COPASI API
4.16.103
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#include <CLNAMethod.h>
Public Member Functions | |
void | calculateCovarianceMatrixFull () |
int | calculateCovarianceMatrixReduced () |
int | CalculateLNA () |
CLNAMethod (const CCopasiContainer *pParent=NULL) | |
CLNAMethod (const CLNAMethod &src, const CCopasiContainer *pParent=NULL) | |
virtual bool | elevateChildren () |
const CMatrix< C_FLOAT64 > & | getBMatrixReduced () const |
const CArrayAnnotation * | getBMatrixReducedAnn () const |
const CMatrix< C_FLOAT64 > & | getCovarianceMatrix () const |
const CArrayAnnotation * | getCovarianceMatrixAnn () const |
const CMatrix< C_FLOAT64 > & | getCovarianceMatrixReduced () const |
const CArrayAnnotation * | getCovarianceMatrixReducedAnn () const |
const CLNAMethod::EVStatus & | getEigenValueStatus () const |
const CModel * | getModel () const |
const CArrayAnnotation * | getScaledBMatrixReducedAnn () const |
const CArrayAnnotation * | getScaledCovarianceMatrixAnn () const |
const CArrayAnnotation * | getScaledCovarianceMatrixReducedAnn () const |
const CSteadyStateMethod::ReturnCode & | getSteadyStateStatus () const |
const CArrayAnnotation * | getUnscaledBMatrixReducedAnn () const |
const CArrayAnnotation * | getUnscaledCovarianceMatrixAnn () const |
const CArrayAnnotation * | getUnscaledCovarianceMatrixReducedAnn () const |
virtual bool | isValidProblem (const CCopasiProblem *pProblem) |
C_INT32 | load (CReadConfig &configBuffer) |
virtual bool | process () |
virtual void | resizeAllMatrices () |
void | setEigenValueStatus (CLNAMethod::EVStatus status) |
void | setModel (CModel *model) |
void | setSteadyStateResolution (C_FLOAT64 factor) |
void | setSteadyStateStatus (CSteadyStateMethod::ReturnCode SSStatus) |
virtual | ~CLNAMethod () |
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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 CLNAMethod * | createMethod (CCopasiMethod::SubType subType=CCopasiMethod::linearNoiseApproximation) |
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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 | |
void | initializeParameter () |
void | initObjects () |
Additional Inherited Members | |
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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 28 of file CLNAMethod.h.
enum CLNAMethod::EVStatus |
Enumerator | |
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allNeg | |
nonNegEigenvaluesExist |
Definition at line 31 of file CLNAMethod.h.
CLNAMethod::CLNAMethod | ( | const CCopasiContainer * | pParent = NULL | ) |
Default constructor
const | CCopasiContainer * pParent (Default: NULL) |
Default constructor
Definition at line 29 of file CLNAMethod.cpp.
References initializeParameter(), and initObjects().
Referenced by createMethod().
CLNAMethod::CLNAMethod | ( | const CLNAMethod & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const | CLNAMethod & src |
const | CCopasiContainer * pParent (Default: NULL) |
Definition at line 39 of file CLNAMethod.cpp.
References initializeParameter(), and initObjects().
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void CLNAMethod::calculateCovarianceMatrixFull | ( | ) |
Re-calculate covariances for the full system
Definition at line 518 of file CLNAMethod.cpp.
References CMatrix< CType >::array(), C_FLOAT64, C_INT, dgemm_(), CModel::getL0(), CModel::getNumDependentReactionMetabs(), CModel::getNumIndependentReactionMetabs(), mCovarianceMatrix, mCovarianceMatrixReduced, mL, mpModel, and CMatrix< CType >::resize().
Referenced by CalculateLNA().
int CLNAMethod::calculateCovarianceMatrixReduced | ( | ) |
Definition at line 127 of file CLNAMethod.cpp.
References CVectorCore< CType >::array(), CMatrix< CType >::array(), CCopasiVector< T >::begin(), C_FLOAT64, C_INT, C_LOGICAL, CModel::calculateJacobianX(), dgees_(), dgemm_(), dtrsyl_(), CCopasiVector< T >::end(), CCopasiVector< T >::getIndex(), CModel::getMetabolitesX(), CModel::getNumIndependentReactionMetabs(), CModel::getParticleFlux(), CModel::getReactions(), CModelEntity::getStatus(), CMetab::isDependent(), LNA_OK, max, mBMatrixReduced, mCovarianceMatrixReduced, mJacobianReduced, mpModel, CMatrix< CType >::numCols(), CMatrix< CType >::numRows(), CModelEntity::REACTIONS, CMatrix< CType >::resize(), CVector< CType >::resize(), CMatrix< CType >::size(), and CCopasiVector< T >::size().
Referenced by CalculateLNA().
int CLNAMethod::CalculateLNA | ( | ) |
the LNA entry point
the LNA entry point
status | refers to the steady-state solution |
res | refers to the resolution |
Definition at line 601 of file CLNAMethod.cpp.
References allNeg, calculateCovarianceMatrixFull(), calculateCovarianceMatrixReduced(), CSteadyStateMethod::found, CSteadyStateMethod::foundEquilibrium, LNA_NOT_OK, LNA_OK, mBMatrixReduced, mCovarianceMatrix, mCovarianceMatrixReduced, mEVStatus, mpModel, and mSSStatus.
Referenced by process().
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Create a LNA method. Note: the returned object has to be released after use with delete
Definition at line 21 of file CLNAMethod.cpp.
References CLNAMethod().
Referenced by CLNATask::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 101 of file CLNAMethod.cpp.
References initializeParameter().
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Definition at line 110 of file CLNAMethod.h.
References mCovarianceMatrixAnn.
Referenced by CLNATask::printResult().
Definition at line 113 of file CLNAMethod.h.
References mCovarianceMatrixReduced.
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Definition at line 116 of file CLNAMethod.h.
References mCovarianceMatrixReducedAnn.
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Definition at line 188 of file CLNAMethod.h.
References mEVStatus.
Referenced by CLNAResultSubwidget::loadAll().
const CModel * CLNAMethod::getModel | ( | ) | const |
Get the Model
Definition at line 657 of file CLNAMethod.cpp.
References mpModel.
Referenced by CLNAResultSubwidget::loadAll().
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Definition at line 121 of file CLNAMethod.h.
References mBMatrixReducedAnn.
Referenced by CLNAResultSubwidget::loadBMatrixReduced().
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Definition at line 127 of file CLNAMethod.h.
References mCovarianceMatrixAnn.
Referenced by CLNAResultSubwidget::loadCovarianceMatrix().
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Definition at line 130 of file CLNAMethod.h.
References mCovarianceMatrixReducedAnn.
Referenced by CLNAResultSubwidget::loadCovarianceMatrixReduced().
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Definition at line 185 of file CLNAMethod.h.
References mSSStatus.
Referenced by CLNAResultSubwidget::loadAll(), and CLNATask::printResult().
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Definition at line 124 of file CLNAMethod.h.
References mBMatrixReducedAnn.
Referenced by CLNAResultSubwidget::loadBMatrixReduced().
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Definition at line 133 of file CLNAMethod.h.
References mCovarianceMatrixAnn.
Referenced by CLNAResultSubwidget::loadCovarianceMatrix().
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Definition at line 136 of file CLNAMethod.h.
References mCovarianceMatrixReducedAnn.
Referenced by CLNAResultSubwidget::loadCovarianceMatrixReduced().
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Intialize the method parameter
Definition at line 87 of file CLNAMethod.cpp.
Referenced by CLNAMethod(), and elevateChildren().
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Definition at line 50 of file CLNAMethod.cpp.
References mBMatrixReduced, mBMatrixReducedAnn, mCovarianceMatrix, mCovarianceMatrixAnn, mCovarianceMatrixReduced, mCovarianceMatrixReducedAnn, CArrayAnnotation::setDescription(), CArrayAnnotation::setDimensionDescription(), CArrayAnnotation::setMode(), and CArrayAnnotation::VECTOR.
Referenced by CLNAMethod().
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Check if the method is suitable for this problem
Reimplemented from CCopasiMethod.
Definition at line 663 of file CLNAMethod.cpp.
References CCopasiVector< T >::begin(), CCopasiVector< T >::end(), CCopasiMessage::ERROR, CModelEntity::FIXED, CModel::getCompartments(), CCopasiProblem::getModel(), CModel::getNumAssignmentMetabs(), CModel::getNumODEMetabs(), CModel::getReactions(), CCopasiMethod::isValidProblem(), and CCopasiVector< T >::size().
C_INT32 CLNAMethod::load | ( | CReadConfig & | configBuffer | ) |
Read some parameters from configuration file
Read some parameters from configuration file.
Definition at line 624 of file CLNAMethod.cpp.
References C_INT32.
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Definition at line 636 of file CLNAMethod.cpp.
References CalculateLNA(), and LNA_OK.
Referenced by CLNATask::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 107 of file CLNAMethod.cpp.
References CModel::getMetabolitesX(), CModel::getNumDependentReactionMetabs(), CModel::getNumIndependentReactionMetabs(), mBMatrixReduced, mBMatrixReducedAnn, mCovarianceMatrix, mCovarianceMatrixAnn, mCovarianceMatrixReduced, mCovarianceMatrixReducedAnn, mpModel, CMatrix< CType >::resize(), CArrayAnnotation::resize(), and CArrayAnnotation::setCopasiVector().
Referenced by CLNATask::updateMatrices().
void CLNAMethod::setEigenValueStatus | ( | CLNAMethod::EVStatus | status | ) |
Definition at line 647 of file CLNAMethod.cpp.
References mEVStatus.
Referenced by CLNATask::process().
Set the Model
Definition at line 591 of file CLNAMethod.cpp.
References mpModel.
Referenced by CLNATask::printResult(), and CLNATask::updateMatrices().
void CLNAMethod::setSteadyStateStatus | ( | CSteadyStateMethod::ReturnCode | SSStatus | ) |
Definition at line 642 of file CLNAMethod.cpp.
References mSSStatus.
Referenced by CLNATask::process().
LNA Matrices
Definition at line 44 of file CLNAMethod.h.
Referenced by calculateCovarianceMatrixReduced(), CalculateLNA(), getBMatrixReduced(), initObjects(), and resizeAllMatrices().
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Definition at line 45 of file CLNAMethod.h.
Referenced by getBMatrixReducedAnn(), getScaledBMatrixReducedAnn(), getUnscaledBMatrixReducedAnn(), initObjects(), and resizeAllMatrices().
Definition at line 50 of file CLNAMethod.h.
Referenced by calculateCovarianceMatrixFull(), CalculateLNA(), getCovarianceMatrix(), initObjects(), and resizeAllMatrices().
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Definition at line 51 of file CLNAMethod.h.
Referenced by getCovarianceMatrixAnn(), getScaledCovarianceMatrixAnn(), getUnscaledCovarianceMatrixAnn(), initObjects(), and resizeAllMatrices().
Definition at line 47 of file CLNAMethod.h.
Referenced by calculateCovarianceMatrixFull(), calculateCovarianceMatrixReduced(), CalculateLNA(), getCovarianceMatrixReduced(), initObjects(), and resizeAllMatrices().
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Definition at line 48 of file CLNAMethod.h.
Referenced by getCovarianceMatrixReducedAnn(), getScaledCovarianceMatrixReducedAnn(), getUnscaledCovarianceMatrixReducedAnn(), initObjects(), and resizeAllMatrices().
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Definition at line 63 of file CLNAMethod.h.
Referenced by CalculateLNA(), getEigenValueStatus(), and setEigenValueStatus().
Definition at line 54 of file CLNAMethod.h.
Referenced by calculateCovarianceMatrixReduced().
Definition at line 57 of file CLNAMethod.h.
Referenced by calculateCovarianceMatrixFull().
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Definition at line 39 of file CLNAMethod.h.
Referenced by calculateCovarianceMatrixFull(), calculateCovarianceMatrixReduced(), CalculateLNA(), getModel(), resizeAllMatrices(), and setModel().
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Definition at line 61 of file CLNAMethod.h.
Referenced by CalculateLNA(), getSteadyStateStatus(), and setSteadyStateStatus().
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Definition at line 59 of file CLNAMethod.h.
Referenced by setSteadyStateResolution().