COPASI API
4.16.103
|
#include <CEFMProblem.h>
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 () |
![]() | |
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 () |
![]() | |
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 () |
![]() | |
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 () |
![]() | |
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 () |
![]() | |
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 () |
![]() | |
CObjectInterface () | |
virtual | ~CObjectInterface () |
Protected Attributes | |
std::vector< CFluxMode > | mFluxModes |
std::vector< const CReaction * > | mReorderedReactions |
![]() | |
CProcessReport * | mpCallBack |
CModel * | mpModel |
CReport * | mpReport |
![]() | |
std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
![]() | |
objectMap | mObjects |
Private Member Functions | |
void | initializeParameter () |
void | initObjects () |
Additional Inherited Members | |
![]() | |
typedef parameterGroup::iterator | index_iterator |
typedef CCopasiContainer::objectMap::iterator | name_iterator |
typedef std::vector < CCopasiParameter * > | parameterGroup |
![]() | |
enum | Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID } |
![]() | |
typedef std::multimap < std::string, CCopasiObject * > | objectMap |
![]() | |
typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
![]() | |
typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
![]() | |
static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
![]() | |
static const std::string | TypeName [] |
static const char * | XMLType [] |
![]() | |
static const std::vector < CCopasiContainer * > | EmptyList |
![]() | |
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 } |
![]() | |
CCopasiProblem (const CCopasiTask::Type &type, const CCopasiContainer *pParent=NULL) | |
![]() | |
CCopasiParameterGroup () | |
![]() | |
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 () |
![]() | |
CCopasiObject () | |
CCopasiObject (const std::string &name, const CCopasiContainer *pParent=NULL, const std::string &type="CN", const unsigned C_INT32 &flag=0) | |
![]() | |
static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 38 of file CEFMProblem.h.
CEFMProblem::CEFMProblem | ( | const CCopasiContainer * | pParent = NULL | ) |
Default constructor
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 35 of file CEFMProblem.cpp.
References initializeParameter(), and initObjects().
CEFMProblem::CEFMProblem | ( | const CEFMProblem & | src, |
const CCopasiContainer * | pParent = NULL |
||
) |
Copy constructor.
const | CEFMProblem & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 45 of file CEFMProblem.cpp.
References initializeParameter(), and initObjects().
|
virtual |
|
virtual |
This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
Definition at line 62 of file CEFMProblem.cpp.
Referenced by initializeParameter().
const std::vector< CFluxMode > & CEFMProblem::getFluxModes | ( | ) | const |
Return the flux modes after a successful analysis.
Definition at line 80 of file CEFMProblem.cpp.
References mFluxModes.
Referenced by CQNewMainWindow::checkForElementaryModesSlot(), QFluxModeAnimation::getScales(), CEFMMethod::initialize(), and QFluxModeAnimation::initialize().
std::vector< CFluxMode > & CEFMProblem::getFluxModes | ( | ) |
Return the flux modes after a successful analysis.
Definition at line 83 of file CEFMProblem.cpp.
References mFluxModes.
const std::vector< const CReaction * > & CEFMProblem::getReorderedReactions | ( | ) | const |
Return the reactions in the order they are used in the flux modes
Definition at line 86 of file CEFMProblem.cpp.
References mReorderedReactions.
Referenced by CEFMTask::getReactionEquation(), QFluxModeAnimation::getScales(), and CEFMMethod::initialize().
std::vector< const CReaction * > & CEFMProblem::getReorderedReactions | ( | ) |
Return the reactions in the order they are used in the flux modes
Definition at line 89 of file CEFMProblem.cpp.
References mReorderedReactions.
|
virtual |
Do all necessary initialization so that calls to calculate will be successful. This is called once from CCopasiTask::process()
Reimplemented from CCopasiProblem.
Definition at line 75 of file CEFMProblem.cpp.
References CCopasiProblem::initialize().
|
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().
|
private |
|
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.
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.
|
virtual |
Set the call back of the problem
CProcessReport | * pCallBack |
Reimplemented from CCopasiProblem.
Definition at line 65 of file CEFMProblem.cpp.
References CCopasiProblem::setCallBack().
|
protected |
The resulting elementary flux modes
Definition at line 130 of file CEFMProblem.h.
Referenced by getFluxModes().
|
protected |
Reactions in the order used in the analysis
Definition at line 135 of file CEFMProblem.h.
Referenced by getReorderedReactions(), and printResult().