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java.lang.Objectfern.network.sbml.SBMLPropensityCalculator
public class SBMLPropensityCalculator
Propensity calculator which is used for SBMLNetwork
s. The propensities are
calculated by using a MathTree
derived by the MathML representation of the
kinetic law for each reaction.
Constructor Summary | |
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SBMLPropensityCalculator(SBMLNetwork net)
Creates the MathTree s and parses the parameters. |
Method Summary | |
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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 |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public SBMLPropensityCalculator(SBMLNetwork net)
MathTree
s and parses the parameters.
net
- sbml netowrkMethod Detail |
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public Map<String,Double> getGlobalParameters()
public double calculatePropensity(int reaction, AmountManager amount, Simulator sim)
PropensityCalculator
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.
calculatePropensity
in interface PropensityCalculator
reaction
- index of the reactionamount
- AmountManagersim
- Simulator
public List<Integer> getKineticLawSpecies(int reaction)
ComplexDependenciesPropensityCalculator
getKineticLawSpecies
in interface ComplexDependenciesPropensityCalculator
reaction
- index of the reaction
public MathTree getMathTree(int reaction)
reaction
- index of the reaction
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