CExperimentSet Class Reference

#include <CExperimentSet.h>

Inheritance diagram for CExperimentSet:

Collaboration diagram for CExperimentSet:

Public Member Functions
CExperiment *	addExperiment (const CExperiment &experiment)
bool	calculateStatistics ()
	CExperimentSet (const CCopasiContainer *pParent, const std::string &name="Experiment Set")
	CExperimentSet (const CExperimentSet &src, const CCopasiContainer *pParent=NULL)
	CExperimentSet (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL)
bool	compile (const std::vector< CCopasiContainer * > listOfContainer=CCopasiContainer::EmptyList)
virtual bool	elevateChildren ()
void	fixBuild55 ()
size_t	getDataPointCount () const
const CMatrix< C_FLOAT64 > &	getDependentData (const size_t &index) const
const CVector< C_FLOAT64 > &	getDependentErrorMean () const
const CVector< C_FLOAT64 > &	getDependentErrorMeanSD () const
const CVector< C_FLOAT64 > &	getDependentObjectiveValues () const
const CVector< CCopasiObject * > &	getDependentObjects () const
const CVector< C_FLOAT64 > &	getDependentRMS () const
CExperiment *	getExperiment (const size_t &index)
const CExperiment *	getExperiment (const size_t &index) const
CExperiment *	getExperiment (const std::string &name)
const CExperiment *	getExperiment (const std::string &name) const
size_t	getExperimentCount () const
const CCopasiTask::Type &	getExperimentType (const size_t &index) const
std::vector< std::string >	getFileNames () const
const CMatrix< C_FLOAT64 > &	getIndependentData (const size_t &index) const
const size_t &	getValidValueCount () const
bool	hasDataForTaskType (const CCopasiTask::Type &type) const
size_t	keyToIndex (const std::string &key) const
void	removeExperiment (const size_t &index)
void	sort ()
virtual	~CExperimentSet ()
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 ()
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)
virtual void	print (std::ostream *ostream) const
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 ()

Private Member Functions
void	initializeParameter ()

Private Attributes
CVector< size_t >	mDependentDataCount
CVector< C_FLOAT64 >	mDependentErrorMean
CVector< C_FLOAT64 >	mDependentErrorMeanSD
CVector< C_FLOAT64 >	mDependentObjectiveValues
CVector< CCopasiObject * >	mDependentObjects
CVector< C_FLOAT64 >	mDependentRMS
size_t	mNonExperiments
std::vector< CExperiment * > *	mpExperiments
size_t	mValidValueCount

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

Definition at line 26 of file CExperimentSet.h.

Constructor & Destructor Documentation

CExperimentSet::CExperimentSet	(	const CCopasiContainer *	pParent,
		const std::string &	name = "Experiment Set"
	)

Default constructor

Parameters

const	CCopasiContainer * pParent
const	std::string & name (default: Experiment Set)

Definition at line 30 of file CExperimentSet.cpp.

References initializeParameter().

                                                      :
  CCopasiParameterGroup(name, pParent, "CExperimentSet"),
  mpExperiments(NULL),
  mNonExperiments(0),
  mDependentObjects(0),
  mDependentObjectiveValues(0),
  mDependentRMS(0),
  mDependentErrorMean(0),
  mDependentErrorMeanSD(0),
  mDependentDataCount(0),
  mValidValueCount(0)
{initializeParameter();}

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

Copy constructor

Parameters

const	CExperimentSet & src
const	CCopasiContainer * pParent (default: src data model)

Definition at line 44 of file CExperimentSet.cpp.

References initializeParameter().

                                                                :
  CCopasiParameterGroup(src, static_cast< const CCopasiContainer * >((pParent != NULL) ? pParent : src.getObjectDataModel())),
  mpExperiments(NULL),
  mNonExperiments(0),
  mDependentObjects(0),
  mDependentObjectiveValues(0),
  mDependentRMS(0),
  mDependentErrorMean(0),
  mDependentErrorMeanSD(0),
  mDependentDataCount(0),
  mValidValueCount(0)
{initializeParameter();}

CExperimentSet::CExperimentSet	(	const CCopasiParameterGroup &	group,
		const CCopasiContainer *	pParent = NULL
	)

Specific constructor used for reading COPASI files

Parameters

const	CCopasiParameterGroup & group
const	CCopasiContainer * pParent (default: group data model)

Definition at line 58 of file CExperimentSet.cpp.

References initializeParameter().

                                                                :
  CCopasiParameterGroup(group, static_cast< const CCopasiContainer * >((pParent != NULL) ? pParent : group.getObjectDataModel())),
  mpExperiments(NULL),
  mNonExperiments(0),
  mDependentObjects(0),
  mDependentObjectiveValues(0),
  mDependentRMS(0),
  mDependentErrorMean(0),
  mDependentErrorMeanSD(0),
  mDependentDataCount(0),
  mValidValueCount(0)
{initializeParameter();}

CExperimentSet::~CExperimentSet ( )

virtual

Destructor

Definition at line 72 of file CExperimentSet.cpp.

{}

Member Function Documentation

CExperiment * CExperimentSet::addExperiment

(

const CExperiment &

experiment

)

Add an experiment

Returns

CExperiment * experiment

Definition at line 327 of file CExperimentSet.cpp.

References CCopasiParameterGroup::addParameter(), CCopasiObject::getObjectName(), CCopasiParameterGroup::getParameter(), CCopasiObject::setObjectName(), sort(), and StringPrint().

Referenced by CQFittingWidget::saveTask(), CQExperimentData::slotExperimentAdd(), and CQExperimentData::slotOK().

{
  // We need to make sure that the experiment name is unique.
  std::string name = experiment.getObjectName();

  int i = 0;

  while (getParameter(name))
    {
      i++;
      name = StringPrint("%s_%d", experiment.getObjectName().c_str(), i);
    }

  CExperiment * pExperiment = new CExperiment(experiment);
  pExperiment->setObjectName(name);
  addParameter(pExperiment);

  sort();

  return pExperiment;
}

bool CExperimentSet::calculateStatistics

(

)

Calculate statistics across all experiments.

Returns

bool success

Definition at line 177 of file CExperimentSet.cpp.

References COutputInterface::AFTER, CVectorCore< CType >::array(), C_FLOAT64, CCopasiObject::getObjectAncestor(), max, mDependentDataCount, mDependentErrorMean, mDependentErrorMeanSD, mDependentObjectiveValues, mDependentObjects, mDependentRMS, mNonExperiments, mpExperiments, mValidValueCount, CCopasiTask::output(), CVector< CType >::resize(), CVectorCore< CType >::size(), and CCopasiTask::timeCourse.

Referenced by CFitProblem::calculateStatistics().

{
  mDependentObjectiveValues.resize(mDependentObjects.size());
  mDependentObjectiveValues = 0.0;

  mDependentRMS.resize(mDependentObjects.size());
  mDependentRMS = 0.0;

  mDependentErrorMean.resize(mDependentObjects.size());
  mDependentErrorMean = 0.0;

  mDependentErrorMeanSD.resize(mDependentObjects.size());
  mDependentErrorMeanSD = 0.0;

  mDependentDataCount.resize(mDependentObjects.size());
  mDependentDataCount = 0;
  mValidValueCount = 0;

  // calculate the per experiment and per dependent value statistics.
  std::vector< CExperiment * >::iterator it = mpExperiments->begin() + mNonExperiments;
  std::vector< CExperiment * >::iterator end = mpExperiments->end();

  size_t i, Count;
  C_FLOAT64 Tmp;

  for (; it != end; ++it)
    {
      (*it)->calculateStatistics();

      CCopasiObject *const* ppObject = mDependentObjects.array();
      CCopasiObject *const* ppEnd = ppObject + mDependentObjects.size();

      for (i = 0; ppObject != ppEnd; ++ppObject, ++i)
        {
          Count = (*it)->getColumnValidValueCount(*ppObject);

          if (Count)
            {
              mDependentObjectiveValues[i] += (*it)->getObjectiveValue(*ppObject);

              Tmp = (*it)->getRMS(*ppObject);
              mDependentRMS[i] += Tmp * Tmp * Count;

              mDependentErrorMean[i] += (*it)->getErrorSum(*ppObject);

              mDependentDataCount[i] += Count;
              mValidValueCount += Count;
            }
        }
    }

  size_t imax = mDependentObjects.size();

  for (i = 0; i != imax; i++)
    {
      Count = mDependentDataCount[i];

      if (Count)
        {
          mDependentRMS[i] = sqrt(mDependentRMS[i] / Count);
          mDependentErrorMean[i] /= Count;
        }
      else
        {
          mDependentRMS[i] = std::numeric_limits<C_FLOAT64>::quiet_NaN();
          mDependentErrorMean[i] = std::numeric_limits<C_FLOAT64>::quiet_NaN();
        }
    }

  it = mpExperiments->begin() + mNonExperiments;

  // We need to loop again to calculate the std. deviation.
  for (; it != end; ++it)  //over experiments
    {
      CCopasiObject *const* ppObject = mDependentObjects.array();
      CCopasiObject *const* ppEnd = ppObject + mDependentObjects.size();

      for (i = 0; ppObject != ppEnd; ++ppObject, ++i)
        {
          Count = (*it)->getColumnValidValueCount(*ppObject);

          if (Count)
            mDependentErrorMeanSD[i] +=
              (*it)->getErrorMeanSD(*ppObject, mDependentErrorMean[i]);
        }
    }

  for (i = 0; i != imax; i++)
    {
      Count = mDependentDataCount[i];

      if (Count)
        mDependentErrorMeanSD[i] = sqrt(mDependentErrorMeanSD[i] / Count);
      else
        mDependentErrorMeanSD[i] = std::numeric_limits<C_FLOAT64>::quiet_NaN();
    }

  // This is the time to call the output handler to plot the fitted points.
  for (it = mpExperiments->begin() + mNonExperiments, imax = 0; it != end; ++it)
    imax = std::max(imax, (*it)->getDependentData().numRows());

  CCopasiTask * pParentTask = dynamic_cast< CCopasiTask *>(getObjectAncestor("Task"));
  assert(pParentTask != NULL);

  for (i = 0; i < imax; i++)
    {
      for (it = mpExperiments->begin() + mNonExperiments; it != end; ++it)
        (*it)->updateFittedPointValues(i, (*it)->getExperimentType() != CCopasiTask::timeCourse); //false means without simulated data

      pParentTask->output(COutputInterface::AFTER);
    }

  //now the extended time series
  for (it = mpExperiments->begin() + mNonExperiments, imax = 0; it != end; ++it)
    imax = std::max(imax, (*it)->extendedTimeSeriesSize());

  for (i = 0; i < imax; i++)
    {
      for (it = mpExperiments->begin() + mNonExperiments; it != end; ++it)
        {
          if ((*it)->getExperimentType() == CCopasiTask::timeCourse)
            {
              (*it)->updateFittedPointValuesFromExtendedTimeSeries(i);
            }
        }

      pParentTask->output(COutputInterface::AFTER);
    }

  return true;
}

bool CExperimentSet::compile

(

const std::vector< CCopasiContainer * >

listOfContainer = CCopasiContainer::EmptyList

)

Compile the experiment set. This function must be called before any evaluations can be performed.

Parameters

const

std::vector< CCopasiContainer * > listOfContainer

Returns

bool success

Definition at line 96 of file CExperimentSet.cpp.

References CVectorCore< CType >::array(), CCopasiMessage::ERROR, CLocaleString::fromUtf8(), MCFitting, mDependentDataCount, mDependentErrorMean, mDependentErrorMeanSD, mDependentObjectiveValues, mDependentObjects, mDependentRMS, mNonExperiments, mpExperiments, CVector< CType >::resize(), CVectorCore< CType >::size(), and sort().

Referenced by CFitProblem::initialize().

{
  bool success = true;

  // First we need to sort the experiments so that we can make use of continued
  // file reading.
  sort();

  std::set< CCopasiObject * > DependentObjects;

  std::ifstream in;
  std::string CurrentFileName("");
  size_t CurrentLineNumber = 1;

  std::vector< CExperiment * >::iterator it = mpExperiments->begin() + mNonExperiments;
  std::vector< CExperiment * >::iterator end = mpExperiments->end();

  for (; it != end; ++it)
    {
      if (CurrentFileName != (*it)->getFileName())
        {
          CurrentFileName = (*it)->getFileName();
          CurrentLineNumber = 1;

          if (in.is_open())
            {
              in.close();
              in.clear();
            }

          in.open(CLocaleString::fromUtf8(CurrentFileName).c_str(), std::ios::binary);

          if (in.fail())
            {
              CCopasiMessage(CCopasiMessage::ERROR, MCFitting + 8, CurrentFileName.c_str());
              return false; // File can not be opened.
            }
        }

      if (!(*it)->read(in, CurrentLineNumber)) return false;

      if (!(*it)->compile(listOfContainer)) return false;

      const std::map< CCopasiObject *, size_t > & ExpDependentObjects
        = (*it)->getDependentObjects();
      std::map< CCopasiObject *, size_t >::const_iterator itObject
        = ExpDependentObjects.begin();
      std::map< CCopasiObject *, size_t >::const_iterator endObject
        = ExpDependentObjects.end();

      for (; itObject != endObject; ++itObject)
        DependentObjects.insert(itObject->first);
    }

  mDependentObjects.resize(DependentObjects.size());
  CCopasiObject ** ppInsert = mDependentObjects.array();
  std::set< CCopasiObject * >::const_iterator itObject = DependentObjects.begin();
  std::set< CCopasiObject * >::const_iterator endObject = DependentObjects.end();

  for (; itObject != endObject; ++itObject, ++ppInsert)
    *ppInsert = *itObject;

  // Allocation and initialization of statistical information
  mDependentObjectiveValues.resize(mDependentObjects.size());
  mDependentObjectiveValues = std::numeric_limits<C_FLOAT64>::quiet_NaN();

  mDependentRMS.resize(mDependentObjects.size());
  mDependentRMS = std::numeric_limits<C_FLOAT64>::quiet_NaN();

  mDependentErrorMean.resize(mDependentObjects.size());
  mDependentErrorMean = std::numeric_limits<C_FLOAT64>::quiet_NaN();

  mDependentErrorMeanSD.resize(mDependentObjects.size());
  mDependentErrorMeanSD = std::numeric_limits<C_FLOAT64>::quiet_NaN();

  mDependentDataCount.resize(mDependentObjects.size());
  mDependentDataCount = std::numeric_limits<size_t>::quiet_NaN();

  return success;
}

bool CExperimentSet::elevateChildren ( )

virtual

This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.

Returns

bool success

Reimplemented from CCopasiParameterGroup.

Definition at line 77 of file CExperimentSet.cpp.

References mpExperiments, CCopasiParameter::mValue, CCopasiParameter::Value::pGROUP, CCopasiParameter::Value::pVOID, and sort().

Referenced by initializeParameter(), and CCrossValidationSet::initializeParameter().

{
  index_iterator it = mValue.pGROUP->begin();
  index_iterator end = mValue.pGROUP->end();

  for (; it != end; ++it)
    {
      if (dynamic_cast< CCopasiParameterGroup * >(*it) == NULL) continue;

      if (!elevate<CExperiment, CCopasiParameterGroup>(*it)) return false;
    }

  mpExperiments = static_cast<std::vector<CExperiment * > * >(mValue.pVOID);

  sort();

  return true;
}

void CExperimentSet::fixBuild55

(

)

Fix files written with Version 4.10.55, which wrote the square root of user defined weights for the parameter fitting task

Definition at line 466 of file CExperimentSet.cpp.

References mNonExperiments, and mpExperiments.

Referenced by CFitProblem::fixBuild55().

{
  std::vector< CExperiment * >::iterator it = mpExperiments->begin() + mNonExperiments;
  std::vector< CExperiment * >::iterator end = mpExperiments->end();

  for (; it != end; ++it)
    {
      (*it)->fixBuild55();
    }

  return;
}

size_t CExperimentSet::getDataPointCount

(

)

const

Retrieve the number of data points of all experiments combined.

Returns

size_t dataPointCount

Definition at line 449 of file CExperimentSet.cpp.

References mNonExperiments, and mpExperiments.

Referenced by CFitProblem::calculateCrossValidation(), CFitProblem::initialize(), and CFitProblem::setResidualsRequired().

{
  size_t Count = 0;
  std::vector< CExperiment * >::iterator it = mpExperiments->begin() + mNonExperiments;
  std::vector< CExperiment * >::iterator end = mpExperiments->end();

  for (; it != end; ++it)
    Count += (*it)->getDependentData().numRows() * (*it)->getDependentData().numCols();

  return Count;
}

const CMatrix< C_FLOAT64 > & CExperimentSet::getDependentData

(

const size_t &

index

)

const

Retrieve the dependent data of the indexed experiment.

Parameters

const

size_t & index,

Returns

const CMatrix< C_FLOAT64 > & dependentData

Definition at line 386 of file CExperimentSet.cpp.

References CExperiment::getDependentData(), and getExperiment().

{return getExperiment(index)->getDependentData();}

const CVector< C_FLOAT64 > & CExperimentSet::getDependentErrorMean

(

)

const

Retrieve all dependent data error mean values.

Returns

const CVector< C_FLOAT64 > & dependentErrorMean

Definition at line 318 of file CExperimentSet.cpp.

References mDependentErrorMean.

Referenced by CQFittingResult::enterProtected().

{return mDependentErrorMean;}

const CVector< C_FLOAT64 > & CExperimentSet::getDependentErrorMeanSD

(

)

const

Retrieve all dependent data error mean std. deviations.

Returns

const CVector< C_FLOAT64 > & dependentErrorMeanSD

Definition at line 321 of file CExperimentSet.cpp.

References mDependentErrorMeanSD.

Referenced by CQFittingResult::enterProtected().

{return mDependentErrorMeanSD;}

const CVector< C_FLOAT64 > & CExperimentSet::getDependentObjectiveValues

(

)

const

Retrieve all dependent data objective values.

Returns

const CVector< C_FLOAT64 > & dependentObjectiveValues

Definition at line 312 of file CExperimentSet.cpp.

References mDependentObjectiveValues.

Referenced by CQFittingResult::enterProtected().

{return mDependentObjectiveValues;}

const CVector< CCopasiObject * > & CExperimentSet::getDependentObjects

(

)

const

Retrieve the list of dependent data objects

Returns

const std::vector< CCopasiObject * > & dependentObjects

Definition at line 309 of file CExperimentSet.cpp.

References mDependentObjects.

Referenced by CQFittingResult::enterProtected().

{return mDependentObjects;}

const CVector< C_FLOAT64 > & CExperimentSet::getDependentRMS

(

)

const

Retrieve all dependent data objective values.

Returns

const CVector< C_FLOAT64 > & dependentRMS

Definition at line 315 of file CExperimentSet.cpp.

References mDependentRMS.

Referenced by CQFittingResult::enterProtected().

{return mDependentRMS;}

CExperiment * CExperimentSet::getExperiment

(

const size_t &

index

)

Retrieve the indexed experiment

Parameters

const

size_t & index,

Returns

CExperiment * experiment

Definition at line 352 of file CExperimentSet.cpp.

References mNonExperiments, and mpExperiments.

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), COutputAssistant::createDefaultOutput(), CFitProblem::elevateChildren(), CQFittingResult::enterProtected(), getDependentData(), getExperimentType(), getIndependentData(), CFitProblem::initialize(), CQExperimentData::isLikePreviousExperiment(), keyToIndex(), CQExperimentSelection::load(), CQExperimentData::load(), CQExperimentData::loadExperiment(), CQFittingWidget::loadTask(), CFitProblem::printResult(), CQExperimentData::saveExperiment(), CQFittingWidget::saveTask(), CQExperimentData::slotCheckNormalizeWeightsPerExperiment(), CQExperimentData::slotCheckTo(), CQExperimentData::slotExperimentDelete(), CQExperimentData::slotFileDelete(), CQExperimentData::slotOK(), CQExperimentData::slotWeightMethod(), and CExperimentFileInfo::sync().

{return (*mpExperiments)[index + mNonExperiments];}

const CExperiment * CExperimentSet::getExperiment

(

const size_t &

index

)

const

Retrieve the indexed experiment

Parameters

const

size_t & index,

Returns

const CExperiment * experiment

Definition at line 355 of file CExperimentSet.cpp.

References mNonExperiments, and mpExperiments.

{return (*mpExperiments)[index + mNonExperiments];}

CExperiment * CExperimentSet::getExperiment

(

const std::string &

name

)

Retrieve the indexed experiment

Parameters

const

std::string & name,

Returns

CExperiment * experiment

Definition at line 358 of file CExperimentSet.cpp.

References CCopasiParameterGroup::getGroup().

{return static_cast<CExperiment *>(getGroup(name));}

const CExperiment * CExperimentSet::getExperiment

(

const std::string &

name

)

const

Retrieve the indexed experiment

Parameters

const

std::string & name,

Returns

const CExperiment * experiment

Definition at line 361 of file CExperimentSet.cpp.

References CCopasiParameterGroup::getGroup().

{return static_cast<const CExperiment *>(getGroup(name));}

size_t CExperimentSet::getExperimentCount

(

)

const

Retrieve the number of the experiments in the set

Returns

size_t experimentCount

Definition at line 324 of file CExperimentSet.cpp.

References mNonExperiments, and CCopasiParameterGroup::size().

Referenced by CFitProblem::calculate(), CFitProblem::calculateCrossValidation(), COutputAssistant::createDefaultOutput(), CQFittingResult::enterProtected(), CFitProblem::initialize(), CQFittingResultTab1::load(), CQExperimentSelection::load(), CQExperimentData::load(), CQFittingWidget::loadTask(), CFitProblem::printResult(), CQFittingWidget::saveTask(), CQFittingItemWidget::setCrossValidationSet(), CFitProblem::setSolution(), CQExperimentData::slotFileDelete(), CQExperimentData::slotOK(), and CExperimentFileInfo::sync().

{return size() - mNonExperiments;}

const CCopasiTask::Type & CExperimentSet::getExperimentType

(

const size_t &

index

)

const

Retrieve the indexed experiment type

Parameters

const

size_t & index,

Returns

const CCopasiTasK::Type & experimentType

Definition at line 380 of file CExperimentSet.cpp.

References getExperiment(), and CExperiment::getExperimentType().

{return getExperiment(index)->getExperimentType();}

std::vector< std::string > CExperimentSet::getFileNames

(

)

const

Retrieve the list of file names

Returns

std::vector< std::string > fileNames

Definition at line 431 of file CExperimentSet.cpp.

References mNonExperiments, and mpExperiments.

Referenced by CQExperimentData::load().

{
  std::vector< std::string > List;
  std::string currentFile = "";

  std::vector< CExperiment * >::iterator it = mpExperiments->begin() + mNonExperiments;
  std::vector< CExperiment * >::iterator end = mpExperiments->end();

  for (; it != end; ++it)
    if (currentFile != (*it)->getFileName())
      {
        currentFile = (*it)->getFileName();
        List.push_back(currentFile);
      }

  return List;
}

const CMatrix< C_FLOAT64 > & CExperimentSet::getIndependentData

(

const size_t &

index

)

const

Retrieve the independent data of the indexed experiment.

Parameters

const

size_t & index,

Returns

const CMatrix< C_FLOAT64 > & independentData

Definition at line 383 of file CExperimentSet.cpp.

References getExperiment(), and CExperiment::getIndependentData().

{return getExperiment(index)->getIndependentData();}

const size_t & CExperimentSet::getValidValueCount

(

)

const

Retrieve the count of valid data points of all experiments combined.

Returns

size_t count

Definition at line 461 of file CExperimentSet.cpp.

References mValidValueCount.

Referenced by CFitProblem::calculateStatistics().

{
  return mValidValueCount;
}

bool CExperimentSet::hasDataForTaskType

(

const CCopasiTask::Type &

type

)

const

Check whether the set contains data for the the given task type

Parameters

const

CCopasiTask::Type & type

Returns

bool hasDataForTaskType

Definition at line 364 of file CExperimentSet.cpp.

References mNonExperiments, and mpExperiments.

Referenced by CFitProblem::initialize().

{
  std::vector< CExperiment * >::const_iterator it = mpExperiments->begin() + mNonExperiments;
  std::vector< CExperiment * >::const_iterator end = mpExperiments->end();

  for (; it != end; ++it)
    {
      if ((*it)->getExperimentType() == type)
        {
          return true;
        }
    }

  return false;
}

void CExperimentSet::initializeParameter ( )

private

Allocates all group parameters and assures that they are properly initialized.

Definition at line 74 of file CExperimentSet.cpp.

References elevateChildren().

Referenced by CExperimentSet().

{elevateChildren();}

size_t CExperimentSet::keyToIndex

(

const std::string &

key

)

const

Convert an experiment key to an index

Parameters

const

std::string & key

Returns

size_t index

Definition at line 389 of file CExperimentSet.cpp.

References C_INVALID_INDEX, CKeyFactory::get(), getExperiment(), CCopasiRootContainer::getKeyFactory(), and CCopasiParameterGroup::size().

Referenced by CFitProblem::initialize(), CQExperimentData::isLikePreviousExperiment(), CQExperimentData::loadExperiment(), CQExperimentData::saveExperiment(), CQExperimentData::slotCheckNormalizeWeightsPerExperiment(), CQExperimentData::slotCheckTo(), CQExperimentData::slotExperimentDelete(), and CQExperimentData::slotWeightMethod().

{
  const CExperiment * pExp = dynamic_cast<const CExperiment *>(CCopasiRootContainer::getKeyFactory()->get(key));

  if (!pExp) return C_INVALID_INDEX;

  size_t i, imax = size();

  for (i = 0; i < imax; i++)
    if (pExp == getExperiment(i)) return i;

  return C_INVALID_INDEX;
}

void CExperimentSet::removeExperiment

(

const size_t &

index

)

Remove an experiment from the set

Parameters

const

size_t & index

Definition at line 349 of file CExperimentSet.cpp.

References mNonExperiments, and CCopasiParameterGroup::removeParameter().

Referenced by CQFittingWidget::saveTask(), CQExperimentData::slotExperimentDelete(), CQExperimentData::slotFileDelete(), and CQExperimentData::slotOK().

{removeParameter(index + mNonExperiments);}

void CExperimentSet::sort

(

)

Sort the experiments in the set

Definition at line 403 of file CExperimentSet.cpp.

References CCopasiParameterGroup::beginIndex(), CExperiment::compare(), CCopasiParameterGroup::endIndex(), mNonExperiments, mpExperiments, and CCopasiParameterGroup::swap().

Referenced by addExperiment(), compile(), elevateChildren(), and CExperimentFileInfo::sync().

{
  // First we make sure that all experiments are at the end of the group
  index_iterator it = beginIndex();
  index_iterator end = endIndex();

  index_iterator swapTarget = beginIndex();
  mNonExperiments = 0;

  for (; it != end; ++it)
    if (dynamic_cast< CExperiment * >(*it) == NULL)
      {
        if (it != swapTarget)
          swap(it, swapTarget);

        swapTarget++;
        mNonExperiments++;
      }

  // Now sort the experiments
  std::vector< CExperiment * >::iterator startSort = mpExperiments->begin() + mNonExperiments;
  std::vector< CExperiment * >::iterator endSort = mpExperiments->end();

  std::sort(startSort, endSort, &CExperiment::compare);

  return;
}

Member Data Documentation

CVector< size_t > CExperimentSet::mDependentDataCount

private

A list of the number of data points for each dependent object;

Definition at line 268 of file CExperimentSet.h.

Referenced by calculateStatistics(), and compile().

CVector< C_FLOAT64 > CExperimentSet::mDependentErrorMean

private

A list of all dependent data error mean values;

Definition at line 258 of file CExperimentSet.h.

Referenced by calculateStatistics(), compile(), and getDependentErrorMean().

CVector< C_FLOAT64 > CExperimentSet::mDependentErrorMeanSD

private

A list of all dependent data error mean std. deviations;

Definition at line 263 of file CExperimentSet.h.

Referenced by calculateStatistics(), compile(), and getDependentErrorMeanSD().

CVector< C_FLOAT64 > CExperimentSet::mDependentObjectiveValues

private

A list of all dependent data objective values;

Definition at line 248 of file CExperimentSet.h.

Referenced by calculateStatistics(), compile(), and getDependentObjectiveValues().

CVector< CCopasiObject * > CExperimentSet::mDependentObjects

private

A set of all dependent data objects;

Definition at line 243 of file CExperimentSet.h.

Referenced by calculateStatistics(), compile(), and getDependentObjects().

CVector< C_FLOAT64 > CExperimentSet::mDependentRMS

private

A list of all dependent data objective values;

Definition at line 253 of file CExperimentSet.h.

Referenced by calculateStatistics(), compile(), and getDependentRMS().

size_t CExperimentSet::mNonExperiments

private

The number of parameters which are not of type CExperiment

Definition at line 238 of file CExperimentSet.h.

Referenced by calculateStatistics(), compile(), fixBuild55(), getDataPointCount(), getExperiment(), getExperimentCount(), getFileNames(), hasDataForTaskType(), removeExperiment(), and sort().

std::vector< CExperiment * >* CExperimentSet::mpExperiments

private

This is realized a CCopasiParameter type GROUP

Definition at line 233 of file CExperimentSet.h.

Referenced by calculateStatistics(), compile(), elevateChildren(), fixBuild55(), getDataPointCount(), getExperiment(), getFileNames(), hasDataForTaskType(), and sort().

size_t CExperimentSet::mValidValueCount

private

The total count of valid data values.

Definition at line 273 of file CExperimentSet.h.

Referenced by calculateStatistics(), and getValidValueCount().

---

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

• CExperimentSet.h
• CExperimentSet.cpp