COPASI API
4.16.103
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#include <CCopasiDataModel.h>
Classes | |
class | CData |
Public Member Functions | |
bool | addDefaultReports () |
bool | addDefaultTasks () |
CReportDefinition * | addReport (const CCopasiTask::Type &taskType) |
CCopasiTask * | addTask (const CCopasiTask::Type &taskType) |
bool | appendDependentTasks (std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependentTasks) const |
bool | autoSave () |
CCopasiDataModel (const bool withGUI=false) | |
CCopasiDataModel (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", bool withGUI=false) | |
void | changed (const bool &changed=true) |
void | deleteOldData () |
bool | exportMathModel (const std::string &fileName, CProcessReport *pProcessReport, const std::string &filter, bool overwriteFile=false) |
std::string | exportMathModelToString (CProcessReport *pProcessReport, const std::string &filter) |
bool | exportSBML (const std::string &fileName, bool overwriteFile=false, int sbmlLevel=2, int sbmlVersion=1, bool exportIncomplete=false, bool exportCOPASIMIRIAM=true, CProcessReport *pExportHandler=NULL) |
std::string | exportSBMLToString (CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion) |
std::map< CCopasiObject *, SBase * > & | getCopasi2SBMLMap () |
SBMLDocument * | getCurrentSBMLDocument () |
CCopasiObject * | getDataObject (const CCopasiObjectName &CN) const |
const std::string & | getFileName () const |
SCopasiXMLGUI * | getGUI () |
CListOfLayouts * | getListOfLayouts () |
const CListOfLayouts * | getListOfLayouts () const |
CModel * | getModel () |
const CModel * | getModel () const |
const COutputDefinitionVector * | getPlotDefinitionList () const |
COutputDefinitionVector * | getPlotDefinitionList () |
const std::string & | getReferenceDirectory () const |
const CReportDefinitionVector * | getReportDefinitionList () const |
CReportDefinitionVector * | getReportDefinitionList () |
const std::string & | getSBMLFileName () const |
CCopasiVectorN< CCopasiTask > * | getTaskList () |
const CCopasiVectorN < CCopasiTask > * | getTaskList () const |
bool | importSBML (const std::string &fileName, CProcessReport *pImportHandler=NULL, const bool &deleteOldData=true) |
bool | importSBMLFromString (const std::string &sbmlDocumentText, CProcessReport *pImportHandler=NULL, const bool &deleteOldData=true) |
bool | isChanged () const |
bool | loadModel (std::istream &in, const std::string &pwd, CProcessReport *pProcessReport, const bool &deleteOldData=true) |
bool | loadModel (const std::string &fileName, CProcessReport *pProcessReport, const bool &deleteOldData=true) |
bool | newModel (CProcessReport *pProcessReport, const bool &deleteOldData) |
CObjectInterface * | ObjectFromCN (const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &objName) const |
CCopasiObject * | ObjectFromName (const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const |
bool | removeLayout (const std::string &key) |
bool | saveModel (const std::string &fileName, CProcessReport *pProcessReport, bool overwriteFile=false, const bool &autoSave=false) |
bool | setSBMLFileName (const std::string &fileName) |
virtual | ~CCopasiDataModel () |
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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 CObjectInterface * | getObject (const CCopasiObjectName &cn) const |
virtual const objectMap & | getObjects () const |
virtual std::string | getUnits () const |
virtual const CCopasiObject * | getValueObject () const |
virtual bool | remove (CCopasiObject *pObject) |
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 () |
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virtual void | addInterface (COutputInterface *pInterface) |
virtual bool | compile (std::vector< CCopasiContainer * > listOfContainer, const CCopasiDataModel *pDataModel) |
COutputHandler () | |
COutputHandler (const COutputHandler &src) | |
virtual void | finish () |
std::set< COutputInterface * > | getInterfaces () const |
bool | isMaster () const |
virtual void | output (const Activity &activity) |
virtual void | removeInterface (COutputInterface *pInterface) |
virtual void | separate (const Activity &activity) |
void | setMaster (COutputHandler *pMaster) |
virtual | ~COutputHandler () |
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virtual void | close () |
COutputInterface () | |
COutputInterface (const COutputInterface &src) | |
virtual const std::set< const CCopasiObject * > & | getObjects () const |
virtual | ~COutputInterface () |
Public Attributes | |
std::set< CCopasiObject * > | mLastAddedObjects |
CCopasiVectorS< CMetabOld > * | pOldMetabolites |
Protected Member Functions | |
void | commonAfterLoad (CProcessReport *pProcessReport, const bool &deleteOldData) |
void | popData () |
void | pushData () |
void | removeSBMLIdFromFunctions () |
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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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bool | compileRefresh (const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiDataModel *pDataModel) |
void | refresh () |
Protected Attributes | |
CData | mData |
CData | mOldData |
CDataModelRenameHandler | mRenameHandler |
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objectMap | mObjects |
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std::set< COutputInterface * > | mInterfaces |
std::vector< Refresh * > | mObjectRefreshes |
COutputHandler * | mpMaster |
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std::set< const CCopasiObject * > | mObjects |
Private Types | |
enum | FileType { CopasiML = 0, SBML, SEDML, Gepasi, unset } |
Additional Inherited Members | |
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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 |
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enum | Activity { BEFORE = 0x01, DURING = 0x02, AFTER = 0x04 } |
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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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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 78 of file CCopasiDataModel.h.
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private |
Enumerator | |
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CopasiML | |
SBML | |
SEDML | |
Gepasi | |
unset |
Definition at line 80 of file CCopasiDataModel.h.
CCopasiDataModel::CCopasiDataModel | ( | const bool | withGUI = false | ) |
Definition at line 113 of file CCopasiDataModel.cpp.
References mRenameHandler, newModel(), CCopasiTimer::PROCESS, CCopasiObject::setRenameHandler(), and CCopasiTimer::WALL.
CCopasiDataModel::CCopasiDataModel | ( | const std::string & | name, |
const CCopasiContainer * | pParent = NULL , |
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const std::string & | type = "CN" , |
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bool | withGUI = false |
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Definition at line 127 of file CCopasiDataModel.cpp.
References mRenameHandler, newModel(), CCopasiTimer::PROCESS, CCopasiObject::setRenameHandler(), and CCopasiTimer::WALL.
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virtual |
Definition at line 144 of file CCopasiDataModel.cpp.
References deleteOldData(), mData, mOldData, pdelete, pOldMetabolites, and CCopasiObject::setRenameHandler().
bool CCopasiDataModel::addDefaultReports | ( | ) |
Definition at line 1727 of file CCopasiDataModel.cpp.
References addReport(), C_INVALID_INDEX, CCopasiVectorN< CType >::getIndex(), CCopasiTask::getReport(), CReport::getReportDefinition(), mData, CCopasiDataModel::CData::pReportDefinitionList, pTask, CCopasiDataModel::CData::pTaskList, CReport::setReportDefinition(), and CCopasiTask::TypeName.
Referenced by commonAfterLoad().
bool CCopasiDataModel::addDefaultTasks | ( | ) |
Definition at line 1501 of file CCopasiDataModel.cpp.
References addTask(), C_INVALID_INDEX, CCopasiVectorN< CType >::getIndex(), mData, CCopasiDataModel::CData::pTaskList, and CCopasiTask::TypeName.
Referenced by commonAfterLoad().
CReportDefinition * CCopasiDataModel::addReport | ( | const CCopasiTask::Type & | taskType | ) |
Definition at line 1544 of file CCopasiDataModel.cpp.
References CCopasiVectorN< CType >::add(), CCopasiTask::fluxMode, CReportDefinition::getBodyAddr(), CReportDefinition::getFooterAddr(), CReportDefinition::getHeaderAddr(), CCopasiTask::lna, CCopasiTask::lyap, CCopasiTask::mca, mData, CCopasiTask::optimization, CCopasiTask::parameterFitting, CCopasiDataModel::CData::pReportDefinitionList, CCopasiTask::scan, CCopasiTask::sens, CReportDefinition::setComment(), CReportDefinition::setIsTable(), CReportDefinition::setSeparator(), CReportDefinition::setTaskType(), CReportDefinition::setTitle(), CCopasiTask::steadyState, CCopasiTask::timeCourse, CCopasiTask::tssAnalysis, and CCopasiTask::TypeName.
Referenced by addDefaultReports().
CCopasiTask * CCopasiDataModel::addTask | ( | const CCopasiTask::Type & | taskType | ) |
Definition at line 1431 of file CCopasiDataModel.cpp.
References CCopasiVectorN< CType >::add(), CCopasiTask::crosssection, CCopasiTask::fluxMode, CCopasiTask::getProblem(), CCopasiTask::lna, CCopasiTask::lyap, CCopasiTask::mca, mData, CCopasiTask::moieties, CCopasiTask::optimization, CCopasiTask::parameterFitting, CCopasiDataModel::CData::pModel, pTask, CCopasiDataModel::CData::pTaskList, CCopasiTask::scan, CCopasiTask::sens, CCopasiProblem::setModel(), CCopasiTask::steadyState, CCopasiTask::timeCourse, and CCopasiTask::tssAnalysis.
Referenced by addDefaultTasks().
bool CCopasiDataModel::appendDependentTasks | ( | std::set< const CCopasiObject * > | candidates, |
std::set< const CCopasiObject * > & | dependentTasks | ||
) | const |
Appends pointers to tasks, which are dependent on any of the candidates to the list dependentTasks.
std::set< | const CCopasiObject * > candidates |
std::set< | const CCopasiObject * > & dependentTasks |
Definition at line 1512 of file CCopasiDataModel.cpp.
References CCopasiVector< T >::begin(), CCopasiVector< T >::end(), mData, and CCopasiDataModel::CData::pTaskList.
Referenced by CQReportDefinition::btnDeleteReportClicked(), CQMessageBox::confirmDelete(), and CQReportDM::removeRows().
bool CCopasiDataModel::autoSave | ( | ) |
Definition at line 482 of file CCopasiDataModel.cpp.
References CDirEntry::baseName(), COptions::getValue(), CCopasiDataModel::CData::mAutoSaveNeeded, mData, CCopasiDataModel::CData::mSaveFileName, saveModel(), and CDirEntry::Separator.
void CCopasiDataModel::changed | ( | const bool & | changed = true | ) |
Definition at line 1829 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::mAutoSaveNeeded, CCopasiDataModel::CData::mChanged, and mData.
Referenced by commonAfterLoad(), CQTabWidget::save(), CQModelWidget::save(), CQSpeciesDetail::save(), CQNotes::save(), saveModel(), ScanWidget::saveTask(), SensitivitiesWidget::saveTask(), SteadyStateWidget::saveTask(), FunctionWidget1::saveToFunction(), and CQPlotSubwidget::saveToPlotSpec().
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protected |
Definition at line 2069 of file CCopasiDataModel.cpp.
References addDefaultReports(), addDefaultTasks(), CCopasiVector< T >::begin(), changed(), CModel::compileIfNecessary(), deleteOldData(), CCopasiVector< T >::end(), CCopasiMessage::getLastMessage(), CModel::getModelParameterSet(), mData, mOldData, CCopasiDataModel::CData::mWithGUI, CCopasiTask::NO_OUTPUT, CCopasiDataModel::CData::pCurrentSBMLDocument, CCopasiDataModel::CData::pGUI, CCopasiDataModel::CData::pListOfLayouts, CCopasiDataModel::CData::pModel, CCopasiDataModel::CData::pPlotDefinitionList, CCopasiDataModel::CData::pReportDefinitionList, CCopasiDataModel::CData::pTaskList, CModelEntity::setObjectParent(), CCopasiObject::setObjectParent(), CCopasiMessage::size(), CModel::updateInitialValues(), and CModelParameterSet::updateModel().
Referenced by importSBML(), importSBMLFromString(), loadModel(), and newModel().
void CCopasiDataModel::deleteOldData | ( | ) |
Definition at line 1389 of file CCopasiDataModel.cpp.
References mOldData, CCopasiDataModel::CData::pCurrentSBMLDocument, pdelete, CCopasiDataModel::CData::pGUI, CCopasiDataModel::CData::pListOfLayouts, CCopasiDataModel::CData::pModel, CCopasiDataModel::CData::pPlotDefinitionList, CCopasiDataModel::CData::pReportDefinitionList, and CCopasiDataModel::CData::pTaskList.
Referenced by commonAfterLoad(), DataModelGUI::linkDataModelToGUI(), and ~CCopasiDataModel().
bool CCopasiDataModel::exportMathModel | ( | const std::string & | fileName, |
CProcessReport * | pProcessReport, | ||
const std::string & | filter, | ||
bool | overwriteFile = false |
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Definition at line 969 of file CCopasiDataModel.cpp.
References CCopasiVector< T >::begin(), CCopasiMessage::clearDeque(), CModel::compileIfNecessary(), CDirEntry::dirName(), CCopasiVector< T >::end(), CCopasiMessage::ERROR, CDirEntry::exist(), CODEExporter::exportToStream(), CLocaleString::fromUtf8(), CModel::getModelValues(), CDirEntry::isWritable(), MCDirEntry, MCODEExporter, mData, CCopasiDataModel::CData::pModel, and CCopasiMessage::WARNING.
Referenced by main().
std::string CCopasiDataModel::exportMathModelToString | ( | CProcessReport * | pProcessReport, |
const std::string & | filter | ||
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Definition at line 917 of file CCopasiDataModel.cpp.
References CCopasiVector< T >::begin(), CModel::compileIfNecessary(), CCopasiVector< T >::end(), CODEExporter::exportToStream(), CModel::getModelValues(), MCODEExporter, mData, CCopasiDataModel::CData::pModel, and CCopasiMessage::WARNING.
bool CCopasiDataModel::exportSBML | ( | const std::string & | fileName, |
bool | overwriteFile = false , |
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int | sbmlLevel = 2 , |
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int | sbmlVersion = 1 , |
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bool | exportIncomplete = false , |
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bool | exportCOPASIMIRIAM = true , |
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CProcessReport * | pExportHandler = NULL |
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Definition at line 798 of file CCopasiDataModel.cpp.
References CCopasiMessage::clearDeque(), CModel::compileIfNecessary(), CSBMLExporter::disownSBMLDocument(), CCopasiMessage::ERROR, CCopasiMessage::EXCEPTION, CDirEntry::exist(), CSBMLExporter::exportModel(), CDirEntry::fileName(), CCopasiMessage::getAllMessageText(), CSBMLExporter::getCOPASI2SBMLMap(), CSBMLExporter::getSBMLDocument(), COptions::getValue(), CDirEntry::isRelativePath(), CDirEntry::isWritable(), CDirEntry::makePathAbsolute(), MCDirEntry, CCopasiDataModel::CData::mCopasi2SBMLMap, mData, CCopasiDataModel::CData::mSBMLFileName, CCopasiDataModel::CData::pCurrentSBMLDocument, pdelete, CCopasiDataModel::CData::pModel, and CSBMLExporter::setExportCOPASIMIRIAM().
std::string CCopasiDataModel::exportSBMLToString | ( | CProcessReport * | pExportHandler, |
int | sbmlLevel, | ||
int | sbmlVersion | ||
) |
Definition at line 709 of file CCopasiDataModel.cpp.
References CCopasiMessage::clearDeque(), CModel::compileIfNecessary(), CSBMLExporter::disownSBMLDocument(), CCopasiMessage::EXCEPTION, CSBMLExporter::exportModelToString(), CCopasiMessage::getAllMessageText(), CSBMLExporter::getCOPASI2SBMLMap(), CSBMLExporter::getSBMLDocument(), CCopasiDataModel::CData::mCopasi2SBMLMap, mData, CCopasiDataModel::CData::pCurrentSBMLDocument, pdelete, CCopasiDataModel::CData::pModel, and CSBMLExporter::setExportCOPASIMIRIAM().
Referenced by test000054::test_bug1002(), test000055::test_bug1004(), test000057::test_bug1006(), test000058::test_bug1025_1(), test000058::test_bug1025_10(), test000058::test_bug1025_2(), test000058::test_bug1025_3(), test000058::test_bug1025_4(), test000058::test_bug1025_5(), test000058::test_bug1025_6(), test000058::test_bug1025_7(), test000058::test_bug1025_8(), test000058::test_bug1025_9(), test000076::test_bug1035_1(), test000076::test_bug1035_2(), test000076::test_bug1035_3(), test000067::test_bug1060(), test000068::test_bug1068(), test000069::test_bug1069(), test000070::test_bug1084(), test000071::test_bug1085(), test000072::test_bug1086(), test000074::test_bug1088(), test000081::test_bug1205(), test000089::test_bug1412(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000100::test_bug1692_1(), test000100::test_bug1692_2(), test000101::test_bug1740(), test000102::test_bug1741(), test000103::test_bug1743_l2(), test000103::test_bug1743_l3(), test000050::test_bug894(), test000049::test_bug894(), test000048::test_bug919(), test000051::test_bug988(), test000060::test_bug_1026(), test000061::test_bug_1044(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000082::test_export_delayAssignment_1(), test000082::test_export_delayAssignment_2(), test000082::test_export_delayAssignment_3(), test000082::test_export_delayAssignment_4(), test000082::test_export_delayAssignment_5(), test000082::test_export_delayAssignment_6(), test000077::test_export_dimensionless(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_1(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_2(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_3(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_4(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_5(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_6(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_7(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_8(), test000097::test_export_global_render_information(), test000097::test_export_local_render_information(), test000098::test_export_notes(), test000087::test_export_reaction_flux_reference_1(), test000087::test_export_reaction_flux_reference_2(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_1(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_2(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_3(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_4(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_5(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_6(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_7(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_8(), test000097::test_importexport_global_render_information(), test000097::test_importexport_local_render_information(), test000092::test_miriam_export_1(), test000092::test_miriam_export_2(), test000092::test_miriam_export_3(), test000092::test_miriam_export_4(), test000092::test_miriam_export_5(), test000092::test_miriam_export_6(), test000092::test_miriam_export_7(), test000092::test_miriam_export_8(), test000092::test_miriam_export_9(), test000097::test_readexport_global_render_information(), test000097::test_readexport_local_render_information(), test000059::test_unique_id_1(), test000059::test_unique_id_10(), test000059::test_unique_id_11(), test000059::test_unique_id_12(), test000059::test_unique_id_13(), test000059::test_unique_id_14(), test000059::test_unique_id_15(), test000059::test_unique_id_16(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_2(), test000059::test_unique_id_20(), test000059::test_unique_id_21(), test000059::test_unique_id_21_2(), test000059::test_unique_id_22(), test000059::test_unique_id_3(), test000059::test_unique_id_4(), test000059::test_unique_id_5(), test000059::test_unique_id_6(), test000059::test_unique_id_7(), test000059::test_unique_id_8(), test000059::test_unique_id_9(), Copasi2SBMLTranslator::translateFileToSBML(), and Copasi2SBMLTranslator::translateToSBML().
std::map< CCopasiObject *, SBase * > & CCopasiDataModel::getCopasi2SBMLMap | ( | ) |
Definition at line 1854 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::mCopasi2SBMLMap, and mData.
Referenced by DataModelGUI::importCellDesigner(), SEDMLImporter::readListOfPlotsFromSedMLOutput(), and test000067::test_bug1060().
SBMLDocument * CCopasiDataModel::getCurrentSBMLDocument | ( | ) |
Definition at line 1835 of file CCopasiDataModel.cpp.
References mData, and CCopasiDataModel::CData::pCurrentSBMLDocument.
Referenced by CSBMLExporter::createSBMLDocument(), DataModelGUI::importCellDesigner(), stress_test::normalizeMath(), test000054::test_bug1002(), test000055::test_bug1004(), test000056::test_bug1005(), test000057::test_bug1006(), test000058::test_bug1025_1(), test000058::test_bug1025_10(), test000058::test_bug1025_2(), test000058::test_bug1025_3(), test000058::test_bug1025_4(), test000058::test_bug1025_5(), test000058::test_bug1025_6(), test000058::test_bug1025_7(), test000058::test_bug1025_8(), test000058::test_bug1025_9(), test000076::test_bug1035_1(), test000076::test_bug1035_2(), test000076::test_bug1035_3(), test000067::test_bug1060(), test000068::test_bug1068(), test000069::test_bug1069(), test000071::test_bug1085(), test000081::test_bug1205(), test000089::test_bug1412(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000049::test_bug894(), test000050::test_bug894(), test000048::test_bug919(), test000051::test_bug988(), test000060::test_bug_1026(), test000061::test_bug_1044(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000082::test_export_delayAssignment_1(), test000082::test_export_delayAssignment_2(), test000082::test_export_delayAssignment_3(), test000082::test_export_delayAssignment_4(), test000082::test_export_delayAssignment_5(), test000082::test_export_delayAssignment_6(), test000077::test_export_dimensionless(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_1(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_2(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_3(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_4(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_5(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_6(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_7(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_8(), test000087::test_export_reaction_flux_reference_1(), test000087::test_export_reaction_flux_reference_2(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_1(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_2(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_3(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_4(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_5(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_6(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_7(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_8(), test000075::test_import_time_dependent_function_definition(), test000092::test_miriam_export_7(), test000094::test_notrequired_package(), test000059::test_unique_id_1(), test000059::test_unique_id_10(), test000059::test_unique_id_11(), test000059::test_unique_id_12(), test000059::test_unique_id_13(), test000059::test_unique_id_14(), test000059::test_unique_id_15(), test000059::test_unique_id_16(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_2(), test000059::test_unique_id_20(), test000059::test_unique_id_21(), test000059::test_unique_id_21_2(), test000059::test_unique_id_22(), test000059::test_unique_id_3(), test000059::test_unique_id_4(), test000059::test_unique_id_5(), test000059::test_unique_id_6(), test000059::test_unique_id_7(), test000059::test_unique_id_8(), and test000059::test_unique_id_9().
CCopasiObject * CCopasiDataModel::getDataObject | ( | const CCopasiObjectName & | CN | ) | const |
Retrieve the data object with the given CN
const | CCopasiObjectName & CN |
Definition at line 1947 of file CCopasiDataModel.cpp.
References CCopasiContainer::getObject().
Referenced by CQPlotSubwidget::addCurve2D(), CSEDMLExporter::createDataGenerators(), CScanItem::CScanItem(), CQOptimizationResult::enterProtected(), CQFittingResult::enterProtected(), CODEExporter::exportExpression(), CSBMLExporter::findModelEntityDependencies(), CArrayAnnotation::getAnnotationsString(), CExperimentObjectMap::CDataColumn::getDefaultScale(), CExpression::getNodeObject(), CSensItem::getSingleObjectDisplayName(), COptItem::getStartValue(), CSensItem::getVariablesPointerList(), CScanWidgetRandom::load(), CScanWidgetScan::load(), Curve2DWidget::LoadFromCurveSpec(), BandedGraphWidget::LoadFromCurveSpec(), HistoWidget::LoadFromCurveSpec(), CQFittingItemWidget::loadSelection(), CQExperimentData::loadTable(), SensitivitiesWidget::loadTask(), CQSimpleSelectionTree::populateTree(), CQReportListItem::refreshText(), COptItem::setObjectCN(), CQFittingItemWidget::setTableText(), CQExperimentData::slotTypeChanged(), and CEvaluationNodeObject::toAST().
const std::string & CCopasiDataModel::getFileName | ( | ) | const |
Definition at line 1823 of file CCopasiDataModel.cpp.
References mData, and CCopasiDataModel::CData::mSaveFileName.
Referenced by main(), CReport::open(), CopasiUI3Window::slotExportMathModel(), and validate().
SCopasiXMLGUI * CCopasiDataModel::getGUI | ( | ) |
Definition at line 1815 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::isValid(), mData, mOldData, and CCopasiDataModel::CData::pGUI.
Referenced by SliderDialog::getCSlidersForObject(), and save_cps_model_to_stream().
CListOfLayouts * CCopasiDataModel::getListOfLayouts | ( | ) |
Definition at line 1807 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::isValid(), mData, mOldData, and CCopasiDataModel::CData::pListOfLayouts.
Referenced by CQNewMainWindow::addGlobalRenderInfoItemsToList(), test000097::addGlobalRenderInformation(), test000097::addLocalRenderInformation(), test000097::createModel(), CSBMLExporter::exportModelToString(), Arguments::handleCommandLine(), DataModelGUI::importCellDesigner(), CQLayoutScene::initializeResolver(), save_cps_model_to_stream(), CQLayoutsWidget::slotBtnNewClicked(), CQLayoutView::slotLayoutChanged(), CQNewMainWindow::slotLayoutChanged(), CQNewMainWindow::slotRenderInfoChanged(), CQLayoutView::slotRenderInformationChanged(), test000097::test_import_global_render_information(), test000097::test_import_local_render_information(), test000097::test_importexport_global_render_information(), test000097::test_importexport_local_render_information(), test000097::test_importwrite_global_render_information(), test000097::test_importwrite_local_render_information(), 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(), CQGLLayoutPainter::update(), updateLayoutList(), CQNewMainWindow::updateLayoutList(), updateRenderInformationList(), and CQNewMainWindow::updateRenderInformationList().
const CListOfLayouts * CCopasiDataModel::getListOfLayouts | ( | ) | const |
Definition at line 1799 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::isValid(), mData, mOldData, and CCopasiDataModel::CData::pListOfLayouts.
CModel * CCopasiDataModel::getModel | ( | ) |
Definition at line 1407 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::isValid(), mData, mOldData, and CCopasiDataModel::CData::pModel.
Referenced by CQPlotSubwidget::addCurve2D(), CCopasiXML::buildFunctionList(), CExperiment::calculateStatistics(), CSBMLExporter::check_for_spatial_size_units(), CSBMLExporter::checkForEvents(), CSBMLExporter::checkForInitialAssignments(), CSBMLExporter::checkForODESpeciesInNonfixedCompartment(), CSBMLExporter::checkForPiecewiseFunctions(), CSBMLExporter::checkForUnsupportedObjectReferences(), CSBMLExporter::collectIds(), CTimeSeries::compile(), COutputHandler::compileRefresh(), CQMessageBox::confirmDelete(), CQSpeciesDetail::copy(), CQCompartment::copy(), ReactionsWidget1::copy(), CSBMLExporter::createAreaUnit(), CSBMLExporter::createCompartments(), CSEDMLExporter::createDataGenerators(), CSBMLExporter::createEvents(), CSBMLExporter::createLengthUnit(), CSBMLExporter::createMetabolites(), test000097::createModel(), CSBMLExporter::createParameters(), createParameterSetsForExperiment(), CSBMLExporter::createReactions(), CSBMLExporter::createSBMLDocument(), CSEDMLExporter::createSEDMLDocument(), CSBMLExporter::createSubstanceUnit(), CSBMLExporter::createTimeUnit(), CSBMLExporter::createVolumeUnit(), CQPlotSubwidget::deletePlot(), CQNewMainWindow::elementaryModeTriggeredSlot(), CQLayoutsWidget::enterProtected(), CODEExporter::exportExpression(), CODEExporter::exportObjectNodesFromModel(), CODEExporter::exportToStream(), CSBMLExporter::findAvogadro(), findObjectByDisplayName(), SliderDialog::getCSlidersForObject(), getQuantityParameterOrValue(), QConservedSpeciesAnimation::getScales(), CSensItem::getVariablesPointerList(), SEDMLUtils::getXPathForObject(), CSBMLExporter::hasVolumeAssignment(), QConservedSpeciesAnimation::initialize(), QFluxModeAnimation::initialize(), QTimeCourseAnimation::initialize(), CTSSAMethod::initializeIntegrationsParameter(), CLsodaMethod::initializeParameter(), CScanTask::initSubtask(), CQSpecieDM::insertRows(), CSBMLExporter::isModelSBMLCompatible(), CSlider::isValid(), CQMoietiesTaskResult::load(), CSteadyStateProblem::load(), CQBrowserPaneDM::load(), CTrajectoryProblem::load(), FunctionWidget1::loadParameterTable(), main(), stress_test::normalizeAndSimplifyExpressions(), CQPlotDM::removeRows(), CQReactionDM::removeRows(), CQFunctionDM::removeRows(), CQEventDM::removeRows(), CQGlobalQuantityDM::removeRows(), CQCompartmentDM::removeRows(), CQSpecieDM::removeRows(), CSBMLExporter::replace_local_parameters(), CSBMLExporter::replaceSpeciesReferences(), CSBMLExporter::restore_local_parameters(), CQFittingWidget::runTask(), save_cps_model_to_stream(), ReactionsWidget1::saveToReaction(), CQReactionDM::setEquation(), CSlider::setSliderObject(), CQCrossSectionTaskWidget::showUnits(), CQTrajectoryWidget::showUnits(), CQPlotsWidget::slotBtnActivateAllClicked(), CQPlotsWidget::slotBtnDeactivateAllClicked(), ReactionsWidget1::slotBtnDelete(), CQCompartment::slotBtnDelete(), CQModelValue::slotBtnDelete(), CQEventWidget1::slotBtnDelete(), ReactionsWidget1::slotBtnNew(), CQSpeciesDetail::slotBtnNew(), CQLayoutsWidget::slotBtnNewClicked(), CQPlotsWidget::slotDoubleClicked(), CQReactionsWidget::slotDoubleClicked(), CQReportsWidget::slotDoubleClicked(), CQCompartmentsWidget::slotDoubleClicked(), CQEventsWidget::slotDoubleClicked(), CQGlobalQuantitiesWidget::slotDoubleClicked(), CQSpeciesWidget::slotDoubleClicked(), CQFittingWidget::taskFinishedEvent(), test000053::test1_bug1000(), test000053::test2_bug1000(), test000053::test3_bug1000(), test000053::test4_bug1000(), test000053::test5_bug1000(), test000054::test_bug1002(), test000055::test_bug1004(), test000057::test_bug1006(), test000058::test_bug1025_1(), test000058::test_bug1025_10(), test000058::test_bug1025_2(), test000058::test_bug1025_3(), test000058::test_bug1025_4(), test000058::test_bug1025_5(), test000058::test_bug1025_6(), test000058::test_bug1025_7(), test000058::test_bug1025_8(), test000058::test_bug1025_9(), test000076::test_bug1035_1(), test000076::test_bug1035_2(), test000076::test_bug1035_3(), test000067::test_bug1060(), test000068::test_bug1068(), test000069::test_bug1069(), test000071::test_bug1085(), test000073::test_bug1087(), test000081::test_bug1205(), test000089::test_bug1412(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000099::test_bug1675(), test000103::test_bug1743_l2(), test000103::test_bug1743_l3(), test000049::test_bug894(), test000050::test_bug894(), test000048::test_bug919(), test000051::test_bug988(), test000052::test_bug988(), test000060::test_bug_1026(), test000061::test_bug_1044(), test000047::test_delay(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000063::test_events_1(), test000082::test_export_delayAssignment_1(), test000082::test_export_delayAssignment_2(), test000082::test_export_delayAssignment_3(), test000082::test_export_delayAssignment_4(), test000082::test_export_delayAssignment_5(), test000082::test_export_delayAssignment_6(), test000077::test_export_dimensionless(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_1(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_2(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_3(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_4(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_5(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_6(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_7(), test000064::test_export_event_assignment_expression_and_hasOnlySubstanceUnits_8(), test000087::test_export_reaction_flux_reference_1(), test000087::test_export_reaction_flux_reference_2(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_1(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_2(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_3(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_4(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_5(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_6(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_7(), test000064::test_export_rule_expression_and_hasOnlySubstanceUnits_8(), test000021::test_hasOnlySubstanceUnits(), test000022::test_hasOnlySubstanceUnits(), test000023::test_hasOnlySubstanceUnits(), test000024::test_hasOnlySubstanceUnits(), test000025::test_hasOnlySubstanceUnits(), test000026::test_hasOnlySubstanceUnits(), test000027::test_hasOnlySubstanceUnits(), test000028::test_hasOnlySubstanceUnits(), test000029::test_hasOnlySubstanceUnits(), test000030::test_hasOnlySubstanceUnits(), test000031::test_hasOnlySubstanceUnits(), test000032::test_hasOnlySubstanceUnits(), test000033::test_hasOnlySubstanceUnits(), test000034::test_hasOnlySubstanceUnits(), test000035::test_hasOnlySubstanceUnits(), test000036::test_hasOnlySubstanceUnits(), test000037::test_hasOnlySubstanceUnits(), test000038::test_hasOnlySubstanceUnits(), test000039::test_hasOnlySubstanceUnits(), test000040::test_hasOnlySubstanceUnits(), test000041::test_hasOnlySubstanceUnits(), test000042::test_hasOnlySubstanceUnits(), test000043::test_hasOnlySubstanceUnits(), test000088::test_import_assignment_without_expression(), test000086::test_import_compartment_units_1(), test000084::test_import_compartment_units_1(), test000083::test_import_compartment_units_1(), test000085::test_import_compartment_units_1(), test000086::test_import_compartment_units_10(), test000083::test_import_compartment_units_10(), test000084::test_import_compartment_units_10(), test000085::test_import_compartment_units_10(), test000086::test_import_compartment_units_11(), test000083::test_import_compartment_units_11(), test000084::test_import_compartment_units_11(), test000085::test_import_compartment_units_11(), test000083::test_import_compartment_units_12(), test000085::test_import_compartment_units_12(), test000084::test_import_compartment_units_12(), test000083::test_import_compartment_units_13(), test000085::test_import_compartment_units_13(), test000084::test_import_compartment_units_13(), test000083::test_import_compartment_units_14(), test000085::test_import_compartment_units_14(), test000084::test_import_compartment_units_14(), test000084::test_import_compartment_units_15(), test000085::test_import_compartment_units_15(), test000083::test_import_compartment_units_15(), test000083::test_import_compartment_units_16(), test000085::test_import_compartment_units_16(), test000084::test_import_compartment_units_16(), test000083::test_import_compartment_units_17(), test000084::test_import_compartment_units_17(), test000085::test_import_compartment_units_17(), test000083::test_import_compartment_units_18(), test000085::test_import_compartment_units_18(), test000084::test_import_compartment_units_18(), test000084::test_import_compartment_units_19(), test000085::test_import_compartment_units_19(), test000083::test_import_compartment_units_19(), test000086::test_import_compartment_units_2(), test000084::test_import_compartment_units_2(), test000085::test_import_compartment_units_2(), test000083::test_import_compartment_units_2(), test000083::test_import_compartment_units_20(), test000084::test_import_compartment_units_20(), test000085::test_import_compartment_units_20(), test000083::test_import_compartment_units_21(), test000084::test_import_compartment_units_21(), test000085::test_import_compartment_units_21(), test000086::test_import_compartment_units_3(), test000083::test_import_compartment_units_3(), test000085::test_import_compartment_units_3(), test000084::test_import_compartment_units_3(), test000086::test_import_compartment_units_4(), test000085::test_import_compartment_units_4(), test000084::test_import_compartment_units_4(), test000083::test_import_compartment_units_4(), test000086::test_import_compartment_units_5(), test000085::test_import_compartment_units_5(), test000084::test_import_compartment_units_5(), test000083::test_import_compartment_units_5(), test000086::test_import_compartment_units_6(), test000085::test_import_compartment_units_6(), test000084::test_import_compartment_units_6(), test000083::test_import_compartment_units_6(), test000086::test_import_compartment_units_7(), test000084::test_import_compartment_units_7(), test000083::test_import_compartment_units_7(), test000085::test_import_compartment_units_7(), test000086::test_import_compartment_units_8(), test000084::test_import_compartment_units_8(), test000085::test_import_compartment_units_8(), test000083::test_import_compartment_units_8(), test000086::test_import_compartment_units_9(), test000084::test_import_compartment_units_9(), test000083::test_import_compartment_units_9(), test000085::test_import_compartment_units_9(), test000082::test_import_delayAssignment_1(), test000082::test_import_delayAssignment_2(), test000082::test_import_delayAssignment_3(), test000082::test_import_delayAssignment_4(), test000082::test_import_delayAssignment_5(), test000082::test_import_delayAssignment_6(), test000082::test_import_delayAssignment_7(), test000082::test_import_delayAssignment_8(), test000077::test_import_dimensionless_1(), test000077::test_import_dimensionless_2(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_1(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_2(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_3(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_4(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_5(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_6(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_7(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_8(), test000088::test_import_eventassignment_without_expression(), test000079::test_import_fast(), test000088::test_import_initialassignment_without_expression(), test000095::test_import_l3_event_1(), test000095::test_import_l3_event_2(), test000095::test_import_l3_event_3(), test000095::test_import_l3_event_4(), test000095::test_import_l3_event_5(), test000098::test_import_notes(), test000087::test_import_reaction_flux_reference_2(), test000066::test_import_reaction_with_constant_flux(), test000066::test_import_reaction_with_constant_flux_function(), test000066::test_import_reaction_with_constant_flux_function_global_parameter(), test000066::test_import_reaction_with_constant_flux_global_parameter(), test000066::test_import_reaction_with_constant_flux_reversible(), test000066::test_import_reaction_with_constant_flux_reversible_function(), test000066::test_import_reaction_with_constant_flux_reversible_function_global_parameter(), test000066::test_import_reaction_with_constant_flux_reversible_global_parameter(), test000065::test_import_reaction_with_unsuitable_kinetic_1(), test000065::test_import_reaction_with_unsuitable_kinetic_2(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_1(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_2(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_3(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_4(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_5(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_6(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_7(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_8(), test000075::test_import_time_dependent_function_definition(), test000062::test_kineticlaw_without_math(), test000078::test_l2v4_import_unordered_functions(), test000080::test_mass_action_recognition_bug(), test000092::test_miriam_export_1(), test000092::test_miriam_export_2(), test000092::test_miriam_export_3(), test000092::test_miriam_export_4(), test000092::test_miriam_export_5(), test000092::test_miriam_export_6(), test000092::test_miriam_export_7(), test000092::test_miriam_export_8(), test000092::test_miriam_export_9(), test000092::test_miriam_import_1(), test000094::test_notrequired_package(), test000087::test_simulate_reaction_flux_reference_1(), test000045::test_stoichiometricExpression(), test000046::test_stoichiometricExpression(), test000044::test_stoichiometricExpression(), test000059::test_unique_id_1(), test000059::test_unique_id_10(), test000059::test_unique_id_11(), test000059::test_unique_id_12(), test000059::test_unique_id_13(), test000059::test_unique_id_14(), test000059::test_unique_id_15(), test000059::test_unique_id_16(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_2(), test000059::test_unique_id_20(), test000059::test_unique_id_21(), test000059::test_unique_id_21_2(), test000059::test_unique_id_22(), test000059::test_unique_id_3(), test000059::test_unique_id_4(), test000059::test_unique_id_5(), test000059::test_unique_id_6(), test000059::test_unique_id_7(), test000059::test_unique_id_8(), test000059::test_unique_id_9(), CQGLLayoutPainter::update(), and validate().
const CModel * CCopasiDataModel::getModel | ( | ) | const |
Definition at line 1404 of file CCopasiDataModel.cpp.
References mData, and CCopasiDataModel::CData::pModel.
const COutputDefinitionVector * CCopasiDataModel::getPlotDefinitionList | ( | ) | const |
Definition at line 1783 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::isValid(), mData, mOldData, and CCopasiDataModel::CData::pPlotDefinitionList.
Referenced by CQPlotSubwidget::addPlot(), CQPlotSubwidget::copyPlot(), CSEDMLExporter::createDataGenerators(), COutputAssistant::createDefaultOutput(), COutputAssistant::createPlot(), CSEDMLExporter::createSEDMLDocument(), CQPlotSubwidget::deletePlot(), CQBrowserPaneDM::load(), Arguments::prepareModel(), CQPlotDM::removeRows(), save_cps_model_to_stream(), CQPlotsWidget::slotBtnActivateAllClicked(), CQPlotsWidget::slotBtnDeactivateAllClicked(), and CQPlotsWidget::slotDoubleClicked().
COutputDefinitionVector * CCopasiDataModel::getPlotDefinitionList | ( | ) |
Definition at line 1791 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::isValid(), mData, mOldData, and CCopasiDataModel::CData::pPlotDefinitionList.
const std::string & CCopasiDataModel::getReferenceDirectory | ( | ) | const |
Definition at line 1952 of file CCopasiDataModel.cpp.
References mData, and CCopasiDataModel::CData::mReferenceDir.
Referenced by CQNewMainWindow::CQNewMainWindow(), and SBMLImporter::parseSBML().
const CReportDefinitionVector * CCopasiDataModel::getReportDefinitionList | ( | ) | const |
Definition at line 1767 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::isValid(), mData, mOldData, and CCopasiDataModel::CData::pReportDefinitionList.
Referenced by CQReportDefinition::btnCopyReportClicked(), CQReportDefinition::btnDeleteReportClicked(), COutputAssistant::createTable(), SEDMLImporter::importTasks(), CQBrowserPaneDM::load(), SEDMLImporter::readListOfPlotsFromSedMLOutput(), CQReportDM::removeRows(), save_cps_model_to_stream(), CQReportsWidget::slotDoubleClicked(), and test000087::test_simulate_reaction_flux_reference_1().
CReportDefinitionVector * CCopasiDataModel::getReportDefinitionList | ( | ) |
Definition at line 1775 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::isValid(), mData, mOldData, and CCopasiDataModel::CData::pReportDefinitionList.
const std::string & CCopasiDataModel::getSBMLFileName | ( | ) | const |
Definition at line 1851 of file CCopasiDataModel.cpp.
References mData, and CCopasiDataModel::CData::mSBMLFileName.
Referenced by CCopasiXML::saveSBMLReference().
CCopasiVectorN< CCopasiTask > * CCopasiDataModel::getTaskList | ( | ) |
Definition at line 1415 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::isValid(), mData, mOldData, and CCopasiDataModel::CData::pTaskList.
Referenced by CQNewMainWindow::checkForElementaryModesSlot(), COutputAssistant::createDefaultOutput(), CSEDMLExporter::createScanTask(), CSEDMLExporter::createSteadyStateTask(), CSEDMLExporter::createTasks(), CSEDMLExporter::createTimeCourseTask(), CQNewMainWindow::elementaryModeTriggeredSlot(), CFitProblem::elevateChildren(), CQFittingResult::enterProtected(), QFluxModeAnimation::getScales(), QTimeCourseAnimation::getScales(), CMCAProblem::getSubTask(), SEDMLImporter::importTasks(), CFitProblem::initialize(), QFluxModeAnimation::initialize(), CSensMethod::initialize(), CNewtonMethod::initialize(), QTimeCourseAnimation::initialize(), CScanTask::initSubtask(), CQBrowserPaneDM::load(), main(), CQSimpleSelectionTree::populateTree(), Arguments::prepareModel(), save_cps_model_to_stream(), CLNAProblem::setSteadyStateRequested(), CMCAProblem::setSteadyStateRequested(), test000087::test_simulate_reaction_flux_reference_1(), SEDMLImporter::updateCopasiTaskForSimulation(), and validate().
const CCopasiVectorN< CCopasiTask > * CCopasiDataModel::getTaskList | ( | ) | const |
Definition at line 1423 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::isValid(), mData, mOldData, and CCopasiDataModel::CData::pTaskList.
bool CCopasiDataModel::importSBML | ( | const std::string & | fileName, |
CProcessReport * | pImportHandler = NULL , |
||
const bool & | deleteOldData = true |
||
) |
Definition at line 603 of file CCopasiDataModel.cpp.
References CCopasiContainer::add(), CDirEntry::baseName(), CCopasiMessage::clearDeque(), commonAfterLoad(), SBMLImporter::deleteCopasiModel(), CDirEntry::dirName(), CDirEntry::fileName(), CLocaleString::fromUtf8(), CCopasiRootContainer::getFunctionList(), CCopasiTask::getProblem(), COptions::getValue(), CDirEntry::isRelativePath(), CDirEntry::makePathAbsolute(), CCopasiDataModel::CData::mCopasi2SBMLMap, mData, CCopasiDataModel::CData::mFileType, CCopasiDataModel::CData::mReferenceDir, mRenameHandler, CCopasiDataModel::CData::mSaveFileName, CCopasiDataModel::CData::mSBMLFileName, CDirEntry::normalize(), CCopasiDataModel::CData::pCurrentSBMLDocument, CCopasiDataModel::CData::pListOfLayouts, CCopasiDataModel::CData::pModel, popData(), CCopasiDataModel::CData::pTaskList, pushData(), SBMLImporter::readSBML(), SBMLImporter::restoreFunctionDB(), SBML, CDirEntry::Separator, CDataModelRenameHandler::setEnabled(), SBMLImporter::setImportCOPASIMIRIAM(), SBMLImporter::setImportHandler(), and CDirEntry::suffix().
Referenced by Arguments::handleCommandLine(), main(), and stress_test::normalizeMath().
bool CCopasiDataModel::importSBMLFromString | ( | const std::string & | sbmlDocumentText, |
CProcessReport * | pImportHandler = NULL , |
||
const bool & | deleteOldData = true |
||
) |
Definition at line 526 of file CCopasiDataModel.cpp.
References CCopasiContainer::add(), CCopasiMessage::clearDeque(), commonAfterLoad(), SBMLImporter::deleteCopasiModel(), CCopasiRootContainer::getFunctionList(), CCopasiTask::getProblem(), CCopasiDataModel::CData::mCopasi2SBMLMap, mData, CCopasiDataModel::CData::mFileType, mRenameHandler, SBMLImporter::parseSBML(), CCopasiDataModel::CData::pCurrentSBMLDocument, CCopasiDataModel::CData::pListOfLayouts, CCopasiDataModel::CData::pModel, popData(), CCopasiDataModel::CData::pTaskList, pushData(), SBMLImporter::restoreFunctionDB(), SBML, CDataModelRenameHandler::setEnabled(), SBMLImporter::setImportCOPASIMIRIAM(), and SBMLImporter::setImportHandler().
Referenced by test000053::test1_bug1000(), test000053::test2_bug1000(), test000053::test3_bug1000(), test000053::test4_bug1000(), test000053::test5_bug1000(), test000055::test_bug1004(), test000056::test_bug1005(), test000057::test_bug1006(), test000058::test_bug1025_1(), test000058::test_bug1025_2(), test000058::test_bug1025_3(), test000058::test_bug1025_4(), test000058::test_bug1025_5(), test000068::test_bug1068(), test000070::test_bug1084(), test000071::test_bug1085(), test000072::test_bug1086(), test000073::test_bug1087(), test000074::test_bug1088(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000099::test_bug1675(), test000101::test_bug1740(), test000102::test_bug1741(), test000103::test_bug1743_l2(), test000103::test_bug1743_l3(), test000104::test_bug1744(), test000052::test_bug988(), test000060::test_bug_1026(), test000047::test_delay(), test000090::test_delay_in_function(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000063::test_events_1(), test000032::test_hasOnlySubstanceUnits(), test000027::test_hasOnlySubstanceUnits(), test000035::test_hasOnlySubstanceUnits(), test000036::test_hasOnlySubstanceUnits(), test000023::test_hasOnlySubstanceUnits(), test000037::test_hasOnlySubstanceUnits(), test000028::test_hasOnlySubstanceUnits(), test000038::test_hasOnlySubstanceUnits(), test000024::test_hasOnlySubstanceUnits(), test000039::test_hasOnlySubstanceUnits(), test000029::test_hasOnlySubstanceUnits(), test000040::test_hasOnlySubstanceUnits(), test000030::test_hasOnlySubstanceUnits(), test000041::test_hasOnlySubstanceUnits(), test000042::test_hasOnlySubstanceUnits(), test000025::test_hasOnlySubstanceUnits(), test000031::test_hasOnlySubstanceUnits(), test000043::test_hasOnlySubstanceUnits(), test000033::test_hasOnlySubstanceUnits(), test000022::test_hasOnlySubstanceUnits(), test000026::test_hasOnlySubstanceUnits(), test000034::test_hasOnlySubstanceUnits(), test000021::test_hasOnlySubstanceUnits(), test000088::test_import_assignment_without_expression(), test000086::test_import_compartment_units_1(), test000084::test_import_compartment_units_1(), test000085::test_import_compartment_units_1(), test000083::test_import_compartment_units_1(), test000086::test_import_compartment_units_10(), test000084::test_import_compartment_units_10(), test000085::test_import_compartment_units_10(), test000083::test_import_compartment_units_10(), test000086::test_import_compartment_units_11(), test000084::test_import_compartment_units_11(), test000085::test_import_compartment_units_11(), test000083::test_import_compartment_units_11(), test000084::test_import_compartment_units_12(), test000085::test_import_compartment_units_12(), test000083::test_import_compartment_units_12(), test000084::test_import_compartment_units_13(), test000085::test_import_compartment_units_13(), test000083::test_import_compartment_units_13(), test000084::test_import_compartment_units_14(), test000085::test_import_compartment_units_14(), test000083::test_import_compartment_units_14(), test000084::test_import_compartment_units_15(), test000085::test_import_compartment_units_15(), test000083::test_import_compartment_units_15(), test000085::test_import_compartment_units_16(), test000084::test_import_compartment_units_16(), test000083::test_import_compartment_units_16(), test000084::test_import_compartment_units_17(), test000085::test_import_compartment_units_17(), test000083::test_import_compartment_units_17(), test000084::test_import_compartment_units_18(), test000085::test_import_compartment_units_18(), test000083::test_import_compartment_units_18(), test000083::test_import_compartment_units_19(), test000084::test_import_compartment_units_19(), test000085::test_import_compartment_units_19(), test000086::test_import_compartment_units_2(), test000084::test_import_compartment_units_2(), test000085::test_import_compartment_units_2(), test000083::test_import_compartment_units_2(), test000083::test_import_compartment_units_20(), test000084::test_import_compartment_units_20(), test000085::test_import_compartment_units_20(), test000083::test_import_compartment_units_21(), test000085::test_import_compartment_units_21(), test000084::test_import_compartment_units_21(), test000086::test_import_compartment_units_3(), test000084::test_import_compartment_units_3(), test000085::test_import_compartment_units_3(), test000083::test_import_compartment_units_3(), test000086::test_import_compartment_units_4(), test000084::test_import_compartment_units_4(), test000085::test_import_compartment_units_4(), test000083::test_import_compartment_units_4(), test000086::test_import_compartment_units_5(), test000084::test_import_compartment_units_5(), test000085::test_import_compartment_units_5(), test000083::test_import_compartment_units_5(), test000086::test_import_compartment_units_6(), test000084::test_import_compartment_units_6(), test000083::test_import_compartment_units_6(), test000085::test_import_compartment_units_6(), test000086::test_import_compartment_units_7(), test000084::test_import_compartment_units_7(), test000085::test_import_compartment_units_7(), test000083::test_import_compartment_units_7(), test000086::test_import_compartment_units_8(), test000084::test_import_compartment_units_8(), test000085::test_import_compartment_units_8(), test000083::test_import_compartment_units_8(), test000086::test_import_compartment_units_9(), test000085::test_import_compartment_units_9(), test000084::test_import_compartment_units_9(), test000083::test_import_compartment_units_9(), test000082::test_import_delayAssignment_1(), test000082::test_import_delayAssignment_2(), test000082::test_import_delayAssignment_3(), test000082::test_import_delayAssignment_4(), test000082::test_import_delayAssignment_5(), test000082::test_import_delayAssignment_6(), test000082::test_import_delayAssignment_7(), test000082::test_import_delayAssignment_8(), test000077::test_import_dimensionless_1(), test000077::test_import_dimensionless_2(), test000077::test_import_dimensionless_3(), test000077::test_import_dimensionless_4(), test000077::test_import_dimensionless_5(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_1(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_2(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_3(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_4(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_5(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_6(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_7(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_8(), test000088::test_import_eventassignment_without_expression(), test000079::test_import_fast(), test000097::test_import_global_render_information(), test000088::test_import_initialassignment_without_expression(), test000095::test_import_l3_event_1(), test000095::test_import_l3_event_2(), test000095::test_import_l3_event_3(), test000095::test_import_l3_event_4(), test000095::test_import_l3_event_5(), test000097::test_import_local_render_information(), test000098::test_import_notes(), test000087::test_import_reaction_flux_reference_1(), test000087::test_import_reaction_flux_reference_2(), test000087::test_import_reaction_flux_reference_3(), test000066::test_import_reaction_with_constant_flux(), test000066::test_import_reaction_with_constant_flux_function(), test000066::test_import_reaction_with_constant_flux_function_global_parameter(), test000066::test_import_reaction_with_constant_flux_global_parameter(), test000066::test_import_reaction_with_constant_flux_reversible(), test000066::test_import_reaction_with_constant_flux_reversible_function(), test000066::test_import_reaction_with_constant_flux_reversible_function_global_parameter(), test000066::test_import_reaction_with_constant_flux_reversible_global_parameter(), test000065::test_import_reaction_with_unsuitable_kinetic_1(), test000065::test_import_reaction_with_unsuitable_kinetic_2(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_1(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_2(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_3(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_4(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_5(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_6(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_7(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_8(), test000075::test_import_time_dependent_function_definition(), test000097::test_importexport_global_render_information(), test000097::test_importexport_local_render_information(), test000097::test_importwrite_global_render_information(), test000097::test_importwrite_local_render_information(), test000062::test_kineticlaw_without_math(), test000078::test_l2v4_import_unordered_functions(), test000080::test_mass_action_recognition_bug(), test000092::test_miriam_export_1(), test000092::test_miriam_export_2(), test000092::test_miriam_export_3(), test000092::test_miriam_export_4(), test000092::test_miriam_export_5(), test000092::test_miriam_export_6(), test000092::test_miriam_export_7(), test000092::test_miriam_export_8(), test000092::test_miriam_export_9(), test000092::test_miriam_import_1(), test000094::test_notrequired_package(), test000094::test_required_package(), test000087::test_simulate_reaction_flux_reference_1(), test000044::test_stoichiometricExpression(), test000046::test_stoichiometricExpression(), test000045::test_stoichiometricExpression(), test000059::test_unique_id_1(), test000059::test_unique_id_10(), test000059::test_unique_id_17(), test000059::test_unique_id_18(), test000059::test_unique_id_19(), test000059::test_unique_id_2(), test000059::test_unique_id_20(), test000059::test_unique_id_22(), test000059::test_unique_id_3(), test000059::test_unique_id_4(), test000059::test_unique_id_5(), test000059::test_unique_id_6(), test000059::test_unique_id_7(), test000059::test_unique_id_8(), test000059::test_unique_id_9(), and Copasi2SBMLTranslator::translate().
bool CCopasiDataModel::isChanged | ( | ) | const |
Definition at line 1826 of file CCopasiDataModel.cpp.
References CCopasiDataModel::CData::mChanged, and mData.
bool CCopasiDataModel::loadModel | ( | std::istream & | in, |
const std::string & | pwd, | ||
CProcessReport * | pProcessReport, | ||
const bool & | deleteOldData = true |
||
) |
Definition at line 158 of file CCopasiDataModel.cpp.
References CCopasiContainer::add(), CCopasiMessage::clearDeque(), commonAfterLoad(), CopasiML, CCopasiMessage::ERROR, CCopasiXML::freeGUI(), CCopasiXML::freeLayoutList(), CCopasiXML::freeModel(), CCopasiXML::freePlotList(), CCopasiXML::freeReportList(), CCopasiXML::freeTaskList(), Gepasi, CCopasiRootContainer::getFunctionList(), CCopasiXML::getLayoutList(), CCopasiXML::getModel(), CCopasiXML::getPlotList(), CCopasiXML::getReportList(), CCopasiXML::getTaskList(), CReadConfig::getVersion(), CCopasiXML::load(), CModel::load(), CTrajectoryTask::load(), CSteadyStateTask::load(), MCXML, mData, CCopasiDataModel::CData::mFileType, mRenameHandler, CCopasiDataModel::CData::mWithGUI, newModel(), CCopasiDataModel::CData::pGUI, CCopasiDataModel::CData::pListOfLayouts, CCopasiDataModel::CData::pModel, popData(), CCopasiDataModel::CData::pPlotDefinitionList, CCopasiDataModel::CData::pReportDefinitionList, CCopasiDataModel::CData::pTaskList, pushData(), CCopasiXML::setDatamodel(), CDataModelRenameHandler::setEnabled(), CCopasiXML::setFunctionList(), and CCopasiXML::setGUI().
Referenced by Arguments::handleCommandLine(), load_cps_model_from_stream(), loadModel(), main(), Arguments::prepareModel(), Copasi2SBMLTranslator::translateFileToSBML(), and Copasi2SBMLTranslator::translateToSBML().
bool CCopasiDataModel::loadModel | ( | const std::string & | fileName, |
CProcessReport * | pProcessReport, | ||
const bool & | deleteOldData = true |
||
) |
Definition at line 303 of file CCopasiDataModel.cpp.
References CDirEntry::baseName(), CopasiML, CDirEntry::dirName(), fatalError, CDirEntry::fileName(), CLocaleString::fromUtf8(), Gepasi, COptions::getValue(), CDirEntry::isRelativePath(), loadModel(), CDirEntry::makePathAbsolute(), mData, CCopasiDataModel::CData::mFileType, CCopasiDataModel::CData::mReferenceDir, CCopasiDataModel::CData::mSaveFileName, CDirEntry::normalize(), CCopasiMessage::RAW, CDirEntry::Separator, and CDirEntry::suffix().
bool CCopasiDataModel::newModel | ( | CProcessReport * | pProcessReport, |
const bool & | deleteOldData | ||
) |
Definition at line 515 of file CCopasiDataModel.cpp.
References commonAfterLoad(), and pushData().
Referenced by CCopasiDataModel(), loadModel(), test000068::test_bug1068(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000103::test_bug1743_l2(), and test000103::test_bug1743_l3().
CObjectInterface * CCopasiDataModel::ObjectFromCN | ( | const std::vector< CCopasiContainer * > & | listOfContainer, |
const CCopasiObjectName & | objName | ||
) | const |
Retrieve the object with the given CN
const | std::vector< CCopasiContainer * > &listOfContainer |
const | CCopasiObjectName& objName |
Definition at line 1890 of file CCopasiDataModel.cpp.
References CCopasiObject::getCN(), CCopasiRootContainer::getFunctionList(), CCopasiContainer::getObject(), and CCopasiObjectName::getRemainder().
Referenced by CExpression::getNodeObject(), CMathContainer::getObject(), and ObjectFromName().
CCopasiObject * CCopasiDataModel::ObjectFromName | ( | const std::vector< CCopasiContainer * > & | listOfContainer, |
const CCopasiObjectName & | CN | ||
) | const |
Retrieve the data object with the given CN
const | std::vector< CCopasiContainer * > &listOfContainer |
const | CCopasiObjectName& CN |
Definition at line 1940 of file CCopasiDataModel.cpp.
References ObjectFromCN().
Referenced by CSBMLExporter::checkForUnsupportedObjectReferences(), CTimeSeries::compile(), CExperiment::compile(), CModelParameter::compile(), CopasiPlot::compile(), CModelParameterReactionParameter::compile(), COutputHandler::compileRefresh(), contains_necessary_mass_action_elements(), SBMLImporter::doMapping(), CReport::generateObjectsFromName(), COptProblem::getSubtaskType(), CFitProblem::initialize(), COptProblem::initializeSubtaskBeforeOutput(), SBMLImporter::isConstantFlux(), SBMLImporter::isMassActionExpression(), CODEExporter::isModelEntityExpressionODEExporterCompatible(), CSlider::isValid(), CReaction::object2variable(), CReportDefinition::preCompileTable(), SBMLImporter::renameMassActionParameters(), CSBMLExporter::replace_local_parameters(), CSBMLExporter::replaceSpeciesReferences(), CSBMLExporter::restore_local_parameters(), SBMLImporter::setCorrectUsage(), CQExpressionWidget::setExpression(), test000093::test_bug1503_1(), test000093::test_bug1503_2(), test000099::test_bug1675(), test000052::test_bug988(), test000047::test_delay(), test000091::test_delay_in_kinetic_law(), test000091::test_delay_in_kinetic_law_local_parameter(), test000026::test_hasOnlySubstanceUnits(), test000027::test_hasOnlySubstanceUnits(), test000028::test_hasOnlySubstanceUnits(), test000029::test_hasOnlySubstanceUnits(), test000030::test_hasOnlySubstanceUnits(), test000031::test_hasOnlySubstanceUnits(), test000032::test_hasOnlySubstanceUnits(), test000038::test_hasOnlySubstanceUnits(), test000036::test_hasOnlySubstanceUnits(), test000037::test_hasOnlySubstanceUnits(), test000039::test_hasOnlySubstanceUnits(), test000033::test_hasOnlySubstanceUnits(), test000040::test_hasOnlySubstanceUnits(), test000041::test_hasOnlySubstanceUnits(), test000042::test_hasOnlySubstanceUnits(), test000043::test_hasOnlySubstanceUnits(), test000034::test_hasOnlySubstanceUnits(), test000035::test_hasOnlySubstanceUnits(), test000021::test_hasOnlySubstanceUnits(), test000022::test_hasOnlySubstanceUnits(), test000023::test_hasOnlySubstanceUnits(), test000024::test_hasOnlySubstanceUnits(), test000025::test_hasOnlySubstanceUnits(), test000082::test_import_delayAssignment_1(), test000082::test_import_delayAssignment_2(), test000082::test_import_delayAssignment_3(), test000082::test_import_delayAssignment_4(), test000082::test_import_delayAssignment_5(), test000082::test_import_delayAssignment_6(), test000082::test_import_delayAssignment_7(), test000082::test_import_delayAssignment_8(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_1(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_2(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_3(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_4(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_5(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_6(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_7(), test000064::test_import_event_assignment_expression_and_hasOnlySubstanceUnits_8(), test000095::test_import_l3_event_1(), test000095::test_import_l3_event_2(), test000095::test_import_l3_event_3(), test000095::test_import_l3_event_4(), test000095::test_import_l3_event_5(), test000087::test_import_reaction_flux_reference_2(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_1(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_2(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_3(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_4(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_5(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_6(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_7(), test000064::test_import_rule_expression_and_hasOnlySubstanceUnits_8(), test000075::test_import_time_dependent_function_definition(), test000087::test_simulate_reaction_flux_reference_1(), and CModelParameter::updateModel().
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protected |
Definition at line 2053 of file CCopasiDataModel.cpp.
References mData, mOldData, CCopasiDataModel::CData::mWithGUI, CCopasiDataModel::CData::pGUI, CCopasiDataModel::CData::pListOfLayouts, CCopasiDataModel::CData::pModel, CCopasiDataModel::CData::pPlotDefinitionList, CCopasiDataModel::CData::pReportDefinitionList, and CCopasiDataModel::CData::pTaskList.
Referenced by importSBML(), importSBMLFromString(), and loadModel().
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protected |
Definition at line 2033 of file CCopasiDataModel.cpp.
References mData, mOldData, CCopasiDataModel::CData::mWithGUI, CCopasiDataModel::CData::pGUI, CCopasiDataModel::CData::pListOfLayouts, CCopasiDataModel::CData::pModel, CCopasiDataModel::CData::pPlotDefinitionList, CCopasiDataModel::CData::pReportDefinitionList, and CCopasiDataModel::CData::pTaskList.
Referenced by importSBML(), importSBMLFromString(), loadModel(), and newModel().
bool CCopasiDataModel::removeLayout | ( | const std::string & | key | ) |
Definition at line 1870 of file CCopasiDataModel.cpp.
References C_INVALID_INDEX, CKeyFactory::get(), CCopasiRootContainer::getKeyFactory(), mData, and CCopasiDataModel::CData::pListOfLayouts.
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protected |
Definition at line 1859 of file CCopasiDataModel.cpp.
References CCopasiRootContainer::getFunctionList(), CFunctionDB::loadedFunctions(), and CCopasiVector< T >::size().
bool CCopasiDataModel::saveModel | ( | const std::string & | fileName, |
CProcessReport * | pProcessReport, | ||
bool | overwriteFile = false , |
||
const bool & | autoSave = false |
||
) |
Definition at line 372 of file CCopasiDataModel.cpp.
References changed(), CCopasiMessage::clearDeque(), CModel::compileIfNecessary(), CDirEntry::createTmpName(), CCopasiMessage::ERROR, CDirEntry::exist(), CDirEntry::fileName(), CModel::getModelParameterSet(), COptions::getValue(), CDirEntry::isRelativePath(), CDirEntry::isWritable(), CDirEntry::makePathAbsolute(), MCDirEntry, mData, CDirEntry::move(), CCopasiDataModel::CData::mSaveFileName, CDirEntry::normalize(), CCopasiDataModel::CData::pGUI, CCopasiDataModel::CData::pListOfLayouts, CCopasiDataModel::CData::pModel, CCopasiDataModel::CData::pPlotDefinitionList, CCopasiDataModel::CData::pReportDefinitionList, CCopasiDataModel::CData::pTaskList, CModelParameterGroup::refreshFromModel(), CDirEntry::remove(), CCopasiXML::setDatamodel(), CCopasiXML::setGUI(), CCopasiXML::setLayoutList(), CCopasiXML::setModel(), CCopasiXML::setPlotList(), CCopasiXML::setReportList(), and CCopasiXML::setTaskList().
Referenced by autoSave(), main(), Arguments::prepareModel(), and Copasi2SBMLTranslator::translate().
bool CCopasiDataModel::setSBMLFileName | ( | const std::string & | fileName | ) |
Definition at line 1840 of file CCopasiDataModel.cpp.
References CDirEntry::fileName(), CDirEntry::isRelativePath(), CDirEntry::makePathAbsolute(), mData, CCopasiDataModel::CData::mSaveFileName, CCopasiDataModel::CData::mSBMLFileName, and CDirEntry::normalize().
Referenced by SEDMLImporter::importFirstSBMLModel(), and CCopasiXMLParser::SBMLReferenceElement::start().
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protected |
Definition at line 301 of file CCopasiDataModel.h.
Referenced by addDefaultReports(), addDefaultTasks(), addReport(), addTask(), appendDependentTasks(), autoSave(), changed(), commonAfterLoad(), exportMathModel(), exportMathModelToString(), exportSBML(), exportSBMLToString(), getCopasi2SBMLMap(), getCurrentSBMLDocument(), getFileName(), getGUI(), getListOfLayouts(), getModel(), getPlotDefinitionList(), getReferenceDirectory(), getReportDefinitionList(), getSBMLFileName(), getTaskList(), importSBML(), importSBMLFromString(), isChanged(), loadModel(), popData(), pushData(), removeLayout(), saveModel(), setSBMLFileName(), and ~CCopasiDataModel().
std::set<CCopasiObject*> CCopasiDataModel::mLastAddedObjects |
Definition at line 312 of file CCopasiDataModel.h.
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protected |
Definition at line 302 of file CCopasiDataModel.h.
Referenced by commonAfterLoad(), deleteOldData(), getGUI(), getListOfLayouts(), getModel(), getPlotDefinitionList(), getReportDefinitionList(), getTaskList(), popData(), pushData(), and ~CCopasiDataModel().
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protected |
Definition at line 303 of file CCopasiDataModel.h.
Referenced by CCopasiDataModel(), importSBML(), importSBMLFromString(), and loadModel().
CCopasiVectorS< CMetabOld >* CCopasiDataModel::pOldMetabolites |
This is a hack at the moment to be able to read Gepasi model files
Definition at line 309 of file CCopasiDataModel.h.
Referenced by CModel::load(), CReaction::loadOneRole(), and ~CCopasiDataModel().