COPASI API
4.16.103
|
#include <CExperimentObjectMap.h>
Classes | |
class | CDataColumn |
Public Member Functions | |
CExperimentObjectMap (const std::string &name="Object Map", const CCopasiContainer *pParent=NULL) | |
CExperimentObjectMap (const CExperimentObjectMap &src, const CCopasiContainer *pParent=NULL) | |
CExperimentObjectMap (const CCopasiParameterGroup &group, const CCopasiContainer *pParent=NULL) | |
bool | compile (const std::vector< CCopasiContainer * > listOfContainer=CCopasiContainer::EmptyList) |
virtual bool | elevateChildren () |
void | fixBuild55 () |
C_FLOAT64 | getDefaultScale (const size_t &index) const |
const size_t & | getLastColumn () const |
size_t | getLastNotIgnoredColumn () const |
const CVector< CCopasiObject * > & | getMappedObjects () const |
virtual const std::string & | getName (const size_t &index) const |
std::string | getObjectCN (const size_t &index) const |
CExperiment::Type | getRole (const size_t &index) const |
C_FLOAT64 | getScale (const size_t &index) const |
bool | setNumCols (const size_t &numCols) |
bool | setObjectCN (const size_t &index, const std::string &objectCN) |
bool | setRole (const size_t &index, const CExperiment::Type &role) |
bool | setScale (const size_t &index, const C_FLOAT64 &scale) |
virtual | ~CExperimentObjectMap () |
![]() | |
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 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) |
virtual void | print (std::ostream *ostream) const |
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 () |
Private Member Functions | |
void | initializeParameter () |
Private Attributes | |
size_t | mLastColumn |
CVector< CCopasiObject * > | mObjects |
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 } |
![]() | |
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) | |
![]() | |
std::string | mKey |
CCopasiObject * | mpValueReference |
size_t | mSize |
Value | mValue |
![]() | |
objectMap | mObjects |
![]() | |
static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 23 of file CExperimentObjectMap.h.
CExperimentObjectMap::CExperimentObjectMap | ( | const std::string & | name = "Object Map" , |
const CCopasiContainer * | pParent = NULL |
||
) |
Default constructor
const | std::string & name (default: Object Map) |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 27 of file CExperimentObjectMap.cpp.
References initializeParameter().
CExperimentObjectMap::CExperimentObjectMap | ( | const CExperimentObjectMap & | src, |
const CCopasiContainer * | pParent = NULL |
||
) |
Copy constructor
const | CExperimentObjectMap & src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 34 of file CExperimentObjectMap.cpp.
References initializeParameter().
CExperimentObjectMap::CExperimentObjectMap | ( | const CCopasiParameterGroup & | group, |
const CCopasiContainer * | pParent = NULL |
||
) |
Specific constructor used for reading copasi files
const | CCopasiParameterGroup & group |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 41 of file CExperimentObjectMap.cpp.
References initializeParameter().
|
virtual |
bool CExperimentObjectMap::compile | ( | const std::vector< CCopasiContainer * > | listOfContainer = CCopasiContainer::EmptyList | ) |
Compile the map. This function must be called before any operations can be performed.
const | std::vector< CCopasiContainer * > listOfContainer |
Definition at line 222 of file CExperimentObjectMap.cpp.
References C_INVALID_INDEX, CCopasiParameter::CN, getName(), getObjectCN(), CCopasiObject::getObjectDataModel(), CCopasiObject::isValueDbl(), mLastColumn, mObjects, CVector< CType >::resize(), and CCopasiParameterGroup::size().
Referenced by CExperiment::compile().
|
virtual |
This methods must be called to elevate subgroups to derived objects. The default implementation does nothing.
Reimplemented from CCopasiParameterGroup.
Definition at line 55 of file CExperimentObjectMap.cpp.
References CCopasiParameterGroup::assertGroup(), CCopasiParameterGroup::assertParameter(), CCopasiParameterGroup::clear(), CCopasiParameter::CN, CCopasiObject::getObjectName(), CCopasiParameter::mValue, and CCopasiParameter::Value::pGROUP.
Referenced by CExperimentObjectMap::CDataColumn::initializeParameter(), and initializeParameter().
void CExperimentObjectMap::fixBuild55 | ( | ) |
Fix files written with Version 4.10.55, which wrote the square root of user defined weights for the parameter fitting task
Definition at line 273 of file CExperimentObjectMap.cpp.
References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), and CExperimentObjectMap::CDataColumn::fixBuild55().
Referenced by CExperiment::fixBuild55().
C_FLOAT64 CExperimentObjectMap::getDefaultScale | ( | const size_t & | index | ) | const |
Retrieve the default scaling factor according to the selected weight method of the indexed column
const | size_t & index |
Definition at line 211 of file CExperimentObjectMap.cpp.
References CExperimentObjectMap::CDataColumn::getDefaultScale(), CCopasiParameterGroup::getGroup(), and StringPrint().
Referenced by CExperimentObjectMap::CDataColumn::getScale(), CQExperimentData::loadTable(), CExperimentObjectMap::CDataColumn::setScale(), and CQExperimentData::updateScales().
const size_t & CExperimentObjectMap::getLastColumn | ( | ) | const |
Retrieve the last mapped column number
Definition at line 270 of file CExperimentObjectMap.cpp.
References mLastColumn.
Referenced by CExperiment::compile().
size_t CExperimentObjectMap::getLastNotIgnoredColumn | ( | ) | const |
Retrieve the last non ignored column
Definition at line 110 of file CExperimentObjectMap.cpp.
References C_INT32, CExperiment::ignore, CCopasiParameter::mValue, and CCopasiParameter::Value::pGROUP.
Referenced by CExperiment::compile(), and CExperiment::printResult().
const CVector< CCopasiObject * > & CExperimentObjectMap::getMappedObjects | ( | ) | const |
Retrieve the vector of mapped objects
Definition at line 267 of file CExperimentObjectMap.cpp.
References mObjects.
Referenced by CExperiment::compile(), and CExperiment::printResult().
|
virtual |
Retrieve the name of a parameter or subgroup
const | size_t & index |
Reimplemented from CCopasiParameterGroup.
Definition at line 129 of file CExperimentObjectMap.cpp.
References CCopasiParameterGroup::getGroup(), CCopasiObject::getObjectName(), and StringPrint().
Referenced by compile().
std::string CExperimentObjectMap::getObjectCN | ( | const size_t & | index | ) | const |
Retrieve the object CN of the object mapped to the indexed column
const | size_t & index |
Definition at line 177 of file CExperimentObjectMap.cpp.
References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::getObjectCN(), and StringPrint().
Referenced by compile(), CExperiment::elevateChildren(), CQExperimentData::loadTable(), CQExperimentData::saveTable(), and CExperiment::updateFittedPoints().
CExperiment::Type CExperimentObjectMap::getRole | ( | const size_t & | index | ) | const |
Retrieve the role of the indexed column
const | size_t & index |
Definition at line 154 of file CExperimentObjectMap.cpp.
References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::getRole(), CExperiment::ignore, and StringPrint().
Referenced by CExperiment::compile(), CQExperimentData::loadTable(), CExperiment::printResult(), CExperiment::read(), CQExperimentData::saveTable(), CExperiment::updateFittedPoints(), and CQExperimentData::updateScales().
C_FLOAT64 CExperimentObjectMap::getScale | ( | const size_t & | index | ) | const |
Retrieve the scaling factor of the indexed column
const | size_t & index |
Definition at line 200 of file CExperimentObjectMap.cpp.
References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::getScale(), and StringPrint().
Referenced by CExperiment::compile(), CQExperimentData::loadTable(), and CQExperimentData::saveTable().
|
private |
Allocates all group parameters and assures that they are properly initialized.
Definition at line 50 of file CExperimentObjectMap.cpp.
References elevateChildren().
Referenced by CExperimentObjectMap().
bool CExperimentObjectMap::setNumCols | ( | const size_t & | numCols | ) |
Set the number of data columns
const | size_t & numCols |
Definition at line 84 of file CExperimentObjectMap.cpp.
References CCopasiParameterGroup::assertGroup(), CCopasiParameter::mValue, CCopasiParameter::Value::pGROUP, and StringPrint().
Referenced by CExperiment::elevateChildren(), and CQExperimentData::saveTable().
bool CExperimentObjectMap::setObjectCN | ( | const size_t & | index, |
const std::string & | objectCN | ||
) |
Set the object CN of the object mapped to the indexed column
const | size_t & index |
const | std::string & objectCN |
Definition at line 165 of file CExperimentObjectMap.cpp.
References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::setObjectCN(), and StringPrint().
Referenced by CExperiment::elevateChildren(), CExperimentObjectMap::CDataColumn::operator=(), and CQExperimentData::saveTable().
bool CExperimentObjectMap::setRole | ( | const size_t & | index, |
const CExperiment::Type & | role | ||
) |
Set the role of the indexed column
const | size_t & index |
const | CExperiment::Type & role |
Definition at line 142 of file CExperimentObjectMap.cpp.
References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::setRole(), and StringPrint().
Referenced by CExperiment::elevateChildren(), CQExperimentData::loadTable(), CQExperimentData::saveTable(), and CQExperimentData::slotExprimentType().
bool CExperimentObjectMap::setScale | ( | const size_t & | index, |
const C_FLOAT64 & | scale | ||
) |
Set the scaling factor for the indexed column
const | size_t & index |
const | C_FLOAT64 & scale |
Definition at line 188 of file CExperimentObjectMap.cpp.
References CCopasiParameterGroup::getGroup(), CExperimentObjectMap::CDataColumn::setScale(), and StringPrint().
Referenced by CExperimentObjectMap::CDataColumn::operator=(), CQExperimentData::saveTable(), and CExperiment::setWeightMethod().
|
private |
The last mapped column
Definition at line 299 of file CExperimentObjectMap.h.
Referenced by compile(), and getLastColumn().
|
private |
A vector of pointer to the objects corresponding to the data column.
Definition at line 294 of file CExperimentObjectMap.h.
Referenced by compile(), and getMappedObjects().