COPASI API
4.16.103
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#include <CMCAMethod.h>
Public Member Functions | |
bool | CalculateMCA (C_FLOAT64 res) |
bool | calculateUnscaledConcentrationCC () |
void | calculateUnscaledElasticities (C_FLOAT64 res) |
bool | calculateUnscaledFluxCC (const bool &status) |
bool | checkSummationTheorems (const C_FLOAT64 &resolution) |
CMCAMethod (const CCopasiContainer *pParent=NULL) | |
CMCAMethod (const CMCAMethod &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | elevateChildren () |
const CModel * | getModel () const |
const CMatrix< C_FLOAT64 > & | getScaledConcentrationCC () const |
const CArrayAnnotation * | getScaledConcentrationCCAnn () const |
const CMatrix< C_FLOAT64 > & | getScaledElasticities () const |
const CArrayAnnotation * | getScaledElasticitiesAnn () const |
const CMatrix< C_FLOAT64 > & | getScaledFluxCC () const |
const CArrayAnnotation * | getScaledFluxCCAnn () const |
const CSteadyStateMethod::ReturnCode & | getSteadyStateStatus () const |
const CMatrix< C_FLOAT64 > & | getUnscaledConcentrationCC () const |
const CArrayAnnotation * | getUnscaledConcentrationCCAnn () const |
const CMatrix< C_FLOAT64 > & | getUnscaledElasticities () const |
const CArrayAnnotation * | getUnscaledElasticitiesAnn () const |
const CMatrix< C_FLOAT64 > & | getUnscaledFluxCC () const |
const CArrayAnnotation * | getUnscaledFluxCCAnn () const |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
C_INT32 | load (CReadConfig &configBuffer) |
virtual bool | process () |
virtual void | resizeAllMatrices () |
bool | scaleMCA (const bool &status, C_FLOAT64 res) |
void | setFactor (C_FLOAT64 factor) |
void | setModel (CModel *model) |
void | setSteadyStateResolution (C_FLOAT64 factor) |
void | setSteadyStateTask (CSteadyStateTask *pSteadyStateTask) |
virtual | ~CMCAMethod () |
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CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL) | |
const CCopasiMethod::SubType & | getSubType () const |
const CCopasiTask::Type & | getType () const |
virtual void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual | ~CCopasiMethod () |
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bool | addGroup (const std::string &name) |
bool | addParameter (const CCopasiParameter ¶meter) |
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) |
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 () |
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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 () |
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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 () |
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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 () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
Static Public Member Functions | |
static CMCAMethod * | createMethod (CCopasiMethod::SubType subType=CCopasiMethod::mcaMethodReder) |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
Private Member Functions | |
bool | createLinkMatrix (const bool &useSmallbone=false) |
void | initializeParameter () |
void | initObjects () |
Additional Inherited Members | |
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enum | SubType { unset = 0, RandomSearch, RandomSearchMaster, SimulatedAnnealing, CoranaWalk, DifferentialEvolution, ScatterSearch, GeneticAlgorithm, EvolutionaryProgram, SteepestDescent, HybridGASA, GeneticAlgorithmSR, HookeJeeves, LevenbergMarquardt, NelderMead, SRES, Statistics, ParticleSwarm, Praxis, TruncatedNewton, Newton, deterministic, LSODAR, directMethod, stochastic, tauLeap, adaptiveSA, hybrid, hybridLSODA, hybridODE45, DsaLsodar, tssILDM, tssILDMModified, tssCSP, mcaMethodReder, scanMethod, lyapWolf, sensMethod, EFMAlgorithm, EFMBitPatternTreeAlgorithm, EFMBitPatternAlgorithm, Householder, crossSectionMethod, linearNoiseApproximation } |
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typedef parameterGroup::iterator | index_iterator |
typedef CCopasiContainer::objectMap::iterator | name_iterator |
typedef std::vector < CCopasiParameter * > | parameterGroup |
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enum | Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID } |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
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static const std::string | SubTypeName [] |
static const char * | XMLSubType [] |
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static const std::string | TypeName [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
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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 } |
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CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL) | |
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CCopasiParameterGroup () | |
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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 () |
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CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
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CProcessReport * | mpCallBack |
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std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
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objectMap | mObjects |
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static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 27 of file CMCAMethod.h.
CMCAMethod::CMCAMethod | ( | const CCopasiContainer * | pParent = NULL | ) |
Default constructor
const | CCopasiContainer * pParent (Default: NULL) |
Default constructor
Definition at line 42 of file CMCAMethod.cpp.
References initializeParameter(), and initObjects().
Referenced by createMethod().
CMCAMethod::CMCAMethod | ( | const CMCAMethod & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CMCAMethod & src |
const | CCopasiContainer * pParent (Default: NULL) |
Definition at line 59 of file CMCAMethod.cpp.
References initializeParameter(), and initObjects().
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Destructor
Deconstructor
Definition at line 132 of file CMCAMethod.cpp.
References DESTRUCTOR_TRACE.
bool CMCAMethod::CalculateMCA | ( | C_FLOAT64 | res | ) |
the steady state MCA entry point
ss_solution | refer to steady-state solution |
refer | to the resolution |
Definition at line 673 of file CMCAMethod.cpp.
References calculateUnscaledConcentrationCC(), calculateUnscaledElasticities(), calculateUnscaledFluxCC(), checkSummationTheorems(), createLinkMatrix(), CSteadyStateMethod::found, MCMCA, mpModel, mpUseReeder, mpUseSmallbone, mSSStatus, mUnscaledConcCC, mUnscaledFluxCC, scaleMCA(), and CCopasiMessage::WARNING.
Referenced by process().
bool CMCAMethod::calculateUnscaledConcentrationCC | ( | ) |
Definition at line 311 of file CMCAMethod.cpp.
References CVectorCore< CType >::array(), CMatrix< CType >::array(), C_FLOAT64, C_INT, dgemm_(), dgetrf_(), dgetri_(), CLinkMatrix::doColumnPivot(), K, CLinkMatrix::leftMultiply(), mLinkZero, mpModel, mReducedStoichiometry, mUnscaledConcCC, mUnscaledElasticities, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CMatrix< CType >::resize(), CVector< CType >::resize(), CLinkMatrix::rightMultiply(), CLinkMatrix::undoColumnPivot(), and CLinkMatrix::undoRowPivot().
Referenced by CalculateMCA().
Definition at line 203 of file CMCAMethod.cpp.
References CVectorCore< CType >::array(), CMatrix< CType >::array(), CCopasiVector< T >::begin(), C_FLOAT64, CCopasiVector< T >::end(), CModel::getMetabolitesX(), CModel::getNumDependentReactionMetabs(), CModel::getNumIndependentReactionMetabs(), CModel::getParticleFlux(), CModel::getReactions(), mElasticityDependencies, mFactor, min, mpModel, mUnscaledElasticities, CMatrix< CType >::size(), CCopasiVector< T >::size(), and CModel::updateSimulatedValues().
Referenced by CalculateMCA().
bool CMCAMethod::calculateUnscaledFluxCC | ( | const bool & | status | ) |
Definition at line 403 of file CMCAMethod.cpp.
References CMatrix< CType >::array(), C_FLOAT64, C_INT, dgemm_(), dlaset_(), K, mpModel, mUnscaledConcCC, mUnscaledElasticities, mUnscaledFluxCC, CMatrix< CType >::numCols(), and CMatrix< CType >::numRows().
Referenced by CalculateMCA().
bool CMCAMethod::checkSummationTheorems | ( | const C_FLOAT64 & | resolution | ) |
Check whether the summation theorems hold.
Definition at line 598 of file CMCAMethod.cpp.
References CVectorCore< CType >::array(), CMatrix< CType >::array(), C_FLOAT64, max, min, mScaledConcCC, mScaledFluxCC, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CVector< CType >::resize(), and CMatrix< CType >::size().
Referenced by CalculateMCA().
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Definition at line 718 of file CMCAMethod.cpp.
References CLinkMatrix::build(), CLinkMatrix::doRowPivot(), CSteadyStateTask::getJacobian(), CModel::getL0(), CLinkMatrix::getNumIndependent(), CModel::getNumIndependentReactionMetabs(), CModel::getRedStoi(), CModel::getStoi(), mLinkZero, mpModel, mpSteadyStateTask, mReducedStoichiometry, CMatrix< CType >::numCols(), and CMatrix< CType >::resize().
Referenced by CalculateMCA().
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Create a MCA method. Note: the returned object has to be released after use with delete
Definition at line 34 of file CMCAMethod.cpp.
References CMCAMethod().
Referenced by CMCATask::createMethod().
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This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
Definition at line 154 of file CMCAMethod.cpp.
References initializeParameter().
const CModel * CMCAMethod::getModel | ( | ) | const |
Get the Model
Definition at line 797 of file CMCAMethod.cpp.
References mpModel.
Referenced by CMCAResultSubwidget::loadAll().
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Definition at line 92 of file CMCAMethod.h.
References mScaledConcCCAnn.
Referenced by CMCAResultSubwidget::loadConcentrationCCs(), and CMCATask::printResult().
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Definition at line 88 of file CMCAMethod.h.
References mScaledElasticitiesAnn.
Referenced by CMCAResultSubwidget::loadElasticities(), and CMCATask::printResult().
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Definition at line 96 of file CMCAMethod.h.
References mScaledFluxCCAnn.
Referenced by CMCAResultSubwidget::loadFluxCCs(), and CMCATask::printResult().
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Definition at line 147 of file CMCAMethod.h.
References mSSStatus.
Referenced by CMCAResultSubwidget::loadAll(), and CMCATask::printResult().
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Definition at line 90 of file CMCAMethod.h.
References mUnscaledConcCCAnn.
Referenced by CMCAResultSubwidget::loadConcentrationCCs(), and CMCATask::printResult().
Definition at line 62 of file CMCAMethod.h.
References mUnscaledElasticities.
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Definition at line 86 of file CMCAMethod.h.
References mUnscaledElasticitiesAnn.
Referenced by CMCAResultSubwidget::loadElasticities(), and CMCATask::printResult().
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Definition at line 94 of file CMCAMethod.h.
References mUnscaledFluxCCAnn.
Referenced by CMCAResultSubwidget::loadFluxCCs(), and CMCATask::printResult().
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Initialize the method parameter
Definition at line 138 of file CMCAMethod.cpp.
References CCopasiParameterGroup::assertParameter(), CCopasiParameter::BOOL, CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), mpUseReeder, mpUseSmallbone, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pUDOUBLE, CCopasiParameterGroup::removeParameter(), CCopasiParameterGroup::setValue(), and CCopasiParameter::UDOUBLE.
Referenced by CMCAMethod(), and elevateChildren().
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Definition at line 77 of file CMCAMethod.cpp.
References mScaledConcCC, mScaledConcCCAnn, mScaledElasticities, mScaledElasticitiesAnn, mScaledFluxCC, mScaledFluxCCAnn, mUnscaledConcCC, mUnscaledConcCCAnn, mUnscaledElasticities, mUnscaledElasticitiesAnn, mUnscaledFluxCC, mUnscaledFluxCCAnn, CArrayAnnotation::setDescription(), CArrayAnnotation::setDimensionDescription(), CArrayAnnotation::setMode(), and CArrayAnnotation::VECTOR.
Referenced by CMCAMethod().
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Check if the method is suitable for this problem
Reimplemented from CCopasiMethod.
Definition at line 803 of file CMCAMethod.cpp.
References CModelEntity::ASSIGNMENT, CCopasiVector< T >::begin(), CStateTemplate::beginIndependent(), CCopasiVector< T >::end(), CStateTemplate::endIndependent(), CCopasiMessage::ERROR, CModel::getCompartments(), CCopasiProblem::getModel(), CModel::getNumIndependentReactionMetabs(), CModel::getStateTemplate(), CCopasiMethod::isValidProblem(), mpUseReeder, and mpUseSmallbone.
C_INT32 CMCAMethod::load | ( | CReadConfig & | configBuffer | ) |
Read SSMCAUnscaled from configuration file
Definition at line 745 of file CMCAMethod.cpp.
References C_INT32, CReadConfig::getVariable(), CReadConfig::LOOP, and mSSReder.
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Definition at line 757 of file CMCAMethod.cpp.
References CalculateMCA(), and mSteadyStateResolution.
Referenced by CMCATask::process().
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Resizes all result matrices and updates the corresponding array annotations. This needs to be called before output initialization (in case the output references parts of the matrix) from the task initialization, but it also needs to be called before selecting elements of the matrices in the object selection dialog. The model needs to be set before calling this.
Definition at line 160 of file CMCAMethod.cpp.
References CModel::getMetabolitesX(), CModel::getNumDependentReactionMetabs(), CModel::getNumIndependentReactionMetabs(), CModel::getReactions(), CModel::getTotSteps(), mElasticityDependencies, mpModel, mScaledConcCC, mScaledConcCCAnn, mScaledElasticities, mScaledElasticitiesAnn, mScaledFluxCC, mScaledFluxCCAnn, mUnscaledConcCC, mUnscaledConcCCAnn, mUnscaledElasticities, mUnscaledElasticitiesAnn, mUnscaledFluxCC, mUnscaledFluxCCAnn, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CMatrix< CType >::resize(), CArrayAnnotation::resize(), and CArrayAnnotation::setCopasiVector().
Referenced by CMCATask::updateMatrices().
bool CMCAMethod::scaleMCA | ( | const bool & | status, |
C_FLOAT64 | res | ||
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Scales the coefficients (i.e. Kacser format, rather than Reder)
Definition at line 440 of file CMCAMethod.cpp.
References CMatrix< CType >::array(), CCopasiVector< T >::begin(), C_FLOAT64, CCopasiVector< T >::end(), CSteadyStateMethod::found, CModel::getMetabolitesX(), CModel::getNumDependentReactionMetabs(), CModel::getNumIndependentReactionMetabs(), CModel::getReactions(), CModelEntity::getValue(), mElasticityDependencies, mpModel, mScaledConcCC, mScaledElasticities, mScaledFluxCC, mSSStatus, mUnscaledConcCC, mUnscaledElasticities, mUnscaledFluxCC, and CMatrix< CType >::numCols().
Referenced by CalculateMCA().
Set the Model
Definition at line 663 of file CMCAMethod.cpp.
References mpModel.
Referenced by CMCATask::printResult(), and CMCATask::updateMatrices().
void CMCAMethod::setSteadyStateTask | ( | CSteadyStateTask * | pSteadyStateTask | ) |
Definition at line 773 of file CMCAMethod.cpp.
References CSteadyStateTask::getResult(), mpSteadyStateTask, mSSStatus, and CSteadyStateMethod::notFound.
Referenced by CMCATask::process().
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Definition at line 225 of file CMCAMethod.h.
Referenced by calculateUnscaledElasticities(), resizeAllMatrices(), and scaleMCA().
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Modulation factor for finite differences derivation
Definition at line 213 of file CMCAMethod.h.
Referenced by calculateUnscaledElasticities(), and setFactor().
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Definition at line 221 of file CMCAMethod.h.
Referenced by calculateUnscaledConcentrationCC(), and createLinkMatrix().
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Definition at line 172 of file CMCAMethod.h.
Referenced by CalculateMCA(), calculateUnscaledConcentrationCC(), calculateUnscaledElasticities(), calculateUnscaledFluxCC(), createLinkMatrix(), getModel(), resizeAllMatrices(), scaleMCA(), and setModel().
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Definition at line 219 of file CMCAMethod.h.
Referenced by createLinkMatrix(), and setSteadyStateTask().
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Definition at line 174 of file CMCAMethod.h.
Referenced by CalculateMCA(), initializeParameter(), and isValidProblem().
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Definition at line 176 of file CMCAMethod.h.
Referenced by CalculateMCA(), initializeParameter(), and isValidProblem().
Definition at line 223 of file CMCAMethod.h.
Referenced by calculateUnscaledConcentrationCC(), and createLinkMatrix().
Definition at line 193 of file CMCAMethod.h.
Referenced by checkSummationTheorems(), getScaledConcentrationCC(), initObjects(), resizeAllMatrices(), and scaleMCA().
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Definition at line 194 of file CMCAMethod.h.
Referenced by getScaledConcentrationCCAnn(), initObjects(), and resizeAllMatrices().
Definition at line 190 of file CMCAMethod.h.
Referenced by getScaledElasticities(), initObjects(), resizeAllMatrices(), and scaleMCA().
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Definition at line 191 of file CMCAMethod.h.
Referenced by getScaledElasticitiesAnn(), initObjects(), and resizeAllMatrices().
Definition at line 196 of file CMCAMethod.h.
Referenced by checkSummationTheorems(), getScaledFluxCC(), initObjects(), resizeAllMatrices(), and scaleMCA().
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Definition at line 197 of file CMCAMethod.h.
Referenced by getScaledFluxCCAnn(), initObjects(), and resizeAllMatrices().
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1 if MCA coeffs are to be unscaled
Definition at line 202 of file CMCAMethod.h.
Referenced by load().
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Definition at line 217 of file CMCAMethod.h.
Referenced by CalculateMCA(), getSteadyStateStatus(), scaleMCA(), and setSteadyStateTask().
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If need to evaluate the elasticities, ss_x will be assigned in calculateTimeMCA()
Definition at line 208 of file CMCAMethod.h.
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Definition at line 215 of file CMCAMethod.h.
Referenced by process(), and setSteadyStateResolution().
Definition at line 184 of file CMCAMethod.h.
Referenced by CalculateMCA(), calculateUnscaledConcentrationCC(), calculateUnscaledFluxCC(), getUnscaledConcentrationCC(), initObjects(), resizeAllMatrices(), and scaleMCA().
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Definition at line 185 of file CMCAMethod.h.
Referenced by getUnscaledConcentrationCCAnn(), initObjects(), and resizeAllMatrices().
MCA Matrices
Definition at line 181 of file CMCAMethod.h.
Referenced by calculateUnscaledConcentrationCC(), calculateUnscaledElasticities(), calculateUnscaledFluxCC(), getUnscaledElasticities(), initObjects(), resizeAllMatrices(), and scaleMCA().
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Definition at line 182 of file CMCAMethod.h.
Referenced by getUnscaledElasticitiesAnn(), initObjects(), and resizeAllMatrices().
Definition at line 187 of file CMCAMethod.h.
Referenced by CalculateMCA(), calculateUnscaledFluxCC(), getUnscaledFluxCC(), initObjects(), resizeAllMatrices(), and scaleMCA().
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Definition at line 188 of file CMCAMethod.h.
Referenced by getUnscaledFluxCCAnn(), initObjects(), and resizeAllMatrices().