CStateTemplate Class Reference

#include <CState.h>

Collaboration diagram for CStateTemplate:

Public Member Functions
void	add (CModelEntity *entity)
CModelEntity **	beginDependent ()
CModelEntity *const *	beginDependent () const
CModelEntity **	beginFixed ()
CModelEntity *const *	beginFixed () const
CModelEntity **	beginIndependent ()
CModelEntity *const *	beginIndependent () const
	CStateTemplate (CModel &model, CState &initialState, CState &currentState)
CModelEntity **	endDependent ()
CModelEntity *const *	endDependent () const
CModelEntity **	endFixed ()
CModelEntity *const *	endFixed () const
CModelEntity **	endIndependent ()
CModelEntity *const *	endIndependent () const
CModelEntity **	getEntities ()
CModelEntity *const *	getEntities () const
size_t	getIndex (const CModelEntity *entity) const
size_t	getNumDependent () const
size_t	getNumFixed () const
size_t	getNumIndependent () const
size_t	getNumVariable () const
const CVector< size_t > &	getUserOrder () const
void	remove (CModelEntity *entity)
void	reorder (const CVector< CModelEntity * > &newOrder)
void	setUserOrder (const CVector< CModelEntity * > &userOrder)
const size_t &	size () const
	~CStateTemplate ()

Protected Member Functions
void	resize ()

Private Member Functions
	CStateTemplate ()

Private Attributes
CState &	mCurrentState
std::map< CModelEntity *, size_t >	mIndexMap
CState &	mInitialState
size_t	mInsert
CModel &	mModel
CModelEntity **	mpBeginDependent
CModelEntity **	mpBeginFixed
CModelEntity **	mpBeginIndependent
C_FLOAT64 *	mpCurrentValues
CModelEntity **	mpEnd
CModelEntity **	mpEntities
C_FLOAT64 *	mpInitialValues
size_t	mSize
CVector< size_t >	mUserOrder

Detailed Description

Definition at line 46 of file CState.h.

Constructor & Destructor Documentation

CStateTemplate::CStateTemplate ( )

private

Default Constructor (inaccessible)

CStateTemplate::CStateTemplate	(	CModel &	model,
		CState &	initialState,
		CState &	currentState
	)

Specific constructor

Parameters

CModel	& model
CState	& initialState
CState	& currentState

Definition at line 41 of file CState.cpp.

                                                                                          :
    mModel(model),
    mInitialState(initialState),
    mCurrentState(currentState),
    mpEntities(NULL),
    mSize(0),
    mpBeginIndependent(NULL),
    mpBeginDependent(NULL),
    mpBeginFixed(NULL),
    mpEnd(NULL),
    mInsert(0),
    mIndexMap(),
    mUserOrder(0),
    mpInitialValues(NULL),
    mpCurrentValues(NULL)
{}

CStateTemplate::~CStateTemplate

(

)

Destructor

Definition at line 58 of file CState.cpp.

References mpEntities, and pdeletev.

{
  pdeletev(mpEntities);
}

Member Function Documentation

void CStateTemplate::add

(

CModelEntity *

entity

)

Add an entity to the template.

Parameters

CModelEntity

* entity

Definition at line 63 of file CState.cpp.

References mIndexMap, mInsert, mModel, mpCurrentValues, mpEntities, mpInitialValues, mSize, resize(), CModel::setCompileFlag(), CModelEntity::setInitialValuePtr(), and CModelEntity::setValuePtr().

Referenced by CModelEntity::initObjects(), CModel::initObjects(), and CModelEntity::setObjectParent().

{
  if (mIndexMap.count(entity))
    return;

  if (mInsert == mSize) resize();

  mpEntities[mInsert] = entity;

  entity->setInitialValuePtr(mpInitialValues + mInsert);
  entity->setValuePtr(mpCurrentValues + mInsert);

  mIndexMap[entity] = mInsert++;

  mModel.setCompileFlag(true);
}

CModelEntity ** CStateTemplate::beginDependent

(

)

Retrieve the array of pointers to all dependent entities, which are only dependent species for a reduced model.

Returns

CModelEntities ** dependentEntities

Definition at line 210 of file CState.cpp.

References mpBeginDependent.

Referenced by CModel::buildSimulatedSequence(), CMathContainer::initializeObjects(), and CQUpdatesWidget::loadObjectsTable().

{return mpBeginDependent;}

CModelEntity *const * CStateTemplate::beginDependent

(

)

const

Retrieve the array of pointers to all dependent entities, which are only dependent species for a reduced model.

Returns

CModelEntities const dependentEntities

Definition at line 217 of file CState.cpp.

References mpBeginDependent.

{return mpBeginDependent;}

CModelEntity ** CStateTemplate::beginFixed

(

)

Retrieve the array of pointers to all fixed entities.

Returns

CModelEntities ** fixedEntities

Definition at line 212 of file CState.cpp.

References mpBeginFixed.

Referenced by CMathContainer::initializeObjects(), and CQUpdatesWidget::loadObjectsTable().

{return mpBeginFixed;}

CModelEntity *const * CStateTemplate::beginFixed

(

)

const

Retrieve the array of pointers to all fixed entities.

Returns

CModelEntities const fixedEntities

Definition at line 219 of file CState.cpp.

References mpBeginFixed.

{return mpBeginFixed;}

CModelEntity ** CStateTemplate::beginIndependent

(

)

Retrieve the array of pointers to all independent entities.

Returns

CModelEntities ** independentEntities

Definition at line 208 of file CState.cpp.

References mpBeginIndependent.

Referenced by CSteadyStateMethod::allPositive(), CModel::buildApplyInitialValuesSequence(), CModel::buildDependencyGraphs(), CModel::buildInitialRefreshSequence(), CModel::buildInitialSequence(), CModel::buildSimulatedSequence(), CModel::buildStateTemplate(), CModel::calculateElasticityMatrix(), CCSPMethod::CSPOutput(), CCSPMethod::cspstep(), CSteadyStateTask::initialize(), CTSSAMethod::initializeAtol(), CModel::initializeAtolVector(), CMathContainer::initializeObjects(), CModel::isStateVariable(), CMCAMethod::isValidProblem(), CStochDirectMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), CQUpdatesWidget::loadObjectsTable(), CCSPMethod::predifineAnnotation(), CCSPMethod::printResult(), CCSPMethod::setAnnotationM(), CNewtonMethod::solveJacobianXeqB(), CTauLeapMethod::start(), CStochDirectMethod::start(), CCSPMethod::start(), CTrajAdaptiveSA::start(), CTrajectoryMethodDsaLsodar::start(), CNewtonMethod::targetFunction(), and CSteadyStateTask::updateMatrices().

{return mpBeginIndependent;}

CModelEntity *const * CStateTemplate::beginIndependent

(

)

const

Retrieve the array of pointers to all independent entities.

Returns

CModelEntities const independentEntities

Definition at line 215 of file CState.cpp.

References mpBeginIndependent.

{return mpBeginIndependent;}

CModelEntity ** CStateTemplate::endDependent

(

)

Retrieve pointer just beyond the dependent entities.

Returns

CModelEntities ** endDependentEntities

Definition at line 211 of file CState.cpp.

References mpBeginFixed.

Referenced by CModel::buildSimulatedSequence(), CModel::calculateElasticityMatrix(), CMathModel::compile(), CMathContainer::initializeObjects(), CModel::isStateVariable(), and CQUpdatesWidget::loadObjectsTable().

{return mpBeginFixed;}

CModelEntity *const * CStateTemplate::endDependent

(

)

const

Retrieve pointer just beyond the dependent entities.

Returns

CModelEntities ** endDependentEntities

Definition at line 218 of file CState.cpp.

References mpBeginFixed.

{return mpBeginFixed;}

CModelEntity ** CStateTemplate::endFixed

(

)

Retrieve pointer just beyond the fixed entities.

Returns

CModelEntities ** endFixedEntities

Definition at line 213 of file CState.cpp.

References mpEnd.

Referenced by CModel::buildApplyInitialValuesSequence(), DataModelGUI::buildChangedObjects(), CModel::buildDependencyGraphs(), CModel::buildInitialRefreshSequence(), CModel::buildInitialSequence(), CModel::buildSimulatedSequence(), CModel::buildStateTemplate(), CTimeSeries::compile(), CMathContainer::initializeObjects(), CQUpdatesWidget::loadObjectsTable(), CTauLeapMethod::start(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), and CTrajectoryMethodDsaLsodar::start().

{return mpEnd;}

CModelEntity *const * CStateTemplate::endFixed

(

)

const

Retrieve pointer just beyond the fixed entities.

Returns

CModelEntities const endFixedEntities

Definition at line 220 of file CState.cpp.

References mpEnd.

{return mpEnd;}

CModelEntity ** CStateTemplate::endIndependent

(

)

Retrieve pointer just beyond the independent entities.

Returns

CModelEntities ** endIndependentEntities

Definition at line 209 of file CState.cpp.

References mpBeginDependent.

Referenced by CModel::buildSimulatedSequence(), CMathContainer::initializeObjects(), CMCAMethod::isValidProblem(), CStochDirectMethod::isValidProblem(), CTrajAdaptiveSA::isValidProblem(), and CQUpdatesWidget::loadObjectsTable().

{return mpBeginDependent;}

CModelEntity *const * CStateTemplate::endIndependent

(

)

const

Retrieve pointer just beyond the independent entities.

Returns

CModelEntities const endIndependentEntities

Definition at line 216 of file CState.cpp.

References mpBeginDependent.

{return mpBeginDependent;}

CModelEntity ** CStateTemplate::getEntities

(

)

Retrieve the array of pointers to all entities.

Returns

CModelEntities ** entities

Definition at line 204 of file CState.cpp.

References mpEntities.

Referenced by DataModelGUI::buildChangedObjects(), CMathModel::buildDependendRefreshList(), CModel::buildUserOrder(), CModel::calculateDerivatives(), CModel::calculateDerivativesX(), CFixLocalReactionParameters::checkModel(), CMathModel::compile(), CTimeSeries::compile(), CModel::getTreesWithDiscontinuities(), CSteadyStateTask::initialize(), CQUpdatesWidget::loadObjectsTable(), CCopasiXML::saveModel(), and CSteadyStateTask::updateMatrices().

{return mpEntities;}

CModelEntity *const * CStateTemplate::getEntities

(

)

const

Retrieve the array of pointers to all entities.

Returns

CModelEntities const entities

Definition at line 205 of file CState.cpp.

References mpEntities.

{return mpEntities;}

size_t CStateTemplate::getIndex

(

const CModelEntity *

entity

)

const

Retrieve the index of an entity in the template. Returns C_INVALID_INDEX if the entity is not found.

Parameters

const

CModelEntity * entity

Returns

size_t index

Definition at line 231 of file CState.cpp.

References C_INVALID_INDEX, and mIndexMap.

Referenced by CTimeSeries::compile(), CCopasiXMLParser::InitialStateElement::end(), setUserOrder(), CTauLeapMethod::start(), CHybridMethod::start(), CStochDirectMethod::start(), CTrajAdaptiveSA::start(), CStochMethod::start(), and CTrajectoryMethodDsaLsodar::start().

{
  std::map< CModelEntity *, size_t >::const_iterator found =
    mIndexMap.find(const_cast< CModelEntity * >(entity));

  if (found != mIndexMap.end())
    return found->second;

  return C_INVALID_INDEX;
}

size_t CStateTemplate::getNumDependent

(

)

const

Retrieve the number of dependent entities.

Returns

size_t numDependent

Definition at line 224 of file CState.cpp.

References mpBeginDependent, and mpBeginFixed.

Referenced by CSteadyStateTask::updateMatrices().

{return mpBeginFixed - mpBeginDependent;}

size_t CStateTemplate::getNumFixed

(

)

const

Retrieve the number of fixed entities.

Returns

size_t numFixed

Definition at line 228 of file CState.cpp.

References mpBeginFixed, and mpEnd.

{return mpEnd - mpBeginFixed;}

size_t CStateTemplate::getNumIndependent

(

)

const

Retrieve the number of independent entities.

Returns

size_t numIndependent

Definition at line 222 of file CState.cpp.

References mpBeginDependent, and mpBeginIndependent.

Referenced by CModel::buildUserOrder(), CModel::calculateDerivatives(), CModel::calculateDerivativesX(), CMathModel::calculateRootDerivatives(), CNewtonMethod::initialize(), CModel::initializeAtolVector(), and CSteadyStateTask::updateMatrices().

{return mpBeginDependent - mpBeginIndependent;}

size_t CStateTemplate::getNumVariable

(

)

const

Retrieve the number of variable entities, i.e., the sum of independent and dependent variables.

Returns

size_t numVariable

Definition at line 226 of file CState.cpp.

References mpBeginFixed, and mpBeginIndependent.

{return mpBeginFixed - mpBeginIndependent;}

const CVector< size_t > & CStateTemplate::getUserOrder

(

)

const

Retrieve a pivot vector which can be used to reconstruct the user order.

Returns

const CVector<size_t> & userOrder

Definition at line 201 of file CState.cpp.

References mUserOrder.

Referenced by CModel::buildUserOrder(), CTimeSeries::compile(), CSteadyStateTask::initialize(), and CSteadyStateTask::updateMatrices().

{return mUserOrder;}

void CStateTemplate::remove

(

CModelEntity *

entity

)

Remove an entity from the template.

Parameters

CModelEntity

* entity

Definition at line 80 of file CState.cpp.

References mIndexMap, mModel, mpEntities, CModel::setCompileFlag(), CModelEntity::setInitialValuePtr(), and CModelEntity::setValuePtr().

Referenced by CModelEntity::setObjectParent(), and CModelEntity::~CModelEntity().

{
  std::map< CModelEntity *, size_t >::iterator it =
    mIndexMap.find(entity);

  if (it == mIndexMap.end())
    return;

  entity->setInitialValuePtr(NULL);
  entity->setValuePtr(NULL);

  mpEntities[it->second] = NULL;

  mIndexMap.erase(it);

  mModel.setCompileFlag(true);
}

void CStateTemplate::reorder

(

const CVector< CModelEntity * > &

newOrder

)

Reorder the template.

Parameters

const

CVector< CModelEntity * > & newOrder

Definition at line 98 of file CState.cpp.

References CVectorCore< CType >::array(), CModelEntity::ASSIGNMENT, C_FLOAT64, CModelEntity::FIXED, mCurrentState, mIndexMap, mInitialState, mInsert, mpBeginDependent, mpBeginFixed, mpBeginIndependent, mpCurrentValues, mpEnd, mpEntities, mpInitialValues, CModelEntity::ODE, CModelEntity::REACTIONS, CVectorCore< CType >::size(), CModelEntity::TIME, and CState::updateIterator().

Referenced by CModel::buildSimulatedSequence(), and CModel::buildStateTemplate().

{
  assert(entitiesX.size() + 1 == mIndexMap.size());

  // Update mpEntities to reflect the new order;

  memcpy(mpEntities + 1, entitiesX.array(), sizeof(CModelEntity *) * entitiesX.size());
  mInsert = entitiesX.size() + 1;

  std::map< CModelEntity *, size_t >::iterator found;
  CVector<C_FLOAT64> InitialValues(entitiesX.size());
  CVector<C_FLOAT64> CurrentValues(entitiesX.size());

  CModelEntity *const*it = entitiesX.array();
  CModelEntity *const*end = it + entitiesX.size();

  size_t i;
  size_t Independent, Dependent, Fixed;
  Independent = Dependent = Fixed = 0;

  for (i = 1; it != end; ++it, i++)
    {
      found = mIndexMap.find(*it);
      assert(found != mIndexMap.end());

      // Build new order
      InitialValues[i - 1] = *(mpInitialValues + found->second);
      CurrentValues[i - 1] = *(mpCurrentValues + found->second);

      // Update pointer if necessary
      if (i != found->second)
        {
          found->second = i;
          found->first->setInitialValuePtr(mpInitialValues + found->second);
          found->first->setValuePtr(mpCurrentValues + found->second);
        }

      // Count numbers for each status type;
      if ((*it)->isUsed())
        switch ((*it)->getStatus())
          {
            case CModelEntity::FIXED:
              Fixed++;
              break;

            case CModelEntity::REACTIONS:

              if (static_cast< CMetab * >(*it)->isDependent())
                {
                  assert(Fixed == 0);
                  Dependent++;
                }
              else
                {
                  assert(Dependent == 0);
                  Independent++;
                }

              break;

            case CModelEntity::ODE:
              assert(Dependent == 0);
              Independent++;
              break;

            case CModelEntity::ASSIGNMENT:
              assert(Fixed == 0);
              Dependent++;
              break;

            case CModelEntity::TIME:
              assert(false);
              break;
          }
      else
        Fixed++;
    }

  mpBeginIndependent = mpEntities + 1;
  mpBeginDependent = mpBeginIndependent + Independent;
  mpBeginFixed = mpBeginDependent + Dependent;
  mpEnd = mpBeginFixed + Fixed;

  memcpy(mpInitialValues + 1, InitialValues.array(), sizeof(C_FLOAT64) * entitiesX.size());
  memcpy(mpCurrentValues + 1, CurrentValues.array(), sizeof(C_FLOAT64) * entitiesX.size());

  // Update the iterators of the states
  mInitialState.updateIterator(Independent, Dependent, Fixed);
  mCurrentState.updateIterator(Independent, Dependent, Fixed);
}

void CStateTemplate::resize ( )

protected

Resize the template

Definition at line 245 of file CState.cpp.

References C_FLOAT64, mCurrentState, mInitialState, mInsert, mpCurrentValues, mpEntities, mpInitialValues, mSize, pdeletev, and CState::resize().

Referenced by add().

{
  size_t OldSize = mSize;

  if (mSize)
    mSize *= 2;
  else
    mSize = 16;

  // Resize the entities array.
  CModelEntity ** pTmp = mpEntities;
  mpEntities = new CModelEntity * [mSize];
  memcpy(mpEntities, pTmp, sizeof(CModelEntity *) * OldSize);
  pdeletev(pTmp);

  // Resize the states
  C_FLOAT64 * pInitialValues = mpInitialValues = mInitialState.resize(mSize);
  C_FLOAT64 * pCurrentValues = mpCurrentValues = mCurrentState.resize(mSize);

  // Update all pointers in the entities
  pTmp = mpEntities;
  CModelEntity ** pEnd = pTmp + mInsert;

  for (; pTmp != pEnd; ++pTmp, ++pInitialValues, ++pCurrentValues)
    if (*pTmp != NULL)
      {
        (*pTmp)->setInitialValuePtr(pInitialValues);
        (*pTmp)->setValuePtr(pCurrentValues);
      }
}

void CStateTemplate::setUserOrder

(

const CVector< CModelEntity * > &

userOrder

)

Set the user preferred order of the entities.

Parameters

const

CVector< CModelEntity * > & userOrder

Definition at line 189 of file CState.cpp.

References CVectorCore< CType >::array(), getIndex(), mUserOrder, CVector< CType >::resize(), and CVectorCore< CType >::size().

Referenced by CModel::buildUserOrder().

{
  mUserOrder.resize(entities.size() + 1);
  size_t * pUserOrder = mUserOrder.array();
  *pUserOrder++ = 0; // for time

  CModelEntity *const *it = entities.array();
  CModelEntity *const *end = it + entities.size();

  while (it != end) *pUserOrder++ = getIndex(*it++);
}

const size_t & CStateTemplate::size

(

)

const

Retrieve size of the template, i.e., the number of entities.

Returns

size_t size

Definition at line 242 of file CState.cpp.

References mInsert.

Referenced by CMathContainer::allocate(), CMathModel::buildDependendRefreshList(), CModel::buildSimulatedSequence(), CFixLocalReactionParameters::checkModel(), CModel::getTreesWithDiscontinuities(), CQUpdatesWidget::loadObjectsTable(), and CCopasiXML::saveModel().

{return mInsert;}

Member Data Documentation

CState& CStateTemplate::mCurrentState

private

A reference to the current state of the model

Definition at line 247 of file CState.h.

Referenced by reorder(), and resize().

std::map< CModelEntity *, size_t > CStateTemplate::mIndexMap

private

A map of pointer to entities to the index it appear in the template

Definition at line 287 of file CState.h.

Referenced by add(), getIndex(), remove(), and reorder().

CState& CStateTemplate::mInitialState

private

A reference to the initial state of the model

Definition at line 242 of file CState.h.

Referenced by reorder(), and resize().

size_t CStateTemplate::mInsert

private

The index in which the next added entity must be inserted.

Definition at line 282 of file CState.h.

Referenced by add(), reorder(), resize(), and size().

CModel& CStateTemplate::mModel

private

A reference to the model

Definition at line 237 of file CState.h.

Referenced by add(), and remove().

CModelEntity** CStateTemplate::mpBeginDependent

private

A pointer to the dependent entities

Definition at line 267 of file CState.h.

Referenced by beginDependent(), endIndependent(), getNumDependent(), getNumIndependent(), and reorder().

CModelEntity** CStateTemplate::mpBeginFixed

private

A pointer to the fixed entities

Definition at line 272 of file CState.h.

Referenced by beginFixed(), endDependent(), getNumDependent(), getNumFixed(), getNumVariable(), and reorder().

CModelEntity** CStateTemplate::mpBeginIndependent

private

A pointer to the independent entities

Definition at line 262 of file CState.h.

Referenced by beginIndependent(), getNumIndependent(), getNumVariable(), and reorder().

C_FLOAT64* CStateTemplate::mpCurrentValues

private

The array of current values of all entities

Definition at line 302 of file CState.h.

Referenced by add(), reorder(), and resize().

CModelEntity** CStateTemplate::mpEnd

private

A pointer just beyond the entities

Definition at line 277 of file CState.h.

Referenced by endFixed(), getNumFixed(), and reorder().

CModelEntity** CStateTemplate::mpEntities

private

The array of entities

Definition at line 252 of file CState.h.

Referenced by add(), getEntities(), remove(), reorder(), resize(), and ~CStateTemplate().

C_FLOAT64* CStateTemplate::mpInitialValues

private

The array of initial values of all entities

Definition at line 297 of file CState.h.

Referenced by add(), reorder(), and resize().

size_t CStateTemplate::mSize

private

The allocate size of the template

Definition at line 257 of file CState.h.

Referenced by add(), and resize().

CVector<size_t> CStateTemplate::mUserOrder

private

A pivot vector storing the user order of the entities

Definition at line 292 of file CState.h.

Referenced by getUserOrder(), and setUserOrder().

---

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

• CState.h
• CState.cpp