COPASI API
4.16.103
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#include <CScanProblem.h>
Public Types | |
enum | Type { SCAN_REPEAT = 0, SCAN_LINEAR, SCAN_RANDOM, SCAN_BREAK } |
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typedef parameterGroup::iterator | index_iterator |
typedef CCopasiContainer::objectMap::iterator | name_iterator |
typedef std::vector < CCopasiParameter * > | parameterGroup |
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enum | Type { DOUBLE = 0, UDOUBLE, INT, UINT, BOOL, GROUP, STRING, CN, KEY, FILE, EXPRESSION, INVALID } |
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typedef std::multimap < std::string, CCopasiObject * > | objectMap |
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typedef std::set< const CCopasiObject * > | DataObjectSet |
typedef std::vector< Refresh * > | DataUpdateSequence |
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typedef std::set< const CObjectInterface * > | ObjectSet |
typedef std::vector < CObjectInterface * > | UpdateSequence |
Public Member Functions | |
CCopasiParameterGroup * | addScanItem (CScanProblem::Type type, size_t steps=5, const CCopasiObject *obj=NULL) |
void | clearScanItems () |
CScanProblem (const CCopasiContainer *pParent=NULL) | |
CScanProblem (const CScanProblem &src, const CCopasiContainer *pParent=NULL) | |
void | fixBuild81 () |
bool | getContinueFromCurrentState () const |
size_t | getNumberOfScanItems () const |
const bool & | getOutputInSubtask () const |
const CCopasiParameterGroup * | getScanItem (size_t index) const |
CCopasiParameterGroup * | getScanItem (size_t index) |
CCopasiTask::Type | getSubtask () const |
void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::NEXT) |
bool | removeScanItem (const size_t &index) |
void | setContinueFromCurrentState (bool aic) |
void | setOutputInSubtask (bool ois) |
void | setSubtask (CCopasiTask::Type type) |
~CScanProblem () | |
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CCopasiProblem (const CCopasiProblem &src, const CCopasiContainer *pParent=NULL) | |
CModel * | getModel () const |
const CCopasiTask::Type & | getType () const |
virtual bool | initialize () |
virtual void | print (std::ostream *ostream) const |
virtual void | printResult (std::ostream *ostream) const |
virtual bool | restore (const bool &updateModel) |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual bool | setModel (CModel *pModel) |
virtual | ~CCopasiProblem () |
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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 () |
virtual bool | elevateChildren () |
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 CCopasiParameterGroup * | createScanItem (CScanProblem::Type type, size_t steps=5, const CCopasiObject *obj=NULL) |
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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 () |
Private Attributes | |
CCopasiParameterGroup * | mpScanItems |
Additional Inherited Members | |
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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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CCopasiProblem (const CCopasiTask::Type &type, 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 |
CModel * | mpModel |
CReport * | mpReport |
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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 |
CScanProblem class.
Definition at line 30 of file CScanProblem.h.
enum CScanProblem::Type |
Enumerator | |
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SCAN_REPEAT | |
SCAN_LINEAR | |
SCAN_RANDOM | |
SCAN_BREAK |
Definition at line 33 of file CScanProblem.h.
CScanProblem::CScanProblem | ( | const CCopasiContainer * | pParent = NULL | ) |
Default constructor.
const | CCopasiContainer * pParent (default: NULL) |
CScanProblem class. Default constructor.
CModel * | pModel |
Definition at line 31 of file CScanProblem.cpp.
References initializeParameter().
CScanProblem::CScanProblem | ( | const CScanProblem & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor.
const | CTrajectoryProblem & src CCopasiContainer * pParent (default: NULL) |
Copy constructor.
const CScanProblem & | src |
Definition at line 42 of file CScanProblem.cpp.
References initializeParameter().
CScanProblem::~CScanProblem | ( | ) |
CCopasiParameterGroup * CScanProblem::addScanItem | ( | CScanProblem::Type | type, |
size_t | steps = 5 , |
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const CCopasiObject * | obj = NULL |
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Definition at line 135 of file CScanProblem.cpp.
References CCopasiParameterGroup::addParameter(), createScanItem(), and mpScanItems.
Referenced by SEDMLImporter::importTasks(), and ScanWidget::saveTask().
void CScanProblem::clearScanItems | ( | ) |
Definition at line 184 of file CScanProblem.cpp.
References CCopasiParameterGroup::clear(), and mpScanItems.
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Definition at line 149 of file CScanProblem.cpp.
References CCopasiParameterGroup::addParameter(), CCopasiParameter::BOOL, C_FLOAT64, C_INT32, CCopasiParameterGroup::CCopasiParameterGroup(), CCopasiParameter::CN, CCopasiParameter::DOUBLE, CCopasiObject::getCN(), SCAN_BREAK, SCAN_LINEAR, SCAN_RANDOM, and CCopasiParameter::UINT.
Referenced by addScanItem(), and ScanWidget::slotAddItem().
void CScanProblem::fixBuild81 | ( | ) |
Fix files written with Version 4.12.81 and earlier, which wrote the exp(mean) and exp(std. deviation) for normal random distributions in the scan task.
Definition at line 189 of file CScanProblem.cpp.
References CCopasiParameterGroup::beginIndex(), CCopasiParameterGroup::endIndex(), CCopasiParameterGroup::getParameter(), CCopasiParameter::getValue(), CCopasiParameter::GROUP, mpScanItems, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pDOUBLE, CCopasiParameter::Value::pUINT, SCAN_RANDOM, and CCopasiParameter::setValue().
Referenced by CScanTask::fixBuild81().
bool CScanProblem::getContinueFromCurrentState | ( | ) | const |
Retrieve whether the subtask should continue with its last result.
Definition at line 94 of file CScanProblem.cpp.
References CCopasiParameter::getValue(), and CCopasiParameter::Value::pBOOL.
Referenced by CSEDMLExporter::createScanTask(), CScanMethod::init(), CScanTask::initSubtask(), CScanMethod::isValidProblem(), CScanWidgetTask::load(), and CScanWidgetTask::save().
size_t CScanProblem::getNumberOfScanItems | ( | ) | const |
Definition at line 103 of file CScanProblem.cpp.
References mpScanItems, and CCopasiParameterGroup::size().
Referenced by CSEDMLExporter::createScanTask(), CScanMethod::init(), CScanMethod::isValidProblem(), ScanWidget::loadTask(), and ScanWidget::saveTask().
const bool & CScanProblem::getOutputInSubtask | ( | ) | const |
Ask if output should be done after every step of the subtask.
Definition at line 84 of file CScanProblem.cpp.
References CCopasiParameter::getValue(), and CCopasiParameter::Value::pBOOL.
Referenced by CScanWidgetTask::load(), and CScanWidgetTask::save().
const CCopasiParameterGroup * CScanProblem::getScanItem | ( | size_t | index | ) | const |
Definition at line 108 of file CScanProblem.cpp.
References CCopasiParameterGroup::getParameter(), CCopasiParameter::getType(), CCopasiParameter::GROUP, and mpScanItems.
Referenced by CSEDMLExporter::createScanTask(), CScanMethod::init(), CScanMethod::isValidProblem(), ScanWidget::loadTask(), and ScanWidget::saveTask().
CCopasiParameterGroup * CScanProblem::getScanItem | ( | size_t | index | ) |
Definition at line 121 of file CScanProblem.cpp.
References CCopasiParameterGroup::getParameter(), CCopasiParameter::getType(), CCopasiParameter::GROUP, and mpScanItems.
CCopasiTask::Type CScanProblem::getSubtask | ( | ) | const |
Get the type of the subtask.
Definition at line 74 of file CScanProblem.cpp.
References CCopasiParameter::getValue(), and CCopasiParameter::Value::pUINT.
Referenced by COutputAssistant::createPlot(), CSEDMLExporter::createScanTask(), CScanWidgetTask::load(), and CScanWidgetTask::save().
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Initialize the method parameter
Definition at line 56 of file CScanProblem.cpp.
References CCopasiParameterGroup::addGroup(), CCopasiParameterGroup::addParameter(), CCopasiParameter::BOOL, C_INT32, CCopasiParameterGroup::getParameter(), mpScanItems, CCopasiTask::timeCourse, and CCopasiParameter::UINT.
Referenced by CScanProblem().
void CScanProblem::load | ( | CReadConfig & | configBuffer, |
CReadConfig::Mode | mode = CReadConfig::NEXT |
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Load a scan problem
CReadConfig & | configBuffer |
"CReadConfig::Mode | mode (Default: CReadConfig::NEXT) |
Definition at line 99 of file CScanProblem.cpp.
bool CScanProblem::removeScanItem | ( | const size_t & | index | ) |
Definition at line 143 of file CScanProblem.cpp.
References mpScanItems, and CCopasiParameterGroup::removeParameter().
Referenced by ScanWidget::saveTask().
void CScanProblem::setContinueFromCurrentState | ( | bool | aic | ) |
Set whether the subtask should continue with its last result.
Definition at line 89 of file CScanProblem.cpp.
References CCopasiParameterGroup::setValue().
Referenced by SEDMLImporter::importTasks(), and CScanWidgetTask::save().
void CScanProblem::setOutputInSubtask | ( | bool | ois | ) |
Set if output should be done after every step of the subtask.
Definition at line 79 of file CScanProblem.cpp.
References CCopasiParameterGroup::setValue().
Referenced by SEDMLImporter::importTasks(), and CScanWidgetTask::save().
void CScanProblem::setSubtask | ( | CCopasiTask::Type | type | ) |
Set the type of the subtask.
Definition at line 69 of file CScanProblem.cpp.
References C_INT32, and CCopasiParameterGroup::setValue().
Referenced by SEDMLImporter::importTasks(), and CScanWidgetTask::save().
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private |
This holds the scan items
Definition at line 46 of file CScanProblem.h.
Referenced by addScanItem(), clearScanItems(), fixBuild81(), getNumberOfScanItems(), getScanItem(), initializeParameter(), and removeScanItem().