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java.lang.Objectfern.network.modification.ModifierNetwork
fern.network.modification.CatalysedNetwork
public class CatalysedNetwork
Modifies the network by adding reactions X+C -> Y+C (where C is each catalyst of the
original reaction). If a reaction has n catalysts, there will be n+1 reactions
generated. It is only possible to create a CatalysedNetwork
out of a
AutocatalyticNetwork
(or at least of a ModifierNetwork
whose original network
is a AutocatalyticNetwork
).
The AmountManager
automatically monitors the food molecules amounts and whenever
it changes, it is reset to the initial value (given by AutocatalyticNetwork.getMonomerAmount()
.
The PropensityCalculator
's constant is AutocatalyticNetwork.getCatalyzedKineticConstant()
for each reaction with a catalyst and AutocatalyticNetwork.getUncatalyzedKineticConstant()
for
the other ones.
The AnnotationManager
uses the underlying one but removes the AutocatalyticNetwork.CATALYSTS_FIELD
and the field Autocatalytic
from not catalyzed reactions.
Constructor Summary | |
---|---|
CatalysedNetwork(Network originalNet)
Create a catalyzed network from an original network. |
Method Summary | |
---|---|
AmountManager |
getAmountManager()
Gets the AmountManager of the original network. |
AnnotationManager |
getAnnotationManager()
Gets the AnnotationManager of the original network |
int |
getNumReactions()
Gets the number of reaction in the original network. |
int[] |
getProducts(int reaction)
Gets the products of a reaction in the original network. |
PropensityCalculator |
getPropensityCalculator()
Gets the PropensityCalculator of the original network. |
int[] |
getReactants(int reaction)
Gets the reactants of a reaction in the original network. |
String |
getReactionName(int index)
Gets a string representation of the reactio in the original network. |
Methods inherited from class fern.network.modification.ModifierNetwork |
---|
getInitialAmount, getName, getNumSpecies, getOriginalNetwork, getParentNetwork, getSpeciesByName, getSpeciesName, setInitialAmount |
Methods inherited from class java.lang.Object |
---|
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
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public CatalysedNetwork(Network originalNet)
originalNet
- the original networkMethod Detail |
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public int getNumReactions()
ModifierNetwork
getNumReactions
in interface Network
getNumReactions
in class ModifierNetwork
public int[] getReactants(int reaction)
ModifierNetwork
getReactants
in interface Network
getReactants
in class ModifierNetwork
reaction
- index of the reaction in the original network
public int[] getProducts(int reaction)
ModifierNetwork
getProducts
in interface Network
getProducts
in class ModifierNetwork
reaction
- index of the reaction in the original network
public PropensityCalculator getPropensityCalculator()
ModifierNetwork
PropensityCalculator
of the original network.
getPropensityCalculator
in interface Network
getPropensityCalculator
in class ModifierNetwork
PropensityCalculator
of the the original networkpublic AmountManager getAmountManager()
ModifierNetwork
AmountManager
of the original network.
getAmountManager
in interface Network
getAmountManager
in class ModifierNetwork
AmountManager
of the the original networkpublic AnnotationManager getAnnotationManager()
ModifierNetwork
AnnotationManager
of the original network
getAnnotationManager
in interface Network
getAnnotationManager
in class ModifierNetwork
AnnotationManager
of the original networkpublic String getReactionName(int index)
ModifierNetwork
getReactionName
in interface Network
getReactionName
in class ModifierNetwork
index
- index of the reaction in the original network
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