COPASI API
4.16.103
|
#include <CScanTask.h>
Public Member Functions | |
void | cleanup () |
virtual CCopasiMethod * | createMethod (const int &type) const |
CScanTask (const CCopasiContainer *pParent=NULL) | |
CScanTask (const CScanTask &src, const CCopasiContainer *pParent=NULL) | |
void | fixBuild81 () |
virtual bool | initialize (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
void | load (CReadConfig &configBuffer) |
bool | outputSeparatorCallback (bool isLast=false) |
virtual bool | process (const bool &useInitialValues) |
bool | processCallback () |
virtual bool | restore () |
~CScanTask () | |
![]() | |
CCopasiTask (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="Task") | |
CCopasiTask (const Type &taskType, const CCopasiContainer *pParent=NULL, const std::string &type="Task") | |
CCopasiTask (const CCopasiTask &src, const CCopasiContainer *pParent=NULL) | |
void | cleanup () |
CProcessReport * | getCallBack () const |
const CDescription & | getDescription () const |
virtual const std::string & | getKey () const |
CCopasiMethod * | getMethod () |
const CCopasiMethod * | getMethod () const |
COutputHandler * | getOutputHandler () const |
const OutputFlag & | getOutputMode () const |
CCopasiProblem * | getProblem () |
const CCopasiProblem * | getProblem () const |
CReport & | getReport () |
const CResult & | getResult () const |
CCopasiParameterGroup * | getSliders () |
Type | getType () const |
const bool & | isScheduled () const |
const bool & | isUpdateModel () const |
virtual void | output (const COutputInterface::Activity &activity) |
virtual void | separate (const COutputInterface::Activity &activity) |
virtual bool | setCallBack (CProcessReport *pCallBack) |
virtual bool | setMethodType (const int &type) |
void | setScheduled (const bool &scheduled) |
void | setType (const Type &type) |
void | setUpdateModel (const bool &updateModel) |
virtual bool | updateMatrices () |
virtual | ~CCopasiTask () |
![]() | |
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 CObjectInterface * | getObject (const CCopasiObjectName &cn) 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 CCopasiObjectName | getCN () const |
virtual const DataObjectSet & | getDirectDependencies (const DataObjectSet &context=DataObjectSet()) const |
CCopasiContainer * | getObjectAncestor (const std::string &type) const |
CCopasiDataModel * | getObjectDataModel () |
const CCopasiDataModel * | getObjectDataModel () const |
virtual std::string | getObjectDisplayName (bool regular=true, bool richtext=false) 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 |
virtual void * | getValuePointer () 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 |
virtual void | print (std::ostream *ostream) 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 Member Functions | |
bool | initSubtask (const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream) |
![]() | |
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) | |
Private Attributes | |
size_t | mhProgress |
bool | mOutputInSubtask |
unsigned C_INT32 | mProgress |
CCopasiTask * | mpSubtask |
bool | mUseInitialValues |
Additional Inherited Members | |
![]() | |
enum | eOutputFlagBase { INITIALIZE = 0x01, STREAM = 0x02, FINISH = 0x04, REPORT = 0x10, PLOT = 0x20, TIME_SERIES = 0x40 } |
enum | OutputFlag { NO_OUTPUT = 0, OUTPUT_BEFORE = INITIALIZE, OUTPUT_AFTER = FINISH, OUTPUT = REPORT | PLOT | STREAM, OUTPUT_SE = REPORT | PLOT | INITIALIZE | STREAM | FINISH, OUTPUT_UI = REPORT | PLOT | TIME_SERIES | INITIALIZE | STREAM | FINISH, ONLY_TIME_SERIES = TIME_SERIES | INITIALIZE | STREAM | FINISH } |
enum | Type { steadyState = 0, timeCourse, scan, fluxMode, optimization, parameterFitting, mca, lyap, tssAnalysis, sens, moieties, crosssection, lna, unset } |
![]() | |
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 bool | isValidMethod (const unsigned int &method, const unsigned int *validMethods) |
![]() | |
static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
![]() | |
std::string | Error |
std::string | Warning |
![]() | |
static const std::string | TypeName [] |
static const unsigned int | ValidMethods [] |
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 } |
![]() | |
CDescription | mDescription |
OutputFlag | mDoOutput |
std::string | mKey |
unsigned C_INT32 | mOutputCounter |
CProcessReport * | mpCallBack |
CState * | mpInitialState |
CCopasiMethod * | mpMethod |
COutputHandler * | mpOutputHandler |
CCopasiProblem * | mpProblem |
CCopasiParameterGroup * | mpSliders |
CReport | mReport |
CResult | mResult |
bool | mScheduled |
Type | mType |
bool | mUpdateModel |
![]() | |
objectMap | mObjects |
![]() | |
static CRenameHandler * | smpRenameHandler = NULL |
Definition at line 34 of file CScanTask.h.
CScanTask::CScanTask | ( | const CCopasiContainer * | pParent = NULL | ) |
default constructor
CScanTask class.
This class implements a scan task which is comprised of a of a problem and a method.
Definition at line 47 of file CScanTask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiMethod::scanMethod.
CScanTask::CScanTask | ( | const CScanTask & | src, |
const CCopasiContainer * | pParent = NULL |
||
) |
Copy constructor
const | CScanTask & src |
Definition at line 61 of file CScanTask.cpp.
References CCopasiContainer::add(), createMethod(), CCopasiTask::mpMethod, CCopasiTask::mpProblem, and CCopasiMethod::scanMethod.
CScanTask::~CScanTask | ( | ) |
void CScanTask::cleanup | ( | ) |
|
virtual |
Create a method of the specified type to solve the task. It is the duty of the caller to release the CCopasiMethod.
const | CCopasiMethod::SubType & type |
Reimplemented from CCopasiTask.
Definition at line 80 of file CScanTask.cpp.
References CScanMethod::createMethod().
Referenced by CScanTask().
void CScanTask::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 322 of file CScanTask.cpp.
References CScanProblem::fixBuild81(), and CCopasiTask::mpProblem.
Referenced by CCopasiXML::fixBuild81().
|
virtual |
Initialize the task. If an ostream is given this ostream is used instead of the target specified in the report. This allows nested tasks to share the same output device.
const | OutputFlag & of |
COutputHandler | * pOutputHandler |
std::ostream | * pOstream (default: NULL) |
Reimplemented from CCopasiTask.
Definition at line 90 of file CScanTask.cpp.
References COutputHandler::addInterface(), CCopasiMessage::COMMANDLINE, CCopasiObject::getObjectDataModel(), CCopasiObject::getObjectName(), CReport::getStream(), CCopasiTask::initialize(), initSubtask(), CCopasiMethod::isValidProblem(), MCCopasiTask, CCopasiTask::mpMethod, CCopasiTask::mpProblem, CCopasiTask::mReport, CReport::open(), and CCopasiTask::REPORT.
|
protected |
Init the subtask
const | OutputFlag & of |
COutputHandler | * pOutputHandler |
Definition at line 235 of file CScanTask.cpp.
References CCopasiTask::crosssection, fatalError, CScanProblem::getContinueFromCurrentState(), CCopasiDataModel::getModel(), CCopasiObject::getObjectDataModel(), CCopasiTask::getProblem(), CCopasiDataModel::getTaskList(), CCopasiParameterGroup::getValue(), CCopasiTask::initialize(), CCopasiTask::lna, CCopasiTask::lyap, CCopasiTask::mca, mOutputInSubtask, CCopasiTask::mpProblem, mpSubtask, mUseInitialValues, CCopasiTask::NO_OUTPUT, CCopasiTask::optimization, CCopasiTask::OUTPUT, CCopasiTask::parameterFitting, CCopasiParameter::Value::pBOOL, CCopasiParameter::Value::pUINT, CCopasiTask::sens, CCopasiTask::setCallBack(), CCopasiProblem::setModel(), CCopasiTask::steadyState, CCopasiTask::timeCourse, CCopasiTask::tssAnalysis, and CCopasiTask::TypeName.
Referenced by initialize().
void CScanTask::load | ( | CReadConfig & | configBuffer | ) |
Loads parameters for this solver with data coming from a CReadConfig object. (CReadConfig object reads an input stream)
configbuffer | reference to a CReadConfig object. |
Definition at line 115 of file CScanTask.cpp.
bool CScanTask::outputSeparatorCallback | ( | bool | isLast = false | ) |
output separators if isLast==true this method has to decide if a separator should be generated dependent on mOutputInSubtask.
Definition at line 227 of file CScanTask.cpp.
References COutputInterface::DURING, mOutputInSubtask, and CCopasiTask::separate().
|
virtual |
Process the task with or without initializing to the initial state.
const | bool & useInitialValues |
Reimplemented from CCopasiTask.
Definition at line 118 of file CScanTask.cpp.
References CProcessReport::addItem(), COutputInterface::AFTER, CModel::applyInitialValues(), COutputInterface::BEFORE, C_INT32, CCrossSectionTask::createEvent(), fatalError, CCopasiProblem::getModel(), CScanMethod::getTotalNumberOfSteps(), CScanMethod::init(), mhProgress, CCopasiTask::mpCallBack, CCopasiTask::mpMethod, CCopasiTask::mpProblem, mProgress, mpSubtask, CCopasiTask::output(), CCrossSectionTask::removeEvent(), CScanMethod::scan(), CCopasiTask::setCallBack(), CProcessReport::setName(), and CScanMethod::setProblem().
bool CScanTask::processCallback | ( | ) |
Do the subtask and the output
Definition at line 201 of file CScanTask.cpp.
References COutputInterface::DURING, CCopasiTask::getProblem(), CCopasiTask::isUpdateModel(), mhProgress, mOutputInSubtask, CCopasiTask::mpCallBack, mProgress, mpSubtask, mUseInitialValues, CCopasiTask::output(), CCopasiTask::process(), CProcessReport::progressItem(), and COptProblem::restoreModel().
Referenced by CScanMethod::calculate().
|
virtual |
Perform necessary cleanup procedures
Reimplemented from CCopasiTask.
Definition at line 187 of file CScanTask.cpp.
References mpSubtask, and CCopasiTask::restore().
|
private |
Handle to process item
Definition at line 52 of file CScanTask.h.
Referenced by process(), and processCallback().
|
private |
Definition at line 59 of file CScanTask.h.
Referenced by initSubtask(), outputSeparatorCallback(), and processCallback().
|
private |
Pointer to the output stream for reporting for progress bar
Definition at line 47 of file CScanTask.h.
Referenced by process(), and processCallback().
|
private |
the subtask
Definition at line 57 of file CScanTask.h.
Referenced by initSubtask(), process(), processCallback(), and restore().
|
private |
Definition at line 61 of file CScanTask.h.
Referenced by initSubtask(), and processCallback().