15 #ifndef COPASI_CCopasiDataModel
16 #define COPASI_CCopasiDataModel
61 virtual void handle(
const std::string & oldCN,
const std::string & newCN)
const;
94 CData(
const bool & withGUI =
false);
141 SedDocument* pCurrentSEDMLDocument;
148 std::map<CCopasiObject*, SedBase*> mCopasi2SEDMLMap;
153 std::string mSEDMLFileName;
164 const std::string & type =
"CN",
165 bool withGUI =
false);
170 const std::string & pwd,
174 bool loadModel(
const std::string & fileName,
178 bool saveModel(
const std::string & fileName,
180 bool overwriteFile =
false,
197 bool exportSBML(
const std::string & fileName,
bool overwriteFile =
false,
int sbmlLevel = 2,
int sbmlVersion = 1,
bool exportIncomplete =
false,
bool exportCOPASIMIRIAM =
true,
CProcessReport* pExportHandler = NULL);
201 const std::string & filter,
bool overwriteFile =
false);
219 std::set< const CCopasiObject * > & dependentTasks)
const;
274 bool importSEDMLFromString(
const std::string & sedmlDocumentText,
278 bool importSEDML(
const std::string & fileName,
282 std::string exportSEDMLToString(
CProcessReport* pExportHandler,
int sedmlLevel,
int sedmlVersion);
283 bool exportSEDML(
const std::string & fileName,
bool overwriteFile =
false,
int sedmlLevel = 1,
int sedmlVersion = 1,
bool exportIncomplete =
false,
bool exportCOPASIMIRIAM =
true,
CProcessReport* pExportHandler = NULL);
285 SedDocument* getCurrentSEDMLDocument();
286 bool setSEDMLFileName(
const std::string & fileName);
287 const std::string & getSEDMLFileName()
const;
289 std::map<CCopasiObject*, SedBase*>& getCopasi2SEDMLMap();
318 #endif // COPASI_CCopasiDataModel
CCopasiObject * getDataObject(const CCopasiObjectName &CN) const
SBMLDocument * getCurrentSBMLDocument()
bool setSBMLFileName(const std::string &fileName)
std::set< CCopasiObject * > mLastAddedObjects
CData & operator=(const CData &rhs)
void commonAfterLoad(CProcessReport *pProcessReport, const bool &deleteOldData)
bool appendDependentTasks(std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependentTasks) const
std::string exportSBMLToString(CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion)
bool newModel(CProcessReport *pProcessReport, const bool &deleteOldData)
CReportDefinitionVector * pReportDefinitionList
CObjectInterface * ObjectFromCN(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &objName) const
bool importSBML(const std::string &fileName, CProcessReport *pImportHandler=NULL, const bool &deleteOldData=true)
std::string mSaveFileName
CData(const bool &withGUI=false)
void changed(const bool &changed=true)
std::string mReferenceDir
COutputDefinitionVector * pPlotDefinitionList
virtual ~CCopasiDataModel()
const std::string & getFileName() const
const CReportDefinitionVector * getReportDefinitionList() const
CCopasiDataModel(const bool withGUI=false)
const std::string & getReferenceDirectory() const
virtual void handle(const std::string &oldCN, const std::string &newCN) const
bool removeLayout(const std::string &key)
CDataModelRenameHandler()
const std::string & getSBMLFileName() const
CListOfLayouts * pListOfLayouts
CCopasiVectorN< CCopasiTask > * getTaskList()
CReportDefinition * addReport(const CCopasiTask::Type &taskType)
void removeSBMLIdFromFunctions()
bool loadModel(std::istream &in, const std::string &pwd, CProcessReport *pProcessReport, const bool &deleteOldData=true)
CListOfLayouts * getListOfLayouts()
void setEnabled(const bool &enabled)
bool saveModel(const std::string &fileName, CProcessReport *pProcessReport, bool overwriteFile=false, const bool &autoSave=false)
CCopasiTask * addTask(const CCopasiTask::Type &taskType)
CCopasiVectorN< CCopasiTask > * pTaskList
SBMLDocument * pCurrentSBMLDocument
virtual ~CDataModelRenameHandler()
bool exportSBML(const std::string &fileName, bool overwriteFile=false, int sbmlLevel=2, int sbmlVersion=1, bool exportIncomplete=false, bool exportCOPASIMIRIAM=true, CProcessReport *pExportHandler=NULL)
const COutputDefinitionVector * getPlotDefinitionList() const
bool importSBMLFromString(const std::string &sbmlDocumentText, CProcessReport *pImportHandler=NULL, const bool &deleteOldData=true)
The class for handling a chemical kinetic function.
bool exportMathModel(const std::string &fileName, CProcessReport *pProcessReport, const std::string &filter, bool overwriteFile=false)
std::map< CCopasiObject *, SBase * > mCopasi2SBMLMap
std::string mSBMLFileName
CDataModelRenameHandler mRenameHandler
std::string exportMathModelToString(CProcessReport *pProcessReport, const std::string &filter)
CCopasiVectorS< CMetabOld > * pOldMetabolites
std::map< CCopasiObject *, SBase * > & getCopasi2SBMLMap()
CCopasiObject * ObjectFromName(const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &CN) const