CCopasiParameter Class Reference

#include <CCopasiParameter.h>

Inheritance diagram for CCopasiParameter:

Collaboration diagram for CCopasiParameter:

Classes
union	Value

Public Types
enum	Type {   DOUBLE = 0, UDOUBLE, INT, UINT,   BOOL, GROUP, STRING, CN,   KEY, FILE, EXPRESSION, INVALID }
Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap
Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet
typedef std::vector< Refresh * >	DataUpdateSequence
Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet
typedef std::vector < CObjectInterface * >	UpdateSequence

Public Member Functions
	CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)
	CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter")
virtual CCopasiObjectName	getCN () const
virtual const std::string &	getKey () const
virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const
const CCopasiParameter::Type &	getType () const
const Value &	getValue () const
Value &	getValue ()
virtual void *	getValuePointer () const
CCopasiObject *	getValueReference () const
bool	isValidValue (const C_FLOAT64 &value) const
bool	isValidValue (const C_INT32 &value) const
bool	isValidValue (const unsigned C_INT32 &value) const
bool	isValidValue (const bool &value) const
bool	isValidValue (const std::string &value) const
bool	isValidValue (const CCopasiObjectName &value) const
bool	isValidValue (const std::vector< CCopasiParameter * > &value) const
CCopasiParameter &	operator= (const CCopasiParameter &rhs)
virtual void	print (std::ostream *ostream) const
template<class CType >
bool	setValue (const CType &value)
bool	setValue (const std::vector< CCopasiParameter * > &value)
virtual	~CCopasiParameter ()
Public Member Functions inherited from CCopasiContainer
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 ()
Public Member Functions inherited from CCopasiObject
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 const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
CCopasiContainer *	getObjectAncestor (const std::string &type) const
CCopasiDataModel *	getObjectDataModel ()
const CCopasiDataModel *	getObjectDataModel () 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
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
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 ()
Public Member Functions inherited from CObjectInterface
	CObjectInterface ()
virtual	~CObjectInterface ()

Static Public Attributes
static const std::string	TypeName []
static const char *	XMLType []
Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Attributes
std::string	mKey
CCopasiObject *	mpValueReference
size_t	mSize
Value	mValue
Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Private Member Functions
	CCopasiParameter ()
Value	createValue (const Value &value)
void	deleteValue ()

Private Attributes
CCopasiParameter::Type	mType

Friends
std::ostream &	operator<< (std::ostream &os, const CCopasiParameter &o)
bool	operator== (const CCopasiParameter &lhs, const CCopasiParameter &rhs)

Additional Inherited Members
Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())
static void	setRenameHandler (CRenameHandler *rh)
Protected Types inherited from CCopasiObject
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 }
Protected Member Functions inherited from CCopasiContainer
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 ()
Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()
	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)
Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

CCopasiParameter class. This class is used to describe parameters. This class is intended to be used with integration or optimization methods or reactions.

Created for COPASI by Stefan Hoops 2002

Definition at line 35 of file CCopasiParameter.h.

Member Enumeration Documentation

enum CCopasiParameter::Type

Enumerator
DOUBLE
UDOUBLE
INT
UINT
BOOL
GROUP
STRING
CN
KEY
FILE
EXPRESSION
INVALID

Definition at line 39 of file CCopasiParameter.h.

  {
    DOUBLE = 0,
    UDOUBLE,
    INT,
    UINT,
    BOOL,
    GROUP,
    STRING,
    CN,
    KEY,
    FILE,
    EXPRESSION,
    INVALID
  };

Constructor & Destructor Documentation

CCopasiParameter::CCopasiParameter ( )

private

Default constructor

Definition at line 65 of file CCopasiParameter.cpp.

References mValue, and CCopasiParameter::Value::pVOID.

Referenced by CCopasiParameterGroup::addParameter(), and CCopasiParameterGroup::operator=().

                                  :
  CCopasiContainer("NoName", NULL, "Parameter"),
  mKey(CCopasiRootContainer::getKeyFactory()->add("Parameter", this)),
  mType(INVALID),
  mSize(0),
  mValue(),
  mpValueReference(NULL)
{mValue.pVOID = NULL;}

CCopasiParameter::CCopasiParameter	(	const CCopasiParameter &	src,
		const CCopasiContainer *	pParent = NULL
	)

Copy constructor

Parameters

const	CCopasiParameter & src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 74 of file CCopasiParameter.cpp.

References createValue(), and mValue.

                                                                    :
  CCopasiContainer(src, pParent),
  mKey(CCopasiRootContainer::getKeyFactory()->add(src.getObjectType(), this)),
  mType(src.mType),
  mSize(0),
  mValue(),
  mpValueReference(NULL)
{
  createValue(src.mValue);
}

CCopasiParameter::CCopasiParameter	(	const std::string &	name,
		const Type &	type,
		const void *	pValue = NULL,
		const CCopasiContainer *	pParent = NULL,
		const std::string &	objectType = "Parameter"
	)

Specific constructor

Parameters

const	string & name
const	CCopasiParameter::Type & type
const	void * pValue (default: NULL)
const	CCopasiContainer * pParent (default: NULL)
const	std::string & objectType (default: "Parameter")

Definition at line 86 of file CCopasiParameter.cpp.

References createValue(), mValue, and CCopasiParameter::Value::pVOID.

                                                                :
  CCopasiContainer(name, pParent, objectType,
                   CCopasiObject::Container |
                   ((type == DOUBLE || type == UDOUBLE) ? CCopasiObject::ValueDbl :
                    ((type == INT || type == UINT) ? CCopasiObject::ValueInt :
                     ((type == STRING || type == CN || type == KEY || type == FILE || type == EXPRESSION) ? CCopasiObject::ValueString :
                      (type == BOOL) ? CCopasiObject::ValueBool : 0)))),
  mKey(CCopasiRootContainer::getKeyFactory()->add(objectType, this)),
  mType(type),
  mSize(0),
  mValue(),
  mpValueReference(NULL)
{
  CCopasiParameter::Value value;
  value.pVOID = const_cast<void *>(pValue);
  mValue = createValue(value);
}

CCopasiParameter::~CCopasiParameter ( )

virtual

Destructor

Definition at line 108 of file CCopasiParameter.cpp.

References deleteValue(), CCopasiRootContainer::getKeyFactory(), CCopasiRootContainer::getRoot(), mKey, and CKeyFactory::remove().

{
  if (CCopasiRootContainer::getRoot())
    CCopasiRootContainer::getKeyFactory()->remove(mKey);

  deleteValue();
}

Member Function Documentation

CCopasiParameter::Value CCopasiParameter::createValue ( const Value &  value )

private

Create or copy the value

Parameters

const

CCopasiParameter::Value & value

Returns

CCopasiParameter::Value Value

Definition at line 429 of file CCopasiParameter.cpp.

References CCopasiContainer::addObjectReference(), BOOL, C_FLOAT64, C_INT32, CN, DOUBLE, EXPRESSION, FILE, GROUP, INT, INVALID, KEY, mpValueReference, mSize, mType, mValue, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pCN, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pGROUP, CCopasiParameter::Value::pINT, CCopasiParameter::Value::pSTRING, CCopasiParameter::Value::pUINT, CCopasiParameter::Value::pVOID, STRING, UDOUBLE, UINT, CCopasiObject::ValueBool, CCopasiObject::ValueDbl, CCopasiObject::ValueInt, and CCopasiObject::ValueString.

Referenced by CCopasiParameter(), and operator=().

{
  switch (mType)
    {
      case CCopasiParameter::DOUBLE:
      case CCopasiParameter::UDOUBLE:
        mValue.pDOUBLE = new C_FLOAT64;

        if (value.pDOUBLE) * mValue.pDOUBLE = * value.pDOUBLE;

        mSize = sizeof(C_FLOAT64);
        mpValueReference = addObjectReference("Value", * mValue.pDOUBLE, CCopasiObject::ValueDbl);
        break;

      case CCopasiParameter::INT:
        mValue.pINT = new C_INT32;

        if (value.pINT) * mValue.pINT = * value.pINT;

        mSize = sizeof(C_INT32);
        mpValueReference = addObjectReference("Value", * mValue.pINT, CCopasiObject::ValueInt);
        break;

      case CCopasiParameter::UINT:
        mValue.pUINT = new unsigned C_INT32;

        if (value.pUINT) * mValue.pUINT = * value.pUINT;

        mSize = sizeof(unsigned C_INT32);
        mpValueReference = addObjectReference("Value", * mValue.pUINT, CCopasiObject::ValueInt);
        break;

      case CCopasiParameter::BOOL:
        mValue.pBOOL = new bool;

        if (value.pBOOL) * mValue.pBOOL = * value.pBOOL;

        mSize = sizeof(bool);
        mpValueReference = addObjectReference("Value", * mValue.pBOOL, CCopasiObject::ValueBool);
        break;

      case CCopasiParameter::STRING:
      case CCopasiParameter::KEY:
      case CCopasiParameter::FILE:
      case CCopasiParameter::EXPRESSION:

        if (value.pSTRING)
          mValue.pSTRING = new std::string(* value.pSTRING);
        else
          mValue.pSTRING = new std::string;

        mSize = sizeof(std::string);
        mpValueReference = addObjectReference("Value", * mValue.pSTRING, CCopasiObject::ValueString);
        break;

      case CCopasiParameter::CN:

        if (value.pCN)
          mValue.pCN = new CRegisteredObjectName(* value.pCN);
        else
          mValue.pCN = new CRegisteredObjectName;

        mSize = sizeof(CRegisteredObjectName);
        mpValueReference = addObjectReference("Value", * mValue.pCN, CCopasiObject::ValueString);
        break;

      case CCopasiParameter::GROUP:
        mValue.pGROUP = new std::vector< CCopasiParameter * >;
        mSize = sizeof(std::vector< CCopasiParameter * >);
        break;

      case CCopasiParameter::INVALID:
        mValue.pVOID = NULL;
        mSize = 0;
        break;
    }

  return mValue;
}

void CCopasiParameter::deleteValue ( )

private

Delete the value

Definition at line 509 of file CCopasiParameter.cpp.

References BOOL, CN, DOUBLE, EXPRESSION, fatalError, FILE, GROUP, INT, INVALID, KEY, mType, mValue, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pCN, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pGROUP, CCopasiParameter::Value::pINT, CCopasiParameter::Value::pSTRING, CCopasiParameter::Value::pUINT, CCopasiParameter::Value::pVOID, STRING, UDOUBLE, and UINT.

Referenced by operator=(), and ~CCopasiParameter().

{
  if (mValue.pVOID == NULL) return;

  switch (mType)
    {
      case CCopasiParameter::DOUBLE:
      case CCopasiParameter::UDOUBLE:
        delete mValue.pDOUBLE;
        break;

      case CCopasiParameter::INT:
        delete mValue.pINT;
        break;

      case CCopasiParameter::UINT:
        delete mValue.pUINT;
        break;

      case CCopasiParameter::BOOL:
        delete mValue.pBOOL;
        break;

      case CCopasiParameter::STRING:
      case CCopasiParameter::KEY:
      case CCopasiParameter::FILE:
      case CCopasiParameter::EXPRESSION:
        delete mValue.pSTRING;
        break;

      case CCopasiParameter::CN:
        delete mValue.pCN;
        break;

      case CCopasiParameter::GROUP:
        delete mValue.pGROUP;
        break;

      case CCopasiParameter::INVALID:
        break;

      default:
        fatalError();
        break;
    }

  mValue.pVOID = NULL;
  return;
}

CCopasiObjectName CCopasiParameter::getCN ( ) const

virtual

Retrieve the CN of the math container The math container provides values for the numerical values of model objects. For the CN mechanism to work properly it has to pretend to be the model.

Returns

CCopasiObjectName

Reimplemented from CCopasiObject.

Definition at line 412 of file CCopasiParameter.cpp.

References CCopasiObjectName::escape(), CCopasiObject::getCN(), CCopasiObject::getObjectParent(), CCopasiObject::getObjectType(), and CCopasiParameterGroup::getUniqueParameterName().

Referenced by CFixLocalReactionParameters::changeModel(), CSBMLExporter::createKineticLaw(), CSensProblem::initDebugProblem(), CSensMethod::initialize(), CSBMLExporter::replace_local_parameters(), SBMLImporter::sbmlId2CopasiCN(), and CEvaluationNodeObject::toAST().

{
  CCopasiContainer * pObjectParent = getObjectParent();
  CCopasiParameterGroup * pGroup;

  if (pObjectParent != NULL &&
      (pGroup = dynamic_cast< CCopasiParameterGroup * >(pObjectParent)) != NULL)
    {
      return pObjectParent->getCN() + "," + CCopasiObjectName::escape(getObjectType()) + "=" + CCopasiObjectName::escape(pGroup->getUniqueParameterName(this));
    }

  return CCopasiObject::getCN();
}

const std::string & CCopasiParameter::getKey ( ) const

virtual

Return the key of this model

Returns

string key

Reimplemented from CCopasiObject.

Definition at line 239 of file CCopasiParameter.cpp.

References mKey.

Referenced by CModelAnalyzer::checkReaction(), CCopasiXMLParser::PlotItemElement::end(), CCopasiXMLParser::PlotSpecificationElement::end(), CCopasiXMLParser::ParameterGroupElement::end(), CODEExporter::exportKineticFunction(), CODEExporterBM::exportSingleParameter(), CODEExporterXPPAUT::exportSingleParameter(), CODEExporterC::exportSingleParameter(), CStochMethod::getAffects(), CCopasiParameterGroup::getKey(), CReaction::initializeParameters(), CReaction::isLocalParameter(), CODEExporterC::KineticFunction2ODEmember(), CReaction::setParameterValue(), CCopasiXMLParser::SourceParameterElement::start(), CCopasiXMLParser::ParameterElement::start(), and CModelParameter::updateModel().

{return mKey;}

std::string CCopasiParameter::getObjectDisplayName ( bool  regular = true, bool  richtext = false  ) const

virtual

Overload display name. Special treatment for reaction parameters to provide a shorter display.

Reimplemented from CCopasiObject.

Definition at line 560 of file CCopasiParameter.cpp.

References CCopasiObject::getObjectAncestor(), getObjectDisplayName(), CCopasiObject::getObjectDisplayName(), CCopasiObject::getObjectName(), CCopasiObject::getObjectParent(), getType(), CCopasiParameterGroup::getUniqueParameterName(), and GROUP.

Referenced by CExperiment::compile(), getObjectDisplayName(), CFitProblem::printResult(), and CExperiment::printResult().

{
  // if one of the ancestors is a reaction and the parameter is not a group
  // it is (hopefully) a kinetic parameter

  CCopasiObject* tmp = this->getObjectAncestor("Reaction");

  if (tmp && getType() != GROUP)
    {
      return tmp->getObjectDisplayName(regular, richtext) + "." + getObjectName();
    }

  CCopasiContainer * pObjectParent = getObjectParent();
  CCopasiParameterGroup * pGroup;

  if (pObjectParent != NULL &&
      (pGroup = dynamic_cast< CCopasiParameterGroup * >(pObjectParent)) != NULL)
    {
      std::string DisplayName = pGroup->getObjectDisplayName(regular, richtext);

      if (DisplayName.length() >= 2 &&
          (DisplayName.substr(DisplayName.length() - 2) == "[]"))
        {
          DisplayName.insert(DisplayName.length() - 1, pGroup->getUniqueParameterName(this));
        }
      else
        {
          if ((DisplayName.length() != 0) && (DisplayName[DisplayName.length() - 1] != '.'))
            {
              DisplayName += ".";
            }

          DisplayName += pGroup->getUniqueParameterName(this);
        }

      if (getType() == GROUP)
        {
          DisplayName += "[]";
        }

      return DisplayName;
    }

  return CCopasiObject::getObjectDisplayName(regular, richtext);
}

const CCopasiParameter::Type & CCopasiParameter::getType

(

void

)

const

Retrieve the type of the parameter.

Returns

CCopasiParameter::Type & type

Definition at line 256 of file CCopasiParameter.cpp.

References mType.

Referenced by CCopasiParameterGroup::addParameter(), CCopasiParameterGroup::assertParameter(), CQProgressItemBar::destroy(), CCopasiXMLParser::PlotItemElement::end(), CCopasiXMLParser::PlotSpecificationElement::end(), CCopasiXMLParser::ParameterGroupElement::end(), CCopasiXMLParser::COPASIElement::end(), getObjectDisplayName(), CScanProblem::getScanItem(), CCopasiParameterGroup::getType(), CQProgressItemText::reset(), CQProgressItemBar::reset(), and CCopasiXMLInterface::saveParameter().

{return mType;}

const CCopasiParameter::Value & CCopasiParameter::getValue

(

)

const

Retrieve the private value of the parameter.

Returns

const CCopasiParameter::Value & Value

Definition at line 247 of file CCopasiParameter.cpp.

References mValue.

Referenced by CLyapWolfMethod::calculate(), CHybridMethod::calculateAmu(), CFixLocalReactionParameters::changeModel(), CFunctionAnalyzer::constructCallParametersActualValues(), CSEDMLExporter::createScanTask(), CSensMethod::CSensMethod(), CSensProblem::CSensProblem(), CTrajectoryTask::CTrajectoryTask(), CTSSATask::CTSSATask(), CFitProblem::elevateChildren(), CFitItem::elevateChildren(), COptProblem::elevateChildren(), CCopasiXMLParser::PlotItemElement::end(), CCopasiXMLParser::PlotSpecificationElement::end(), CCopasiXMLParser::TaskElement::end(), CCopasiXMLParser::COPASIElement::end(), CODEExporter::exportReacParamsAndFuncs(), CScanProblem::fixBuild81(), CPlotItem::getActivity(), CScanProblem::getContinueFromCurrentState(), CHybridMethodODE45::getDefaultAtol(), CHybridMethodLSODA::getDefaultAtol(), CScanProblem::getOutputInSubtask(), CSteadyStateMethod::getStabilityResolution(), CScanProblem::getSubtask(), CLNAProblem::getSubTask(), CMCAProblem::getSubTask(), CCopasiParameterGroup::getValue(), SEDMLImporter::importTasks(), CQPreferenceDialog::init(), CQProgressItemText::initFromProcessReportItem(), CQProgressItemBar::initFromProcessReportItem(), COptMethodEP::initialize(), COptMethodSteepestDescent::initialize(), CRandomSearch::initialize(), COptMethodDE::initialize(), COptMethodSRES::initialize(), COptMethodGA::initialize(), COptMethodPS::initialize(), COptMethodGASR::initialize(), COptMethodHookeJeeves::initialize(), COptMethodLevenbergMarquardt::initialize(), COptMethodNelderMead::initialize(), COptMethodSA::initialize(), COptMethodCoranaWalk::initialize(), COptMethodPraxis::initialize(), COptMethodSS::initialize(), CTSSATask::initialize(), CTrajectoryTask::initialize(), CNewtonMethod::initialize(), CCrossSectionTask::initialize(), CTSSAMethod::initializeIntegrationsParameter(), CExperimentObjectMap::CDataColumn::initializeParameter(), CRecentFiles::initializeParameter(), CSteadyStateMethod::initializeParameter(), CMIRIAMResource::initializeParameter(), CLyapProblem::initializeParameter(), CNewtonMethod::initializeParameter(), CTrajectoryProblem::initializeParameter(), CTSSAProblem::initializeParameter(), CMCAMethod::initializeParameter(), CCrossSectionProblem::initializeParameter(), CHybridMethodODE45::initializeParameter(), CLyapWolfMethod::initializeParameter(), CTauLeapMethod::initializeParameter(), CStochMethod::initializeParameter(), CConfigurationFile::initializeParameter(), COptItem::initializeParameter(), CFitProblem::initializeParameter(), CLsodaMethod::initializeParameter(), CMIRIAMResources::initializeParameter(), CCrossValidationSet::initializeParameter(), CTrajectoryMethodDsaLsodar::initializeParameter(), COptProblem::initializeParameter(), CHybridMethod::initializeParameter(), CHybridMethodLSODA::initializeParameter(), CExperiment::initializeParameter(), CHybridMethod::initMethod(), CHybridMethodODE45::initMethod(), CHybridMethodLSODA::initMethod(), CSteadyStateProblem::isJacobianRequested(), CPlotSpecification::isLogX(), CPlotSpecification::isLogY(), CSteadyStateProblem::isStabilityAnalysisRequested(), CLNAProblem::isSteadyStateRequested(), CMCAProblem::isSteadyStateRequested(), CNewtonMethod::isValidProblem(), CHybridMethod::isValidProblem(), CHybridMethodLSODA::isValidProblem(), CStochDirectMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), CLyapWolfMethod::isValidProblem(), CStochMethod::isValidProblem(), CTrajectoryMethodDsaLsodar::isValidProblem(), CSteadyStateProblem::load(), CTrajectoryTask::load(), CReactionInterface::loadMappingAndValues(), CExperiment::operator=(), COptMethodEP2::optimise(), COptMethodHGASA::optimise(), CHybridMethod::partitionSystem(), CHybridMethodLSODA::partitionSystem(), CCSPMethod::predifineAnnotation(), CModel::printParameterOverview(), CModelParameter::refreshFromModel(), CSBMLExporter::replace_local_parameters(), CCopasiXMLInterface::saveParameter(), CTrajectoryTask::setMethodType(), CCrossSectionTask::setMethodType(), CExperimentObjectMap::CDataColumn::setObjectCN(), CExperimentObjectMap::CDataColumn::setScale(), CPlotItem::setType(), CHybridMethod::setupPartition(), CHybridMethodLSODA::setupPartition(), CQPreferenceDialog::slotBtnOk(), CILDMMethod::start(), CILDMModifiedMethod::start(), CTauLeapMethod::start(), CStochDirectMethod::start(), CCSPMethod::start(), CLyapWolfMethod::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), and SteadyStateWidget::taskFinishedEvent().

{return mValue;}

CCopasiParameter::Value & CCopasiParameter::getValue

(

)

Retrieve the private value of the parameter.

Returns

CCopasiParameter::Value & Value

Definition at line 249 of file CCopasiParameter.cpp.

References mValue.

{return mValue;}

void * CCopasiParameter::getValuePointer ( ) const

virtual

Retrieve a pointer to the value of the object

Reimplemented from CCopasiObject.

Definition at line 426 of file CCopasiParameter.cpp.

References mValue, and CCopasiParameter::Value::pVOID.

Referenced by CSensMethod::calculate_one_level(), CExperiment::compile(), CSensMethod::do_target_calculation(), and CSensMethod::scaling_variables().

{return const_cast<void *>(mValue.pVOID);}

CCopasiObject * CCopasiParameter::getValueReference

(

)

const

Retrieve the object which represents the value of the parameter

Returns

CCopasiObject * pValueReference

Definition at line 251 of file CCopasiParameter.cpp.

References mpValueReference.

Referenced by CModel::buildInitialSequence(), CModel::convert2NonReversible(), CObjectLists::getListOfConstObjects(), CTrajectoryProblem::initObjects(), CTSSAProblem::initObjects(), CModel::removeLocalReactionParameter(), SBMLImporter::setInitialValues(), test000058::test_bug1025_1(), test000058::test_bug1025_6(), test000059::test_unique_id_10(), test000059::test_unique_id_13(), test000059::test_unique_id_15(), test000059::test_unique_id_16(), test000059::test_unique_id_4(), test000059::test_unique_id_7(), and test000059::test_unique_id_9().

{
  return mpValueReference;
}

bool CCopasiParameter::isValidValue

(

const C_FLOAT64 &

value

)

const

Check whether the value corresponds to the type

Parameters

const

C_FLOAT64 & value

Returns

bool isValidValue

Definition at line 259 of file CCopasiParameter.cpp.

References DOUBLE, mType, and UDOUBLE.

Referenced by CCopasiParameterGroup::addParameter(), and setValue().

{
  if ((mType != CCopasiParameter::DOUBLE &&
       mType != CCopasiParameter::UDOUBLE) ||
      (mType == CCopasiParameter::UDOUBLE &&
       value < 0.0)) return false;

  return true;
}

bool CCopasiParameter::isValidValue

(

const C_INT32 &

value

)

const

Check whether the value corresponds to the type

Parameters

const

C_INT32 & value

Returns

bool isValidValue

Definition at line 269 of file CCopasiParameter.cpp.

References INT, and mType.

{
  if (mType != CCopasiParameter::INT) return false;

  return true;
}

bool CCopasiParameter::isValidValue

(

const unsigned C_INT32 &

value

)

const

Check whether the value corresponds to the type

Parameters

const

unsigned C_INT32 & value

Returns

bool isValidValue

Definition at line 276 of file CCopasiParameter.cpp.

References mType, and UINT.

{
  if (mType != CCopasiParameter::UINT) return false;

  return true;
}

bool CCopasiParameter::isValidValue

(

const bool &

value

)

const

Check whether the value corresponds to the type

Parameters

const

bool & value

Returns

bool isValidValue

bool CCopasiParameter::isValidValue

(

const std::string &

value

)

const

Check whether the value corresponds to the type

Parameters

const

std::string & value

Returns

bool isValidValue

Definition at line 290 of file CCopasiParameter.cpp.

References EXPRESSION, FILE, CKeyFactory::isValidKey(), KEY, mType, and STRING.

{
  if (mType == CCopasiParameter::KEY)
    return CKeyFactory::isValidKey(value);

  if (mType != CCopasiParameter::STRING &&
      mType != CCopasiParameter::FILE &&
      mType != CCopasiParameter::EXPRESSION) return false;

  return true;
}

bool CCopasiParameter::isValidValue

(

const CCopasiObjectName &

value

)

const

Check whether the value corresponds to the type

Parameters

const

CRegisteredObjectName & value

Returns

bool isValidValue

bool CCopasiParameter::isValidValue

(

const std::vector< CCopasiParameter * > &

value

)

const

Check whether the value corresponds to the type

Parameters

const

CCopasiParameterGroup::parameterGroup & value

Returns

bool isValidValue

CCopasiParameter & CCopasiParameter::operator=

(

const CCopasiParameter &

rhs

)

Assignment operator

Parameters

const

CCopasiParameter & rhs

Returns

CCopasiParameter & lhs

Definition at line 116 of file CCopasiParameter.cpp.

References BOOL, CN, createValue(), deleteValue(), DOUBLE, EXPRESSION, FILE, CCopasiObject::getObjectName(), GROUP, INT, INVALID, KEY, mType, mValue, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pCN, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pINT, CCopasiParameter::Value::pSTRING, CCopasiObject::setObjectName(), STRING, UDOUBLE, and UINT.

{
  if (getObjectName() != rhs.getObjectName())
    setObjectName(rhs.getObjectName());

  switch (rhs.mType)
    {
      case CCopasiParameter::DOUBLE:
      case CCopasiParameter::UDOUBLE:

        if (mType != DOUBLE &&
            mType != UDOUBLE)
          {
            deleteValue();
            mType = rhs.mType;
            createValue(rhs.mValue);
          }
        else
          {
            mType = rhs.mType;
            *mValue.pDOUBLE = *rhs.mValue.pDOUBLE;
          }

        break;

      case CCopasiParameter::INT:
      case CCopasiParameter::UINT:

        if (mType != INT &&
            mType != UINT)
          {
            deleteValue();
            mType = rhs.mType;
            createValue(rhs.mValue);
          }
        else
          {
            mType = rhs.mType;
            *mValue.pINT = *rhs.mValue.pINT;
          }

        break;

      case CCopasiParameter::BOOL:

        if (mType != BOOL)
          {
            deleteValue();
            mType = BOOL;
            createValue(rhs.mValue);
          }
        else
          {
            *mValue.pBOOL = *rhs.mValue.pBOOL;
          }

        break;

      case CCopasiParameter::STRING:
      case CCopasiParameter::KEY:
      case CCopasiParameter::FILE:
      case CCopasiParameter::EXPRESSION:

        if (mType != STRING &&
            mType != KEY &&
            mType != FILE &&
            mType != EXPRESSION)
          {
            deleteValue();
            mType = rhs.mType;
            createValue(rhs.mValue);
          }
        else
          {
            mType = rhs.mType;
            *mValue.pSTRING = *rhs.mValue.pSTRING;
          }

        break;

      case CCopasiParameter::CN:

        if (mType != CN)
          {
            deleteValue();
            mType = CN;
            createValue(rhs.mValue);
          }
        else
          {
            *mValue.pCN = *rhs.mValue.pCN;
          }

        break;

      case CCopasiParameter::GROUP:

        if (mType != GROUP)
          {
            deleteValue();
            mType = GROUP;
            createValue(rhs.mValue);
          }

        *static_cast<CCopasiParameterGroup *>(this) =
          *static_cast<const CCopasiParameterGroup *>(&rhs);

        break;

      case CCopasiParameter::INVALID:

        if (mType != INVALID)
          {
            deleteValue();
            mType = INVALID;
            createValue(rhs.mValue);
          }

        break;
    }

  return *this;
}

void CCopasiParameter::print ( std::ostream *  ostream ) const

virtual

This is the output method for any object. The default implementation provided with CCopasiObject uses the ostream operator<< of the object to print the object.To override this default behavior one needs to reimplement the virtual print function.

Parameters

std::ostream

* ostream

Reimplemented from CCopasiObject.

Reimplemented in CCopasiParameterGroup, COptProblem, CCopasiMethod, CCopasiProblem, CSensProblem, CCrossSectionProblem, CLNAProblem, CMCAProblem, CFitProblem, and COscillationProblem.

Definition at line 316 of file CCopasiParameter.cpp.

{*ostream << *this;}

template<class CType >

bool CCopasiParameter::setValue ( const CType &  value )

inline

Set the value of the parameter

Parameters

const

const CType & value

Returns

bool isValidValue

Definition at line 164 of file CCopasiParameter.h.

References isValidValue(), mValue, and CCopasiParameter::Value::pVOID.

Referenced by CCopasiParameterGroup::addParameter(), CCopasiXMLParser::PlotItemElement::end(), CCopasiXMLParser::PlotSpecificationElement::end(), CCopasiXMLParser::ParameterTextElement::end(), CCopasiXMLParser::COPASIElement::end(), CScanProblem::fixBuild81(), CExperiment::initializeParameter(), SBMLImporter::sbmlId2CopasiCN(), CCopasiParameterGroup::setValue(), CQPreferenceDialog::slotBtnOk(), test000087::test_simulate_reaction_flux_reference_1(), and CModelParameter::updateModel().

  {
    if (!isValidValue(value)) return false;

    *(CType *) mValue.pVOID = value;
    return true;
  }

bool CCopasiParameter::setValue

(

const std::vector< CCopasiParameter * > &

value

)

Set the value of the parameter when the origin is a parameter group. This function is currently not implemented and creates a fatalError when called.

Parameters

const

CCopasiParameter::parameterGroup& value

Returns

bool false

Definition at line 241 of file CCopasiParameter.cpp.

References fatalError.

{
  fatalError();
  return false;
}

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  os, const CCopasiParameter &  o  )

friend

Output stream operator

Parameters

ostream	& os
const	CCopasiParameter & A

Returns

ostream & os

Definition at line 319 of file CCopasiParameter.cpp.

{
  os << "    " << o.getObjectName() << ": ";

  switch (o.mType)
    {
      case CCopasiParameter::DOUBLE:
      case CCopasiParameter::UDOUBLE:
        os << * o.mValue.pDOUBLE;
        break;

      case CCopasiParameter::INT:
        os << * o.mValue.pINT;
        break;

      case CCopasiParameter::UINT:
        os << * o.mValue.pUINT;
        break;

      case CCopasiParameter::BOOL:
        os << * o.mValue.pBOOL;
        break;

      case CCopasiParameter::STRING:
      case CCopasiParameter::KEY:
      case CCopasiParameter::FILE:
      case CCopasiParameter::EXPRESSION:
        os << * o.mValue.pSTRING;
        break;

      case CCopasiParameter::CN:
        os << * o.mValue.pCN;
        break;

      case CCopasiParameter::GROUP:
      case CCopasiParameter::INVALID:
        break;
    }

  return os;
}

bool operator== ( const CCopasiParameter &  lhs, const CCopasiParameter &  rhs  )

friend

Comparison operator

Parameters

const	CCopasiParameter & lhs
const	CCopasiParameter & rhs

Returns

bool equal

Definition at line 361 of file CCopasiParameter.cpp.

{
  if (lhs.getObjectName() != rhs.getObjectName()) return false;

  if (lhs.mType != rhs.mType) return false;

  switch (lhs.mType)
    {
      case CCopasiParameter::DOUBLE:
      case CCopasiParameter::UDOUBLE:
        return *lhs.mValue.pDOUBLE == *rhs.mValue.pDOUBLE;
        break;

      case CCopasiParameter::INT:
        return *lhs.mValue.pINT == *rhs.mValue.pINT;
        break;

      case CCopasiParameter::UINT:
        return *lhs.mValue.pUINT == *rhs.mValue.pUINT;
        break;

      case CCopasiParameter::BOOL:
        return *lhs.mValue.pBOOL == *rhs.mValue.pBOOL;
        break;

      case CCopasiParameter::STRING:
      case CCopasiParameter::KEY:
      case CCopasiParameter::FILE:
      case CCopasiParameter::EXPRESSION:
        return *lhs.mValue.pSTRING == *rhs.mValue.pSTRING;
        break;

      case CCopasiParameter::CN:
        return *lhs.mValue.pCN == *rhs.mValue.pCN;
        break;

      case CCopasiParameter::GROUP:
        return *static_cast<const CCopasiParameterGroup *>(&lhs) ==
               *static_cast<const CCopasiParameterGroup *>(&rhs);
        break;

      case CCopasiParameter::INVALID:
      default:
        return !memcmp(lhs.mValue.pVOID, rhs.mValue.pVOID, lhs.mSize);
        break;
    }

  return false;
}

Member Data Documentation

std::string CCopasiParameter::mKey

protected

The key of the parameter.

Definition at line 86 of file CCopasiParameter.h.

Referenced by getKey(), CExperiment::initializeParameter(), and ~CCopasiParameter().

CCopasiObject* CCopasiParameter::mpValueReference

mutableprotected

A pointer to the object reference for the value

Definition at line 108 of file CCopasiParameter.h.

Referenced by createValue(), and getValueReference().

size_t CCopasiParameter::mSize

protected

The size allocated for the value of the parameter.

Definition at line 98 of file CCopasiParameter.h.

Referenced by createValue(), and operator==().

CCopasiParameter::Type CCopasiParameter::mType

private

The type of the parameter

Definition at line 92 of file CCopasiParameter.h.

Referenced by createValue(), deleteValue(), getType(), isValidValue(), operator<<(), operator=(), and operator==().

Value CCopasiParameter::mValue

protected

A pointer to the value of the parameter.

Definition at line 103 of file CCopasiParameter.h.

Referenced by CCopasiParameterGroup::addParameter(), CCopasiParameterGroup::beginIndex(), CCopasiParameter(), CCopasiParameterGroup::clear(), CProcessReportItem::CProcessReportItem(), createValue(), deleteValue(), CExperimentSet::elevateChildren(), CExperimentObjectMap::elevateChildren(), CCopasiParameterGroup::endIndex(), CCopasiParameterGroup::getIndex(), CExperimentObjectMap::getLastNotIgnoredColumn(), CCopasiParameterGroup::getObject(), CCopasiParameterGroup::getParameter(), CCopasiParameterGroup::getUniqueParameterName(), getValue(), getValuePointer(), operator<<(), operator=(), operator==(), CHybridMethod::partitionSystem(), CHybridMethodLSODA::partitionSystem(), CCopasiParameterGroup::removeParameter(), CExperimentObjectMap::setNumCols(), CHybridMethod::setupPartition(), CHybridMethodLSODA::setupPartition(), setValue(), CCopasiParameterGroup::size(), and CProcessReportItem::~CProcessReportItem().

const std::string CCopasiParameter::TypeName

static

Initial value:

=
{
  "float",
  "unsigned float",
  "integer",
  "unsigned integer",
  "bool",
  "group",
  "string",
  "common name",
  "key",
  "file",
  "expression",
  ""
}

String literals for the GUI to display type names of parameters known to COPASI.

CCopasiParameter class. This class is used to describe method paramters. This class is intended to be used with integration or optimization methods.

Created for Copasi by Stefan Hoops 2002

Definition at line 75 of file CCopasiParameter.h.

const char * CCopasiParameter::XMLType

static

Initial value:

=
{
  "float",
  "unsignedFloat",
  "integer",
  "unsignedInteger",
  "bool",
  "group",
  "string",
  "cn",
  "key",
  "file",
  "expression",
  NULL
}

XML type names of parameters known to COPASI.

Definition at line 80 of file CCopasiParameter.h.

Referenced by CCopasiXMLInterface::saveParameter(), CCopasiXMLParser::ParameterElement::start(), and CCopasiXMLParser::ParameterTextElement::start().

---

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

• CCopasiParameter.h
• CCopasiParameter.cpp