COPASI API
4.16.103
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#include <CMassAction.h>
Public Member Functions | |
virtual const C_FLOAT64 & | calcValue (const CCallParameters< C_FLOAT64 > &callParameters) |
CMassAction (const std::string &name="NoName", const CCopasiContainer *pParent=NULL) | |
CMassAction (const CFunction &src, const CCopasiContainer *pParent=NULL) | |
CMassAction (const TriLogic &reversible, const CCopasiContainer *pParent=NULL) | |
virtual bool | compile () |
virtual bool | dependsOn (const C_FLOAT64 *parameter, const CCallParameters< C_FLOAT64 > &callParameters) const |
virtual bool | setInfix (const std::string &infix) |
virtual std::string | writeMathML (const std::vector< std::vector< std::string > > &variables, bool expand=true, bool fullExpand=true) const |
~CMassAction () | |
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bool | addVariable (const std::string &name, CFunctionParameter::Role usage=CFunctionParameter::VARIABLE, const CFunctionParameter::DataType &type=CFunctionParameter::FLOAT64) |
CFunction (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const Type &type=Function) | |
CFunction (const CFunction &src, const CCopasiContainer *pParent=NULL) | |
CFunction * | createCopy () const |
void | createListOfParametersForMathML (std::vector< std::vector< std::string > > &env) |
const std::string & | getKey () const |
const std::string & | getSBMLId () const |
virtual size_t | getVariableIndex (const std::string &name) const |
CFunctionParameters & | getVariables () |
const CFunctionParameters & | getVariables () const |
virtual const C_FLOAT64 & | getVariableValue (const size_t &index) const |
const TriLogic & | isReversible () const |
bool | isSuitable (const size_t noSubstrates, const size_t noProducts, const TriLogic reversible) |
virtual void | load (CReadConfig &configBuffer, CReadConfig::Mode mode=CReadConfig::SEARCH) |
bool | operator== (const CFunction &rhs) const |
virtual bool | setInfix (const std::string &infix, bool compile) |
void | setReversible (const TriLogic &reversible) |
void | setSBMLId (const std::string &id) |
std::pair< CFunction *, CFunction * > | splitFunction (const CEvaluationNode *node, const std::string &name1, const std::string &name2) const |
virtual void | writeMathML (std::ostream &out, size_t l=0) const |
virtual | ~CFunction () |
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bool | calls (std::set< std::string > &list) const |
CEvaluationTree (const std::string &name="NoName", const CCopasiContainer *pParent=NULL, const Type &type=Function) | |
CEvaluationTree (const CEvaluationTree &src, const CCopasiContainer *pParent=NULL) | |
bool | dependsOnTree (const std::string &name) const |
CCopasiObject::DataObjectSet | getDeletedObjects () const |
std::string::size_type | getErrorPosition () const |
const std::string & | getInfix () const |
const std::vector < CEvaluationNode * > & | getNodeList () const |
CEvaluationNode * | getRoot () |
const CEvaluationNode * | getRoot () const |
const CEvaluationTree::Type & | getType () const |
bool | hasCircularDependency () const |
bool | hasDiscontinuity () const |
bool | isBoolean () const |
bool | isUsable () const |
bool | operator== (const CEvaluationTree &rhs) const |
virtual bool | setRoot (CEvaluationNode *pRootNode) |
bool | setTree (const ASTNode &pRootNode) |
virtual ASTNode * | toAST (const CCopasiDataModel *pDataModel) const |
bool | updateTree () |
virtual | ~CEvaluationTree () |
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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 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 () |
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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 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 () |
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CObjectInterface () | |
virtual | ~CObjectInterface () |
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bool | addUnsupportedAnnotation (const std::string &name, const std::string &xml) |
CAnnotation () | |
CAnnotation (const CAnnotation &src) | |
const std::string & | getMiriamAnnotation () const |
const std::string & | getNotes () const |
UnsupportedAnnotation & | getUnsupportedAnnotations () |
const UnsupportedAnnotation & | getUnsupportedAnnotations () const |
bool | operator== (const CAnnotation &rhs) const |
bool | removeUnsupportedAnnotation (const std::string &name) |
bool | replaceUnsupportedAnnotation (const std::string &name, const std::string &xml) |
void | setMiriamAnnotation (const std::string &miriamAnnotation, const std::string &newId, const std::string &oldId) |
void | setNotes (const std::string ¬es) |
virtual | ~CAnnotation () |
Static Public Attributes | |
static const char * | Infix [] |
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static const std::string | TypeName [] |
static const char * | XMLType [] |
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static const std::vector < CCopasiContainer * > | EmptyList |
Additional Inherited Members | |
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enum | Type { Function = 0, MassAction, PreDefined, UserDefined, Expression, MathExpression } |
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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 |
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typedef std::map< std::string, std::string > | UnsupportedAnnotation |
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static bool | completeFunctionList (std::vector< CFunction * > &list, const size_t &added=0) |
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static CEvaluationTree * | copy (const CEvaluationTree &src) |
static CEvaluationTree * | create (CEvaluationTree::Type type) |
static CEvaluationNode * | fromAST (const ASTNode *pASTNode) |
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static std::vector< Refresh * > | buildUpdateSequence (const DataObjectSet &objects, const DataObjectSet &uptoDateObjects, const DataObjectSet &context=DataObjectSet()) |
static void | setRenameHandler (CRenameHandler *rh) |
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static CAnnotation * | castObject (CCopasiObject *pObject) |
static const CAnnotation * | castObject (const CCopasiObject *pObject) |
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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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bool | initVariables () |
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void | buildCalculationSequence () |
void | calculate () |
bool | compileNodes () |
bool | parse () |
void | setType (const CEvaluationTree::Type &type) |
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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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std::vector< CEvaluationNode * > | mCalculationSequence |
std::string | mInfix |
std::vector< CEvaluationNode * > * | mpNodeList |
CEvaluationNode * | mpRoot |
CEvaluationTree::Type | mType |
bool | mUsable |
C_FLOAT64 | mValue |
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objectMap | mObjects |
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std::string | mKey |
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static CRenameHandler * | smpRenameHandler = NULL |
Created for Copasi by Stefan Hoops (C) Stefan Hoops 2001
Definition at line 30 of file CMassAction.h.
CMassAction::CMassAction | ( | const std::string & | name = "NoName" , |
const CCopasiContainer * | pParent = NULL |
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Default constructor
const | std::string & name (default: "NoName") |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 38 of file CMassAction.cpp.
CMassAction::CMassAction | ( | const CFunction & | src, |
const CCopasiContainer * | pParent = NULL |
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Copy constructor
const CFunction & | src |
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 43 of file CMassAction.cpp.
CMassAction::CMassAction | ( | const TriLogic & | reversible, |
const CCopasiContainer * | pParent = NULL |
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Specified constructor
const | CCopasiContainer * pParent (default: NULL) |
Definition at line 48 of file CMassAction.cpp.
References CONSTRUCTOR_TRACE, CCopasiMessage::ERROR, Infix, MCMassAction, setInfix(), TriFalse, and TriTrue.
CMassAction::~CMassAction | ( | ) |
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Calculates the value of the function
const | CCallParameters<C_FLOAT64> & callParameters |
Reimplemented from CFunction.
Definition at line 69 of file CMassAction.cpp.
References CCallParameters< Type >::begin(), C_FLOAT64, CCallParameters< Type >::end(), CFunction::isReversible(), CEvaluationTree::mValue, and TriFalse.
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Compile the evaluation tree.
Reimplemented from CEvaluationTree.
Definition at line 164 of file CMassAction.cpp.
References CEvaluationTree::mUsable.
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Returns whether the function depends on the given parameter ¶m const void * parameter ¶m const CCallParameters<C_FLOAT64> & callParameters ¶m bool dependsOn
Reimplemented from CFunction.
Definition at line 107 of file CMassAction.cpp.
References CCallParameters< Type >::begin(), CCallParameters< Type >::end(), CFunction::isReversible(), and TriTrue.
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Set the infix description of the tree and compile it.
const | std::string & infix |
Reimplemented from CFunction.
Definition at line 132 of file CMassAction.cpp.
References CFunctionParameters::add(), CFunctionParameters::cleanup(), CFunctionParameter::FLOAT64, CFunction::getVariables(), CFunction::isReversible(), CFunctionParameter::PARAMETER, CFunctionParameter::PRODUCT, CFunction::setInfix(), CFunction::setReversible(), CFunctionParameter::SUBSTRATE, TriFalse, TriTrue, and CFunctionParameter::VFLOAT64.
Referenced by CMassAction().
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Function to write the mathematical formula in format of MathML.
std::ostream | & out |
const | std::vector< std::vector< std::string > > & variables |
bool | expand = true |
bool | fullExpand |
Reimplemented from CFunction.
Definition at line 173 of file CMassAction.cpp.
References CFunction::isReversible(), and TriTrue.
Referenced by CQExpressionWidget::writeMathML().
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Created for COPASI by Stefan Hoops (C) Stefan Hoops 2001
Definition at line 34 of file CMassAction.h.
Referenced by CMassAction(), CQValidatorFunction::validate(), and CQExpressionWidget::writeMathML().