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java.lang.Objectfern.network.sbml.SBMLPropensityCalculator
fern.cellDesigner.CellDesignerPropensityCalculator
public class CellDesignerPropensityCalculator
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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CellDesignerPropensityCalculator(PluginModel model,
CellDesignerNetworkWrapper 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. |
Methods inherited from class fern.network.sbml.SBMLPropensityCalculator |
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getMathTree |
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 CellDesignerPropensityCalculator(PluginModel model, CellDesignerNetworkWrapper net)
MathTree
s and parses the parameters.
net
- sbml netowrkMethod Detail |
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public Map<String,Double> getGlobalParameters()
getGlobalParameters
in class SBMLPropensityCalculator
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
calculatePropensity
in class SBMLPropensityCalculator
reaction
- index of the reactionamount
- AmountManagersim
- Simulator
public List<Integer> getKineticLawSpecies(int reaction)
ComplexDependenciesPropensityCalculator
getKineticLawSpecies
in interface ComplexDependenciesPropensityCalculator
getKineticLawSpecies
in class SBMLPropensityCalculator
reaction
- index of the reaction
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