinuousCreationPointer(), CMathContainer::initializeEvents(), CMathContainer::initializeObjects(), CExperiment::initializeScalingMatrix(), CHybridMethodLSODA::integrateDeterministicPart(), CTSSAMethod::integrationStep(), CProcessReport::isValidHandle(), CLinkMatrix::leftMultiply(), StateSubwidget::loadJacobian(), CQUpdatesWidget::loadObjectsTable(), LUfactor(), CLsodaMethod::maskRoots(), CPermutation::next(), CZeroSet::operator&=(), CFluxScore::operator<(), operator<<(), CZeroSet::operator==(), CZeroSet::operator>=(), CZeroSet::operator|=(), PaintWidget::paintEvent(), CQTSSATimeScaleWidget::paintTimeScale(), CLsodaMethod::peekAhead(), CBitPatternMethod::performRankTest(), CPermutation::pick(), CFitProblem::printResult(), COptProblem::printResult(), CExperiment::printResult(), CSteadyStateTask::process(), CMathModel::processRoots(), CProcessReport::progress(), CMathContainer::pushInitialState(), CMathContainer::pushState(), CExperiment::read(), C2DCurveData::reallocated(), CBandedGraphData::reallocated(), CHistoCurveData::reallocated(), CStateTemplate::reorder(), CProcessReport::reset(), CVector< CProcessReportItem * >::resize(), CopasiPlot::resizeCurveData(), CExperiment::restoreModelIndependentData(), CLinkMatrix::rightMultiply(), CProcessQueue::rootsFound(), CopasiPlot::saveData(), CILDMMethod::setAnnotationM(), CMathContainer::setInitialState(), CFitProblem::setResidualsRequired(), CMathContainer::setState(), CMathContainer::setStateReduced(), CStateTemplate::setUserOrder(), CMathContainer::setValues(), CILDMMethod::setVectors(), CCSPMethod::setVectors(), CPermutation::shuffle(), CHistoCurveData::size(), CProgressBar::slotAddItem(), CProgressBar::slotProgressAll(), CQFittingItemWidget::slotReset(), CNewtonMethod::solveJacobianXeqB(), CEigen::stabilityAnalysis(), CLyapWolfMethod::step(), CLsodaMethod::step(), CNewtonMethod::targetFunction(), CSSAMethod::testForMixingStability(), CopasiPlot::updateCurves(), CSteadyStateTask::updateMatrices(), CExperiment::updateModelWithIndependentData(), CProcessReport::~CProcessReport(), and CProgressBar::~CProgressBar().

{return mSize;}

Friends And Related Function Documentation

template<typename CType>

std::ostream& operator<< ( std::ostream &  os, const CVectorCore< CType > &  A  )

friend

Output stream operator

Parameters

ostream	& os
const	CVector< CType > & A

Returns

ostream & os

Definition at line 380 of file CVector.h.

{
  os << "(\t";

  if (A.mSize)
    {
      size_t i;
      CType * tmp = A.mVector;
      os << *(tmp++);

      for (i = 1; i < A.mSize; i++)
        os << "\t" << *(tmp++);
    }

  os << "\t)";
  return os;
}

Member Data Documentation

template<typename CType>

size_t CVectorCore< CType >::mSize

protected

Size of the vector.

Definition at line 44 of file CVector.h.

Referenced by CVectorCore< CProcessReportItem * >::applyPivot(), CVectorCore< CProcessReportItem * >::operator=(), and CVectorCore< CProcessReportItem * >::size().

template<typename CType>

CType* CVectorCore< CType >::mVector

protected

The array storing the vector elements

Definition at line 49 of file CVector.h.

Referenced by CVectorCore< CProcessReportItem * >::applyPivot(), CVectorCore< CProcessReportItem * >::array(), CVectorCore< CProcessReportItem * >::operator()(), CVectorCore< CProcessReportItem * >::operator=(), and CVectorCore< CProcessReportItem * >::operator[]().

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

• CVector.h