CCopasiDataModel Class Reference

#include <CCopasiDataModel.h>

Inheritance diagram for CCopasiDataModel:

List of all members.

Public Member Functions
	CCopasiDataModel (const bool withGUI=false)
	CCopasiDataModel (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", bool withGUI=false)
	~CCopasiDataModel ()
bool	loadModel (const std::string &fileName, CProcessReport *pProcessReport)
bool	saveModel (const std::string &fileName, CProcessReport *pProcessReport, bool overwriteFile=false, const bool &autoSave=false)
bool	autoSave ()
bool	newModel (CModel *pModel, CProcessReport *pProcessReport, CListOfLayouts *pLol=NULL)
bool	importSBMLFromString (const std::string &sbmlDocumentText, CProcessReport *pImportHandler=NULL)
bool	importSBML (const std::string &fileName, CProcessReport *pImportHandler=NULL)
std::string	exportSBMLToString (CProcessReport *pExportHandler, int sbmlLevel, int sbmlVersion)
bool	exportSBML (const std::string &fileName, bool overwriteFile=false, int sbmlLevel=2, int sbmlVersion=1, bool exportIncomplete=false, bool exportCOPASIMIRIAM=true, CProcessReport *pExportHandler=NULL)
bool	exportMathModel (const std::string &fileName, CProcessReport *pProcessReport, const std::string &filter, bool overwriteFile=false)
CModel *	getModel ()
const CModel *	getModel () const
CCopasiVectorN< CCopasiTask > *	getTaskList ()
const CCopasiVectorN < CCopasiTask > *	getTaskList () const
CCopasiTask *	addTask (const CCopasiTask::Type &taskType)
bool	addDefaultTasks ()
bool	appendDependentTasks (std::set< const CCopasiObject * > candidates, std::set< const CCopasiObject * > &dependentTasks) const
CReportDefinitionVector *	getReportDefinitionList ()
CReportDefinition *	addReport (const CCopasiTask::Type &taskType)
bool	addDefaultReports ()
COutputDefinitionVector *	getPlotDefinitionList ()
CListOfLayouts *	getListOfLayouts ()
const CListOfLayouts *	getListOfLayouts () const
bool	removeLayout (const std::string &key)
SCopasiXMLGUI *	getGUI ()
const std::string &	getFileName () const
bool	isChanged () const
void	changed (const bool &changed=true)
SBMLDocument *	getCurrentSBMLDocument ()
bool	setSBMLFileName (const std::string &fileName)
const std::string &	getSBMLFileName () const
std::map< CCopasiObject *, SBase * > &	getCopasi2SBMLMap ()
CCopasiObject *	ObjectFromName (const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &objName)
const CCopasiObject *	ObjectFromName (const std::vector< CCopasiContainer * > &listOfContainer, const CCopasiObjectName &objName) const
Public Attributes
CCopasiVectorS< CMetabOld > *	pOldMetabolites
Protected Member Functions
void	removeSBMLIdFromFunctions ()
Protected Attributes
CModel *	mpModel
CCopasiVectorN< CCopasiTask > *	mpTaskList
CReportDefinitionVector *	mpReportDefinitionList
COutputDefinitionVector *	mpPlotDefinitionList
CListOfLayouts *	mpListOfLayouts
bool	mWithGUI
SCopasiXMLGUI *	mpGUI
std::string	mSaveFileName
bool	mChanged
bool	mAutoSaveNeeded
CDataModelRenameHandler	mRenameHandler
SBMLDocument *	mpCurrentSBMLDocument
std::string	mSBMLFileName
std::map< CCopasiObject *, SBase * >	mCopasi2SBMLMap

---

Constructor & Destructor Documentation

CCopasiDataModel::CCopasiDataModel

(

const bool

withGUI = false

)

CCopasiDataModel::CCopasiDataModel	(	const std::string &	name,
		const CCopasiContainer *	pParent = NULL,
		const std::string &	type = "CN",
		bool	withGUI = false
	)

CCopasiDataModel::~CCopasiDataModel

(

)

---

Member Function Documentation

bool CCopasiDataModel::addDefaultReports

(

)

bool CCopasiDataModel::addDefaultTasks

(

)

CReportDefinition * CCopasiDataModel::addReport

(

const CCopasiTask::Type &

taskType

)

CCopasiTask * CCopasiDataModel::addTask

(

const CCopasiTask::Type &

taskType

)

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.

Parameters:

std::set<	const CCopasiObject * > candidates
std::set<	const CCopasiObject * > & dependentTasks

Returns:

bool functionsAppended

bool CCopasiDataModel::autoSave

(

)

void CCopasiDataModel::changed

(

const bool &

changed = true

)

bool CCopasiDataModel::exportMathModel	(	const std::string &	fileName,
		CProcessReport *	pProcessReport,
		const std::string &	filter,
		bool	overwriteFile = false
	)

bool CCopasiDataModel::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 CCopasiDataModel::exportSBMLToString	(	CProcessReport *	pExportHandler,
		int	sbmlLevel,
		int	sbmlVersion
	)

std::map< CCopasiObject *, SBase * > & CCopasiDataModel::getCopasi2SBMLMap

(

)

SBMLDocument * CCopasiDataModel::getCurrentSBMLDocument

(

)

const std::string & CCopasiDataModel::getFileName

(

)

const

SCopasiXMLGUI * CCopasiDataModel::getGUI

(

)

CListOfLayouts * CCopasiDataModel::getListOfLayouts

(

)

const CListOfLayouts * CCopasiDataModel::getListOfLayouts

(

)

const

CModel * CCopasiDataModel::getModel

(

)

const CModel * CCopasiDataModel::getModel

(

)

const

COutputDefinitionVector * CCopasiDataModel::getPlotDefinitionList

(

)

CReportDefinitionVector * CCopasiDataModel::getReportDefinitionList

(

)

const std::string & CCopasiDataModel::getSBMLFileName

(

)

const

CCopasiVectorN< CCopasiTask > * CCopasiDataModel::getTaskList

(

)

const CCopasiVectorN< CCopasiTask > * CCopasiDataModel::getTaskList

(

)

const

bool CCopasiDataModel::importSBML	(	const std::string &	fileName,
		CProcessReport *	pImportHandler = NULL
	)

bool CCopasiDataModel::importSBMLFromString	(	const std::string &	sbmlDocumentText,
		CProcessReport *	pImportHandler = NULL
	)

bool CCopasiDataModel::isChanged

(

)

const

bool CCopasiDataModel::loadModel	(	const std::string &	fileName,
		CProcessReport *	pProcessReport
	)

bool CCopasiDataModel::newModel	(	CModel *	pModel,
		CProcessReport *	pProcessReport,
		CListOfLayouts *	pLol = NULL
	)

CCopasiObject * CCopasiDataModel::ObjectFromName	(	const std::vector< CCopasiContainer * > &	listOfContainer,
		const CCopasiObjectName &	objName
	)

Parameters:

const	std::vector< CCopasiContainer * > &listOfContainer
const	CCopasiObjectName& objName

Returns:

CCopasiObject * pObject

const CCopasiObject * CCopasiDataModel::ObjectFromName	(	const std::vector< CCopasiContainer * > &	listOfContainer,
		const CCopasiObjectName &	objName
	)		const

Parameters:

const	std::vector< CCopasiContainer * > &listOfContainer
const	CCopasiObjectName& objName

Returns:

CCopasiObject * pObject

bool CCopasiDataModel::removeLayout

(

const std::string &

key

)

void CCopasiDataModel::removeSBMLIdFromFunctions

(

)

[protected]

bool CCopasiDataModel::saveModel	(	const std::string &	fileName,
		CProcessReport *	pProcessReport,
		bool	overwriteFile = false,
		const bool &	autoSave = false
	)

bool CCopasiDataModel::setSBMLFileName

(

const std::string &

fileName

)

---

Member Data Documentation

bool CCopasiDataModel::mAutoSaveNeeded [protected]

bool CCopasiDataModel::mChanged [protected]

std::map<CCopasiObject*, SBase*> CCopasiDataModel::mCopasi2SBMLMap [protected]

This will map each Copasi object to the corresponding SBML object if the current model was created by an SBML import.

SBMLDocument* CCopasiDataModel::mpCurrentSBMLDocument [protected]

This will hold the SBMLDocument that was imported to create the current Model.

SCopasiXMLGUI* CCopasiDataModel::mpGUI [protected]

CListOfLayouts* CCopasiDataModel::mpListOfLayouts [protected]

CModel* CCopasiDataModel::mpModel [protected]

COutputDefinitionVector* CCopasiDataModel::mpPlotDefinitionList [protected]

CReportDefinitionVector* CCopasiDataModel::mpReportDefinitionList [protected]

CCopasiVectorN< CCopasiTask >* CCopasiDataModel::mpTaskList [protected]

CDataModelRenameHandler CCopasiDataModel::mRenameHandler [protected]

std::string CCopasiDataModel::mSaveFileName [protected]

std::string CCopasiDataModel::mSBMLFileName [protected]

The name of the referenced SBML file

bool CCopasiDataModel::mWithGUI [protected]

CCopasiVectorS< CMetabOld >* CCopasiDataModel::pOldMetabolites

This is a hack at the moment to be able to read Gepasi model files

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The documentation for this class was generated from the following files:

• copasi/CopasiDataModel/CCopasiDataModel.h
• copasi/CopasiDataModel/CCopasiDataModel.cpp