COPASI API  4.16.103
Public Member Functions | Static Public Member Functions | Protected Member Functions | Protected Attributes | Private Member Functions | List of all members
CEFMMethod Class Reference

#include <CEFMMethod.h>

Inheritance diagram for CEFMMethod:
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Collaboration diagram for CEFMMethod:
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Public Member Functions

virtual bool calculate ()
 
 CEFMMethod (const CEFMMethod &src, const CCopasiContainer *pParent=NULL)
 
virtual bool initialize ()
 
virtual bool isValidProblem (const CCopasiProblem *pProblem)
 
virtual ~CEFMMethod ()
 
- Public Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiMethod &src, const CCopasiContainer *pParent=NULL)
 
const CCopasiMethod::SubTypegetSubType () const
 
const CCopasiTask::TypegetType () 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 ()
 
- 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)
 
CCopasiParameterGroupassertGroup (const std::string &name)
 
template<class CType >
CCopasiParameterassertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)
 
index_iterator beginIndex () const
 
name_iterator beginName () const
 
 CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL)
 
 CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup")
 
void clear ()
 
virtual bool elevateChildren ()
 
index_iterator endIndex () const
 
name_iterator endName () const
 
CCopasiParameterGroupgetGroup (const std::string &name)
 
const CCopasiParameterGroupgetGroup (const std::string &name) const
 
CCopasiParameterGroupgetGroup (const size_t &index)
 
const CCopasiParameterGroupgetGroup (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 CObjectInterfacegetObject (const CCopasiObjectName &cn) const
 
CCopasiParametergetParameter (const std::string &name)
 
const CCopasiParametergetParameter (const std::string &name) const
 
CCopasiParametergetParameter (const size_t &index)
 
const CCopasiParametergetParameter (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::ValuegetValue (const std::string &name) const
 
const CCopasiParameter::ValuegetValue (const size_t &index) const
 
CCopasiParameter::ValuegetValue (const std::string &name)
 
CCopasiParameter::ValuegetValue (const size_t &index)
 
CCopasiParameterGroupoperator= (const CCopasiParameterGroup &rhs)
 
bool removeParameter (const std::string &name)
 
bool removeParameter (const size_t &index)
 
template<class CType >
bool setValue (const std::string &name, const CType &value)
 
template<class CType >
bool setValue (const size_t &index, const CType &value)
 
size_t size () const
 
bool swap (const size_t &iFrom, const size_t &iTo)
 
bool swap (index_iterator &from, index_iterator &to)
 
virtual ~CCopasiParameterGroup ()
 
- Public Member Functions inherited from CCopasiParameter
 CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)
 
 CCopasiParameter (const std::string &name, const Type &type, const void *pValue=NULL, const CCopasiContainer *pParent=NULL, const std::string &objectType="Parameter")
 
virtual CCopasiObjectName getCN () const
 
virtual const std::string & getKey () const
 
virtual std::string getObjectDisplayName (bool regular=true, bool richtext=false) const
 
const CCopasiParameter::TypegetType () const
 
const ValuegetValue () const
 
ValuegetValue ()
 
virtual voidgetValuePointer () const
 
CCopasiObjectgetValueReference () 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
 
CCopasiParameteroperator= (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 objectMapgetObjects () const
 
virtual std::string getUnits () const
 
virtual const CCopasiObjectgetValueObject () 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 DataObjectSetgetDirectDependencies (const DataObjectSet &context=DataObjectSet()) const
 
CCopasiContainergetObjectAncestor (const std::string &type) const
 
CCopasiDataModelgetObjectDataModel ()
 
const CCopasiDataModelgetObjectDataModel () const
 
const std::string & getObjectName () const
 
CCopasiContainergetObjectParent () const
 
const std::string & getObjectType () const
 
virtual const
CObjectInterface::ObjectSet
getPrerequisites () const
 
virtual RefreshgetRefresh () const
 
UpdateMethodgetUpdateMethod () const
 
bool hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const
 
bool hasUpdateMethod () const
 
bool isArray () const
 
bool isContainer () const
 
bool isDataModel () const
 
bool isMatrix () const
 
bool isNameVector () const
 
bool isNonUniqueName () const
 
virtual bool isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const
 
bool isReference () const
 
bool isRoot () const
 
bool isSeparator () const
 
bool isStaticString () const
 
bool isValueBool () const
 
bool isValueDbl () const
 
bool isValueInt () const
 
bool isValueInt64 () const
 
bool isValueString () const
 
bool isVector () const
 
virtual bool mustBeDeleted (const DataObjectSet &deletedObjects) const
 
void removeDirectDependency (const CCopasiObject *pObject)
 
void setDirectDependencies (const DataObjectSet &directDependencies)
 
bool setObjectName (const std::string &name)
 
virtual bool setObjectParent (const CCopasiContainer *pParent)
 
void setObjectValue (const C_FLOAT64 &value)
 
void setObjectValue (const C_INT32 &value)
 
void setObjectValue (const bool &value)
 
template<class CType >
void setRefresh (CType *pType, void(CType::*method)(void))
 
template<class CType >
void setUpdateMethod (CType *pType, void(CType::*method)(const C_FLOAT64 &))
 
template<class CType >
void setUpdateMethod (CType *pType, void(CType::*method)(const C_INT32 &))
 
template<class CType >
void setUpdateMethod (CType *pType, void(CType::*method)(const bool &))
 
virtual ~CCopasiObject ()
 
- Public Member Functions inherited from CObjectInterface
 CObjectInterface ()
 
virtual ~CObjectInterface ()
 

Static Public Member Functions

static CEFMMethodcreateMethod (CCopasiMethod::SubType subType=CCopasiMethod::EFMAlgorithm)
 
- 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)
 

Protected Member Functions

 CEFMMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)
 
- Protected Member Functions inherited from CCopasiMethod
 CCopasiMethod (const CCopasiTask::Type &taskType, const SubType &subType, const CCopasiContainer *pParent=NULL)
 
- Protected Member Functions inherited from CCopasiParameterGroup
 CCopasiParameterGroup ()
 
- Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObjectaddMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
template<class CType >
CCopasiObjectaddObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
 
template<class CType >
CCopasiObjectaddVectorReference (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

std::vector< CFluxMode > * mpFluxModes
 
std::vector< const CReaction * > * mpReorderedReactions
 
- Protected Attributes inherited from CCopasiMethod
CProcessReportmpCallBack
 
- Protected Attributes inherited from CCopasiParameter
std::string mKey
 
CCopasiObjectmpValueReference
 
size_t mSize
 
Value mValue
 
- Protected Attributes inherited from CCopasiContainer
objectMap mObjects
 

Private Member Functions

 CEFMMethod ()
 

Additional Inherited Members

- Public Types inherited from CCopasiMethod
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
}
 
- 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 Attributes inherited from CCopasiMethod
static const std::string SubTypeName []
 
static const char * XMLSubType []
 
- 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
}
 
- Static Protected Attributes inherited from CCopasiObject
static CRenameHandlersmpRenameHandler = NULL
 

Detailed Description

Definition at line 25 of file CEFMMethod.h.

Constructor & Destructor Documentation

CEFMMethod::CEFMMethod ( )
private

Default constructor.

Definition at line 80 of file CEFMMethod.cpp.

References CONSTRUCTOR_TRACE.

80  :
82  mpFluxModes(NULL),
std::vector< CFluxMode > * mpFluxModes
Definition: CEFMMethod.h:91
std::vector< const CReaction * > * mpReorderedReactions
Definition: CEFMMethod.h:96
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CEFMMethod::CEFMMethod ( const CCopasiTask::Type taskType,
const SubType subType,
const CCopasiContainer pParent = NULL 
)
protected

Specific constructor

Parameters
constCCopasiTask::Type & type
constCCopasiMethod::SubType & subType
constCCopasiContainer * pParent (default: NULL)

Definition at line 86 of file CEFMMethod.cpp.

References CONSTRUCTOR_TRACE.

88  :
89  CCopasiMethod(taskType, subType, pParent),
90  mpFluxModes(NULL),
std::vector< CFluxMode > * mpFluxModes
Definition: CEFMMethod.h:91
std::vector< const CReaction * > * mpReorderedReactions
Definition: CEFMMethod.h:96
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CEFMMethod::CEFMMethod ( const CEFMMethod src,
const CCopasiContainer pParent = NULL 
)

Copy constructor

Parameters
constCEFMMethod & src
constCCopasiContainer * pParent (default: NULL)

Definition at line 94 of file CEFMMethod.cpp.

References CONSTRUCTOR_TRACE.

95  :
96  CCopasiMethod(src, pParent),
std::vector< CFluxMode > * mpFluxModes
Definition: CEFMMethod.h:91
std::vector< const CReaction * > * mpReorderedReactions
Definition: CEFMMethod.h:96
#define CONSTRUCTOR_TRACE
Definition: copasi.h:202
CEFMMethod::~CEFMMethod ( )
virtual

Destructor

Definition at line 101 of file CEFMMethod.cpp.

102 {}

Member Function Documentation

bool CEFMMethod::calculate ( void  )
virtual

Execute the optimization algorithm calling simulation routine when needed. It is noted that this procedure can give feedback of its progress by the callback function set with SetCallback. @ return success;

Reimplemented in CBitPatternTreeMethod, CBitPatternMethod, CEFMAlgorithm, and CSSAMethod.

Definition at line 104 of file CEFMMethod.cpp.

105 {
106  return false;
107 }
CEFMMethod * CEFMMethod::createMethod ( CCopasiMethod::SubType  subType = CCopasiMethod::EFMAlgorithm)
static

Create a EFM method. Note: the returned object has to be released after use with delete

CEFMMethod class This class describes the interface to all optimization methods. The various method like RandomSearch or GA have to be derived from this class.

Created for COPASI by Stefan Hoops 2002

Definition at line 47 of file CEFMMethod.cpp.

References CCopasiMethod::EFMAlgorithm, CCopasiMethod::EFMBitPatternAlgorithm, and CCopasiMethod::EFMBitPatternTreeAlgorithm.

Referenced by CEFMTask::CEFMTask(), and CEFMTask::createMethod().

48 {
49  CEFMMethod * pMethod = NULL;
50 
51  switch (subType)
52  {
53  case EFMAlgorithm:
54  pMethod = new CEFMAlgorithm();
55  break;
56 
58  pMethod = new CBitPatternTreeMethod();
59  break;
60 
62  pMethod = new CBitPatternMethod();
63  break;
64 
65 #ifdef COPASI_SSA
66  case stoichiometricStabilityAnalysis:
67  pMethod = new CSSAMethod();
68  break;
69 #endif
70 
71  default:
72  pMethod = new CEFMAlgorithm();
73  break;
74  }
75 
76  return pMethod;
77 }
bool CEFMMethod::initialize ( )
virtual

Initialize arrays and pointer.

Returns
bool success

Reimplemented in CBitPatternTreeMethod, CBitPatternMethod, CEFMAlgorithm, and CSSAMethod.

Definition at line 109 of file CEFMMethod.cpp.

References CCopasiMessage::ERROR, CEFMProblem::getFluxModes(), CCopasiObject::getObjectParent(), CCopasiTask::getProblem(), CEFMProblem::getReorderedReactions(), MCEFMAnalysis, mpFluxModes, mpReorderedReactions, and pTask.

Referenced by CEFMAlgorithm::initialize(), CBitPatternMethod::initialize(), and CBitPatternTreeMethod::initialize().

110 {
111  CEFMTask * pTask = dynamic_cast< CEFMTask * >(getObjectParent());
112 
113  if (pTask == NULL)
114  {
116  return false;
117  }
118 
119  CEFMProblem * pProblem = dynamic_cast< CEFMProblem *>(pTask->getProblem());
120 
121  if (pProblem == NULL)
122  {
124  return false;
125  }
126 
127  mpFluxModes = & pProblem->getFluxModes();
129 
130  mpReorderedReactions->clear();
131  mpFluxModes->clear();
132 
133  return true;
134 }
CCopasiProblem * getProblem()
std::vector< CFluxMode > * mpFluxModes
Definition: CEFMMethod.h:91
CTSSATask * pTask
const std::vector< CFluxMode > & getFluxModes() const
Definition: CEFMProblem.cpp:80
std::vector< const CReaction * > * mpReorderedReactions
Definition: CEFMMethod.h:96
const std::vector< const CReaction * > & getReorderedReactions() const
Definition: CEFMProblem.cpp:86
#define MCEFMAnalysis
CCopasiContainer * getObjectParent() const
bool CEFMMethod::isValidProblem ( const CCopasiProblem pProblem)
virtual

Check if the method is suitable for this problem

Returns
bool suitability of the method

Reimplemented from CCopasiMethod.

Definition at line 136 of file CEFMMethod.cpp.

References CMatrix< CType >::array(), C_FLOAT64, CCopasiMessage::ERROR, CCopasiProblem::getModel(), CCopasiObject::getObjectName(), CModel::getReactions(), CModel::getRedStoi(), CCopasiMethod::isValidProblem(), MCEFMAnalysis, CMatrix< CType >::numCols(), and CMatrix< CType >::size().

137 {
138  if (!CCopasiMethod::isValidProblem(pProblem)) return false;
139 
140  if (pProblem == NULL)
141  {
142  return false;
143  }
144 
145  const CModel * pModel = pProblem ->getModel();
146 
147  if (pModel == NULL)
148  {
149  return false;
150  }
151 
152  // Check that the stoichiometry matrix contains only integers.
153 
154  const CMatrix< C_FLOAT64 > & RedStoi = pModel->getRedStoi();
155  const C_FLOAT64 * pValue = RedStoi.array();
156  const C_FLOAT64 * pValueEnd = pValue + RedStoi.size();
157 
158  for (; pValue != pValueEnd; ++pValue)
159  {
160  if (fabs(*pValue - floor(*pValue + 0.5)) > 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
161  {
162  break;
163  }
164  }
165 
166  if (pValue != pValueEnd)
167  {
168  const CReaction * pReaction = pModel->getReactions()[(pValue - RedStoi.array()) % RedStoi.numCols()];
169 
171 
172  return false;
173  }
174 
175  return true;
176 }
const std::string & getObjectName() const
const CMatrix< C_FLOAT64 > & getRedStoi() const
Definition: CModel.cpp:1154
virtual bool isValidProblem(const CCopasiProblem *pProblem)
#define MCEFMAnalysis
#define C_FLOAT64
Definition: copasi.h:92
virtual size_t size() const
Definition: CMatrix.h:132
CCopasiVectorNS< CReaction > & getReactions()
Definition: CModel.cpp:1039
Definition: CModel.h:50
virtual size_t numCols() const
Definition: CMatrix.h:144
virtual CType * array()
Definition: CMatrix.h:337
CModel * getModel() const

Member Data Documentation

std::vector< CFluxMode >* CEFMMethod::mpFluxModes
protected
std::vector< const CReaction * >* CEFMMethod::mpReorderedReactions
protected

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