|
copasi API
0.1
|
|
copasi API
0.1
|
#include <CReactionInterface.h>
Public Member Functions | |
| CReactionInterface (CModel *pModel) | |
| ~CReactionInterface () | |
| void | setReactionName (const std::string &name) |
| const std::string & | getReactionName () const |
| void | setChemEqString (const std::string &eq, const std::string &newFunction) |
| std::string | getChemEqString () const |
| const CChemEqInterface & | getChemEqInterface () const |
| bool | isReversible () const |
| bool | isMulticompartment () const |
| void | setReversibility (bool rev, const std::string &newFunction) |
| void | reverse (bool rev, const std::string &newFunction) |
| const std::vector< std::string > & | getListOfMetabs (CFunctionParameter::Role role) const |
| void | setFunctionWithEmptyMapping (const std::string &fn) |
| void | setFunctionAndDoMapping (const std::string &fn) |
| const std::string & | getFunctionName () const |
| const std::string & | getFunctionDescription () const |
| const CFunction * | getFunction () const |
| std::vector< std::string > | getListOfPossibleFunctions () const |
| C_INT32 | size () const |
| bool | isVector (unsigned C_INT32 index) const |
| CFunctionParameter::Role | getUsage (unsigned C_INT32 index) const |
| std::string | getParameterName (unsigned C_INT32 index) const |
| void | setMapping (unsigned C_INT32 index, std::string mn) |
| void | removeMapping (unsigned C_INT32 index, std::string mn) |
| const std::vector< std::string > & | getMappings (unsigned C_INT32 index) const |
| const std::string & | getMapping (unsigned C_INT32 index) const |
| void | setLocalValue (unsigned C_INT32 index, C_FLOAT64 value) |
| void | setLocal (unsigned C_INT32 index) |
| const C_FLOAT64 & | getLocalValue (unsigned C_INT32 index) const |
| bool | isLocalValue (unsigned C_INT32 index) const |
| void | initFromReaction (const std::string &key) |
| void | initFromReaction (const C_INT32 index) |
| void | initFromReaction (const CReaction *rea) |
| bool | writeBackToReaction (CReaction *rea) |
| bool | createMetabolites () |
| bool | createOtherObjects () const |
| bool | isValid () const |
| bool | isLocked (unsigned C_INT32 index) const |
| bool | isLocked (CFunctionParameter::Role usage) const |
| std::set< const CCopasiObject * > | getDeletedParameters () const |
This class provides an interface for dealing with reactions. For representing the parameter mappings it uses object names. A CReactionInterface allows editing a reaction while trying to keep everything consistent.
Note: Many of the methods need to be provided with a model. While handling of the metabolites is completely independent of the model (they are handled by name, and they don't need to exist), the mapping of Compartments and global parameters is done with the entities that exist in the model. This may seem inconsistent, but the idea is that metabolites can be created from the gui by entering them into the reaction equation. Compartments and global parameters can only be chosen from the list of existing objects.
| CReactionInterface::CReactionInterface | ( | CModel * | pModel | ) |
| CReactionInterface::~CReactionInterface | ( | ) |
| bool CReactionInterface::createMetabolites | ( | ) |
create all metabolites that are needed by the reaction but do not exist in the model yet.
| bool CReactionInterface::createOtherObjects | ( | ) | const |
create all other objects that are needed by the reaction but do not exist in the model yet.
| const CChemEqInterface& CReactionInterface::getChemEqInterface | ( | ) | const [inline] |
| std::string CReactionInterface::getChemEqString | ( | ) | const [inline] |
| std::set< const CCopasiObject * > CReactionInterface::getDeletedParameters | ( | ) | const |
Retrieve the list of parameters which will be deleted
| const CFunction* CReactionInterface::getFunction | ( | ) | const [inline] |
| const std::string& CReactionInterface::getFunctionDescription | ( | ) | const [inline] |
| const std::string& CReactionInterface::getFunctionName | ( | ) | const [inline] |
| const std::vector< std::string > & CReactionInterface::getListOfMetabs | ( | CFunctionParameter::Role | role | ) | const |
This produces a list of metab names (from the chem eq) for use in the combo boxes. The role must be given like a usage, e.g. "SUBSTRATE".
| std::vector< std::string > CReactionInterface::getListOfPossibleFunctions | ( | ) | const |
| const C_FLOAT64& CReactionInterface::getLocalValue | ( | unsigned C_INT32 | index | ) | const [inline] |
| const std::string& CReactionInterface::getMapping | ( | unsigned C_INT32 | index | ) | const [inline] |
| const std::vector< std::string >& CReactionInterface::getMappings | ( | unsigned C_INT32 | index | ) | const [inline] |
| std::string CReactionInterface::getParameterName | ( | unsigned C_INT32 | index | ) | const [inline] |
| const std::string& CReactionInterface::getReactionName | ( | ) | const [inline] |
| CFunctionParameter::Role CReactionInterface::getUsage | ( | unsigned C_INT32 | index | ) | const [inline] |
| void CReactionInterface::initFromReaction | ( | const std::string & | key | ) |
associate the function parameter referenced by "index" with the global parameter named pn. Only valid if the role for this function parameter is "PARAMETER". returns success
| void CReactionInterface::initFromReaction | ( | const C_INT32 | index | ) |
| void CReactionInterface::initFromReaction | ( | const CReaction * | rea | ) |
| bool CReactionInterface::isLocalValue | ( | unsigned C_INT32 | index | ) | const [inline] |
| bool CReactionInterface::isLocked | ( | unsigned C_INT32 | index | ) | const |
Is the mapping of this parameter locked? The bahaviour of this method is different for different roles: SUBSTRATE, PRODUCT: according to the chemical equation MODIFIER: always unlocked TIME: always locked VOLUME, PARAMETER: according to the model
The idea is that in the reaction GUI new species can be entered in the chemical equation that are then created automatically. Compartments and global parameters can only be chosen from those existing in the model.
| bool CReactionInterface::isLocked | ( | CFunctionParameter::Role | usage | ) | const |
| bool CReactionInterface::isMulticompartment | ( | ) | const |
this method tries to find out if the REACTION involves several compartments It only takes into account the metabs that actually exist in the model. A non existing metabolite is assumed not to be in a different compartment
| bool CReactionInterface::isReversible | ( | ) | const [inline] |
| bool CReactionInterface::isValid | ( | ) | const |
| bool CReactionInterface::isVector | ( | unsigned C_INT32 | index | ) | const [inline] |
| void CReactionInterface::removeMapping | ( | unsigned C_INT32 | index, |
| std::string | mn | ||
| ) |
| void CReactionInterface::reverse | ( | bool | rev, |
| const std::string & | newFunction | ||
| ) |
reverse the reaction and set the reversibility. newFunction suggests a new kinetic function which is only used if adequate.
| void CReactionInterface::setChemEqString | ( | const std::string & | eq, |
| const std::string & | newFunction | ||
| ) |
set a new chemical equation. newFunction suggests a new kinetic function which is only used if adequate.
| void CReactionInterface::setFunctionAndDoMapping | ( | const std::string & | fn | ) |
set the function. a new mapping is created that tries to preserve as much information as possible from the old mapping. Then a default mapping is set from the chemical equation and the model (if possible).
| void CReactionInterface::setFunctionWithEmptyMapping | ( | const std::string & | fn | ) |
set the function. an empty mapping is created
| void CReactionInterface::setLocal | ( | unsigned C_INT32 | index | ) | [inline] |
| void CReactionInterface::setLocalValue | ( | unsigned C_INT32 | index, |
| C_FLOAT64 | value | ||
| ) | [inline] |
| void CReactionInterface::setMapping | ( | unsigned C_INT32 | index, |
| std::string | mn | ||
| ) |
| void CReactionInterface::setReactionName | ( | const std::string & | name | ) | [inline] |
| void CReactionInterface::setReversibility | ( | bool | rev, |
| const std::string & | newFunction | ||
| ) |
set the reversibility. newFunction suggests a new kinetic function which is only used if adequate.
| C_INT32 CReactionInterface::size | ( | ) | const [inline] |
| bool CReactionInterface::writeBackToReaction | ( | CReaction * | rea | ) |
writes the information back to a CReaction. createMetabolites() and createOtherObjects() should be called before.
1.7.5.1
