COPASI API
4.16.103
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#include <CCopasiDataModel.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::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, const bool &adopt=false) |
CCopasiVectorN (const std::string &name="NoName", const CCopasiContainer *pParent=NULL) | |
CCopasiVectorN (const CCopasiVectorN< CType > &src, const CCopasiContainer *pParent=NULL) | |
virtual size_t | getIndex (const std::string &name) const |
virtual const CObjectInterface * | getObject (const CCopasiObjectName &name) const |
CCopasiVectorN< CType > & | operator= (const std::vector< CType * > &rhs) |
value_type & | operator[] (const size_t &index) |
const value_type & | operator[] (const size_t &index) const |
value_type & | operator[] (const std::string &name) |
const value_type & | operator[] (const std::string &name) const |
virtual void | remove (const std::string &name) |
virtual | ~CCopasiVectorN () |
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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 |
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 () |
Private Member Functions | |
virtual bool | isInsertAllowed (const CType *src) |
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 |
Definition at line 47 of file CCopasiDataModel.h.
typedef std::vector< CType * >::const_iterator CCopasiVectorN< CType >::const_iterator |
Definition at line 573 of file CCopasiVector.h.
typedef std::vector< CType * >::iterator CCopasiVectorN< CType >::iterator |
Definition at line 572 of file CCopasiVector.h.
typedef std::vector< CType * >::value_type CCopasiVectorN< CType >::value_type |
Definition at line 571 of file CCopasiVector.h.
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inline |
Default constructor
const | std::string & name (Default: "NoName") |
const | CCopasiContainer * pParent (Default: NULL) |
Definition at line 582 of file CCopasiVector.h.
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inline |
Copy constructor
const | CCopasiVectorN < CType > & src |
const | CCopasiContainer * pParent (Default: NULL) |
Definition at line 595 of file CCopasiVector.h.
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inlinevirtual |
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inlinevirtual |
Add a copy of the object to the end of the vector.
const | CType & src |
Reimplemented from CCopasiVector< CType >.
Definition at line 621 of file CCopasiVector.h.
Referenced by CFunctionParameters::add(), CFunctionDB::add(), CModelAdd::addEvents(), CCompartment::addMetabolite(), CCopasiDataModel::addReport(), CCopasiDataModel::addTask(), CQReportDefinition::btnCopyReportClicked(), CQPlotSubwidget::copyPlot(), CModel::createCompartment(), CModel::createEvent(), CModel::createModelValue(), CKinFunction::createParameters(), createParameterSetsForExperiment(), CModel::createReaction(), CModelExpansion::duplicateEvent(), CCopasiXMLParser::ListOfPlotsElement::end(), CCopasiXMLParser::ListOfTasksElement::end(), CCopasiXMLParser::FunctionElement::end(), SBMLImporter::importEvent(), SEDMLImporter::importTasks(), CFunctionDB::load(), CQEventWidget1::saveToEvent(), CQParameterOverviewWidget::slotBtnCopy(), CQParameterOverviewWidget::slotBtnNew(), CQParameterOverviewWidget::slotBtnSaveAs(), CCopasiXMLParser::ModelParameterSetElement::start(), CCopasiXMLParser::ReactionElement::start(), CCopasiXMLParser::CompartmentElement::start(), CCopasiXMLParser::ModelValueElement::start(), CCopasiXMLParser::EventElement::start(), CCopasiXMLParser::AssignmentElement::start(), CCopasiXMLParser::ReportElement::start(), and test000087::test_simulate_reaction_flux_reference_1().
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inlinevirtual |
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 655 of file CCopasiVector.h.
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inlinevirtual |
Retrieve the index of the named object in the vector. If an object with the given name is not found C_INVALID_INDEX is returned.
const | std::string & name |
Definition at line 774 of file CCopasiVector.h.
Referenced by CFunctionParameters::add(), CFunctionDB::addAndAdaptName(), CCopasiDataModel::addDefaultReports(), CCopasiDataModel::addDefaultTasks(), CModelAdd::addEvents(), CQReportDefinition::btnCopyReportClicked(), CFunction::completeFunctionList(), CQPlotSubwidget::copyPlot(), SBMLImporter::createCCompartmentFromCompartment(), SBMLImporter::createCMetabFromSpecies(), SBMLImporter::createCModelValueFromParameter(), CModel::createCompartment(), SBMLImporter::createCReactionFromReaction(), CCrossSectionTask::createEvent(), CModel::createEvent(), CModel::createMetabolite(), CModel::createModelValue(), CChemEqInterface::createNonExistingMetabs(), CKinFunction::createParameters(), createParameterSetsForExperiment(), CModel::createReaction(), CMetabNameInterface::doesExist(), COptProblem::elevateChildren(), CCopasiXMLParser::COPASIElement::end(), CFunctionDB::findFunction(), CCopasiXML::fixBuild55(), CCopasiXML::fixBuild81(), CMetabNameInterface::getMetabolite(), CCopasiVectorN< CReportDefinition >::getObject(), SBMLImporter::importEvent(), CCopasiVectorN< CReportDefinition >::isInsertAllowed(), CCopasiVectorN< CReportDefinition >::operator[](), CCopasiVectorN< CReportDefinition >::remove(), CQEventWidget1::saveToEvent(), CQParameterOverviewWidget::slotBtnCopy(), FunctionWidget1::slotBtnNew(), ReactionsWidget1::slotNewFunction(), CCopasiXMLParser::AssignmentElement::start(), CCopasiXMLParser::ReportElement::start(), and CCopasiXMLParser::FunctionElement::start().
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inlinevirtual |
Retrieve a pointer to the named object.
const | std::string & name |
Reimplemented from CCopasiVector< CType >.
Definition at line 742 of file CCopasiVector.h.
Referenced by CCopasiXMLParser::getObjectFromName().
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inlineprivatevirtual |
Check whether an insert of the given src into the vector is allowed to avoid naming conflicts.
const | CType * src |
Definition at line 796 of file CCopasiVector.h.
Referenced by CCopasiVectorN< CReportDefinition >::add().
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inline |
Assignment operator.
const | std::vector< CType * > & rhs |
Definition at line 610 of file CCopasiVector.h.
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inline |
Retrieve the indexed object.
const | size_t & index |
Definition at line 694 of file CCopasiVector.h.
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inline |
Retrieve the indexed object.
const | size_t & index |
Definition at line 702 of file CCopasiVector.h.
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inline |
Retrieve the named object.
const | std::string & name |
Definition at line 710 of file CCopasiVector.h.
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inline |
Retrieve the named object.
const | std::string & name |
Definition at line 726 of file CCopasiVector.h.
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inlinevirtual |
Remove the object with the given name from the vector.
const | std::string & name |
Definition at line 674 of file CCopasiVector.h.
Referenced by CCopasiXMLParser::COPASIElement::end(), CFunctionParameters::remove(), SBMLImporter::removeUnusedFunctions(), CModelExpansion::replaceInMetab(), CQSpeciesDetail::save(), CQEventWidget1::saveToEvent(), CQParameterOverviewWidget::slotBtnDelete(), and test000087::test_simulate_reaction_flux_reference_1().