51 "Elementary Flux Modes",
53 "Parameter Estimation",
54 "Metabolic Control Analysis",
56 "Time Scale Separation Analysis",
60 "Linear Noise Approximation",
73 "metabolicControlAnalysis",
75 "timeScaleSeparationAnalysis",
79 "linearNoiseApproximation",
90 const unsigned int * validMethods)
95 if (method == validMethods[i])
return true;
102 const std::string & type):
110 mpInitialState(NULL),
116 mDoOutput(OUTPUT_SE),
122 const std::string & type):
130 mpInitialState(NULL),
136 mDoOutput(OUTPUT_SE),
137 mpOutputHandler(NULL),
146 mDescription(src.mDescription, this),
147 mResult(src.mResult, this),
148 mScheduled(src.mScheduled),
149 mUpdateModel(src.mUpdateModel),
150 mpInitialState(src.mpInitialState ? new
CState(*src.mpInitialState) : NULL),
153 mReport(src.mReport),
156 mDoOutput(OUTPUT_SE),
157 mpOutputHandler(NULL),
209 std::ostream * pOstream)
254 else if (pOstream == NULL)
258 std::vector< CCopasiContainer * > ListOfContainer;
259 ListOfContainer.push_back(
this);
262 assert(pDataModel != NULL);
416 os << Task.
getObjectName() <<
" Task" << std::endl << std::endl;
424 os <<
"No Problem Specified!" << std::endl;
432 os <<
"No Method Specified!" << std::endl;
456 os << Task.
getObjectName() <<
" Result:" << std::endl << std::endl;
464 os <<
"No Problem Specified!" << std::endl;
CCopasiDataModel * getObjectDataModel()
virtual void separate(const Activity &activity)
bool remove(const std::string &key)
virtual bool setCallBack(CProcessReport *pCallBack)
virtual void print(std::ostream *ostream) const
void setScheduled(const bool &scheduled)
virtual void separate(const COutputInterface::Activity &activity)
static const std::string TypeName[]
CCopasiProblem * getProblem()
friend std::ostream & operator<<(std::ostream &os, const CCopasiObject &o)
const std::string & getObjectName() const
virtual void print(std::ostream *ostream) const
virtual bool initialize(const OutputFlag &of, COutputHandler *pOutputHandler, std::ostream *pOstream)
static const unsigned int ValidMethods[]
const bool & isUpdateModel() const
CDescription(const CCopasiContainer *pParent=NULL)
void setInitialState(const CState &state)
CCopasiTask(const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const std::string &type="Task")
CProcessReport * mpCallBack
void setType(const Type &type)
CCopasiParameterGroup * getSliders()
const bool & isScheduled() const
const std::string & getTarget() const
CProcessReport * getCallBack() const
virtual void output(const COutputInterface::Activity &activity)
CCopasiProblem * mpProblem
static const char * XMLType[]
virtual void addInterface(COutputInterface *pInterface)
const CDescription & getDescription() const
virtual void print(std::ostream *ostream) const
virtual bool setMethodType(const int &type)
unsigned C_INT32 mOutputCounter
CCopasiParameterGroup * mpSliders
CDescription mDescription
virtual bool compile(std::vector< CCopasiContainer * > listOfContainer, const CCopasiDataModel *pDataModel)
virtual bool process(const bool &useInitialValues)
virtual bool restore(const bool &updateModel)
CCopasiMethod * getMethod()
virtual void output(const Activity &activity)
static CKeyFactory * getKeyFactory()
const CState & getInitialState() const
const CResult & getResult() const
bool compileIfNecessary(CProcessReport *pProcessReport)
virtual const std::string & getKey() const
virtual void print(std::ostream *ostream) const
std::ostream * open(const CCopasiDataModel *pDataModel, std::ostream *pOstream=NULL)
static bool isValidMethod(const unsigned int &method, const unsigned int *validMethods)
virtual CCopasiMethod * createMethod(const int &type) const
COutputHandler * getOutputHandler() const
CResult(const CCopasiContainer *pParent=NULL)
bool updateInitialValues()
COutputHandler * mpOutputHandler
void setUpdateModel(const bool &updateModel)
virtual void printResult(std::ostream *ostream) const
CCopasiObject * addObjectReference(const std::string &name, CType &reference, const unsigned C_INT32 &flag=0)
CModel * getModel() const
CCopasiContainer * getObjectParent() const