#include <CSensProblem.h>

Inheritance diagram for CSensProblem:

Collaboration diagram for CSensProblem:

Public Types
enum	SubTaskType { Evaluation, SteadyState, TimeSeries, ParameterEstimation, Optimization, CrossSection }

Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator	index_iterator

typedef CCopasiContainer::objectMap::iterator	name_iterator

typedef std::vector < CCopasiParameter * >	parameterGroup

Public Types inherited from CCopasiParameter
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
void	addVariables (const CSensItem &item)

void	changeTargetFunctions (const CSensItem item)

bool	changeVariables (size_t index, const CSensItem &item)

bool	collapsRequested () const

	CSensProblem (const CCopasiContainer *pParent=NULL)

	CSensProblem (const CSensProblem &src, const CCopasiContainer *pParent=NULL)

CCopasiArray &	getCollapsedResult ()

const CCopasiArray &	getCollapsedResult () const

CArrayAnnotation *	getCollapsedResultAnnotated ()

const CArrayAnnotation *	getCollapsedResultAnnotated () const

size_t	getNumberOfVariables () const

CCopasiArray &	getResult ()

const CCopasiArray &	getResult () const

CArrayAnnotation *	getResultAnnotated ()

const CArrayAnnotation *	getResultAnnotated () const

CCopasiArray &	getScaledResult ()

const CCopasiArray &	getScaledResult () const

CArrayAnnotation *	getScaledResultAnnotated ()

const CArrayAnnotation *	getScaledResultAnnotated () const

CSensProblem::SubTaskType	getSubTaskType () const

CSensItem	getTargetFunctions () const

CSensItem	getVariables (size_t index) const

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

virtual void	printResult (std::ostream *ostream) const

bool	removeVariables (size_t index)

bool	removeVariables ()

void	setSubTaskType (const CSensProblem::SubTaskType &type)

virtual	~CSensProblem ()

Public Member Functions inherited from CCopasiProblem
	CCopasiProblem (const CCopasiProblem &src, const CCopasiContainer *pParent=NULL)

CModel *	getModel () const

const CCopasiTask::Type &	getType () const

virtual bool	initialize ()

virtual bool	restore (const bool &updateModel)

virtual bool	setCallBack (CProcessReport *pCallBack)

virtual bool	setModel (CModel *pModel)

virtual	~CCopasiProblem ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type)

template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value)

void	addParameter (CCopasiParameter *pParameter)

CCopasiParameterGroup *	assertGroup (const std::string &name)

template<class CType >
CCopasiParameter *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)

index_iterator	beginIndex () const

name_iterator	beginName () const

	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL)

	CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup")

void	clear ()

virtual bool	elevateChildren ()

index_iterator	endIndex () const

name_iterator	endName () const

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

size_t	getIndex (const std::string &name) const

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

std::string	getKey (const size_t &index) const

virtual const std::string &	getName (const size_t &index) const

virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const

CCopasiParameter *	getParameter (const std::string &name)

const CCopasiParameter *	getParameter (const std::string &name) const

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

CCopasiParameter::Type	getType (const std::string &name) const

CCopasiParameter::Type	getType (const size_t &index) const

std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const

const CCopasiParameter::Value &	getValue (const std::string &name) const

const CCopasiParameter::Value &	getValue (const size_t &index) const

CCopasiParameter::Value &	getValue (const std::string &name)

CCopasiParameter::Value &	getValue (const size_t &index)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

bool	removeParameter (const std::string &name)

bool	removeParameter (const size_t &index)

template<class CType >
bool	setValue (const std::string &name, const CType &value)

template<class CType >
bool	setValue (const size_t &index, const CType &value)

size_t	size () const

bool	swap (const size_t &iFrom, const size_t &iTo)

bool	swap (index_iterator &from, index_iterator &to)

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	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)

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 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 Member Functions
static std::vector < CObjectLists::ListType >	getPossibleTargetFunctions (CSensProblem::SubTaskType)

static std::vector < CObjectLists::ListType >	getPossibleVariables (CSensProblem::SubTaskType)

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)

Static Public Attributes
static const std::string	SubTaskName []

static const char *	XMLSubTask []

Static Public Attributes inherited from CCopasiParameter
static const std::string	TypeName []

static const char *	XMLType []

Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Private Member Functions
void	initDebugProblem ()

void	initObjects ()

Static Private Member Functions
static void	copyParameterGroupToSensItem (const CCopasiParameterGroup pg, CSensItem si)

static void	copySensItemToParameterGroup (const CSensItem si, CCopasiParameterGroup pg)

static void	createParametersInGroup (CCopasiParameterGroup *pg)

Private Attributes
CCopasiArray	mCollapsedResult

CArrayAnnotation *	mpCollapsedResultAnnotation

CArrayAnnotation *	mpResultAnnotation

CArrayAnnotation *	mpScaledResultAnnotation

CSensProblem::SubTaskType *	mpSubTaskType

CCopasiParameterGroup *	mpTargetFunctions

CCopasiParameterGroup *	mpVariablesGroup

CCopasiArray	mResult

CCopasiArray	mScaledResult

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

Additional Inherited Members
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 CCopasiProblem
	CCopasiProblem (const CCopasiTask::Type &type, const CCopasiContainer *pParent=NULL)

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

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)

Protected Attributes inherited from CCopasiProblem
CProcessReport *	mpCallBack

CModel *	mpModel

CReport *	mpReport

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

CSensProblem class.

Definition at line 64 of file CSensProblem.h.

Member Enumeration Documentation

enum CSensProblem::SubTaskType

this enumeration

Enumerator
Evaluation
SteadyState
TimeSeries
ParameterEstimation
Optimization
CrossSection

Definition at line 71 of file CSensProblem.h.

   {
     Evaluation,
     SteadyState,
     TimeSeries,
     ParameterEstimation,
     Optimization,
     CrossSection
     //LyapunovExp
   };

Constructor & Destructor Documentation

CSensProblem::CSensProblem ( const CCopasiContainer * pParent = NULL )

Default constructor.

Parameters

const CCopasiContainer * pParent (default: NULL)

Default constructor.

Parameters

CModel * pModel

Definition at line 192 of file CSensProblem.cpp.

References CCopasiParameterGroup::addGroup(), CCopasiParameterGroup::addParameter(), addVariables(), CObjectLists::ALL_PARAMETER_VALUES, C_INT32, changeTargetFunctions(), CONSTRUCTOR_TRACE, createParametersInGroup(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), initObjects(), mpSubTaskType, mpTargetFunctions, mpVariablesGroup, CObjectLists::NON_CONST_METAB_CONCENTRATIONS, CCopasiParameter::Value::pUINT, CSensItem::setListType(), setSubTaskType(), SteadyState, and CCopasiParameter::UINT.

                                                           :
   CCopasiProblem(CCopasiTask::sens, pParent),
   mpSubTaskType(NULL),
   mpTargetFunctions(NULL),
   mpVariablesGroup(NULL),
   mpResultAnnotation(NULL),
   mpScaledResultAnnotation(NULL),
   mpCollapsedResultAnnotation(NULL)
 {
   addParameter("SubtaskType", CCopasiParameter::UINT, (unsigned C_INT32) 0);
   mpSubTaskType = (CSensProblem::SubTaskType*)getValue("SubtaskType").pUINT;
 
   //---------------------------------------------------
   addGroup("TargetFunctions");
   mpTargetFunctions = dynamic_cast<CCopasiParameterGroup*>(getParameter("TargetFunctions"));
   createParametersInGroup(mpTargetFunctions);
 
   //---------------------------------------------------
   addGroup("ListOfVariables");
   mpVariablesGroup = dynamic_cast<CCopasiParameterGroup*>(getParameter("ListOfVariables"));
 
   //create a useful default problem
   setSubTaskType(SteadyState);
 
   CSensItem item;
 
   item.setListType(CObjectLists::NON_CONST_METAB_CONCENTRATIONS);
   changeTargetFunctions(item);
 
   item.setListType(CObjectLists::ALL_PARAMETER_VALUES);
   addVariables(item);
 
   //  initDebugProblem();
   initObjects();
   CONSTRUCTOR_TRACE;
 }

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

Copy constructor.

Parameters

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

Copy constructor.

Parameters

const CSensProblem & src

Definition at line 233 of file CSensProblem.cpp.

References CONSTRUCTOR_TRACE, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), initObjects(), mpSubTaskType, mpTargetFunctions, mpVariablesGroup, and CCopasiParameter::Value::pUINT.

                                                             :
   CCopasiProblem(src, pParent),
   mpSubTaskType(NULL),
   mpTargetFunctions(NULL),
   mpVariablesGroup(NULL),
   mpResultAnnotation(NULL),
   mpScaledResultAnnotation(NULL),
   mpCollapsedResultAnnotation(NULL)
 {
   mpSubTaskType = (CSensProblem::SubTaskType*)getValue("SubtaskType").pUINT;
   mpTargetFunctions = dynamic_cast<CCopasiParameterGroup*>(getParameter("TargetFunctions"));
   mpVariablesGroup = dynamic_cast<CCopasiParameterGroup*>(getParameter("ListOfVariables"));
 
   initObjects();
   CONSTRUCTOR_TRACE;
 }

CSensProblem::~CSensProblem ( )

virtual

Destructor.

Definition at line 269 of file CSensProblem.cpp.

References DESTRUCTOR_TRACE.

270 {DESTRUCTOR_TRACE;}

DESTRUCTOR_TRACE

#define DESTRUCTOR_TRACE

Definition: copasi.h:206

Member Function Documentation

void CSensProblem::addVariables ( const CSensItem & item )

Definition at line 324 of file CSensProblem.cpp.

References CCopasiParameterGroup::addGroup(), copySensItemToParameterGroup(), createParametersInGroup(), getNumberOfVariables(), CCopasiParameterGroup::getParameter(), and mpVariablesGroup.

Referenced by changeVariables(), CSensProblem(), initDebugProblem(), and SensitivitiesWidget::saveTask().

 {
   //create parameter group corresponding to sens item
   CCopasiParameterGroup* tmp;
   mpVariablesGroup->addGroup("Variables");
   tmp = (CCopasiParameterGroup*)(mpVariablesGroup->getParameter(getNumberOfVariables() - 1));
 
   createParametersInGroup(tmp);
 
   copySensItemToParameterGroup(&item, tmp);
 }

void CSensProblem::changeTargetFunctions ( const CSensItem item )

Definition at line 302 of file CSensProblem.cpp.

References copySensItemToParameterGroup(), and mpTargetFunctions.

Referenced by CSensProblem(), and SensitivitiesWidget::saveTask().

 {
   copySensItemToParameterGroup(&item, mpTargetFunctions);
 }

bool CSensProblem::changeVariables	(	size_t	index,
		const CSensItem &	item
	)

Definition at line 351 of file CSensProblem.cpp.

References addVariables(), copySensItemToParameterGroup(), getNumberOfVariables(), CCopasiParameterGroup::getParameter(), and mpVariablesGroup.

 {
   size_t num = getNumberOfVariables();
 
   if (index > num)
     return false;
 
   if (index == num)
     addVariables(item);
   else
     {
       CCopasiParameterGroup * tmp =
         (CCopasiParameterGroup *)(mpVariablesGroup->getParameter(index));
       copySensItemToParameterGroup(&item, tmp);
     }
 
   return true;
 }

bool CSensProblem::collapsRequested ( ) const

Definition at line 430 of file CSensProblem.cpp.

References getTargetFunctions(), and CSensItem::isSingleObject().

Referenced by CSensMethod::do_collapsing(), CSensMethod::initialize(), and CQSensResultWidget::newResult().

 {
   return !getTargetFunctions().isSingleObject();
 }

void CSensProblem::copyParameterGroupToSensItem	(	const CCopasiParameterGroup *	pg,
		CSensItem *	si
	)

staticprivate

Definition at line 166 of file CSensProblem.cpp.

References CCopasiParameterGroup::getValue(), CCopasiParameter::Value::pCN, CCopasiParameter::Value::pUINT, CSensItem::setListType(), and CSensItem::setSingleObjectCN().

Referenced by getTargetFunctions(), and getVariables().

 {
 
   if (!pg) return; if (!si) return;
 
   CCopasiObjectName* pCN = pg->getValue("SingleObject").pCN;
   CObjectLists::ListType* pLT = (CObjectLists::ListType*)pg->getValue("ObjectListType").pUINT;
 
   CCopasiObjectName cn("");
 
   if (pCN) cn = *pCN;
 
   CObjectLists::ListType lt = (CObjectLists::ListType)0;
 
   if (pLT) lt = *pLT;
 
   //  if (cn != "")
   si->setSingleObjectCN(cn);
   //  else
   si->setListType(lt);
 }

void CSensProblem::copySensItemToParameterGroup	(	const CSensItem *	si,
		CCopasiParameterGroup *	pg
	)

staticprivate

Definition at line 152 of file CSensProblem.cpp.

References C_INT32, CSensItem::getListType(), CSensItem::getSingleObjectCN(), CSensItem::isSingleObject(), and CCopasiParameterGroup::setValue().

Referenced by addVariables(), changeTargetFunctions(), and changeVariables().

 {
   CCopasiObjectName cn("");
 
   if (!pg) return; if (!si) return;
 
   if (si->isSingleObject())
     cn = si->getSingleObjectCN();
 
   pg->setValue("SingleObject", cn);
   pg->setValue("ObjectListType", (unsigned C_INT32)si->getListType());
 }

void CSensProblem::createParametersInGroup ( CCopasiParameterGroup * pg )

staticprivate

create the copasi parameters corresponding to the members of a CSensItem

Definition at line 143 of file CSensProblem.cpp.

References CCopasiParameterGroup::addParameter(), C_INT32, CCopasiParameter::CN, and CCopasiParameter::UINT.

Referenced by addVariables(), and CSensProblem().

 {
   if (!pg) return;
 
   pg->addParameter("SingleObject", CCopasiParameter::CN, CCopasiObjectName(""));
   pg->addParameter("ObjectListType", CCopasiParameter::UINT, (unsigned C_INT32) 0);
 }

CCopasiArray & CSensProblem::getCollapsedResult ( )

Definition at line 410 of file CSensProblem.cpp.

References mCollapsedResult.

Referenced by CSensMethod::do_collapsing(), and CSensMethod::initialize().

 {
   return mCollapsedResult;
 }

const CCopasiArray & CSensProblem::getCollapsedResult ( ) const

Definition at line 415 of file CSensProblem.cpp.

References mCollapsedResult.

 {
   return mCollapsedResult;
 }

CArrayAnnotation * CSensProblem::getCollapsedResultAnnotated ( )

Definition at line 420 of file CSensProblem.cpp.

References mpCollapsedResultAnnotation.

Referenced by CSensMethod::initialize(), and CQSensResultWidget::newResult().

 {
   return mpCollapsedResultAnnotation;
 }

const CArrayAnnotation * CSensProblem::getCollapsedResultAnnotated ( ) const

Definition at line 425 of file CSensProblem.cpp.

References mpCollapsedResultAnnotation.

 {
   return mpCollapsedResultAnnotation;
 }

size_t CSensProblem::getNumberOfVariables ( ) const

Definition at line 307 of file CSensProblem.cpp.

References mpVariablesGroup, and CCopasiParameterGroup::size().

Referenced by addVariables(), changeVariables(), CSensMethod::initialize(), SensitivitiesWidget::loadTask(), and operator<<().

 {
   return mpVariablesGroup->size();
 }

std::vector< CObjectLists::ListType > CSensProblem::getPossibleTargetFunctions ( CSensProblem::SubTaskType type )

static

Definition at line 437 of file CSensProblem.cpp.

References CObjectLists::ALL_VARIABLES, CrossSection, Evaluation, CObjectLists::GLOBAL_PARAMETER_RATES, CObjectLists::METAB_CONC_RATES, CObjectLists::METAB_PART_RATES, CObjectLists::NON_CONST_GLOBAL_PARAMETER_VALUES, CObjectLists::NON_CONST_METAB_CONCENTRATIONS, CObjectLists::NON_CONST_METAB_NUMBERS, Optimization, ParameterEstimation, CObjectLists::REACTION_CONC_FLUXES, CObjectLists::REACTION_PART_FLUXES, CObjectLists::REDUCED_JACOBIAN_EV_IM, CObjectLists::REDUCED_JACOBIAN_EV_RE, CObjectLists::SINGLE_OBJECT, SteadyState, and TimeSeries.

Referenced by SensitivitiesWidget::updateComboBoxes().

 {
   std::vector<CObjectLists::ListType> list;
 
   //list.push_back(CObjectLists::EMPTY_LIST);
 
   // Add new functions here, under applicable SubTaskType case.
   // Don't forget to provide for a string value in
   //   getTargetFunctionName()
   switch (type)
     {
       case (CSensProblem::Evaluation):
         list.push_back(CObjectLists::SINGLE_OBJECT);
         list.push_back(CObjectLists::REACTION_CONC_FLUXES);
         list.push_back(CObjectLists::REACTION_PART_FLUXES);
         list.push_back(CObjectLists::METAB_CONC_RATES);
         list.push_back(CObjectLists::METAB_PART_RATES);
         list.push_back(CObjectLists::GLOBAL_PARAMETER_RATES);
         break;
 
       case (CSensProblem::SteadyState):
         list.push_back(CObjectLists::SINGLE_OBJECT);
         list.push_back(CObjectLists::ALL_VARIABLES);
         list.push_back(CObjectLists::NON_CONST_METAB_CONCENTRATIONS);
         list.push_back(CObjectLists::NON_CONST_METAB_NUMBERS);
         list.push_back(CObjectLists::METAB_CONC_RATES);
         list.push_back(CObjectLists::METAB_PART_RATES);
         list.push_back(CObjectLists::NON_CONST_GLOBAL_PARAMETER_VALUES);
         list.push_back(CObjectLists::REACTION_CONC_FLUXES);
         list.push_back(CObjectLists::REACTION_PART_FLUXES);
         list.push_back(CObjectLists::REDUCED_JACOBIAN_EV_RE);
         list.push_back(CObjectLists::REDUCED_JACOBIAN_EV_IM);
         break;
 
       case (CSensProblem::TimeSeries):
         list.push_back(CObjectLists::SINGLE_OBJECT);
         list.push_back(CObjectLists::ALL_VARIABLES);
         list.push_back(CObjectLists::NON_CONST_METAB_CONCENTRATIONS);
         list.push_back(CObjectLists::NON_CONST_METAB_NUMBERS);
         list.push_back(CObjectLists::METAB_CONC_RATES);
         list.push_back(CObjectLists::METAB_PART_RATES);
         list.push_back(CObjectLists::NON_CONST_GLOBAL_PARAMETER_VALUES);
         list.push_back(CObjectLists::REACTION_CONC_FLUXES);
         list.push_back(CObjectLists::REACTION_PART_FLUXES);
         //TODO all model variables
         break;
 
       case (CSensProblem::ParameterEstimation):
       case (CSensProblem::Optimization):
       case (CSensProblem::CrossSection):
         list.push_back(CObjectLists::SINGLE_OBJECT);
         break;
 
         /*case (CSensProblem::LyapunovExp):
                 list.push_back(CObjectLists::SINGLE_OBJECT);
                 list.push_back(CObjectLists::NON_CONST_METAB_NUMBERS);
                 list.push_back(CObjectLists::NON_CONST_METAB_CONCENTRATIONS);
                 list.push_back(CObjectLists::REACTION_CONC_FLUXES);
                 list.push_back(CObjectLists::NON_CONST_METAB_PART_RATES);
           break;*/
     }
 
   return list;
 }

std::vector< CObjectLists::ListType > CSensProblem::getPossibleVariables ( CSensProblem::SubTaskType type )

static

Definition at line 504 of file CSensProblem.cpp.

References CObjectLists::ALL_LOCAL_PARAMETER_VALUES, CObjectLists::ALL_PARAMETER_AND_INITIAL_VALUES, CObjectLists::ALL_PARAMETER_VALUES, CrossSection, Evaluation, CObjectLists::GLOBAL_PARAMETER_VALUES, CObjectLists::METAB_CONCENTRATIONS, CObjectLists::METAB_INITIAL_CONCENTRATIONS, CObjectLists::NON_CONST_GLOBAL_PARAMETER_VALUES, CObjectLists::NON_CONST_METAB_CONCENTRATIONS, CObjectLists::NON_CONST_METAB_NUMBERS, Optimization, ParameterEstimation, CObjectLists::SINGLE_OBJECT, SteadyState, and TimeSeries.

Referenced by SensitivitiesWidget::updateComboBoxes().

 {
   std::vector<CObjectLists::ListType> list;
 
   // the 'unset' type, abusing CObjectLists::ALL_METABS
   list.push_back((CObjectLists::ListType) 0);
 
   // Add new variables here, to applicable SubTaskType case.
   // Don't forget to provide for a string value in
   //   getVariableName()
   switch (type)
     {
       case (Evaluation):
         list.push_back(CObjectLists::SINGLE_OBJECT);
         list.push_back(CObjectLists::NON_CONST_METAB_CONCENTRATIONS);
         list.push_back(CObjectLists::METAB_CONCENTRATIONS);
         list.push_back(CObjectLists::NON_CONST_METAB_NUMBERS);
         list.push_back(CObjectLists::NON_CONST_GLOBAL_PARAMETER_VALUES);
         list.push_back(CObjectLists::GLOBAL_PARAMETER_VALUES);
         list.push_back(CObjectLists::ALL_LOCAL_PARAMETER_VALUES);
         list.push_back(CObjectLists::ALL_PARAMETER_VALUES);
         break;
 
       case (SteadyState):
         list.push_back(CObjectLists::SINGLE_OBJECT);
         list.push_back(CObjectLists::ALL_LOCAL_PARAMETER_VALUES);
         list.push_back(CObjectLists::ALL_PARAMETER_VALUES);
         list.push_back(CObjectLists::METAB_INITIAL_CONCENTRATIONS);
         //TODO all const values, all model parameters
         break;
 
       case (TimeSeries):
         list.push_back(CObjectLists::SINGLE_OBJECT);
         list.push_back(CObjectLists::ALL_LOCAL_PARAMETER_VALUES);
         list.push_back(CObjectLists::ALL_PARAMETER_VALUES);
         list.push_back(CObjectLists::METAB_INITIAL_CONCENTRATIONS);
         list.push_back(CObjectLists::ALL_PARAMETER_AND_INITIAL_VALUES);
         //TODO all const values, all model parameters, all initial values
         break;
 
       case (CSensProblem::ParameterEstimation):
       case (CSensProblem::Optimization):
         list.push_back(CObjectLists::SINGLE_OBJECT);
         list.push_back(CObjectLists::ALL_LOCAL_PARAMETER_VALUES);
         list.push_back(CObjectLists::ALL_PARAMETER_VALUES);
         list.push_back(CObjectLists::METAB_INITIAL_CONCENTRATIONS);
         list.push_back(CObjectLists::ALL_PARAMETER_AND_INITIAL_VALUES);
         break;
 
       case (CSensProblem::CrossSection):
         list.push_back(CObjectLists::SINGLE_OBJECT);
         list.push_back(CObjectLists::ALL_LOCAL_PARAMETER_VALUES);
         list.push_back(CObjectLists::ALL_PARAMETER_VALUES);
         list.push_back(CObjectLists::METAB_INITIAL_CONCENTRATIONS);
         list.push_back(CObjectLists::ALL_PARAMETER_AND_INITIAL_VALUES);
         break;
 
         /*case (LyapunovExp):
                 list.push_back(CObjectLists::SINGLE_OBJECT);
                 list.push_back(CObjectLists::NON_CONST_METAB_CONCENTRATIONS);
                 list.push_back(CObjectLists::GLOBAL_PARAMETER_VALUES);
                 list.push_back(CObjectLists::ALL_LOCAL_PARAMETER_VALUES);
                 list.push_back(CObjectLists::ALL_PARAMETER_VALUES);
                 list.push_back(CObjectLists::ALL_PARAMETER_AND_INITIAL_VALUES);
           break;*/
     }
 
   return list;
 }

CCopasiArray & CSensProblem::getResult ( )

Definition at line 370 of file CSensProblem.cpp.

References mResult.

Referenced by CSensMethod::do_scaling(), CSensMethod::initialize(), CSensMethod::process(), and CSensMethod::scaling_targetfunction().

 {
   return mResult;
 }

const CCopasiArray & CSensProblem::getResult ( ) const

Definition at line 375 of file CSensProblem.cpp.

References mResult.

 {
   return mResult;
 }

CArrayAnnotation * CSensProblem::getResultAnnotated ( )

Definition at line 380 of file CSensProblem.cpp.

References mpResultAnnotation.

Referenced by CQSensResultWidget::enterProtected(), CSensMethod::initialize(), and CQSensResultWidget::newResult().

 {
   return mpResultAnnotation;
 }

const CArrayAnnotation * CSensProblem::getResultAnnotated ( ) const

Definition at line 385 of file CSensProblem.cpp.

References mpResultAnnotation.

 {
   return mpResultAnnotation;
 }

CCopasiArray & CSensProblem::getScaledResult ( )

Definition at line 390 of file CSensProblem.cpp.

References mScaledResult.

Referenced by CSensMethod::do_collapsing(), CSensMethod::do_collapsing_innerloop(), CSensMethod::initialize(), and CSensMethod::scaling_targetfunction().

 {
   return mScaledResult;
 }

const CCopasiArray & CSensProblem::getScaledResult ( ) const

Definition at line 395 of file CSensProblem.cpp.

References mScaledResult.

 {
   return mScaledResult;
 }

CArrayAnnotation * CSensProblem::getScaledResultAnnotated ( )

Definition at line 400 of file CSensProblem.cpp.

References mpScaledResultAnnotation.

Referenced by CSensMethod::initialize(), and CQSensResultWidget::newResult().

 {
   return mpScaledResultAnnotation;
 }

const CArrayAnnotation * CSensProblem::getScaledResultAnnotated ( ) const

Definition at line 405 of file CSensProblem.cpp.

References mpScaledResultAnnotation.

 {
   return mpScaledResultAnnotation;
 }

CSensProblem::SubTaskType CSensProblem::getSubTaskType ( ) const

get the problem's SubTaskType:

Definition at line 282 of file CSensProblem.cpp.

References Evaluation, and mpSubTaskType.

Referenced by CSensMethod::initialize(), SensitivitiesWidget::loadTask(), and operator<<().

 {
   if (mpSubTaskType)
     return *mpSubTaskType;
   else
     return CSensProblem::Evaluation;
 }

CSensItem CSensProblem::getTargetFunctions ( ) const

Definition at line 290 of file CSensProblem.cpp.

References copyParameterGroupToSensItem(), and mpTargetFunctions.

Referenced by collapsRequested(), CSensMethod::initialize(), SensitivitiesWidget::loadTask(), and operator<<().

 {
   CSensItem ret;
   CCopasiParameterGroup* tmp;
 
   tmp = (CCopasiParameterGroup*)(mpTargetFunctions);
 
   copyParameterGroupToSensItem(tmp, &ret);
 
   return ret;
 }

CSensItem CSensProblem::getVariables ( size_t index ) const

Definition at line 312 of file CSensProblem.cpp.

References copyParameterGroupToSensItem(), CCopasiParameterGroup::getParameter(), and mpVariablesGroup.

Referenced by CSensMethod::initialize(), SensitivitiesWidget::loadTask(), and operator<<().

 {
   CSensItem ret;
   CCopasiParameterGroup* tmp;
 
   tmp = (CCopasiParameterGroup*)(mpVariablesGroup->getParameter(index));
 
   copyParameterGroupToSensItem(tmp, &ret);
 
   return ret;
 }

void CSensProblem::initDebugProblem ( )

private

this sets up a problem for debugging purposes

Definition at line 636 of file CSensProblem.cpp.

References addVariables(), CCopasiParameter::getCN(), CObjectLists::NON_CONST_METAB_CONCENTRATIONS, CSensItem::setListType(), and CSensItem::setSingleObjectCN().

 {
   CSensItem item;
 
   item.setSingleObjectCN(this->getCN());
   addVariables(item);
 
   item.setListType(CObjectLists::NON_CONST_METAB_CONCENTRATIONS);
   addVariables(item);
 }

void CSensProblem::initObjects ( )

private

Definition at line 251 of file CSensProblem.cpp.

References mCollapsedResult, mpCollapsedResultAnnotation, mpResultAnnotation, mpScaledResultAnnotation, mResult, mScaledResult, CArrayAnnotation::OBJECTS, CArrayAnnotation::setDescription(), and CArrayAnnotation::setMode().

Referenced by CSensProblem().

 {
   mpResultAnnotation = new CArrayAnnotation("Sensitivities array", this, &mResult, false);
   mpResultAnnotation->setDescription("");
   mpResultAnnotation->setMode(CArrayAnnotation::OBJECTS);
 
   mpScaledResultAnnotation = new CArrayAnnotation("Scaled sensitivities array", this, &mScaledResult, false);
   mpScaledResultAnnotation->setDescription("");
   mpScaledResultAnnotation->setMode(CArrayAnnotation::OBJECTS);
 
   mpCollapsedResultAnnotation = new CArrayAnnotation("Summarized sensitivities array", this, &mCollapsedResult, false);
   mpCollapsedResultAnnotation->setDescription("");
   mpCollapsedResultAnnotation->setMode(CArrayAnnotation::OBJECTS);
 }

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

virtual

This is the output method for any object. It calls the insert operator<<

Parameters

std::ostream * ostream

Reimplemented from CCopasiProblem.

Definition at line 633 of file CSensProblem.cpp.

634 {*ostream << *this;}

void CSensProblem::printResult ( std::ostream * ostream ) const

virtual

This is the output method for any result of a problem. The default implementation provided with CCopasiProblem. Does only print "Not implemented." To overide this default behaviour one needs to reimplement the virtual printResult function.

Parameters

std::ostream * ostream

Reimplemented from CCopasiProblem.

Definition at line 574 of file CSensProblem.cpp.

References mpResultAnnotation, and mpScaledResultAnnotation.

 {
   std::ostream & os = *ostream;
 
   //os << "Sensitivities result." << std::endl;
   if (mpResultAnnotation)
     os << *mpResultAnnotation << std::endl;
 
   if (mpScaledResultAnnotation)
     os << *mpScaledResultAnnotation << std::endl;
 }

bool CSensProblem::removeVariables ( size_t index )

Definition at line 346 of file CSensProblem.cpp.

References mpVariablesGroup, and CCopasiParameterGroup::removeParameter().

Referenced by SensitivitiesWidget::saveTask().

 {
   return mpVariablesGroup->removeParameter(index);
 }

bool CSensProblem::removeVariables ( )

Definition at line 336 of file CSensProblem.cpp.

References mpVariablesGroup, CCopasiParameterGroup::removeParameter(), and CCopasiParameterGroup::size().

 {
   size_t imax = mpVariablesGroup->size();
 
   for (size_t i = 0; i < imax; ++i)
     mpVariablesGroup->removeParameter(0);
 
   return true;
 }

void CSensProblem::setSubTaskType ( const CSensProblem::SubTaskType & type )

set the problem's SubTaskType:

Definition at line 276 of file CSensProblem.cpp.

References mpSubTaskType.

Referenced by CSensProblem(), and SensitivitiesWidget::saveTask().

277 {*mpSubTaskType = type;}

CSensProblem::mpSubTaskType

CSensProblem::SubTaskType * mpSubTaskType

Definition: CSensProblem.h:192

Friends And Related Function Documentation

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

friend

Output stream operator. Prints description of the problem

Parameters

ostream	& os
const	Problem & A

Returns: ostream & os

Definition at line 612 of file CSensProblem.cpp.

 {
   os << "Function(s) to be derived:" << std::endl;
   const CCopasiDataModel* pDataModel = o.getObjectDataModel();
   assert(pDataModel != NULL);
   os << o.getTargetFunctions().print(pDataModel) << std::endl << std::endl;
 
   os << "Calculation to perform: "
      << CSensProblem::SubTaskName[o.getSubTaskType()] << std::endl << std::endl;
 
   size_t i, imax = o.getNumberOfVariables();
 
   for (i = 0; i < imax; ++i)
     {
       os << "Variable(s) for " << i + 1 << ". derivation:" << std::endl;
       os << o.getVariables(i).print(pDataModel) << std::endl << std::endl;
     }
 
   return os;
 }

Member Data Documentation

CCopasiArray CSensProblem::mCollapsedResult

private

This holds the collapsed result

Definition at line 220 of file CSensProblem.h.

Referenced by getCollapsedResult(), and initObjects().

CArrayAnnotation* CSensProblem::mpCollapsedResultAnnotation

private

Definition at line 222 of file CSensProblem.h.

Referenced by getCollapsedResultAnnotated(), and initObjects().

CArrayAnnotation* CSensProblem::mpResultAnnotation

private

Definition at line 208 of file CSensProblem.h.

Referenced by getResultAnnotated(), initObjects(), and printResult().

CArrayAnnotation* CSensProblem::mpScaledResultAnnotation

private

Definition at line 215 of file CSensProblem.h.

Referenced by getScaledResultAnnotated(), initObjects(), and printResult().

CSensProblem::SubTaskType* CSensProblem::mpSubTaskType

private

Definition at line 192 of file CSensProblem.h.

Referenced by CSensProblem(), getSubTaskType(), and setSubTaskType().

CCopasiParameterGroup* CSensProblem::mpTargetFunctions

private

Definition at line 194 of file CSensProblem.h.

Referenced by changeTargetFunctions(), CSensProblem(), and getTargetFunctions().

CCopasiParameterGroup* CSensProblem::mpVariablesGroup

private

This holds the variables items

Definition at line 201 of file CSensProblem.h.

Referenced by addVariables(), changeVariables(), CSensProblem(), getNumberOfVariables(), getVariables(), and removeVariables().

CCopasiArray CSensProblem::mResult

private

This holds the result

Definition at line 206 of file CSensProblem.h.

Referenced by getResult(), and initObjects().

CCopasiArray CSensProblem::mScaledResult

private

This holds the scaled result

Definition at line 213 of file CSensProblem.h.

Referenced by getScaledResult(), and initObjects().

const std::string CSensProblem::SubTaskName

static

Initial value:

=
{
  "Evaluation",
  "Steady State",
  "Time Series",
  "Parameter Estimation",
  "Optimization",
  "Cross Section",
  
  ""
}

Definition at line 82 of file CSensProblem.h.

Referenced by SensitivitiesWidget::initCombos(), and operator<<().

const char * CSensProblem::XMLSubTask

static

Initial value:

=
{
  "Evaluation",
  "SteadyState",
  "TimeSeries",
  "ParameterEstimation",
  "Optimization",
  "CrossSection",
  
  NULL
}

Definition at line 84 of file CSensProblem.h.

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

Public Types

Public Member Functions

Static Public Member Functions

Static Public Attributes

Private Member Functions

Static Private Member Functions

Private Attributes

Friends

Additional Inherited Members

Detailed Description

Member Enumeration Documentation

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation