COPASI API
4.16.103
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#include <CVector.h>
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typedef CType | elementType |
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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 () | |
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size_t | mSize |
CType * | mVector |
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std::ostream & | operator<< (std::ostream &os, const CVectorCore< CType > &A) |
typedef CType CVectorCore< CType >::elementType |
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Reorder the elements according to the provided pivots
const | CVectorCore<size_t> & pivot |
Definition at line 172 of file CVector.h.
Referenced by CExperiment::read(), and CEigen::stabilityAnalysis().
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Retrieve the array of the vector elements. This is suitable for interfacing with clapack routines.
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().
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The number of elements stored in the vector.
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().
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Size of the vector.
Definition at line 44 of file CVector.h.
Referenced by CVectorCore< CProcessReportItem * >::applyPivot(), CVectorCore< CProcessReportItem * >::operator=(), and CVectorCore< CProcessReportItem * >::size().
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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[]().