COPASI API
4.16.103
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#include <compare_utilities.h>
Public Types | |
typedef std::vector< CType * > ::const_iterator | const_iterator |
typedef std::vector< CType * > ::iterator | iterator |
typedef std::vector< CType * > ::value_type | value_type |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
Public Member Functions | |
virtual bool | add (const CType &src) |
virtual bool | add (CType *src, bool adopt=false) |
iterator | begin () |
const_iterator | begin () const |
CCopasiVector (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const unsigned C_INT32 &flag=CCopasiObject::Vector) | |
CCopasiVector (const CCopasiVector< CType > &src, const CCopasiContainer *pParent=NULL) | |
virtual void | cleanup () |
virtual void | clear () |
void | deepCopy (const CCopasiVector< CType > &source) |
iterator | end () |
const_iterator | end () const |
virtual size_t | getIndex (const CCopasiObject *pObject) const |
virtual const CObjectInterface * | getObject (const CCopasiObjectName &name) const |
CCopasiVector< CType > & | operator= (const CCopasiVector< CType > &rhs) |
CCopasiVector< CType > & | operator= (const std::vector< CType * > &rhs) |
const value_type & | operator[] (const size_t &index) const |
value_type & | operator[] (const size_t &index) |
virtual void | remove (const size_t &index) |
virtual bool | remove (CCopasiObject *pObject) |
virtual void | resize (const size_t &newSize) |
virtual size_t | size () const |
virtual void | swap (const size_t &indexFrom, const size_t &indexTo) |
virtual | ~CCopasiVector () |
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virtual bool | add (CCopasiObject *pObject, const bool &adopt=true) |
CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container) | |
CCopasiContainer (const CCopasiContainer &src, const CCopasiContainer *pParent=NULL) | |
virtual std::string | getChildObjectUnits (const CCopasiObject *pObject) const |
virtual const objectMap & | getObjects () const |
virtual std::string | getUnits () const |
virtual const CCopasiObject * | getValueObject () const |
virtual | ~CCopasiContainer () |
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void | addDirectDependency (const CCopasiObject *pObject) |
CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL) | |
void | clearDirectDependencies () |
void | clearRefresh () |
bool | dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const |
void | getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const |
virtual CCopasiObjectName | getCN () const |
virtual const DataObjectSet & | getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const |
virtual const std::string & | getKey () const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) const |
const std::string & | getObjectName () const |
CCopasiContainer * | getObjectParent () const |
const std::string & | getObjectType () const |
virtual const CObjectInterface::ObjectSet & | getPrerequisites () const |
virtual Refresh * | getRefresh () const |
UpdateMethod * | getUpdateMethod () const |
virtual void * | getValuePointer () const |
bool | hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const |
bool | hasUpdateMethod () const |
bool | isArray () const |
bool | isContainer () const |
bool | isDataModel () const |
bool | isMatrix () const |
bool | isNameVector () const |
bool | isNonUniqueName () const |
virtual bool | isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const |
bool | isReference () const |
bool | isRoot () const |
bool | isSeparator () const |
bool | isStaticString () const |
bool | isValueBool () const |
bool | isValueDbl () const |
bool | isValueInt () const |
bool | isValueInt64 () const |
bool | isValueString () const |
bool | isVector () const |
virtual bool | mustBeDeleted (const DataObjectSet &deletedObjects) const |
virtual void | print (std::ostream *ostream) const |
void | removeDirectDependency (const CCopasiObject *pObject) |
void | setDirectDependencies (const DataObjectSet &directDependencies) |
bool | setObjectName (const std::string &name) |
virtual bool | setObjectParent (const CCopasiContainer *pParent) |
void | setObjectValue (const C_FLOAT64 &value) |
void | setObjectValue (const C_INT32 &value) |
void | setObjectValue (const bool &value) |
template<class CType > | |
void | setRefresh (CType *pType, void(CType::*method)(void)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &)) |
template<class CType > | |
void | setUpdateMethod (CType *pType, void(CType::*method)(const bool &)) |
virtual | ~CCopasiObject () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Friends | |
std::ostream & | operator<< (std::ostream &os, const CCopasiVector< CType > &d) |
Additional Inherited Members | |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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static const std::vector < CCopasiContainer * > | EmptyList |
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enum | Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 } |
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template<class CType > | |
CCopasiObject * | addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
template<class CType > | |
CCopasiObject * | addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
template<class CType > | |
CCopasiObject * | addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0) |
void | initObjects () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
CCopasiXMLInterface class. The class CCopasiXMLInterface is the interface to various XML document containing COPASI relevant information.
Created for COPASI by Stefan Hoops 2003
Definition at line 34 of file compare_utilities.h.
typedef std::vector< CType * >::const_iterator CCopasiVector< T >::const_iterator |
Definition at line 57 of file CCopasiVector.h.
typedef std::vector< CType * >::iterator CCopasiVector< T >::iterator |
Definition at line 56 of file CCopasiVector.h.
typedef std::vector< CType * >::value_type CCopasiVector< T >::value_type |
Definition at line 55 of file CCopasiVector.h.
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Default constructor
const | const std::string & name (Default: "NoName") |
const | CCopasiContainer * pParent (Default: NULL) |
const | size_t & flag (Default: flag | CCopasiObject::Vector) |
Definition at line 68 of file CCopasiVector.h.
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Copy constructor
const | CCopasiVector < CType > & src |
const | CCopasiContainer * pParent (Default: NULL) |
Definition at line 81 of file CCopasiVector.h.
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Add a copy of the object to the end of the vector.
const | CType & src |
Reimplemented in CCopasiVectorN< CType >.
Definition at line 223 of file CCopasiVector.h.
Referenced by CLGroup::addChildElement(), CLRenderInformationBase::addColorDefinition(), CLayout::addCompartmentGlyph(), CCopasiRootContainer::addDatamodel(), CChemEq::addElement(), CLayout::addGeneralGlyph(), CListOfLayouts::addGlobalRenderInformation(), CLRenderInformationBase::addGradientDefinition(), CLGradientBase::addGradientStop(), CLRenderInformationBase::addLineEnding(), CLayout::addLocalRenderInformation(), CLayout::addMetaboliteGlyph(), CLReactionGlyph::addMetabReferenceGlyph(), CLayout::addReactionGlyph(), CLGeneralGlyph::addReferenceGlyph(), SliderDialog::addSlider(), CLLocalRenderInformation::addStyle(), CLGlobalRenderInformation::addStyle(), CLGeneralGlyph::addSubglyph(), CLayout::addTextGlyph(), CModel::buildMoieties(), CLayout::CLayout(), CLGlobalRenderInformation::CLGlobalRenderInformation(), CLGroup::CLGroup(), CLLocalRenderInformation::CLLocalRenderInformation(), CLRenderInformationBase::CLRenderInformationBase(), CMathModel::compile(), CMIRIAMInfo::createBiologicalDescription(), CLRenderInformationBase::createColorDefinition(), CMIRIAMInfo::createCreator(), CLGroup::createCurve(), CMathContainer::createDiscontinuityDataEvent(), CLGroup::createEllipse(), CLGradientBase::createGradientStop(), CLGroup::createGroup(), CLGroup::createImage(), CPlotSpecification::createItem(), CLRenderInformationBase::createLinearGradientDefinition(), CLRenderInformationBase::createLineEnding(), CModel::createMetabolite(), CMIRIAMInfo::createModification(), CLGroup::createPolygon(), CLRenderInformationBase::createRadialGradientDefinition(), CLGroup::createRectangle(), CMIRIAMInfo::createReference(), CLLocalRenderInformation::createStyle(), CLGlobalRenderInformation::createStyle(), CLGroup::createText(), CCopasiXMLParser::ListOfLayoutsElement::end(), CModel::initializeMetabolites(), CMIRIAMInfo::loadBiologicalDescriptions(), CMIRIAMInfo::loadCreators(), loadDefaultStyles(), CQEventWidget1::loadFromEvent(), CMIRIAMInfo::loadModifications(), CMIRIAMInfo::loadReferences(), CCopasiVector< CLGeneralGlyph >::operator=(), CQPlotSubwidget::saveToPlotSpec(), CQEventWidget1::slotAddTarget(), CCopasiXMLParser::MetaboliteElement::start(), CCopasiXMLParser::SliderElement::start(), and CExperiment::updateFittedPoints().
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Add an object to the end of the vector, if adobt is true the vector. becomes the parent of the object.
CType | * src |
const | bool & adopt (Default: false) |
Definition at line 275 of file CCopasiVector.h.
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Definition at line 185 of file CCopasiVector.h.
Referenced by CQLayoutScene::addGlyph(), CMathContainer::allocate(), CModel::appendDependentCompartments(), CModel::appendDependentEvents(), CFunctionDB::appendDependentFunctions(), CModel::appendDependentMetabolites(), CModel::appendDependentModelValues(), CModel::appendDependentReactions(), CCopasiDataModel::appendDependentTasks(), CMathModel::applyInitialValues(), SBMLImporter::applyStoichiometricExpressions(), CLayoutState::applyTo(), CSBMLExporter::assignSBMLIdsToReactions(), DataModelGUI::buildChangedObjects(), CModel::buildDependencyGraphs(), CMathModel::buildDependendRefreshList(), CModel::buildInitialRefreshSequence(), CModel::buildInitialSequence(), CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CSSAMethod::buildKineticMatrix(), CModel::buildMoieties(), CModel::buildNonSimulatedSequence(), CModel::buildRedStoi(), CModel::buildSimulatedSequence(), CModel::buildStateTemplate(), CModel::buildStoi(), CModel::buildUserOrder(), CLNAMethod::calculateCovarianceMatrixReduced(), CModel::calculateElasticityMatrix(), CMCAMethod::calculateUnscaledElasticities(), CCopasiVector< CLGeneralGlyph >::CCopasiVector(), CSBMLExporter::check_for_spatial_size_units(), CSBMLExporter::checkForInitialAssignments(), CSBMLExporter::checkForODESpeciesInNonfixedCompartment(), CFixLocalReactionParameters::checkModel(), CLayout::CLayout(), CLayoutState::CLayoutState(), CCopasiVector< CLGeneralGlyph >::cleanup(), CCopasiVector< CLGeneralGlyph >::clear(), CCopasiDataModel::commonAfterLoad(), CMathModel::compile(), CEvent::compile(), CMathEventN::compile(), CMetab::compile(), CReaction::compile(), CMathEvent::compile(), CModel::compile(), CMathContainer::compileEvents(), CModel::compileEvents(), CMathObject::compilePropensity(), contains_necessary_mass_action_elements(), containsKey(), CModel::convert2NonReversible(), CQSpeciesDetail::copy(), CQCompartment::copy(), ReactionsWidget1::copy(), CQConnectionGraphicsItem::CQConnectionGraphicsItem(), CSBMLExporter::createCompartments(), SBMLImporter::createCReactionFromReaction(), COutputAssistant::createDefaultOutput(), CSBMLExporter::createEvents(), CMathObject::createExtensiveReactionRateExpression(), CModelParameterSet::createFromModel(), CCopasiSpringLayout::createLayout(), CSBMLExporter::createMetabolites(), CSBMLExporter::createParameters(), CSBMLExporter::createReactions(), CQEventDM::data(), CCopasiVector< CLGeneralGlyph >::deepCopy(), CQLayoutsWidget::enterProtected(), CSBMLExporter::exportEventAssignments(), CCopasiDataModel::exportMathModel(), CCopasiDataModel::exportMathModelToString(), CQLayoutScene::fillFromLayout(), CSBMLExporter::findAvogadro(), CModel::findMetabByName(), findObjectByDisplayName(), CChemEq::getCompartments(), CObjectLists::getEventTargets(), getFunctionForKey(), CCopasiVector< CLGeneralGlyph >::getIndex(), CCopasiVectorN< CReportDefinition >::getIndex(), CObjectLists::getListOfConstObjects(), getMetabGlyphForKey(), CEFMTask::getNetReactionData(), CCopasiVector< CLGeneralGlyph >::getObject(), CCopasiVectorN< CReportDefinition >::getObject(), getQuantityParameterOrValue(), CEFMTask::getSpeciesChanges(), getTextForItem(), CModel::getTreesWithDiscontinuities(), CFunctionDB::getUsedFunctions(), CModel::handleUnusedMetabolites(), CSBMLExporter::hasVolumeAssignment(), CMathContainer::init(), CopasiPlot::initFromSpec(), CMathReaction::initialize(), QConservedSpeciesAnimation::initialize(), QFluxModeAnimation::initialize(), QTimeCourseAnimation::initialize(), CMathContainer::initializeMathObjects(), CModel::initializeMetabolites(), CSteadyStateMethod::isEquilibrium(), CSBMLExporter::isEventSBMLCompatible(), CSBMLExporter::isModelSBMLCompatible(), CTSSAMethod::isValidProblem(), CMCAMethod::isValidProblem(), CLNAMethod::isValidProblem(), CFunctionDB::listDependentTrees(), CQMoietiesTaskResult::load(), CQBrowserPaneDM::load(), CCopasiVectorS< CMetabOld >::load(), CCopasiVectorNS< CMetab >::load(), StateSubwidget::loadCompartments(), CQEventWidget1::loadFromEvent(), CQPlotSubwidget::loadFromPlotSpec(), StateSubwidget::loadMetabolites(), StateSubwidget::loadModelValues(), StateSubwidget::loadReactions(), moveObject(), CEvent::mustBeDeleted(), CCopasiVector< CLGeneralGlyph >::operator=(), CCopasiVector< CLGeneralGlyph >::operator[](), CCopasiVectorN< CReportDefinition >::operator[](), CMoietiesProblem::printResult(), CEFMProblem::printResult(), CCopasiVector< CLGeneralGlyph >::remove(), CFunctionDB::removeFunction(), CQParameterSetsDM::removeRows(), CQFunctionDM::removeRows(), CQReactionDM::removeRows(), CQEventDM::removeRows(), CQLayoutsDM::removeRows(), CQGlobalQuantityDM::removeRows(), CQCompartmentDM::removeRows(), CQSpecieDM::removeRows(), SBMLImporter::removeUnusedFunctions(), CCopasiVector< CLGeneralGlyph >::resize(), CCopasiXML::saveModel(), CQEventWidget1::saveToEvent(), CMCAMethod::scaleMCA(), CQNewMainWindow::selectMetabolite(), CQNewMainWindow::selectReaction(), SBMLImporter::setInitialValues(), CChemEq::setMultiplicity(), CQEFMSpeciesDM::setTask(), CQParameterOverviewWidget::slotBtnNew(), CQParameterOverviewWidget::slotBtnSaveAs(), CTauLeapMethod::start(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), CTrajectoryMethodDsaLsodar::start(), CCopasiVector< CLGeneralGlyph >::swap(), CLayoutState::tagLayout(), CExperiment::updateFittedPointValues(), CExperiment::updateFittedPointValuesFromExtendedTimeSeries(), updateLayoutList(), CModel::updateMatrixAnnotations(), CModel::updateMoietyValues(), updateRenderInformationList(), and CModel::updateSimulatedValues().
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Definition at line 188 of file CCopasiVector.h.
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Cleanup
Reimplemented in CReportDefinitionVector, and COutputDefinitionVector.
Definition at line 200 of file CCopasiVector.h.
Referenced by CModel::buildMoieties(), CPlotSpecification::cleanup(), CFunctionParameters::cleanup(), CChemEq::cleanup(), CFunctionDB::cleanup(), CCompartment::cleanup(), CKinFunction::createParameters(), CCopasiVector< CLGeneralGlyph >::deepCopy(), CSSAMethod::initialize(), CModel::load(), CCopasiVectorS< CMetabOld >::load(), CCopasiVectorNS< CMetab >::load(), CMIRIAMInfo::loadBiologicalDescriptions(), CMIRIAMInfo::loadCreators(), CMIRIAMInfo::loadModifications(), CMIRIAMInfo::loadReferences(), CCopasiVector< CLGeneralGlyph >::operator=(), and CCopasiVector< CLGeneralGlyph >::~CCopasiVector().
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Definition at line 431 of file CCopasiVector.h.
Referenced by CCopasiVector< CLGeneralGlyph >::cleanup(), CModel::clearMoieties(), CMathModel::compile(), CMathContainer::init(), CModel::initializeMetabolites(), CQEventWidget1::loadFromEvent(), CLGeneralGlyph::operator=(), CCopasiXMLParser::ListOfModelParameterSetsElement::start(), CCopasiXMLParser::ListOfReactionsElement::start(), CCopasiXMLParser::ListOfCompartmentsElement::start(), and CExperiment::updateFittedPoints().
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This creates a deep copy of the source, i.e., all objects are copied and the parent of these copies is the current vector.
const | CCopasiVector< CType > & source |
Definition at line 160 of file CCopasiVector.h.
Referenced by CFunctionParameters::operator=().
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Definition at line 191 of file CCopasiVector.h.
Referenced by CQLayoutScene::addGlyph(), CMathContainer::allocate(), CModel::appendDependentCompartments(), CModel::appendDependentEvents(), CFunctionDB::appendDependentFunctions(), CModel::appendDependentMetabolites(), CModel::appendDependentModelValues(), CModel::appendDependentReactions(), CCopasiDataModel::appendDependentTasks(), CMathModel::applyInitialValues(), SBMLImporter::applyStoichiometricExpressions(), CLayoutState::applyTo(), CSBMLExporter::assignSBMLIdsToReactions(), DataModelGUI::buildChangedObjects(), CModel::buildDependencyGraphs(), CMathModel::buildDependendRefreshList(), CModel::buildInitialRefreshSequence(), CModel::buildInitialSequence(), CBitPatternMethod::buildKernelMatrix(), CBitPatternTreeMethod::buildKernelMatrix(), CSSAMethod::buildKineticMatrix(), CModel::buildNonSimulatedSequence(), CModel::buildSimulatedSequence(), CModel::buildStateTemplate(), CModel::buildStoi(), CModel::buildUserOrder(), CLNAMethod::calculateCovarianceMatrixReduced(), CModel::calculateElasticityMatrix(), CMCAMethod::calculateUnscaledElasticities(), CSBMLExporter::check_for_spatial_size_units(), CSBMLExporter::checkForInitialAssignments(), CSBMLExporter::checkForODESpeciesInNonfixedCompartment(), CFixLocalReactionParameters::checkModel(), CLayout::CLayout(), CLayoutState::CLayoutState(), CCopasiVector< CLGeneralGlyph >::cleanup(), CCopasiVector< CLGeneralGlyph >::clear(), CCopasiDataModel::commonAfterLoad(), CMathModel::compile(), CEvent::compile(), CMetab::compile(), CReaction::compile(), CMathEvent::compile(), CModel::compile(), CMathContainer::compileEvents(), CModel::compileEvents(), CMathObject::compilePropensity(), contains_necessary_mass_action_elements(), containsKey(), CModel::convert2NonReversible(), CQSpeciesDetail::copy(), CQCompartment::copy(), ReactionsWidget1::copy(), CQConnectionGraphicsItem::CQConnectionGraphicsItem(), CSBMLExporter::createCompartments(), SBMLImporter::createCReactionFromReaction(), COutputAssistant::createDefaultOutput(), CSBMLExporter::createEvents(), CMathObject::createExtensiveReactionRateExpression(), CModelParameterSet::createFromModel(), CCopasiSpringLayout::createLayout(), CSBMLExporter::createMetabolites(), CSBMLExporter::createParameters(), CSBMLExporter::createReactions(), CQEventDM::data(), CQLayoutsWidget::enterProtected(), CSBMLExporter::exportEventAssignments(), CCopasiDataModel::exportMathModel(), CCopasiDataModel::exportMathModelToString(), CQLayoutScene::fillFromLayout(), CSBMLExporter::findAvogadro(), findObjectByDisplayName(), CChemEq::getCompartments(), CObjectLists::getEventTargets(), getFunctionForKey(), CObjectLists::getListOfConstObjects(), getMetabGlyphForKey(), CEFMTask::getNetReactionData(), getQuantityParameterOrValue(), CEFMTask::getSpeciesChanges(), getTextForItem(), CModel::getTreesWithDiscontinuities(), CFunctionDB::getUsedFunctions(), CSBMLExporter::hasVolumeAssignment(), CopasiPlot::initFromSpec(), QConservedSpeciesAnimation::initialize(), QFluxModeAnimation::initialize(), QTimeCourseAnimation::initialize(), CMathContainer::initializeMathObjects(), CModel::initializeMetabolites(), CSteadyStateMethod::isEquilibrium(), CSBMLExporter::isEventSBMLCompatible(), CSBMLExporter::isModelSBMLCompatible(), CTSSAMethod::isValidProblem(), CMCAMethod::isValidProblem(), CLNAMethod::isValidProblem(), CFunctionDB::listDependentTrees(), CQMoietiesTaskResult::load(), CQBrowserPaneDM::load(), StateSubwidget::loadCompartments(), CQEventWidget1::loadFromEvent(), CQPlotSubwidget::loadFromPlotSpec(), StateSubwidget::loadMetabolites(), StateSubwidget::loadModelValues(), StateSubwidget::loadReactions(), moveObject(), CEvent::mustBeDeleted(), CCopasiVector< CLGeneralGlyph >::operator=(), CMoietiesProblem::printResult(), CEFMProblem::printResult(), CFunctionDB::removeFunction(), SBMLImporter::removeUnusedFunctions(), CCopasiVector< CLGeneralGlyph >::resize(), CCopasiXML::saveModel(), CQEventWidget1::saveToEvent(), CMCAMethod::scaleMCA(), CQNewMainWindow::selectMetabolite(), CQNewMainWindow::selectReaction(), SBMLImporter::setInitialValues(), CChemEq::setMultiplicity(), CQParameterOverviewWidget::slotBtnNew(), CQParameterOverviewWidget::slotBtnSaveAs(), CTauLeapMethod::start(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), CTrajectoryMethodDsaLsodar::start(), CLayoutState::tagLayout(), CExperiment::updateFittedPointValues(), CExperiment::updateFittedPointValuesFromExtendedTimeSeries(), updateLayoutList(), CModel::updateMoietyValues(), updateRenderInformationList(), and CModel::updateSimulatedValues().
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Definition at line 194 of file CCopasiVector.h.
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Retrieve the index of the pointed to object in the vector. If the object is not found C_INVALID_INDEX is returned.
const | CCopasiObject * pObject |
Definition at line 462 of file CCopasiVector.h.
Referenced by CQReportDefinition::btnDeleteReportClicked(), CLNAMethod::calculateCovarianceMatrixReduced(), CModel::createMetabolite(), CCopasiObject::getCN(), CCopasiVector< CLGeneralGlyph >::remove(), COutputDefinitionVector::removePlotSpec(), CReportDefinitionVector::removeReportDefinition(), CQReportDM::removeRows(), CQLayoutsDM::removeRows(), CHybridMethodODE45::setupBalances(), CHybridMethod::setupBalances(), CHybridMethodLSODA::setupBalances(), CStochMethod::setupDependencyGraphAndBalances(), and CHybridMethodODE45::setupMetab2React().
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Retrieve a the CCopasiObject with the given name.
const | CCopasiObjectName &name |
Reimplemented from CCopasiContainer.
Reimplemented in CCopasiVectorN< CType >, CCopasiVectorN< CReaction >, CCopasiVectorN< CEventAssignment >, CCopasiVectorN< CFunctionParameter >, CCopasiVectorN< CCopasiTask >, CCopasiVectorN< CPlotSpecification >, CCopasiVectorN< CCompartment >, CCopasiVectorN< CModelParameterSet >, CCopasiVectorN< CEvent >, CCopasiVectorN< CMetab >, CCopasiVectorN< CFunction >, CCopasiVectorN< CModelValue >, and CCopasiVectorN< CReportDefinition >.
Definition at line 364 of file CCopasiVector.h.
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Assignment operator. The effect of this operator is that both vectors will share the same objects. However, the parentship of the objects is not affected This means that the assigned vector must be used with some care.
const | CCopasiVector< CType > & rhs |
Definition at line 124 of file CCopasiVector.h.
Referenced by CCopasiVectorN< CReportDefinition >::operator=().
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Assignment operator.
const | std::vector< CType * > & rhs |
Definition at line 142 of file CCopasiVector.h.
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Retrieve the indexed object.
const | size_t & index |
Definition at line 338 of file CCopasiVector.h.
Referenced by CCopasiVectorN< CReportDefinition >::operator[]().
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Retrieve the indexed object.
const | size_t & index |
Definition at line 351 of file CCopasiVector.h.
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Removes the index-th element from the vector
const | size_t & index |
Definition at line 287 of file CCopasiVector.h.
Referenced by CQReportDefinition::btnDeleteReportClicked(), contains_necessary_mass_action_elements(), SliderDialog::getCSlidersForObject(), CCopasiVectorN< CReportDefinition >::remove(), CMIRIAMInfo::removeBiologicalDescription(), CLRenderInformationBase::removeColorDefinition(), CMIRIAMInfo::removeCreator(), CCopasiRootContainer::removeDatamodel(), CLRenderInformationBase::removeGradientDefinition(), CLRenderInformationBase::removeLineEnding(), CModel::removeMetabolite(), CMIRIAMInfo::removeModification(), COutputDefinitionVector::removePlotSpec(), CMIRIAMInfo::removeReference(), CReportDefinitionVector::removeReportDefinition(), CQReportDM::removeRows(), SliderDialog::removeSlider(), and CQEventWidget1::slotDeleteTarget().
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Removes the pointed to object from the vector
CCopasiObject | * pObject |
Reimplemented from CCopasiContainer.
Definition at line 314 of file CCopasiVector.h.
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Resizes the vector but does not create new member objects
const | size_t & newSize |
Definition at line 393 of file CCopasiVector.h.
Referenced by CCopasiVector< CLGeneralGlyph >::deepCopy(), CModel::initializeMetabolites(), CCopasiVectorS< CMetabOld >::load(), CCopasiVectorNS< CMetab >::load(), CCSPMethod::predifineAnnotation(), CCSPMethod::setAnnotationM(), and CCSPMethod::start().
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Retrieves the size of the vector
Definition at line 386 of file CCopasiVector.h.
Referenced by CModelAdd::addCompartments(), CModelAdd::addCompartmentsExpressions(), CChemEq::addElement(), CModelAdd::addEvents(), CQNewMainWindow::addGlobalRenderInfoItemsToList(), test000097::addGlobalRenderInformation(), test000097::addLocalRenderInformation(), CModelAdd::addMetabolites(), CModelAdd::addMetabolitesExpressions(), CModelAdd::addModelValues(), CModelAdd::addModelValuesExpressions(), CModelAdd::addReactions(), CLGradientBase::addSBMLAttributes(), CLRenderInformationBase::addSBMLAttributes(), CMathEventN::allocate(), CMathContainer::allocate(), CQReportDefinition::btnDeleteReportClicked(), CSSAMethod::buildKineticMatrix(), CModel::buildStateTemplate(), CModel::buildStoi(), CModel::buildUserOrder(), CLayout::calculateBoundingBox(), CLNAMethod::calculateCovarianceMatrixReduced(), CModel::calculateDerivatives(), CModel::calculateDerivativesX(), CMCAMethod::calculateUnscaledElasticities(), CCopasiVector< CLGeneralGlyph >::CCopasiVector(), CSBMLExporter::checkForEvents(), CSBMLExporter::checkForPiecewiseFunctions(), CHybridMethod::checkModel(), CHybridMethodLSODA::checkModel(), CHybridMethodODE45::checkModel(), CModelAnalyzer::checkReaction(), CLayout::CLayout(), CCopasiVector< CLGeneralGlyph >::clear(), CLGeneralGlyph::CLGeneralGlyph(), CLGroup::CLGroup(), CModel::CModel(), CSBMLExporter::collectIds(), COutputHandlerPlot::compile(), CopasiPlot::compile(), CChemEqInterface::completeCompartments(), CReactionInterface::connectNonMetabolites(), contains_necessary_mass_action_elements(), CModel::convert2NonReversible(), SBMLDocumentLoader::convertRenderInformationReferencesIds(), CArrayAnnotation::createAnnotationsCNFromCopasiVector(), SBMLImporter::createCFunctionFromFunctionDefinition(), SBMLImporter::createCModelFromSBMLDocument(), SBMLImporter::createCReactionFromReaction(), CSEDMLExporter::createDataGenerators(), COutputAssistant::createDefaultOutput(), CPlotSpecification::createDefaultPlot(), CQGLNetworkPainter::createGraph(), CSBMLExporter::createKineticLaw(), CCopasiSpringLayout::createLayout(), CModel::createMetabolite(), test000097::createModel(), CKinFunction::createParameters(), COutputDefinitionVector::createPlotSpec(), CSBMLExporter::createReaction(), CLayoutInitializer::createReactionGlyph(), CReportDefinitionVector::createReportDefinition(), CSBMLExporter::createTimesTree(), CCopasiSpringLayout::createVariables(), CCSPMethod::CSPImportanceIndex(), CCSPMethod::CSPParticipationIndex(), CCSPMethod::CSPradicalPointer(), CCSPMethod::cspstep(), CQPlotDM::data(), CQSpecieDM::data(), CCopasiVector< CLGeneralGlyph >::deepCopy(), CQPlotSubwidget::deletePlot(), CModel::determineIsAutonomous(), SBMLImporter::doMapping(), CModelExpansion::duplicateEvent(), CModelExpansion::duplicateReaction(), CQNewMainWindow::elementaryModeTriggeredSlot(), CFitProblem::elevateChildren(), CCopasiXMLParser::ListOfFunctionsElement::end(), CQLayoutsWidget::enterProtected(), SliderDialog::equivalentSliderExists(), CObjectLists::existsFixedMetab(), CODEExporter::exportCompartments(), CODEExporter::exportKineticFunction(), CODEExporterC::exportKineticFunctionGroup(), CODEExporter::exportMetabolites(), CODEExporter::exportMetabolitesConcentrations(), CODEExporter::exportModelValues(), CODEExporter::exportModelValuesExpressions(), CODEExporter::exportODEs(), CODEExporter::exportReacParamsAndFuncs(), CODEExporterC::exportTitleData(), CLayout::exportToDotFile(), CListOfLayouts::exportToSBML(), CLayout::exportToSBML(), CLGeneralGlyph::exportToSBML(), CLReactionGlyph::exportToSBML(), CModelExpansion::SetOfModelElements::fillComplete(), CQMergingData::fillTree(), CQSelectionWizardPage::fillTree(), CCopasiSpringLayout::finalizeState(), CCopasiSpringLayout::findCompartmentForReactionNode(), SBMLImporter::findCorrespondingFunction(), findFunction(), CFunctionDB::findLoadFunction(), CModel::findMetabByName(), CModel::findMoiety(), CFunctionParameters::findParameterByName(), CLRenderFlattener::flatten(), CStochMethod::generateReactionIndex(), CStochMethod::getAffects(), CLRenderInformationBase::getColorDefinition(), CChemEqInterface::getCompartment(), SliderDialog::getCSlidersForObject(), CHybridMethodODE45::getDefaultAtol(), CHybridMethodLSODA::getDefaultAtol(), CStochMethod::getDependsOn(), CMetabNameInterface::getDisplayName(), CLGroup::getElement(), Arguments::getFirstScheduledTask(), CLRenderInformationBase::getGradientDefinition(), CLGradientBase::getGradientStop(), CCopasiVector< CLGeneralGlyph >::getIndex(), CCopasiVectorN< CReportDefinition >::getIndex(), CChemEq::getLargestCompartment(), CLRenderInformationBase::getLineEnding(), ParameterTable::getListOfAllCompartmentNames(), ParameterTable::getListOfAllMetabNames(), CChemEq::getMolecularity(), CFunctionParameters::getNumberOfParametersByUsage(), CLRenderInformationBase::getNumColorDefinitions(), getNumDefaultStyles(), CLGroup::getNumElements(), CLRenderInformationBase::getNumGradientDefinitions(), CLGradientBase::getNumGradientStops(), CLRenderInformationBase::getNumLineEndings(), CModel::getNumMetabs(), CModel::getNumModelValues(), CLLocalRenderInformation::getNumStyles(), CLGlobalRenderInformation::getNumStyles(), CCopasiVector< CLGeneralGlyph >::getObject(), SEDMLUtils::getObjectForSbmlId(), CLLayoutRenderer::getObjectsAt(), CLLayoutRenderer::getObjectsInBoundingBox(), CFunctionParameters::getParameterByUsage(), CCopasiSpringLayout::getPotential(), getReactionIndex(), CListOfLayouts::getRenderInformation(), CLayout::getRenderInformation(), QConservedSpeciesAnimation::getScales(), CLLocalRenderInformation::getStyle(), CLGlobalRenderInformation::getStyle(), Arguments::getTaskForName(), CModel::getTotSteps(), Arguments::handleCommandLine(), hasLayout(), CModel::hasReversibleReaction(), CMathContainer::init(), CCopasiSpringLayout::initFromLayout(), CopasiPlot::initFromSpec(), CMathReaction::initialize(), QConservedSpeciesAnimation::initialize(), CTSSAMethod::initializeIntegrationsParameter(), CModel::initializeMetabolites(), CLsodaMethod::initializeParameter(), CQLayoutScene::initializeResolver(), CHybridMethod::initMethod(), CHybridMethodODE45::initMethod(), CHybridMethodLSODA::initMethod(), CQParameterSetsDM::insertRows(), CQLayoutsDM::insertRows(), CQSpecieDM::insertRows(), CReactionInterface::isLocked(), SBMLImporter::isMassActionExpression(), CQSimpleSelectionTree::isMetaboliteNameUnique(), CMetabNameInterface::isUnique(), CTSSAMethod::isValidProblem(), CTauLeapMethod::isValidProblem(), CHybridMethod::isValidProblem(), CHybridMethodODE45::isValidProblem(), CCopasiMethod::isValidProblem(), CHybridMethodLSODA::isValidProblem(), CStochDirectMethod::isValidProblem(), CLNAMethod::isValidProblem(), CStochMethod::isValidProblem(), CTrajectoryMethodDsaLsodar::isValidProblem(), CFunctionParameters::isVector(), CODEExporterC::KineticFunction2ODEmember(), CMMLOutput::listReactionsForMetab(), CQSpeciesDetail::load(), CQExpandModelData::load(), CModel::load(), ObjectBrowserWidget::loadChild(), StateSubwidget::loadCompartments(), ObjectBrowserWidget::loadField(), CChemEqInterface::loadFromChemEq(), CQEventWidget1::loadFromEvent(), CQPlotSubwidget::loadFromPlotSpec(), StateSubwidget::loadMetabolites(), CQCompartment::loadMetaboliteTable(), StateSubwidget::loadModelValues(), CQUpdatesWidget::loadObjectsTable(), StateSubwidget::loadReactions(), CQReportDefinitionSelect::loadReportDefinitionVector(), CQLayoutMainWindow::loadSBMLFile(), main(), CModelMerging::mergeMetabolites(), CStochMethod::modelHasAssignments(), CHybridMethod::modelHasAssignments(), CHybridMethodLSODA::modelHasAssignments(), CHybridMethodODE45::modelHasAssignments(), CLayout::moveBy(), CLGeneralGlyph::moveBy(), CLReactionGlyph::moveBy(), stress_test::normalizeAndSimplifyExpressions(), stress_test::normalizeFunctionDB(), CReaction::object2variable(), operator<<(), CLGeneralGlyph::operator=(), CLReactionGlyph::operator=(), CCopasiVector< CLGeneralGlyph >::operator[](), CHybridMethod::outputData(), CHybridMethodODE45::outputData(), CHybridMethodLSODA::outputData(), CHybridMethod::outputDebug(), CHybridMethodODE45::outputDebug(), CHybridMethodLSODA::outputDebug(), placeTextGlyphs(), CQSimpleSelectionTree::populateTree(), CCSPMethod::predifineAnnotation(), Arguments::prepareModel(), CODEExporterC::preprocess(), CODEExporter::preprocess(), CModel::printParameterOverview(), CCSPMethod::printResult(), CCopasiSpringLayout::randomize(), CModelAdd::reactionInvolvesCompartment(), CQSpeciesWidget::refreshCompartments(), CCopasiVector< CLGeneralGlyph >::remove(), CLRenderInformationBase::removeColorDefinition(), CLRenderInformationBase::removeGradientDefinition(), CLRenderInformationBase::removeLineEnding(), CCopasiDataModel::removeSBMLIdFromFunctions(), SliderDialog::removeSlider(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInEvent(), CModelExpansion::replaceInModel(), CModelExpansion::replaceInReaction(), CCopasiVector< CLGeneralGlyph >::resize(), CQParameterSetsDM::rowCount(), CQLayoutsDM::rowCount(), CQModifiedDM::rowCount(), CQReferenceDM::rowCount(), CQBiologicalDescriptionDM::rowCount(), CQCreatorDM::rowCount(), CQFunctionDM::rowCount(), CQFittingWidget::runTask(), CCopasiXML::saveFunctionList(), CCopasiXML::saveGUI(), CCopasiXML::saveLayoutList(), CCopasiXML::saveListOfGlobalRenderInformation(), CCopasiXML::saveListOfLocalRenderInformation(), CCopasiXML::saveModel(), CCopasiXML::savePlotList(), CCopasiXML::saveReportList(), CCopasiXML::saveTaskList(), CQEventWidget1::saveToEvent(), CILDMMethod::setAnnotationM(), CCSPMethod::setAnnotationM(), ConverterASTNode::setChildren(), SBMLImporter::setCorrectUsage(), CLLayoutRenderer::setDeduceSpeciesReferenceRoles(), CModel::setQuantityUnit(), CReaction::setScalingFactor(), COptProblem::setSubtaskType(), CQEFMSpeciesDM::setTask(), CHybridMethodODE45::setupBalances(), CHybridMethod::setupBalances(), CHybridMethodLSODA::setupBalances(), CHybridMethodODE45::setupDependencyGraph(), CHybridMethod::setupDependencyGraph(), CHybridMethodLSODA::setupDependencyGraph(), CStochMethod::setupDependencyGraphAndBalances(), CHybridMethodODE45::setupMetab2React(), CHybridMethod::setupMetab2React(), CHybridMethodLSODA::setupMetab2React(), CHybridMethod::setupMetab2ReactComplete(), CHybridMethodLSODA::setupMetab2ReactComplete(), CHybridMethod::setupMetab2ReactPlusModifier(), CHybridMethodLSODA::setupMetab2ReactPlusModifier(), CStochNextReactionMethod::setupPriorityQueue(), CHybridMethod::setupPriorityQueue(), CHybridMethodLSODA::setupPriorityQueue(), CILDMMethod::setVectors(), CCSPMethod::setVectors(), CCSPMethod::setVectorsToNaN(), CModelMerging::simpleCall(), CFunctionParameters::size(), CQEventWidget1::slotActualizeAssignmentExpression(), CQEventWidget1::slotAddTarget(), CQPlotsWidget::slotBtnActivateAllClicked(), CQMiriamWidget::slotBtnBrowseDescription(), CQMiriamWidget::slotBtnBrowseReference(), CQPlotsWidget::slotBtnDeactivateAllClicked(), CQSpeciesDetail::slotBtnNew(), CQLayoutsWidget::slotBtnNewClicked(), CQNewMainWindow::slotCalculateDimensions(), CQExpandModelData::slotCompartmentActivated(), CQMoietiesTaskResult::slotCreateGlobalQuantity(), CQEventWidget1::slotDeleteTarget(), CQNewMainWindow::slotRenderInfoChanged(), CQLayoutView::slotRenderInformationChanged(), CQNewMainWindow::slotRunRandomizeLayout(), CTauLeapMethod::start(), CStochDirectMethod::start(), CCSPMethod::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), CTrajectoryMethodDsaLsodar::start(), CCopasiXMLParser::LocalRenderInformationElement::start(), CCopasiXMLParser::GlobalRenderInformationElement::start(), CModel::suitableForStochasticSimulation(), CFunctionDB::suitableFunctions(), CCopasiVector< CLGeneralGlyph >::swap(), CQFittingWidget::taskFinishedEvent(), test000069::test_bug1069(), test000073::test_bug1087(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000060::test_bug_1026(), test000061::test_bug_1044(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000021::test_hasOnlySubstanceUnits(), test000027::test_hasOnlySubstanceUnits(), test000029::test_hasOnlySubstanceUnits(), test000039::test_hasOnlySubstanceUnits(), test000030::test_hasOnlySubstanceUnits(), test000032::test_hasOnlySubstanceUnits(), test000035::test_hasOnlySubstanceUnits(), test000031::test_hasOnlySubstanceUnits(), test000034::test_hasOnlySubstanceUnits(), test000025::test_hasOnlySubstanceUnits(), test000038::test_hasOnlySubstanceUnits(), test000033::test_hasOnlySubstanceUnits(), test000036::test_hasOnlySubstanceUnits(), test000037::test_hasOnlySubstanceUnits(), test000040::test_hasOnlySubstanceUnits(), test000022::test_hasOnlySubstanceUnits(), test000028::test_hasOnlySubstanceUnits(), test000024::test_hasOnlySubstanceUnits(), test000023::test_hasOnlySubstanceUnits(), test000041::test_hasOnlySubstanceUnits(), test000026::test_hasOnlySubstanceUnits(), test000042::test_hasOnlySubstanceUnits(), test000043::test_hasOnlySubstanceUnits(), test000088::test_import_assignment_without_expression(), test000088::test_import_eventassignment_without_expression(), test000097::test_import_global_render_information(), test000088::test_import_initialassignment_without_expression(), test000097::test_import_local_render_information(), test000087::test_import_reaction_flux_reference_2(), test000097::test_importexport_global_render_information(), test000097::test_importexport_local_render_information(), test000097::test_importwrite_global_render_information(), test000097::test_importwrite_local_render_information(), test000078::test_l2v4_import_unordered_functions(), test000080::test_mass_action_recognition_bug(), test000092::test_miriam_export_7(), test000092::test_miriam_export_8(), test000092::test_miriam_export_9(), test000092::test_miriam_import_1(), test000097::test_read_global_render_information(), test000097::test_read_local_render_information(), test000097::test_readexport_global_render_information(), test000097::test_readexport_local_render_information(), test000097::test_readwrite_global_render_information(), test000097::test_readwrite_local_render_information(), test000087::test_simulate_reaction_flux_reference_1(), test000044::test_stoichiometricExpression(), test000045::test_stoichiometricExpression(), test000046::test_stoichiometricExpression(), CLLocalRenderInformation::toSBML(), CLGlobalRenderInformation::toSBML(), CLGroup::toSBML(), CLLayoutRenderer::update_associations(), CQNewMainWindow::updateLayoutList(), CSBMLExporter::updateMIRIAMAnnotation(), CHybridMethod::updatePriorityQueue(), CHybridMethodLSODA::updatePriorityQueue(), updateRenderInformationList(), CQNewMainWindow::updateRenderInformationList(), validate(), CMMLOutput::writeDifferentialEquations(), and CMMLOutput::writeRHS().
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inlinevirtual |
Swap two objects in the vector.
const | size_t & indexFrom |
const | size_t & indexTo |
Definition at line 250 of file CCopasiVector.h.
Referenced by CFunctionParameters::swap().
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friend |
ostream operator
std::ostream | & os |
const | CCopasiVector<CType> & d |
Definition at line 870 of file CCopasiVector.h.