#include <CEFMProblem.h>

Inheritance diagram for CEFMProblem:

Collaboration diagram for CEFMProblem:

Public Member Functions
	CEFMProblem (const CCopasiContainer *pParent=NULL)

	CEFMProblem (const CEFMProblem &src, const CCopasiContainer *pParent=NULL)

virtual bool	elevateChildren ()

const std::vector< CFluxMode > &	getFluxModes () const

std::vector< CFluxMode > &	getFluxModes ()

const std::vector< const CReaction * > &	getReorderedReactions () const

std::vector< const CReaction * > &	getReorderedReactions ()

virtual bool	initialize ()

virtual void	printResult (std::ostream *ostream) const

virtual bool	setCallBack (CProcessReport *pCallBack)

virtual	~CEFMProblem ()

Public Member Functions inherited from CCopasiProblem
	CCopasiProblem (const CCopasiProblem &src, const CCopasiContainer *pParent=NULL)

CModel *	getModel () const

const CCopasiTask::Type &	getType () const

virtual void	print (std::ostream *ostream) const

virtual bool	restore (const bool &updateModel)

virtual bool	setModel (CModel *pModel)

virtual	~CCopasiProblem ()

Public Member Functions inherited from CCopasiParameterGroup
bool	addGroup (const std::string &name)

bool	addParameter (const CCopasiParameter &parameter)

bool	addParameter (const std::string &name, const CCopasiParameter::Type type)

template<class CType >
bool	addParameter (const std::string &name, const CCopasiParameter::Type type, const CType &value)

void	addParameter (CCopasiParameter *pParameter)

CCopasiParameterGroup *	assertGroup (const std::string &name)

template<class CType >
CCopasiParameter *	assertParameter (const std::string &name, const CCopasiParameter::Type type, const CType &defaultValue)

index_iterator	beginIndex () const

name_iterator	beginName () const

	CCopasiParameterGroup (const CCopasiParameterGroup &src, const CCopasiContainer *pParent=NULL)

	CCopasiParameterGroup (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &objectType="ParameterGroup")

void	clear ()

index_iterator	endIndex () const

name_iterator	endName () const

CCopasiParameterGroup *	getGroup (const std::string &name)

const CCopasiParameterGroup *	getGroup (const std::string &name) const

CCopasiParameterGroup *	getGroup (const size_t &index)

const CCopasiParameterGroup *	getGroup (const size_t &index) const

size_t	getIndex (const std::string &name) const

std::string	getKey (const std::string &name) const

std::string	getKey (const size_t &index) const

virtual const std::string &	getName (const size_t &index) const

virtual const CObjectInterface *	getObject (const CCopasiObjectName &cn) const

CCopasiParameter *	getParameter (const std::string &name)

const CCopasiParameter *	getParameter (const std::string &name) const

CCopasiParameter *	getParameter (const size_t &index)

const CCopasiParameter *	getParameter (const size_t &index) const

CCopasiParameter::Type	getType (const std::string &name) const

CCopasiParameter::Type	getType (const size_t &index) const

std::string	getUniqueParameterName (const CCopasiParameter *pParameter) const

const CCopasiParameter::Value &	getValue (const std::string &name) const

const CCopasiParameter::Value &	getValue (const size_t &index) const

CCopasiParameter::Value &	getValue (const std::string &name)

CCopasiParameter::Value &	getValue (const size_t &index)

CCopasiParameterGroup &	operator= (const CCopasiParameterGroup &rhs)

bool	removeParameter (const std::string &name)

bool	removeParameter (const size_t &index)

template<class CType >
bool	setValue (const std::string &name, const CType &value)

template<class CType >
bool	setValue (const size_t &index, const CType &value)

size_t	size () const

bool	swap (const size_t &iFrom, const size_t &iTo)

bool	swap (index_iterator &from, index_iterator &to)

virtual	~CCopasiParameterGroup ()

Public Member Functions inherited from CCopasiParameter
	CCopasiParameter (const CCopasiParameter &src, const CCopasiContainer *pParent=NULL)

	CCopasiParameter (const std::string &name, const Type &type, const void pValue=NULL, const CCopasiContainer pParent=NULL, const std::string &objectType="Parameter")

virtual CCopasiObjectName	getCN () const

virtual const std::string &	getKey () const

virtual std::string	getObjectDisplayName (bool regular=true, bool richtext=false) const

const CCopasiParameter::Type &	getType () const

const Value &	getValue () const

Value &	getValue ()

virtual void *	getValuePointer () const

CCopasiObject *	getValueReference () const

bool	isValidValue (const C_FLOAT64 &value) const

bool	isValidValue (const C_INT32 &value) const

bool	isValidValue (const unsigned C_INT32 &value) const

bool	isValidValue (const bool &value) const

bool	isValidValue (const std::string &value) const

bool	isValidValue (const CCopasiObjectName &value) const

bool	isValidValue (const std::vector< CCopasiParameter * > &value) const

CCopasiParameter &	operator= (const CCopasiParameter &rhs)

template<class CType >
bool	setValue (const CType &value)

bool	setValue (const std::vector< CCopasiParameter * > &value)

virtual	~CCopasiParameter ()

Public Member Functions inherited from CCopasiContainer
virtual bool	add (CCopasiObject *pObject, const bool &adopt=true)

	CCopasiContainer (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=CCopasiObject::Container)

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

virtual std::string	getChildObjectUnits (const CCopasiObject *pObject) const

virtual const objectMap &	getObjects () const

virtual std::string	getUnits () const

virtual const CCopasiObject *	getValueObject () const

virtual bool	remove (CCopasiObject *pObject)

virtual	~CCopasiContainer ()

Public Member Functions inherited from CCopasiObject
void	addDirectDependency (const CCopasiObject *pObject)

	CCopasiObject (const CCopasiObject &src, const CCopasiContainer *pParent=NULL)

void	clearDirectDependencies ()

void	clearRefresh ()

bool	dependsOn (DataObjectSet candidates, const DataObjectSet &context=DataObjectSet()) const

void	getAllDependencies (DataObjectSet &dependencies, const DataObjectSet &context) const

virtual const DataObjectSet &	getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const

CCopasiContainer *	getObjectAncestor (const std::string &type) const

CCopasiDataModel *	getObjectDataModel ()

const CCopasiDataModel *	getObjectDataModel () const

const std::string &	getObjectName () const

CCopasiContainer *	getObjectParent () const

const std::string &	getObjectType () const

virtual const CObjectInterface::ObjectSet &	getPrerequisites () const

virtual Refresh *	getRefresh () const

UpdateMethod *	getUpdateMethod () const

bool	hasCircularDependencies (DataObjectSet &candidates, DataObjectSet &verified, const DataObjectSet &context) const

bool	hasUpdateMethod () const

bool	isArray () const

bool	isContainer () const

bool	isDataModel () const

bool	isMatrix () const

bool	isNameVector () const

bool	isNonUniqueName () const

virtual bool	isPrerequisiteForContext (const CObjectInterface *pObject, const CMath::SimulationContextFlag &context, const CObjectInterface::ObjectSet &changedObjects) const

bool	isReference () const

bool	isRoot () const

bool	isSeparator () const

bool	isStaticString () const

bool	isValueBool () const

bool	isValueDbl () const

bool	isValueInt () const

bool	isValueInt64 () const

bool	isValueString () const

bool	isVector () const

virtual bool	mustBeDeleted (const DataObjectSet &deletedObjects) const

void	removeDirectDependency (const CCopasiObject *pObject)

void	setDirectDependencies (const DataObjectSet &directDependencies)

bool	setObjectName (const std::string &name)

virtual bool	setObjectParent (const CCopasiContainer *pParent)

void	setObjectValue (const C_FLOAT64 &value)

void	setObjectValue (const C_INT32 &value)

void	setObjectValue (const bool &value)

template<class CType >
void	setRefresh (CType pType, void(CType::method)(void))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_FLOAT64 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const C_INT32 &))

template<class CType >
void	setUpdateMethod (CType pType, void(CType::method)(const bool &))

virtual	~CCopasiObject ()

Public Member Functions inherited from CObjectInterface
	CObjectInterface ()

virtual	~CObjectInterface ()

Protected Attributes
std::vector< CFluxMode >	mFluxModes

std::vector< const CReaction * >	mReorderedReactions

Protected Attributes inherited from CCopasiProblem
CProcessReport *	mpCallBack

CModel *	mpModel

CReport *	mpReport

Protected Attributes inherited from CCopasiParameter
std::string	mKey

CCopasiObject *	mpValueReference

size_t	mSize

Value	mValue

Protected Attributes inherited from CCopasiContainer
objectMap	mObjects

Private Member Functions
void	initializeParameter ()

void	initObjects ()

Additional Inherited Members
Public Types inherited from CCopasiParameterGroup
typedef parameterGroup::iterator	index_iterator

typedef CCopasiContainer::objectMap::iterator	name_iterator

typedef std::vector < CCopasiParameter * >	parameterGroup

Public Types inherited from CCopasiParameter
enum	Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID }

Public Types inherited from CCopasiContainer
typedef std::multimap < std::string, CCopasiObject * >	objectMap

Public Types inherited from CCopasiObject
typedef std::set< const CCopasiObject * >	DataObjectSet

typedef std::vector< Refresh * >	DataUpdateSequence

Public Types inherited from CObjectInterface
typedef std::set< const CObjectInterface * >	ObjectSet

typedef std::vector < CObjectInterface * >	UpdateSequence

Static Public Member Functions inherited from CCopasiObject
static std::vector< Refresh * >	buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet())

static void	setRenameHandler (CRenameHandler *rh)

Static Public Attributes inherited from CCopasiParameter
static const std::string	TypeName []

static const char *	XMLType []

Static Public Attributes inherited from CCopasiContainer
static const std::vector < CCopasiContainer * >	EmptyList

Protected Types inherited from CCopasiObject
enum	Flag { Container = 0x1, Vector = 0x2, Matrix = 0x4, NameVector = 0x8, Reference = 0x10, ValueBool = 0x20, ValueInt = 0x40, ValueInt64 = 0x80, ValueDbl = 0x100, NonUniqueName = 0x200, StaticString = 0x400, ValueString = 0x800, Separator = 0x1000, ModelEntity = 0x2000, Array = 0x4000, DataModel = 0x8000, Root = 0x10000, Gui = 0x20000 }

Protected Member Functions inherited from CCopasiProblem
	CCopasiProblem (const CCopasiTask::Type &type, const CCopasiContainer *pParent=NULL)

Protected Member Functions inherited from CCopasiParameterGroup
	CCopasiParameterGroup ()

Protected Member Functions inherited from CCopasiContainer
template<class CType >
CCopasiObject *	addMatrixReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addObjectReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

template<class CType >
CCopasiObject *	addVectorReference (const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)

void	initObjects ()

Protected Member Functions inherited from CCopasiObject
	CCopasiObject ()

	CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0)

Static Protected Attributes inherited from CCopasiObject
static CRenameHandler *	smpRenameHandler = NULL

Detailed Description

Definition at line 38 of file CEFMProblem.h.

Constructor & Destructor Documentation

CEFMProblem::CEFMProblem ( const CCopasiContainer * pParent = NULL )

Default constructor

Parameters

const CCopasiContainer * pParent (default: NULL)

Definition at line 35 of file CEFMProblem.cpp.

References initializeParameter(), and initObjects().

                                                         :
     CCopasiProblem(CCopasiTask::optimization, pParent),
     mFluxModes(),
     mReorderedReactions()
 {
   initializeParameter();
   initObjects();
 }

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

Copy constructor.

Parameters

const	CEFMProblem & src
const	CCopasiContainer * pParent (default: NULL)

Definition at line 45 of file CEFMProblem.cpp.

References initializeParameter(), and initObjects().

                                                           :
     CCopasiProblem(src, pParent),
     mFluxModes(src.mFluxModes),
     mReorderedReactions(src.mReorderedReactions)
 {
   initializeParameter();
   initObjects();
 }

CEFMProblem::~CEFMProblem ( )

virtual

Destructor

Definition at line 56 of file CEFMProblem.cpp.

57 {}

Member Function Documentation

bool CEFMProblem::elevateChildren ( )

virtual

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

Returns: bool success

Reimplemented from CCopasiParameterGroup.

Definition at line 62 of file CEFMProblem.cpp.

Referenced by initializeParameter().

63 {return true;}

const std::vector< CFluxMode > & CEFMProblem::getFluxModes ( ) const

Return the flux modes after a successful analysis.

Returns: const std::vector< CFluxMode > & fluxModes

Definition at line 80 of file CEFMProblem.cpp.

References mFluxModes.

Referenced by CQNewMainWindow::checkForElementaryModesSlot(), QFluxModeAnimation::getScales(), CEFMMethod::initialize(), and QFluxModeAnimation::initialize().

81 {return mFluxModes;}

CEFMProblem::mFluxModes

std::vector< CFluxMode > mFluxModes

Definition: CEFMProblem.h:130

std::vector< CFluxMode > & CEFMProblem::getFluxModes ( )

Return the flux modes after a successful analysis.

Returns: std::vector< CFluxMode > & fluxModes

Definition at line 83 of file CEFMProblem.cpp.

References mFluxModes.

84 {return mFluxModes;}

CEFMProblem::mFluxModes

std::vector< CFluxMode > mFluxModes

Definition: CEFMProblem.h:130

const std::vector< const CReaction * > & CEFMProblem::getReorderedReactions ( ) const

Return the reactions in the order they are used in the flux modes

Returns: const std::vector< const CReaction * > & reorderedReactions

Definition at line 86 of file CEFMProblem.cpp.

References mReorderedReactions.

Referenced by CEFMTask::getReactionEquation(), QFluxModeAnimation::getScales(), and CEFMMethod::initialize().

87 {return mReorderedReactions;}

CEFMProblem::mReorderedReactions

std::vector< const CReaction * > mReorderedReactions

Definition: CEFMProblem.h:135

std::vector< const CReaction * > & CEFMProblem::getReorderedReactions ( )

Return the reactions in the order they are used in the flux modes

Returns: std::vector< const CReaction * > & reorderedReactions

Definition at line 89 of file CEFMProblem.cpp.

References mReorderedReactions.

90 {return mReorderedReactions;}

CEFMProblem::mReorderedReactions

std::vector< const CReaction * > mReorderedReactions

Definition: CEFMProblem.h:135

bool CEFMProblem::initialize ( )

virtual

Do all necessary initialization so that calls to calculate will be successful. This is called once from CCopasiTask::process()

Returns: bool success

Reimplemented from CCopasiProblem.

Definition at line 75 of file CEFMProblem.cpp.

References CCopasiProblem::initialize().

 {
   return CCopasiProblem::initialize();
 }

void CEFMProblem::initializeParameter ( )

private

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

Definition at line 59 of file CEFMProblem.cpp.

References elevateChildren().

Referenced by CEFMProblem().

60 {elevateChildren();}

CEFMProblem::elevateChildren

virtual bool elevateChildren()

Definition: CEFMProblem.cpp:62

void CEFMProblem::initObjects ( )

private

Definition at line 72 of file CEFMProblem.cpp.

Referenced by CEFMProblem().

73 {}

void CEFMProblem::printResult ( std::ostream * ostream ) const

virtual

This is the output method for any result of a problem. The default implementation provided with CCopasiProblem. Does only print "Not implemented." To override this default behavior one needs to reimplement the virtual printResult function.

Parameters

std::ostream * ostream

Reimplemented from CCopasiProblem.

Definition at line 92 of file CEFMProblem.cpp.

References CCopasiVector< T >::begin(), C_INT32, CCopasiVector< T >::end(), CMetabNameInterface::getDisplayName(), CEFMTask::getFluxModeDescription(), CEFMTask::getFluxModes(), CEFMTask::getInternalSpecies(), CModel::getMetabolites(), CEFMTask::getNetReaction(), CCopasiObject::getObjectParent(), CEFMTask::getReactionEquation(), CEFMTask::getSpeciesChanges(), CCopasiProblem::mpModel, mReorderedReactions, and pTask.

 {
   CEFMTask * pTask = dynamic_cast< CEFMTask * >(getObjectParent());
 
   if (pTask)
     {
       const std::vector< CFluxMode > & FluxModes = pTask->getFluxModes();
 
       // List
       *ostream << "\tNumber of Modes:\t" << FluxModes.size() << std::endl;
 
       // Column header
       *ostream << "#\t\tReactions\tEquations" << std::endl;
 
       std::vector< CFluxMode >::const_iterator itMode = FluxModes.begin();
       std::vector< CFluxMode >::const_iterator endMode = FluxModes.end();
 
       unsigned C_INT32 j;
 
       for (j = 0; itMode != endMode; ++itMode, j++)
         {
           *ostream << j + 1;
 
           if (itMode->isReversible() == true)
             *ostream << "\tReversible";
           else
             *ostream << "\tIrreversible";
 
           std::string Description = pTask->getFluxModeDescription(*itMode);
           CFluxMode::const_iterator itReaction = itMode->begin();
           CFluxMode::const_iterator endReaction = itMode->end();
 
           std::string::size_type start = 0;
           std::string::size_type end = 0;
 
           for (; itReaction != endReaction; ++itReaction)
             {
               if (itReaction != itMode->begin())
                 *ostream << "\t";
 
               end = Description.find("\n", start);
               *ostream << "\t" << Description.substr(start, end - start);
               start = end + 1;
               *ostream << "\t" << pTask->getReactionEquation(itReaction) << std::endl;
             }
         }
 
       *ostream << std::endl;
 
       // Net Reactions
       // Column header
       *ostream << "#\tNet Reaction\tInternal Species" << std::endl;
 
       itMode = FluxModes.begin();
 
       for (j = 0; itMode != endMode; ++itMode, j++)
         {
           *ostream << j + 1;
           *ostream << "\t" << pTask->getNetReaction(*itMode);
           *ostream << "\t" << pTask->getInternalSpecies(*itMode) << std::endl;
         }
 
       *ostream << std::endl;
 
       // EFM vs Reaction
       std::vector< const CReaction * >::const_iterator itReaction = mReorderedReactions.begin();
       std::vector< const CReaction * >::const_iterator endReaction = mReorderedReactions.end();
 
       // Column header
       *ostream << "#";
 
       for (; itReaction != endReaction; ++itReaction)
         {
           *ostream << "\t" << (*itReaction)->getObjectName();
         }
 
       *ostream << std::endl;
 
       itMode = FluxModes.begin();
       size_t k;
 
       for (j = 0; itMode != endMode; ++itMode, j++)
         {
           itReaction = mReorderedReactions.begin();
 
           *ostream << j + 1;
 
           for (k = 0; itReaction != endReaction; ++itReaction, k++)
             {
               *ostream << "\t" << itMode->getMultiplier(k);
             }
 
           *ostream << std::endl;
         }
 
       *ostream << std::endl;
 
       if (mpModel == NULL) return;
 
       // EFM vs Species
       std::vector< CMetab * >::const_iterator itSpecies = mpModel->getMetabolites().begin();
       std::vector< CMetab * >::const_iterator endSpecies = mpModel->getMetabolites().end();
       // Column header
       *ostream << "#";
 
       for (; itSpecies != endSpecies; ++itSpecies)
         {
           *ostream << "\t" << CMetabNameInterface::getDisplayName(mpModel, **itSpecies, false);
         }
 
       *ostream << std::endl;
 
       itMode = FluxModes.begin();
 
       for (j = 0; itMode != endMode; ++itMode, j++)
         {
           itSpecies = mpModel->getMetabolites().begin();
 
           *ostream << j + 1;
 
           for (; itSpecies != endSpecies; ++itSpecies)
             {
               std::pair< C_FLOAT64, C_FLOAT64 > Changes =
                 pTask->getSpeciesChanges(*itMode, **itSpecies);
 
               *ostream << "\t";
 
               if (Changes.first > 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon() ||
                   Changes.second > 100.0 * std::numeric_limits< C_FLOAT64 >::epsilon())
                 {
                   *ostream << "-" << Changes.first << " | +" << Changes.second;
                 }
             }
 
           *ostream << std::endl;
         }
 
       *ostream << std::endl;
     }
 }

bool CEFMProblem::setCallBack ( CProcessReport * pCallBack )

virtual

Set the call back of the problem

Parameters

CProcessReport * pCallBack

Returns: bool success

Reimplemented from CCopasiProblem.

Definition at line 65 of file CEFMProblem.cpp.

References CCopasiProblem::setCallBack().

 {
   CCopasiProblem::setCallBack(pCallBack);
 
   return true;
 }

Member Data Documentation

std::vector< CFluxMode > CEFMProblem::mFluxModes

protected

The resulting elementary flux modes

Definition at line 130 of file CEFMProblem.h.

Referenced by getFluxModes().

std::vector< const CReaction * > CEFMProblem::mReorderedReactions

protected

Reactions in the order used in the analysis

Definition at line 135 of file CEFMProblem.h.

Referenced by getReorderedReactions(), and printResult().

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

Public Member Functions

Protected Attributes

Private Member Functions

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation