COPASI API  4.16.103
Macros | Enumerations
copasi.h File Reference
#include <assert.h>
#include <fstream>
#include <limits>
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Macros

#define abs64   abs
 
#define AVOGADRO   6.0221415e23
 
#define C_FLOAT32   float
 
#define C_FLOAT64   double
 
#define C_INT   long
 
#define C_INT16   short
 
#define C_INT32   int
 
#define C_INT64   long long int
 
#define C_INVALID_INDEX   (std::numeric_limits< size_t >::max())
 
#define C_LOGICAL   C_INT
 
#define C_UNUSED(p)
 
#define CONSTRUCTOR_TRACE
 
#define COPASI_DEPRECATED
 
#define DEBUG_OUT(s)
 
#define DESTRUCTOR_TRACE
 
#define LLONG_CONST(n)   n ## LL
 
#define NDEBUG
 
#define pcleanup(p)   {if (p) {p->cleanup(); delete p; p = NULL;}}
 
#define pdelete(p)   {if (p) {delete p; p = NULL;}}
 
#define pdeletev(p)   {if (p) {delete[] p; p = NULL;}}
 
#define pfree(p)   {if (p) {free(p); p = NULL;}}
 
#define SS_DAMPING_LIMIT   3
 
#define SS_FOUND   1
 
#define SS_ITERATION_LIMIT   4
 
#define SS_NOT_FOUND   0
 
#define SS_SINGULAR_JACOBIAN   2
 
#define TIME_TRACE(f, l)
 

Enumerations

enum  TriLogic { TriUnspecified = -1, TriFalse = 0, TriTrue = 1 }
 

Macro Definition Documentation

#define abs64   abs
#define AVOGADRO   6.0221415e23

Definition at line 25 of file copasi.h.

#define C_FLOAT32   float

Definition at line 93 of file copasi.h.

#define C_FLOAT64   double

Definition at line 92 of file copasi.h.

Referenced by CLabel::adaptToHeight(), CFunctionParameterMap::addCallParameter(), CCopasiSpringLayout::addReactionVariables(), addToInitialValueMap(), CMathContainer::allocate(), CSteadyStateMethod::allPositive(), CMathContainer::applyInitialValues(), CLinkMatrix::applyRowPivot(), BezierCurve::bernstein(), COptMethodHookeJeeves::bestNearby(), BezierCurve::bezierPt(), C2DCurveData::boundingRect(), CBandedGraphData::boundingRect(), CHistoCurveData::boundingRect(), CLinkMatrix::build(), CSSAMethod::buildExtremeCurrents(), CBitPatternTreeMethod::buildFluxModes(), CBitPatternMethod::buildFluxModes(), CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CSSAMethod::buildKineticMatrix(), CModel::buildMoieties(), CModel::buildStoi(), CSSAMethod::buildStoichiometry(), CEigen::calcEigenValues(), CLyapWolfMethod::calculate(), CEvaluationNodeOperator::calculate(), CFitProblem::calculate(), CSensMethod::calculate_one_level(), CStochMethod::calculateAmu(), CStochDirectMethod::calculateAmu(), CTrajAdaptiveSA::calculateAmu(), CTauLeapMethod::calculateAmu(), CHybridMethod::calculateAmu(), CHybridMethodODE45::calculateAmu(), CHybridMethodLSODA::calculateAmu(), CTrajectoryMethodDsaLsodar::calculateAmu(), CLNAMethod::calculateCovarianceMatrixFull(), CLNAMethod::calculateCovarianceMatrixReduced(), CFitProblem::calculateCrossValidation(), CMathEvent::calculateDelayedTime(), CTSSAMethod::calculateDerivatives(), CModel::calculateDerivatives(), CTSSAMethod::calculateDerivativesX(), CModel::calculateDerivativesX(), CModel::calculateElasticityMatrix(), CInterpolation::calculateFiringTime(), CModel::calculateJacobian(), CModel::calculateJacobianX(), CBitPatternMethod::CalculateKernel(), CBitPatternTreeMethod::CalculateKernel(), CEFMAlgorithm::calculateNextTableau(), CReaction::calculatePartialDerivative(), CTrajectoryMethodDsaLsodar::calculatePropensities(), CMathModel::calculateRootDerivatives(), CMathModel::calculateRootJacobian(), CInterpolation::calculateState(), CExperimentSet::calculateStatistics(), CFitProblem::calculateStatistics(), COptProblem::calculateStatistics(), CExperiment::calculateStatistics(), CMCAMethod::calculateUnscaledConcentrationCC(), CMCAMethod::calculateUnscaledElasticities(), CMCAMethod::calculateUnscaledFluxCC(), CExperiment::calculateWeights(), CMassAction::calcValue(), CNormalFraction::cancel(), CFunctionParameterMap::CFunctionParameterMap(), CScanWidgetRandom::changeType(), CQGLNetworkPainter::checkCurve(), CNormalSum::checkFactor(), CHybridMethod::checkModel(), CHybridMethodLSODA::checkModel(), CHybridMethodODE45::checkModel(), CMCAMethod::checkSummationTheorems(), COptMethodSS::childLocalMin(), COptMethodSS::closerChild(), COptMethodSS::closerRefSet(), CMathContainer::CMathContainer(), CMathExpression::CMathExpression(), cnvtst_(), COptMethodSS::combination(), CMathModel::compile(), CMathEventN::CTrigger::CRoot::compile(), CEvaluationNodeObject::compile(), CMathExpression::compile(), COptItem::compile(), CExperiment::compile(), CopasiPlot::compile(), CMathEvent::CAssignment::compile(), CMathObject::compileDependentMass(), CMathObject::compileInitialValue(), COptItem::compileLowerBound(), CMathObject::compilePropensity(), CMathObject::compileTotalMass(), COptItem::compileUpperBound(), CNewtonMethod::containsNaN(), CMathExpression::convertToInitialExpression(), COptMethodCoranaWalk::COptMethodCoranaWalk(), COptMethodGASR::COptMethodGASR(), COptMethodHookeJeeves::COptMethodHookeJeeves(), COptMethodLevenbergMarquardt::COptMethodLevenbergMarquardt(), COptMethodNelderMead::COptMethodNelderMead(), COptMethodPraxis::COptMethodPraxis(), COptMethodPS::COptMethodPS(), COptMethodSA::COptMethodSA(), COptMethodSRES::COptMethodSRES(), COptMethodSteepestDescent::COptMethodSteepestDescent(), CMathObject::copy(), CMathExpression::copy(), COptMethodPS::create(), SBMLImporter::createCReactionFromReaction(), CQGLNetworkPainter::createDataSets(), CMathObject::createExtensiveReactionRateExpression(), createItemPower(), CMathContainer::createNodeFromObject(), CMathExpression::createNodeFromValue(), CMathContainer::createNodeFromValue(), CLsodaMethod::createRootMask(), CScanProblem::createScanItem(), CMathEventN::CTrigger::CRoot::createTriggerExpressionNode(), CCopasiParameter::createValue(), COptMethodDE::creation(), COptMethodEP::creation(), COptMethodSRES::creation(), COptMethodGA::creation(), COptMethodGASR::creation(), COptMethodSS::creation(), CSensMethod::CSensMethod(), CCSPMethod::CSPImportanceIndex(), CCSPMethod::CSPParticipationIndex(), CCSPMethod::CSPradicalPointer(), CCSPMethod::cspstep(), CState::CState(), CStateRecord::CStateRecord(), BezierCurve::curvePts(), CSSAMethod::decomposeJacobian(), CMathModel::determineInitialRoots(), CILDMMethod::deuflhard(), CILDMModifiedMethod::deuflhard_metab(), CSensMethod::do_collapsing_innerloop(), CSensMethod::do_target_calculation(), CSensMethod::do_variation(), CNewtonMethod::doIntegration(), CHybridMethodODE45::doInverseInterpolation(), CNewtonMethod::doNewtonStep(), CTrajAdaptiveSA::doSingleSSAStep(), CHybridNextReactionLSODAMethod::doSingleStep(), CHybridNextReactionRKMethod::doSingleStep(), CStochNextReactionMethod::doSingleStep(), CStochDirectMethod::doSingleStep(), CTauLeapMethod::doSingleStep(), CHybridMethodODE45::doSingleStep(), CTrajectoryMethodDsaLsodar::doSingleStep(), CTrajAdaptiveSA::doSingleTauLeapStep(), CQGLNetworkPainter::drawGraph(), CTrajectoryProblem::elevateChildren(), CTSSAProblem::elevateChildren(), CCopasiXMLParser::InitialStateElement::end(), CQOptimizationResult::enterProtected(), CQFittingResult::enterProtected(), CLyapWolfMethod::evalF(), CHybridMethodODE45::evalF(), CTrajectoryMethodDsaLsodar::evalF(), CILDMModifiedMethod::evalsort(), CMathModel::evaluateRoots(), CCrossSectionTask::eventCallBack(), CQGLNetworkPainter::export_bitmap(), CODEExporter::exportMetabolites(), CEvaluationNodeFunction::factorial(), CMathContainer::fetchInitialState(), CMathContainer::fetchState(), CReactionInterface::findAndSetFunction(), CCSPMethod::findCandidatesNumber(), CColorScaleSimple::finishAutomaticParameterCalculation(), CHybridMethod::fireReaction(), CHybridMethodLSODA::fireReaction(), CTrajectoryMethodDsaLsodar::fireReaction(), CHybridMethodODE45::fireReaction(), COptMethodDE::fittest(), COptMethodEP::fittest(), COptMethodSRES::fittest(), COptMethodGA::fittest(), COptMethodGASR::fittest(), CPraxis::flin_(), CStochMethod::generateReactionIndex(), CStochMethod::generateReactionTime(), CHybridMethod::generateReactionTime(), CHybridMethodLSODA::generateReactionTime(), CHybridMethodODE45::generateReactionTime(), CColorScaleSimple::getColor(), CColorScaleAdvanced::getColor(), CColorScaleBiLog::getColor(), CHybridMethodODE45::getDefaultAtol(), CHybridMethodLSODA::getDefaultAtol(), CExperiment::getErrorMeanSD(), CExperiment::getErrorSum(), CReactionInterface::getExpandedMetabList(), CMathContainer::getInitialValuePointer(), CChemEq::getLargestCompartment(), CMathContainer::getMathObject(), CQLayoutMainWindow::getMaxNodeSize(), CQLayoutMainWindow::getMinNodeSize(), CQGLNetworkPainter::getPointNearCircle(), CQGLNetworkPainter::getPointOnCircle(), CQGLNetworkPainter::getPointOnRectangle(), CProcessQueue::getProcessQueueExecutionTime(), CTruncatedNewton::getptc_(), Cmt19937::getRandomCC(), Cmt19937::getRandomCO(), CRandom::getRandomNormal01(), CRandom::getRandomNormalPositive(), Cmt19937::getRandomOO(), CRandom::getRandomStdGamma(), COptItem::getRandomValue(), CHybridMethodODE45::getReactionIndex4Hybrid(), CEFMTask::getSpeciesChanges(), CSteadyStateMethod::getStabilityResolution(), COptItem::getStartValue(), CMathEvent::getTargetValues(), CModelEntity::getValuePointer(), CMetab::getValuePointer(), CReadConfig::getVariable(), CEvaluationTree::getVariableValue(), COptMethodSteepestDescent::gradient(), COptMethodLevenbergMarquardt::gradient(), CTruncatedNewton::gtims_(), CModel::handleUnusedMetabolites(), COptMethodLevenbergMarquardt::hessian(), CScanWidgetRandom::initFromObject(), CScanWidgetScan::initFromObject(), CopasiPlot::initFromSpec(), CMathReaction::initialize(), COptMethodSRES::initialize(), COptMethodGASR::initialize(), COptMethodSS::initialize(), CTSSAMethod::initializeAtol(), CModel::initializeAtolVector(), CMathContainer::initializeDiscontinuousCreationPointer(), CTSSAMethod::initializeIntegrationsParameter(), CILDMMethod::initializeParameter(), CILDMModifiedMethod::initializeParameter(), CSteadyStateMethod::initializeParameter(), CLyapProblem::initializeParameter(), CNewtonMethod::initializeParameter(), CTrajectoryProblem::initializeParameter(), CTSSAProblem::initializeParameter(), CCrossSectionProblem::initializeParameter(), CCSPMethod::initializeParameter(), CTrajAdaptiveSA::initializeParameter(), CHybridMethodODE45::initializeParameter(), CLyapWolfMethod::initializeParameter(), CTauLeapMethod::initializeParameter(), CLsodaMethod::initializeParameter(), CCrossValidationSet::initializeParameter(), CTrajectoryMethodDsaLsodar::initializeParameter(), CHybridMethod::initializeParameter(), CHybridMethodLSODA::initializeParameter(), CReaction::initializeParameters(), CMathContainer::initializePointers(), CExperiment::initializeScalingMatrix(), CHybridMethodODE45::initMethod(), CMathTrigger::CRootFinder::initObjects(), CModelEntity::initObjects(), CMetab::initObjects(), CModel::initObjects(), initp3_(), CQLayoutMainWindow::insertValueTable(), CHybridMethod::integrateDeterministicPart(), CHybridMethodLSODA::integrateDeterministicPart(), CHybridMethodODE45::integrateDeterministicPart(), CHybridMethod::integrateDeterministicPartEuler(), CTSSAMethod::integrationStep(), CInterpolation::interpolation(), CTrajectoryMethodDsaLsodar::CPartition::intialize(), is_mass_action(), CCSPMethod::isBlockDiagonal(), CState::isValid(), CEFMMethod::isValidProblem(), CLyapWolfMethod::isValidProblem(), CLinkMatrix::leftMultiply(), CTruncatedNewton::linder_(), CTruncatedNewton::lmqn_(), CTruncatedNewton::lmqnbc_(), CQFittingResultTab1::load(), CScanWidgetScan::load(), CCompartment::load(), CNewtonMethod::load(), CQLyapResultWidget::loadFromBackend(), Curve2DWidget::LoadFromCurveSpec(), HistoWidget::LoadFromCurveSpec(), CQUpdatesWidget::loadObjectsTable(), CReaction::loadOld(), CQExperimentData::loadTable(), CQTrajectoryWidget::loadTask(), lsout_(), LUfactor(), main(), CMathContainer::map(), CTSSAMethod::map_index(), CTSSAMethod::map_index_desc(), CLsodaMethod::maskRoots(), CTSSAMethod::mat_anal_fast_space(), CTSSAMethod::mat_anal_fast_space_thomas(), CTSSAMethod::mat_anal_mod_space(), mchpr1_(), CPraxis::min_(), CPraxis::minfit_(), CopasiSlider::minorTickInterval(), CCSPMethod::modesAreExhausted(), CTruncatedNewton::modlnp_(), modz_(), monit_(), COptMethodPS::move(), mslv_(), CNormalFraction::multiply(), BezierCurve::multiplyFromTo(), COptMethodEP::mutate(), COptMethodGA::mutate(), COptMethodGASR::mutate(), COptMethodSRES::mutate(), ndia3_(), CILDMMethod::newton(), CILDMModifiedMethod::newton_for_timestep(), CILDMModifiedMethod::newton_new(), CLyapWolfMethod::norm(), CSparseMatrix::operator const CMatrix< C_FLOAT64 >(), FPraxis::operator()(), CLinkMatrixView::operator()(), operator<<(), CStateRecord::operator=(), CSparseMatrix::operator=(), CCompressedColumnFormat::operator=(), CMetab::operator=(), CState::operator=(), COptMethodDE::optimise(), COptMethodSS::optimise(), COptMethodGA::optimise(), COptMethodPS::optimise(), COptMethodHookeJeeves::optimise(), COptMethodCoranaWalk::optimise(), COptMethodLevenbergMarquardt::optimise(), COptMethodNelderMead::optimise(), COptMethodSA::optimise(), COptMethodTruncatedNewton::optimise(), COptMethodPraxis::optimise(), COptMethodStatistics::optimise(), COptMethodSteepestDescent::optimise(), CRandomSearch::optimise(), CTSSAMethod::orthog(), CLyapWolfMethod::orthonormalize(), CTimeSeries::output(), CHybridMethodODE45::outputState(), CHybridMethod::partitionSystem(), CHybridMethodLSODA::partitionSystem(), CColorScaleBiLog::passValue(), CLsodaMethod::peekAhead(), COptMethodSRES::phi(), COptMethodGASR::phi(), CPraxis::praxis_(), CPraxis::print_(), CFitProblem::printResult(), COptProblem::printResult(), CExperiment::printResult(), CLyapTask::process(), CTSSATask::process(), CTrajectoryTask::process(), CSteadyStateTask::process(), CCrossSectionTask::process(), CNewtonMethod::processNewton(), CTSSATask::processStep(), CTrajectoryTask::processStep(), CCrossSectionTask::processStep(), CLyapWolfMethod::product(), CMathContainer::pushInitialState(), CMathContainer::pushState(), CPraxis::quad_(), COptMethodSS::randomize(), COptMethodPS::reachedStdDeviation(), CInterpolation::recordState(), CTableauLine::reduce(), CMetab::refreshTransitionTime(), CCrossSectionTask::relativeDifferenceOfStates(), CNormalLcm::remove(), CNormalProduct::remove(), CStateTemplate::reorder(), CTrajectoryMethodDsaLsodar::CPartition::rePartition(), CMathContainer::replaceDiscontinuousNode(), COptMethodDE::replicate(), COptMethodSRES::replicate(), CQGLNetworkPainter::rescaleDataSets(), CQGLNetworkPainter::rescaleDataSetsWithNewMinMax(), CQGLNetworkPainter::rescaleNode(), CQProgressItemBar::reset(), CSlider::resetRange(), CMatrix< CFitConstraint * >::resize(), CStateTemplate::resize(), CVector< CProcessReportItem * >::resize(), CState::resize(), COptProblem::restoreModel(), CLinkMatrix::rightMultiply(), CProcessQueue::rootsFound(), CTimeSeries::save(), CQTrajectoryWidget::saveTask(), Curve2DWidget::SaveToCurveSpec(), HistoWidget::SaveToCurveSpec(), CMCAMethod::scaleMCA(), CSensMethod::scaling_variables(), CTimeSeries::separate(), CFunctionParameterMap::setCallParameter(), CFindDimensions::setChemicalEquation(), CQArrayAnnotationsWidget::setColumnSize(), CQSpecieDM::setData(), CMathContainer::setInitialState(), CModelEntity::setInitialValuePtr(), CQGLNetworkPainter::setItemAnimated(), COptItem::setLowerBound(), CChemEq::setMultiplicity(), CQGLNetworkPainter::setNodeSize(), CModelEntity::setObjectParent(), setParameterValue(), CExperimentObjectMap::CDataColumn::setScale(), CReaction::setScalingFactor(), CSlider::setSliderObject(), CMathContainer::setState(), CMathContainer::setStateReduced(), CMathEvent::setTargetValues(), CPlotItem::setType(), CHybridMethod::setupPartition(), CHybridMethodLSODA::setupPartition(), COptItem::setUpperBound(), CStochNextReactionMethod::setupPriorityQueue(), CHybridMethodODE45::setupPriorityQueue(), CHybridMethod::setupPriorityQueue(), CHybridMethodLSODA::setupPriorityQueue(), CModelParameterCompartment::setValue(), CModelEntity::setValuePtr(), CWriteConfig::setVariable(), CQOptimizationResult::slotSave(), CQFittingResult::slotSave(), CQFittingItemWidget::slotStartLostFocus(), CCSPMethod::smnorm(), CNewtonMethod::solveJacobianXeqB(), sort_(), COptMethodSS::sortRefSet(), ssbfgs_(), CEigen::stabilityAnalysis(), CCopasiXMLParser::ModelParameterElement::start(), CTauLeapMethod::start(), CStochDirectMethod::start(), CLyapWolfMethod::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), CTrajectoryMethodDsaLsodar::start(), CCopasiXMLParser::ConstantElement::start(), CCopasiXMLParser::ModelElement::start(), CCopasiXMLParser::ParameterElement::start(), CCopasiXMLParser::SliderElement::start(), CCopasiXMLParser::CurveElement::start(), CLsodaMethod::stateChanged(), CILDMMethod::step(), CILDMModifiedMethod::step(), CScanItemLinear::step(), CScanItemRandom::step(), CTauLeapMethod::step(), CHybridMethod::step(), CHybridMethodLSODA::step(), CStochDirectMethod::step(), CLyapWolfMethod::step(), CTrajAdaptiveSA::step(), CStochMethod::step(), CLsodaMethod::step(), CTrajectoryMethodDsaLsodar::step(), CHybridMethodODE45::step(), step1_(), CExperiment::storeExtendedTimeSeriesData(), CScanItem::storeValue(), stpmax_(), CModel::suitableForStochasticSimulation(), CExperiment::sumOfSquares(), CExperiment::sumOfSquaresStore(), COptMethodEP::swap(), COptMethodSRES::swap(), COptMethodGA::swap(), COptMethodGASR::swap(), CIndexedPriorityQueue::swapNodes(), CTSSAMethod::sylvester(), CTrajectoryProblem::sync(), CTSSAProblem::sync(), CSlider::sync(), CNewtonMethod::targetFunction(), test000087::test_simulate_reaction_flux_reference_1(), CSSAMethod::testForMixingStability(), CTruncatedNewton::tn_(), CTruncatedNewton::tnbc_(), CIndexedPriorityQueue::updateAux(), CExperiment::updateFittedPointValues(), CQTrajectoryWidget::updateIntervals(), CModelParameter::updateModel(), CStochNextReactionMethod::updatePriorityQueue(), CHybridMethod::updatePriorityQueue(), CHybridMethodLSODA::updatePriorityQueue(), CHybridMethodODE45::updatePriorityQueue(), CQExperimentData::updateScales(), CModel::updateSimulatedValues(), CTauLeapMethod::updateSystem(), CStochMethod::updateSystemState(), CHybridMethod::updateTauMu(), CHybridMethodLSODA::updateTauMu(), CHybridMethodODE45::updateTauMu(), CQLayoutMainWindow::updateValueTable(), CMMLOutput::writeRHS(), and CQGLNetworkPainter::zoom().

#define C_INT   long

Definition at line 115 of file copasi.h.

Referenced by CLinkMatrix::applyColumnPivot(), CCSPMethod::basisRefinement(), CLinkMatrix::build(), CEigen::calcEigenValues(), CLNAMethod::calculateCovarianceMatrixFull(), CLNAMethod::calculateCovarianceMatrixReduced(), CTSSAMethod::calculateDerivatives(), CModel::calculateDerivatives(), CModel::calculateDerivativesX(), CMathModel::calculateRootDerivatives(), CFitProblem::calculateStatistics(), CMCAMethod::calculateUnscaledConcentrationCC(), CMCAMethod::calculateUnscaledFluxCC(), cnvtst_(), TaskWidget::commonRunTask(), CLinkMatrix::completePivotInformation(), crash_(), CCSPMethod::CSPImportanceIndex(), CCSPMethod::CSPOutput(), CCSPMethod::CSPParticipationIndex(), CCSPMethod::CSPradicalPointer(), CCSPMethod::cspstep(), dbnorm_(), dcfode_(), CSSAMethod::decomposeJacobian(), CMathModel::determineInitialRoots(), CILDMMethod::deuflhard(), CILDMModifiedMethod::deuflhard_metab(), dewset_(), dfnorm_(), CInternalSolver::dintdy_(), CQTSSAResultSubWidget::displayResult(), CInternalSolver::dprja_(), CInternalSolver::drchek_(), CInternalSolver::droots_(), CInternalSolver::dsolsy_(), CInternalSolver::dstoda_(), dxpy_(), CCSPMethod::emptyOutputData(), CLsodaMethod::evalR(), CILDMModifiedMethod::evalsort(), COptMethodPraxis::evaluateFunction(), CHybridMethodODE45::fehl_(), CCSPMethod::findCandidatesNumber(), CPraxis::flin_(), CNodeK::getName(), CTruncatedNewton::getptc_(), CTruncatedNewton::gtims_(), COptMethodLevenbergMarquardt::hessian(), COptions::init(), COptMethodPraxis::initialize(), COptMethodTruncatedNewton::initialize(), CNewtonMethod::initialize(), CHybridMethodODE45::initMethod(), CHybridMethodLSODA::initMethod(), initp3_(), CHybridMethodLSODA::integrateDeterministicPart(), CTSSAMethod::integrationStep(), CCSPMethod::isBlockDiagonal(), CLinkMatrix::leftMultiply(), CTruncatedNewton::linder_(), CTruncatedNewton::lmqn_(), CTruncatedNewton::lmqnbc_(), CTSSAMethod::map_index(), CTSSAMethod::map_index_desc(), maprnt_(), CTSSAMethod::mat_anal_fast_space(), CTSSAMethod::mat_anal_fast_space_thomas(), CTSSAMethod::mat_anal_metab(), CTSSAMethod::mat_anal_mod(), CTSSAMethod::mat_anal_mod_space(), CPraxis::min_(), CPraxis::minfit_(), CCSPMethod::modesAmplitude(), CCSPMethod::modesAreExhausted(), CTruncatedNewton::modlnp_(), modz_(), monit_(), mslv_(), ndia3_(), negvec_(), CILDMMethod::newton(), CILDMModifiedMethod::newton_for_timestep(), CILDMModifiedMethod::newton_new(), CLSODAR::operator()(), CLSODA::operator()(), COptMethodLevenbergMarquardt::optimise(), COptMethodPraxis::optimise(), COptMethodTruncatedNewton::optimise(), CTSSAMethod::orthog(), CLsodaMethod::peekAhead(), CCSPMethod::perturbateA(), CPraxis::praxis_(), CCSPMethod::predifineAnnotation(), CPraxis::print_(), CILDMModifiedMethod::printResult(), CILDMMethod::printResult(), CCSPMethod::printResult(), CMathModel::processRoots(), CPraxis::quad_(), CTableRow::readLine(), CopasiUI3Window::refreshRecentFileMenu(), CopasiUI3Window::refreshRecentSBMLFileMenu(), CLinkMatrix::rightMultiply(), CHybridMethodODE45::rkf45_(), CHybridMethodODE45::rkfs_(), CProcessQueue::rootsFound(), CTSSAMethod::schur(), CTSSAMethod::schur_desc(), CILDMModifiedMethod::setAnnotationM(), CILDMMethod::setAnnotationM(), CCSPMethod::setAnnotationM(), CTruncatedNewton::setpar_(), CCSPMethod::setVectors(), CCSPMethod::setVectorsToNaN(), COptMethodTruncatedNewton::sFun(), CCSPMethod::smadd(), CCSPMethod::sminverse(), CCSPMethod::smmult(), CCSPMethod::smnorm(), CCSPMethod::smsubst(), CNewtonMethod::solveJacobianXeqB(), sort_(), ssbfgs_(), CEigen::stabilityAnalysis(), CCSPMethod::start(), CLyapWolfMethod::start(), CLsodaMethod::start(), CILDMMethod::step(), CILDMModifiedMethod::step(), CCSPMethod::step(), CLyapWolfMethod::step(), CLsodaMethod::step(), stpmax_(), CTSSAMethod::sylvester(), CTruncatedNewton::tn_(), CTruncatedNewton::tnbc_(), CTSSAMethod::update_nid(), CTSSAMethod::update_pid(), vcprnt_(), CCSPMethod::yCorrection(), and ztime_().

#define C_INT16   short
#define C_INT32   int

Definition at line 90 of file copasi.h.

Referenced by CQReportDefinitionSelect::accept(), BezierCurve::bezierPt(), CHistoCurveData::boundingRect(), CQReportDefinition::btnAdvancedClicked(), CLinkMatrix::build(), CSSAMethod::buildExtremeCurrents(), CModel::buildStoi(), CEvaluationNodeOperator::calculate(), CBitPatternMethod::calculate(), CBitPatternTreeMethod::calculate(), CStochMethod::calculateAmu(), CHybridMethod::calculateAmu(), CHybridMethodODE45::calculateAmu(), CHybridMethodLSODA::calculateAmu(), CHybridMethodLSODA::calculateDerivative(), CHybridMethod::calculateDerivative(), CEFMAlgorithm::calculateNextTableau(), CLyapTask::calculationsBeforeOutput(), CCopasiMessage::CCopasiMessage(), FontChooser::changeFontSize(), CQTaskMethodWidget::changeMethod(), CFixLocalReactionParameters::changeModel(), CScanWidgetRandom::changeType(), CHybridMethod::checkModel(), CHybridMethodLSODA::checkModel(), CHybridMethodODE45::checkModel(), COptMethodSS::childLocalMin(), CKinFunction::CKinFunction(), CLCurve::CLCurve(), CLGeneralGlyph::CLGeneralGlyph(), COptMethodSS::closerChild(), COptMethodSS::closerRefSet(), CLReactionGlyph::CLReactionGlyph(), COptMethodSS::combination(), CModel::compile(), COptMethodCoranaWalk::COptMethodCoranaWalk(), COptMethodDE::COptMethodDE(), COptMethodEP::COptMethodEP(), COptMethodEP2::COptMethodEP2(), COptMethodGA::COptMethodGA(), COptMethodGASR::COptMethodGASR(), COptMethodHGASA::COptMethodHGASA(), COptMethodHookeJeeves::COptMethodHookeJeeves(), COptMethodLevenbergMarquardt::COptMethodLevenbergMarquardt(), COptMethodNelderMead::COptMethodNelderMead(), COptMethodPS::COptMethodPS(), COptMethodSA::COptMethodSA(), COptMethodSRES::COptMethodSRES(), COptMethodSS::COptMethodSS(), COptMethodSteepestDescent::COptMethodSteepestDescent(), CSensProblem::copySensItemToParameterGroup(), CQReportDefinition::CQReportDefinition(), CRandomSearch::CRandomSearch(), SBMLImporter::createCModelFromSBMLDocument(), COutputAssistant::createDefaultOutput(), CQSpinBoxDelegate::createEditor(), CQPlotSubwidget::createHistograms(), CHybridMethod::createHybridMethod(), CHybridMethodLSODA::createHybridMethodLSODA(), SBMLDocumentLoader::createLayout(), CQBaseDataModel::createNewName(), CSensProblem::createParametersInGroup(), COutputAssistant::createPlot(), CScanProblem::createScanItem(), CQLayoutMainWindow::createStartIcon(), CQLayoutMainWindow::createStopIcon(), COutputAssistant::createTable(), CQGLNetworkPainter::createTextureForAllLabels(), CDirEntry::createTmpName(), CCopasiParameter::createValue(), COptMethodSS::creation(), COptMethodGA::crossover(), COptMethodGASR::crossover(), CSensProblem::CSensProblem(), BezierCurve::curvePts(), CVersion::CVersion(), CNewtonMethod::doIntegration(), CQGLNetworkPainter::drawColorLegend(), CQGLNetworkPainter::drawGraph(), CQOptimizationResult::enterProtected(), ObjectBrowserWidget::eXport(), CEFMAlgorithm::findMinimalCombinationIndex(), CRDFUtilities::fixLocalFileAboutReference(), CRDFUtilities::fixSBMLRdf(), FontChooser::FontChooser(), CReport::generateObjectsFromName(), Cmt19937::genrand_res53(), CMIRIAMResources::getActDateInSeconds(), CExpatTemplate< CExpat >::getAttributeValue(), CEFMTask::getFluxModeDescription(), CExperimentObjectMap::getLastNotIgnoredColumn(), CCopasiContainer::getObject(), CArrayAnnotation::getObject(), Cmt19937HR::getRandomCC(), Cmt19937HR::getRandomCO(), Cmt19937HR::getRandomOO(), CRandom::getRandomS(), CRandom::getRandomU(), CRandom::getSystemSeed(), CArrayElementReference::getValuePointer(), CReadConfig::getVariable(), SBMLImporter::importEvents(), SBMLImporter::importInitialAssignments(), CScanWidgetRandom::initFromObject(), CopasiPlot::initFromSpec(), CSSAMethod::initialize(), CEFMAlgorithm::initialize(), COptMethodSS::initialize(), CBitPatternMethod::initialize(), CBitPatternTreeMethod::initialize(), CTSSAMethod::initializeIntegrationsParameter(), CExperimentObjectMap::CDataColumn::initializeParameter(), CRecentFiles::initializeParameter(), CScanProblem::initializeParameter(), CLyapProblem::initializeParameter(), CNewtonMethod::initializeParameter(), CTrajectoryProblem::initializeParameter(), CTSSAProblem::initializeParameter(), CCrossSectionProblem::initializeParameter(), CCSPMethod::initializeParameter(), CStochDirectMethod::initializeParameter(), CTrajAdaptiveSA::initializeParameter(), CHybridMethodODE45::initializeParameter(), CLyapWolfMethod::initializeParameter(), CTauLeapMethod::initializeParameter(), CStochMethod::initializeParameter(), CLsodaMethod::initializeParameter(), CMIRIAMResources::initializeParameter(), CCrossValidationSet::initializeParameter(), CTrajectoryMethodDsaLsodar::initializeParameter(), CHybridMethod::initializeParameter(), CHybridMethodLSODA::initializeParameter(), CExperiment::initializeParameter(), CTrajectoryProblem::initObjects(), CTSSAProblem::initObjects(), CScanContainerWidget::insertWidget(), CCopasiTask::isValidMethod(), CLyapMethod::isValidProblem(), CQFittingResultTab1::load(), CScanWidgetRandom::load(), CScanWidgetRepeat::load(), CScanWidgetScan::load(), CFunctionDB::load(), CCompartment::load(), CReaction::load(), CNewtonMethod::load(), CMCAMethod::load(), CModel::load(), CFunction::load(), CLNAMethod::load(), CNodeK::load(), CMetab::load(), CMetabOld::load(), StateSubwidget::loadCompartments(), CQLyapResultWidget::loadFromBackend(), Curve2DWidget::LoadFromCurveSpec(), CQTaskMethodWidget::loadMethod(), StateSubwidget::loadModelValues(), CReaction::loadOld(), CReaction::loadOneRole(), StateSubwidget::loadReactions(), CQReportDefinitionSelect::loadReportDefinitionVector(), COptMethodSS::localmin(), BezierCurve::multiplyFromTo(), Cmt19937::next_state(), NodeSizePanel::NodeSizePanel(), SBMLImporter::normalizeSBMLUnit(), CRandomSearch::optimise(), COptMethodEP2::optimise(), COptMethodHGASA::optimise(), CopasiPlot::output(), CHybridMethod::outputData(), CHybridMethodLSODA::outputData(), PaintWidget::paintEvent(), CRDFParser::parse(), SBMLImporter::parseSBML(), SEDMLImporter::parseSEDML(), PlotWindow::printAsImage(), CEFMProblem::printResult(), CLyapTask::printResult(), CILDMModifiedMethod::printResult(), CILDMMethod::printResult(), CCSPMethod::printResult(), CSensMethod::process(), CScanTask::process(), CTrajectoryTask::process(), CSteadyStateTask::process(), CNewtonMethod::processNewton(), COptMethodSS::randomize(), SBMLDocumentLoader::readListOfLayouts(), CTableauLine::reduce(), CQSpeciesWidget::refreshCompartments(), SBMLImporter::removeUnusedFunctions(), CQProgressItemBar::reset(), CScanWidgetRandom::save(), CQReportDefinition::save(), CQCompartment::save(), CopasiPlot::saveData(), CQTSSAResultSubWidget::saveDataToFile(), CQBarChart::saveDataToFile(), CQTaskMethodWidget::saveMethod(), Curve2DWidget::SaveToCurveSpec(), BandedGraphWidget::SaveToCurveSpec(), HistoWidget::SaveToCurveSpec(), CQLyapResultWidget::saveToFile(), CQSensResultWidget::saveToFile(), SBMLIncompatibility::SBMLIncompatibility(), COptMethodEP::select(), COptMethodGA::select(), CopasiPlot::separate(), CCSPMethod::setAnnotationM(), CQArrayAnnotationsWidget::setColumnSize(), CQSpinBoxDelegate::setEditorData(), NodeSizePanel::setMaxValue(), NodeSizePanel::setMinAndMaxValues(), NodeSizePanel::setMinValue(), CMIRIAMResources::setMIRIAMUpdateFrequencyInDays(), setParameterValue(), CScanProblem::setSubtask(), CPlotItem::setType(), CHybridMethodODE45::setupBalances(), CHybridMethod::setupBalances(), CHybridMethodLSODA::setupBalances(), CStochMethod::setupDependencyGraphAndBalances(), CQTaskMethodWidget::setValidMethods(), CopasiSlider::setValue(), CQProgressItemBar::setValueFromDOUBLE(), CQProgressItemBar::setValueFromINT(), CQProgressItemBar::setValueFromUINT(), CWriteConfig::setVariable(), CPermutation::shuffle(), CQPreferenceDialog::slotBtnOk(), CQParameterOverviewWidget::slotBtnSaveToFile(), CopasiUI3Window::slotCapture(), CQExperimentData::slotCheckFrom(), CQExperimentData::slotCheckTo(), CQMoietiesTaskResult::slotCreateGlobalQuantity(), CQReportDefinitionSelect::slotEdit(), CQExperimentData::slotExperimentAdd(), CopasiUI3Window::slotExportMathModel(), CopasiUI3Window::slotExportSBML(), CopasiUI3Window::slotFileSaveAs(), CopasiUI3Window::slotFunctionDBSave(), CQDifferentialEquations::slotSave(), CQSteadyStateResult::slotSave(), CQTimeSeriesWidget::slotSave(), CQMoietiesTaskResult::slotSave(), CMCAResultSubwidget::slotSave(), CLNAResultSubwidget::slotSave(), CQOptimizationResult::slotSave(), CQFittingResult::slotSave(), CQEFMResultWidget::slotSave(), PlotWindow::slotSaveData(), CQExpressionMmlStackedWidget::slotSaveExpression(), CQExperimentData::slotSeparator(), CQSpeciesDetail::slotSwitchToReaction(), COptMethodSS::sortRefSet(), CEigen::stabilityAnalysis(), CTauLeapMethod::start(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), CCopasiXMLParser::ParameterElement::start(), CCopasiXMLParser::COPASIElement::start(), CCopasiXMLParser::ParameterDescriptionElement::start(), CCopasiXMLParser::SliderElement::start(), CCopasiXMLParser::MetaboliteReferenceGlyphElement::start(), StringPrint(), strToInt(), strToUnsignedInt(), CModel::suitableForStochasticSimulation(), CTrajectoryProblem::sync(), CTSSAProblem::sync(), CSlider::sync(), test000087::test_simulate_reaction_flux_reference_1(), CSSAMethod::testForMixingStability(), CopasiPlot::updateCurves(), CScanContainerWidget::updateIndices(), CMIRIAMResources::updateMIRIAMResources(), CMIRIAMResources::updateMIRIAMResourcesFromFile(), CQExperimentData::updateScales(), ObjectBrowserWidget::updateSelectedItemsView(), CopasiSlider::updateValue(), CQExperimentDataValidator::validate(), CChemEqInterface::writeElement(), CSlider::writeToObject(), and CFunctionParameter::xmlRole2Enum().

#define C_INT64   long long int
#define C_INVALID_INDEX   (std::numeric_limits< size_t >::max())

Definition at line 222 of file copasi.h.

Referenced by CFunctionParameters::add(), CFunctionDB::addAndAdaptName(), CCopasiDataModel::addDefaultReports(), CCopasiDataModel::addDefaultTasks(), CModelAdd::addEvents(), CReaction::addParameterMapping(), CQPlotSubwidget::addPlot(), CQReportDefinition::btnCopyReportClicked(), CQReportDefinition::btnNewReportClicked(), CIndexedPriorityQueue::buildHeap(), CSensMethod::calculate_difference(), CReaction::clearParameterMapping(), CTimeSeries::compile(), CEvaluationNodeVariable::compile(), CMathEventN::CTrigger::compile(), CExperiment::compile(), CExperimentObjectMap::compile(), CMathEventN::CTrigger::compileVARIABLE(), CFunction::completeFunctionList(), CCompressedColumnFormat::const_row_iterator::const_row_iterator(), CRDFGraphConverter::convert(), CQSpeciesDetail::copy(), CQCompartment::copy(), ReactionsWidget1::copy(), CMathTrigger::copyBranch(), CMathContainer::copyBranch(), FunctionWidget1::copyFunctionContentsToFunction(), CQPlotSubwidget::copyPlot(), CMathEventN::CTrigger::countRootsVARIABLE(), CRDFPredicate::createAllowedLocationsRelative(), SBMLImporter::createCCompartmentFromCompartment(), SBMLImporter::createCMetabFromSpecies(), SBMLImporter::createCModelFromSBMLDocument(), SBMLImporter::createCModelValueFromParameter(), CModel::createCompartment(), SBMLImporter::createCReactionFromReaction(), CCrossSectionTask::createEvent(), CModel::createEvent(), CModel::createMetabolite(), CRDFNode::createMissingAncestors(), CModel::createModelValue(), CChemEqInterface::createNonExistingMetabs(), CKinFunction::createParameters(), createParameterSetsForExperiment(), CModel::createReaction(), SliderDialog::createSlidersForFolder(), CQFittingItemWidget::currentRow(), CZeroSet::CZeroSet(), CSensMethod::do_collapsing(), CMetabNameInterface::doesExist(), CTrajAdaptiveSA::doSingleSSAStep(), CHybridNextReactionLSODAMethod::doSingleStep(), CHybridNextReactionRKMethod::doSingleStep(), CStochDirectMethod::doSingleStep(), CTrajectoryMethodDsaLsodar::doSingleStep(), CTrajAdaptiveSA::doSingleTauLeapStep(), COptProblem::elevateChildren(), CCopasiXMLParser::InitialStateElement::end(), CCopasiXMLParser::COPASIElement::end(), CCopasiXMLParser::ListOfFunctionsElement::end(), CCopasiXMLParser::ListOfParameterDescriptionsElement::end(), CQEventWidget1::enterProtected(), CODEExporter::exportExpression(), CMIRIAMResourceObject::extractId(), SBMLImporter::findCorrespondingFunction(), CFunctionDB::findFunction(), CModel::findMetabByName(), CModel::findMoiety(), CFunctionParameters::findParameterByName(), ListViews::findWidgetFromIndex(), COptMethodDE::fittest(), COptMethodSRES::fittest(), COptMethodGA::fittest(), COptMethodGASR::fittest(), CCopasiXML::fixBuild55(), CCopasiXML::fixBuild81(), CTimeSeries::getConcentrationData(), ListViews::getCurrentItemId(), CMIRIAMResourceObject::getDisplayName(), CCopasiObjectName::getElementIndex(), CQBrowserPaneDM::getIdFromIndex(), CStateTemplate::getIndex(), CModelParameter::getIndex(), QTimeCourseAnimation::getIndex(), CCopasiParameterGroup::getIndex(), CCopasiVector< CLGeneralGlyph >::getIndex(), CCopasiVectorN< CReportDefinition >::getIndex(), CChemEq::getLargestCompartment(), QTimeCourseAnimation::getMax(), CMetabNameInterface::getMetabolite(), CMIRIAMResources::getMIRIAMResourceIndex(), CChemEqInterface::getMolecularity(), CExperimentFileInfo::getNextUnusedSection(), CCopasiParameterGroup::getObject(), CCopasiVectorN< CReportDefinition >::getObject(), CFunctionParameterMap::getObjects(), CReaction::getParameterMapping(), getReactionIndex(), CMIRIAMResources::getResourceIndexFromDisplayName(), CQBrowserPaneDM::CNode::getSortRole(), CRDFPredicate::getSubPathIndex(), CCopasiParameterGroup::getUniqueParameterName(), CEvaluationTree::getVariableIndex(), CTableRow::guessColumnNumber(), SBMLImporter::importEvent(), SBMLImporter::importEvents(), SBMLImporter::importInitialAssignments(), CQBrowserPaneDM::index(), CQFittingItemWidget::init(), CScanMethod::init(), CFitProblem::initialize(), CSensMethod::initialize(), CIndexedPriorityQueue::initializeIndexPointer(), CReaction::initializeParameters(), CFunction::initVariables(), CCopasiVectorN< CReportDefinition >::isInsertAllowed(), CQExperimentData::isLikePreviousExperiment(), CReaction::isLocalParameter(), CFunction::isSuitable(), CMIRIAMResourceObject::isValid(), CExperimentSet::keyToIndex(), CQFittingItemWidget::load(), CQBrowserPaneDM::load(), CQEventWidget1::loadFromEvent(), CQExperimentData::loadTable(), LUfactor(), SliderDialog::mapFolderId2EntryId(), COptMethodSRES::mutate(), CZeroSet::CIndex::operator++(), CZeroSet::CIndex::operator=(), CMath::CVariableStack::operator[](), CMath::CAllocationStack::operator[](), CCopasiVectorN< CReportDefinition >::operator[](), COptMethodDE::optimise(), COptMethodSRES::optimise(), COptMethodGA::optimise(), COptMethodGASR::optimise(), COptMethodEP::optimise(), SBMLImporter::parseSBML(), SEDMLImporter::parseSEDML(), CExperiment::read(), CTableRow::readLine(), CCopasiVector< CLGeneralGlyph >::remove(), CCopasiVectorN< CReportDefinition >::remove(), CModel::removeCompartment(), CModel::removeEvent(), CFunctionDB::removeFunction(), CCopasiDataModel::removeLayout(), CModel::removeModelValue(), CCopasiParameterGroup::removeParameter(), COutputDefinitionVector::removePlotSpec(), CModel::removeReaction(), CReportDefinitionVector::removeReportDefinition(), CQParameterSetsDM::removeRows(), CQModifiedDM::removeRows(), CQReportDM::removeRows(), CQLayoutsDM::removeRows(), CQBiologicalDescriptionDM::removeRows(), CQReferenceDM::removeRows(), CQCreatorDM::removeRows(), CQFunctionDM::removeRows(), CQReactionDM::removeRows(), CQEventDM::removeRows(), CQGlobalQuantityDM::removeRows(), CQCompartmentDM::removeRows(), CQSpecieDM::removeRows(), CIndexedPriorityQueue::removeStochReaction(), SBMLImporter::removeUnusedFunctions(), COptMethodDE::replicate(), CopasiPlot::replot(), SliderDialog::reset(), CQFittingItemWidget::save(), CQFittingWidget::saveTask(), CQEventWidget1::saveToEvent(), CSensMethod::scaling_targetfunction(), CQFittingItemWidget::selectRow(), CQArrayAnnotationsWidget::setArrayAnnotation(), SliderDialog::setCurrentFolderId(), CMIRIAMResourceObject::setDisplayName(), CMIRIAMResourceObject::setId(), CFindDimensions::setMolecularitiesForMassAction(), CReaction::setParameterMapping(), CReaction::setParameterMappingVector(), CReaction::setParameterValue(), CMIRIAMResourceObject::setURI(), SliderDialog::SliderDialog(), CQEventWidget1::slotActualizeAssignmentExpression(), CProgressBar::slotAddItem(), CQParameterOverviewWidget::slotBtnCopy(), FunctionWidget1::slotBtnNew(), ReactionsWidget1::slotBtnNew(), CQSpeciesDetail::slotBtnNew(), CQCompartment::slotBtnNew(), CQModelValue::slotBtnNew(), CQEventWidget1::slotBtnNew(), ParameterTable::slotCellChanged(), CQExperimentData::slotCheckFrom(), CQParameterSetsWidget::slotDoubleClicked(), CQPlotsWidget::slotDoubleClicked(), CQReactionsWidget::slotDoubleClicked(), CQReportsWidget::slotDoubleClicked(), CQFunctionsWidget::slotDoubleClicked(), CQEventsWidget::slotDoubleClicked(), CQCompartmentsWidget::slotDoubleClicked(), CQGlobalQuantitiesWidget::slotDoubleClicked(), CQSpeciesWidget::slotDoubleClicked(), CQFittingItemWidget::slotDuplicatePerExperiment(), CQReportDefinitionSelect::slotEdit(), CQExperimentData::slotExperimentDelete(), CQExperimentData::slotFileDelete(), CQExperimentData::slotFirst(), ReactionsWidget1::slotGotoFunction(), CQExperimentData::slotLast(), CQCompartment::slotMetaboliteTableCurrentChanged(), ReactionsWidget1::slotNewFunction(), CQBrowserPaneDM::slotNotify(), CQExperimentData::slotOK(), CQFittingItemWidget::slotParamEdit(), CQEventWidget1::slotSelectObject(), CQSpeciesDetail::slotSwitchToReaction(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), CTrajectoryMethodDsaLsodar::start(), CCopasiXMLParser::AssignmentElement::start(), CCopasiXMLParser::ReportElement::start(), CCopasiXMLParser::ParameterDescriptionElement::start(), CCopasiXMLParser::FunctionElement::start(), CExperimentFileInfo::sync(), SliderDialog::updateAllSliders(), CIndexedPriorityQueue::updateAux(), CopasiPlot::updateCurves(), CHybridMethod::updatePriorityQueue(), CHybridMethodLSODA::updatePriorityQueue(), CHybridMethodODE45::updatePriorityQueue(), CReaction::variable2object(), and CDotOutput::writeObjectNode().

#define C_LOGICAL   C_INT

Definition at line 122 of file copasi.h.

Referenced by CLNAMethod::calculateCovarianceMatrixReduced().

#define C_UNUSED (   p)

Definition at line 220 of file copasi.h.

#define CONSTRUCTOR_TRACE
#define COPASI_DEPRECATED

Definition at line 221 of file copasi.h.

#define DEBUG_OUT (   s)

Definition at line 198 of file copasi.h.

#define DESTRUCTOR_TRACE

Definition at line 206 of file copasi.h.

Referenced by CChemEq::~CChemEq(), CChemEqElement::~CChemEqElement(), CCompartment::~CCompartment(), CCopasiVector< CLGeneralGlyph >::~CCopasiVector(), CCrossSectionMethod::~CCrossSectionMethod(), CCrossSectionProblem::~CCrossSectionProblem(), CEFMAlgorithm::~CEFMAlgorithm(), CEigen::~CEigen(), CFluxScore::~CFluxScore(), CFunctionDB::~CFunctionDB(), CFunctionParameter::~CFunctionParameter(), CFunctionParameters::~CFunctionParameters(), CHybridMethod::~CHybridMethod(), CHybridMethodLSODA::~CHybridMethodLSODA(), CHybridMethodODE45::~CHybridMethodODE45(), CKinFunction::~CKinFunction(), CLinkMatrixView::~CLinkMatrixView(), CLNAMethod::~CLNAMethod(), CLNAProblem::~CLNAProblem(), CLyapMethod::~CLyapMethod(), CLyapProblem::~CLyapProblem(), CMassAction::~CMassAction(), CMCAMethod::~CMCAMethod(), CMCAProblem::~CMCAProblem(), CMetab::~CMetab(), CMetabOld::~CMetabOld(), CModel::~CModel(), CModelEntity::~CModelEntity(), CModelValue::~CModelValue(), CMoiety::~CMoiety(), CNodeK::~CNodeK(), COptions::~COptions(), COptions::COptionValue::~COptionValue(), COptions::COptionValueTemplate< CType >::~COptionValueTemplate(), CReaction::~CReaction(), CSensMethod::~CSensMethod(), CSensProblem::~CSensProblem(), CSteadyStateMethod::~CSteadyStateMethod(), CSteadyStateProblem::~CSteadyStateProblem(), CTableauLine::~CTableauLine(), CTauLeapMethod::~CTauLeapMethod(), CTrajectoryMethod::~CTrajectoryMethod(), CTrajectoryMethodDsaLsodar::~CTrajectoryMethodDsaLsodar(), CTrajectoryProblem::~CTrajectoryProblem(), and CTSSAProblem::~CTSSAProblem().

#define LLONG_CONST (   n)    n ## LL
#define NDEBUG

Definition at line 196 of file copasi.h.

#define pcleanup (   p)    {if (p) {p->cleanup(); delete p; p = NULL;}}

Definition at line 217 of file copasi.h.

#define pdelete (   p)    {if (p) {delete p; p = NULL;}}

Definition at line 215 of file copasi.h.

Referenced by CFunctionDB::addAndAdaptName(), CTableauMatrix::addLine(), COptProblem::calculate(), CBitPatternTreeMethod::calculate(), CEFMAlgorithm::calculateFluxModes(), CEFMAlgorithm::calculateNextTableau(), CFitTask::CFitTask(), CFunctionAnalyzer::checkKineticFunction(), CReportBody::cleanup(), COptMethodEP::cleanup(), COptMethodDE::cleanup(), COptMethodSRES::cleanup(), COptMethodGA::cleanup(), COptMethodPS::cleanup(), COptMethodGASR::cleanup(), CReportTable::cleanup(), COptMethodSS::cleanup(), COptions::cleanup(), CNewtonMethod::cleanup(), CTSSATask::cleanup(), CTrajectoryTask::cleanup(), CCrossSectionTask::cleanup(), CQRDFTreeView::clear(), SliderDialog::clear(), CModelParameterGroup::clear(), CCopasiParameterGroup::clear(), CReactionInterface::clearFunction(), CCopasiObject::clearRefresh(), CReport::close(), CModelEntity::compile(), CMetab::compile(), CModel::compile(), CMathTrigger::compileEQ(), CMathObject::compileFlux(), CModel::convert2NonReversible(), CQSpeciesDetail::copy(), CQCompartment::copy(), ReactionsWidget1::copy(), CReactionInterface::copyMapping(), ObjectList::createBucketIndex(), SBMLImporter::createCFunctionFromFunctionDefinition(), SBMLImporter::createCReactionFromReaction(), CKinFunction::createParameters(), CDirEntry::createTmpName(), ObjectList::delDuplicate(), CCopasiDataModel::deleteOldData(), SliderDialog::deleteSlider(), CQCrossSectionTaskWidget::destroy(), CQProgressItemBar::destroy(), CQFittingWidget::destroy(), CQTSSAWidget::destroy(), CQTrajectoryWidget::destroy(), CQFittingItemWidget::destroy(), CCopasiRootContainer::destroy(), CQExperimentData::destroy(), CCopasiXMLParser::PlotItemElement::end(), CCopasiXMLParser::PlotSpecificationElement::end(), CCopasiXMLParser::ParameterGroupElement::end(), CCopasiXMLParser::TaskElement::end(), CCopasiXMLParser::FunctionElement::end(), CCopasiXMLParser::LineEndingElement::end(), CQParameterOverviewWidget::enterProtected(), CSEDMLExporter::exportModelAndTasksToString(), CSBMLExporter::exportModelToString(), CCopasiDataModel::exportSBML(), CCopasiDataModel::exportSBMLToString(), CListOfLayouts::exportToSBML(), CReport::finish(), CProcessReport::finishItem(), CCopasiXML::freeFunctionList(), CCopasiXML::freeGUI(), CCopasiXML::freeLayoutList(), CCopasiXML::freeModel(), CEvaluationParserBase::freeNodeList(), CCopasiXML::freePlotList(), CCopasiXML::freeReportList(), CCopasiXML::freeTaskList(), SBMLImporter::importEvent(), CReactionInterface::initFromReaction(), CopasiPlot::initFromSpec(), CFitProblem::initialize(), CBitPatternMethod::initialize(), CBitPatternTreeMethod::initialize(), CTrajectoryTask::initialize(), CTSSATask::initialize(), CSteadyStateTask::initialize(), CCrossSectionTask::initialize(), CCopasiTask::initialize(), CFunctionParameterMap::initializeFromFunctionParameters(), CMetab::initObjects(), CModel::initObjects(), CTSSAMethod::integrationMethodStart(), SBMLImporter::isMassActionExpression(), CQExperimentData::load(), CQFittingItemWidget::load(), CMIRIAMInfo::load(), CFunctionDB::load(), CCopasiXML::load(), CTrajectoryTask::load(), ObjectBrowserWidget::loadChild(), FunctionWidget1::loadFromFunction(), ReactionsWidget1::loadFromReaction(), CQCrossSectionTaskWidget::loadTask(), CQFittingWidget::loadTask(), CQTSSAWidget::loadTask(), CQTrajectoryWidget::loadTask(), main(), DataModelGUI::miriamDownloadFinished(), SBMLImporter::multiplySubstanceOnlySpeciesByVolume(), CReport::open(), CNormalChoiceLogical::operator=(), CNormalChoice::operator=(), CCompressedColumnFormat::operator=(), COptMethodHGASA::optimise(), CRDFParser::parse(), ObjectList::pop(), SBMLImporter::preprocessNode(), CModelParameterGroup::remove(), CCopasiRootContainer::removeDatamodel(), CQSimpleSelectionTree::removeEmptySubTree(), CModel::removeMetabolite(), CCopasiParameterGroup::removeParameter(), CQParameterSetsDM::removeRows(), CQLayoutsDM::removeRows(), SBMLImporter::replaceAmountReferences(), CMathContainer::replaceDiscontinuousNode(), CopasiPlot::resizeCurveData(), CFitProblem::restore(), TaskWidget::revertBtnClicked(), CQPlotSubwidget::selectPlotItem(), CNormalChoice::setCondition(), CNormalChoiceLogical::setCondition(), CEvent::setDelayExpressionPtr(), CEventAssignment::setExpressionPtr(), CMathObject::setExpressionPtr(), CModelEntity::setExpressionPtr(), CNormalChoice::setFalseExpression(), CNormalChoiceLogical::setFalseExpression(), CReaction::setFunctionFromExpressionTree(), CReactionInterface::setFunctionWithEmptyMapping(), CModelParameter::setInitialExpression(), CModelEntity::setInitialExpressionPtr(), CRDFObject::setLiteral(), CFitTask::setMethodType(), CMoietiesTask::setMethodType(), COscillationTask::setMethodType(), COptTask::setMethodType(), CEFMTask::setMethodType(), CTrajectoryTask::setMethodType(), CTSSATask::setMethodType(), CLyapTask::setMethodType(), CCrossSectionTask::setMethodType(), CRDFNode::setObject(), CModelEntity::setObjectParent(), CEvent::setPriorityExpressionPtr(), CCopasiObject::setRefresh(), CQAnimationWindow::setScene(), CModelEntity::setStatus(), CRDFNode::setSubject(), CEvent::setTriggerExpressionPtr(), CNormalChoice::setTrueExpression(), CNormalChoiceLogical::setTrueExpression(), CCopasiObject::setUpdateMethod(), ScanWidget::slotAddItem(), CQFittingWidget::slotCrossValidationData(), CQFittingItemWidget::slotDelete(), CQEventWidget1::slotDeleteTarget(), CQFittingWidget::slotExperimentData(), CQExperimentData::slotFileDelete(), CQExperimentData::slotOK(), CQFittingItemWidget::slotReset(), CLyapWolfMethod::start(), CCopasiXMLParser::FunctionElement::start(), CQPlotSubwidget::storeChanges(), CExperimentFileInfo::sync(), TestOptimization(), CMIRIAMResources::updateMIRIAMResources(), CMIRIAMResources::updateMIRIAMResourcesFromFile(), ObjectBrowserWidget::updateSelectedItemsView(), CChemEqParserBase::yyparse(), AboutDialog::~AboutDialog(), CCopasiXMLParser::BodyElement::~BodyElement(), CCopasiXMLParser::BoundingBoxElement::~BoundingBoxElement(), CArrayAnnotation::~CArrayAnnotation(), CBitPatternTree::~CBitPatternTree(), CBitPatternTreeMethod::~CBitPatternTreeMethod(), CBitPatternTreeNode::~CBitPatternTreeNode(), CBrowserObject::~CBrowserObject(), CCompressedColumnFormat::~CCompressedColumnFormat(), CConcentrationReference::~CConcentrationReference(), CCopasiContainer::~CCopasiContainer(), CCopasiDataModel::~CCopasiDataModel(), CCopasiObject::~CCopasiObject(), CCopasiRootContainer::~CCopasiRootContainer(), CCopasiSelectionWidget::~CCopasiSelectionWidget(), CCopasiTask::~CCopasiTask(), CCopasiTree< _Node >::~CCopasiTree(), CCSPMethod::~CCSPMethod(), CEFMAlgorithm::~CEFMAlgorithm(), CEvent::~CEvent(), CEventAssignment::~CEventAssignment(), CExperimentFileInfo::~CExperimentFileInfo(), CFitItem::~CFitItem(), CFitProblem::~CFitProblem(), CFunctionParameterMap::~CFunctionParameterMap(), CILDMMethod::~CILDMMethod(), CILDMModifiedMethod::~CILDMModifiedMethod(), CInterpolation::~CInterpolation(), CLyapWolfMethod::~CLyapWolfMethod(), CMathObject::~CMathObject(), CMIRIAMInfo::~CMIRIAMInfo(), CModel::~CModel(), CModelEntity::~CModelEntity(), CNormalChoice::~CNormalChoice(), CNormalChoiceLogical::~CNormalChoiceLogical(), CCopasiXMLParser::ColorDefinitionElement::~ColorDefinitionElement(), CopasiUI3Window::~CopasiUI3Window(), COptMethodPraxis::~COptMethodPraxis(), COptMethodSteepestDescent::~COptMethodSteepestDescent(), COptMethodTruncatedNewton::~COptMethodTruncatedNewton(), CPlotSelectionDialog::~CPlotSelectionDialog(), CPraxis::~CPraxis(), CProcessReport::~CProcessReport(), CProgressBar::~CProgressBar(), CQAnimationWindow::~CQAnimationWindow(), CQBrowserPaneDM::~CQBrowserPaneDM(), CQCompartmentsWidget::~CQCompartmentsWidget(), CQEFMListWidget::~CQEFMListWidget(), CQEFMResultWidget::~CQEFMResultWidget(), CQEventsWidget::~CQEventsWidget(), CQFunctionsWidget::~CQFunctionsWidget(), CQGlobalQuantitiesWidget::~CQGlobalQuantitiesWidget(), CQLayoutsWidget::~CQLayoutsWidget(), CQLayoutThread::~CQLayoutThread(), CQMiriamWidget::~CQMiriamWidget(), CQParameterSetsWidget::~CQParameterSetsWidget(), CQPlotsWidget::~CQPlotsWidget(), CQProgressItem::~CQProgressItem(), CQReactionsWidget::~CQReactionsWidget(), CQReportsWidget::~CQReportsWidget(), CQSpeciesWidget::~CQSpeciesWidget(), CRDFGraph::~CRDFGraph(), CRDFNode::~CRDFNode(), CRDFObject::~CRDFObject(), CReactionInterface::~CReactionInterface(), CSBMLExporter::~CSBMLExporter(), CSBMLunitInterface::~CSBMLunitInterface(), CSteadyStateTask::~CSteadyStateTask(), CStochDirectMethod::~CStochDirectMethod(), CTableauLine::~CTableauLine(), CTableauMatrix::~CTableauMatrix(), CTrajAdaptiveSA::~CTrajAdaptiveSA(), CCopasiXMLParser::CurveElementElement::~CurveElementElement(), CCopasiXMLParser::EllipseElement::~EllipseElement(), CCopasiXMLParser::EventElement::~EventElement(), CCopasiXMLParser::FooterElement::~FooterElement(), CCopasiXMLParser::FunctionElement::~FunctionElement(), FunctionWidget1::~FunctionWidget1(), CCopasiXMLParser::GlobalStyleElement::~GlobalStyleElement(), CCopasiXMLParser::GradientStopElement::~GradientStopElement(), CCopasiXMLParser::GroupElement::~GroupElement(), CCopasiXMLParser::HeaderElement::~HeaderElement(), CCopasiXMLParser::ImageElement::~ImageElement(), CCopasiXMLParser::LinearGradientElement::~LinearGradientElement(), CCopasiXMLParser::LineEndingElement::~LineEndingElement(), CCopasiXMLParser::ListOfColorDefinitionsElement::~ListOfColorDefinitionsElement(), CCopasiXMLParser::ListOfCurveElementsElement::~ListOfCurveElementsElement(), CCopasiXMLParser::ListOfGlobalRenderInformationElement::~ListOfGlobalRenderInformationElement(), CCopasiXMLParser::ListOfGlobalStylesElement::~ListOfGlobalStylesElement(), CCopasiXMLParser::ListOfGradientDefinitionsElement::~ListOfGradientDefinitionsElement(), CCopasiXMLParser::ListOfLineEndingsElement::~ListOfLineEndingsElement(), CCopasiXMLParser::ListOfLocalRenderInformationElement::~ListOfLocalRenderInformationElement(), CCopasiXMLParser::ListOfLocalStylesElement::~ListOfLocalStylesElement(), CCopasiXMLParser::ListOfModelParameterSetsElement::~ListOfModelParameterSetsElement(), CCopasiXMLParser::ListOfUnsupportedAnnotationsElement::~ListOfUnsupportedAnnotationsElement(), CCopasiXMLParser::LocalStyleElement::~LocalStyleElement(), CCopasiXMLParser::MethodElement::~MethodElement(), CCopasiXMLParser::ModelParameterGroupElement::~ModelParameterGroupElement(), CCopasiXMLParser::ModelParameterSetElement::~ModelParameterSetElement(), CCopasiXMLParser::ModelValueElement::~ModelValueElement(), ObjectBrowserItem::~ObjectBrowserItem(), CCopasiXMLParser::ParameterGroupElement::~ParameterGroupElement(), CCopasiXMLParser::PlotItemElement::~PlotItemElement(), CCopasiXMLParser::PolygonElement::~PolygonElement(), CCopasiXMLParser::RadialGradientElement::~RadialGradientElement(), CCopasiXMLParser::ReactionElement::~ReactionElement(), ReactionsWidget1::~ReactionsWidget1(), CCopasiXMLParser::RectangleElement::~RectangleElement(), CCopasiXMLParser::RenderCurveElement::~RenderCurveElement(), CCopasiXMLParser::ReportElement::~ReportElement(), CCopasiXMLParser::TaskElement::~TaskElement(), TaskWidget::~TaskWidget(), and CCopasiXMLParser::TextElement::~TextElement().

#define pdeletev (   p)    {if (p) {delete[] p; p = NULL;}}
#define pfree (   p)    {if (p) {free(p); p = NULL;}}

Definition at line 214 of file copasi.h.

#define SS_DAMPING_LIMIT   3

Definition at line 49 of file copasi.h.

#define SS_FOUND   1

Definition at line 46 of file copasi.h.

#define SS_ITERATION_LIMIT   4

Definition at line 50 of file copasi.h.

#define SS_NOT_FOUND   0

Definition at line 47 of file copasi.h.

#define SS_SINGULAR_JACOBIAN   2

Definition at line 48 of file copasi.h.

#define TIME_TRACE (   f,
 
)

Definition at line 210 of file copasi.h.

Enumeration Type Documentation

enum TriLogic
Enumerator
TriUnspecified 
TriFalse 
TriTrue 

Definition at line 125 of file copasi.h.

126 {
127  TriUnspecified = -1,
128  TriFalse = 0,
129  TriTrue = 1
130 };