fern.network.sbml

Class SBMLPropensityCalculator

java.lang.Object

fern.network.sbml.SBMLPropensityCalculator

All Implemented Interfaces:

ComplexDependenciesPropensityCalculator, PropensityCalculator

public class SBMLPropensityCalculator
extends Object
implements ComplexDependenciesPropensityCalculator

Propensity calculator which is used for SBMLNetworks. The propensities are calculated by using a MathTree derived by the MathML representation of the kinetic law for each reaction.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
SBMLPropensityCalculator(SBMLinterpreter interpreter) Creates the MathTrees and parses the parameters.

Method Summary

Modifier and Type	Method and Description
double	calculatePropensity(int reaction, AmountManager amount, Simulator sim) Calculates the propensity for a reaction given the amounts of the AmountManager.
Map<String,Double>	getGlobalParameters() Gets the global parameters.
List<Integer>	getKineticLawSpecies(int reaction) Gets the indices of the species that are included in the calculation of the given reaction.
MathTree	getMathTree(int reaction) Gets the internal representation of the sbml kinetic law.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

SBMLPropensityCalculator

public SBMLPropensityCalculator(SBMLinterpreter interpreter)
                         throws org.sbml.jsbml.validator.ModelOverdeterminedException

Creates the MathTrees and parses the parameters.

Parameters:

interpreter - instance of the SBMLinterpreter

Throws:

org.sbml.jsbml.validator.ModelOverdeterminedException

Method Detail

getGlobalParameters

public Map<String,Double> getGlobalParameters()

Gets the global parameters.

Returns:

global parameters

calculatePropensity

public double calculatePropensity(int reaction,
                                  AmountManager amount,
                                  Simulator sim)

Description copied from interface: PropensityCalculator

Calculates the propensity for a reaction given the amounts of the AmountManager. If a positive value for volume is given, it is assumed that the constants are deterministic rate constants and are hence to be transformed to specific reaction rate constants.

Specified by:

calculatePropensity in interface PropensityCalculator

Parameters:

reaction - index of the reaction

amount - AmountManager

sim - Simulator

Returns:

actual propensity of the reaction

getKineticLawSpecies

public List<Integer> getKineticLawSpecies(int reaction)

Description copied from interface: ComplexDependenciesPropensityCalculator

Gets the indices of the species that are included in the calculation of the given reaction.

Specified by:

getKineticLawSpecies in interface ComplexDependenciesPropensityCalculator

Parameters:

reaction - index of the reaction

Returns:

indices of the species included in the reaction's kinetic law

getMathTree

public MathTree getMathTree(int reaction)

Gets the internal representation of the sbml kinetic law.

Parameters:

reaction - index of the reaction

Returns:

a MathTree representation of the kinetic law