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java.lang.Objectfern.network.modification.ModifierNetwork
fern.network.modification.MultiplierNetwork
public class MultiplierNetwork
Multiplies the whole network by a factor. Each species and each reaction is copied factor times and
connected corresponding to the original network.
As proposed by ModifierNetwork
, the reactions are not copied
but the indices are redirected. The reactions and species are relabelled to the pattern oldid_nr, where
oldid is the original id of the reaction/species and nr is the zero based number of the copy.
Constructor Summary | |
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MultiplierNetwork(Network originalNet,
int factor)
Creates a new network from an original network and virtually multiplies each reaction and species factor times. |
Method Summary | |
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AmountManager |
getAmountManager()
Gets the AmountManager for the modified network. |
AnnotationManager |
getAnnotationManager()
Gets the AnnotationManager for the modified network. |
int |
getNumReactions()
Gets the number of reactions in the modified network (which is 2*number of reaction in the original network). |
int[] |
getProducts(int reaction)
Gets the products of a reaction |
PropensityCalculator |
getPropensityCalculator()
Gets the PropensityCalculator for the modified network. |
int[] |
getReactants(int reaction)
Gets the reactants of a reaction |
String |
getReactionName(int index)
Gets a string representation of the reaction in the modified network. |
Methods inherited from class fern.network.modification.ModifierNetwork |
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getInitialAmount, getName, getNumSpecies, getOriginalNetwork, getParentNetwork, getSpeciesByName, getSpeciesName, setInitialAmount |
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 MultiplierNetwork(Network originalNet, int factor)
originalNet
- the original networkreversiblePropensityCalculator
- the PropensityCalculator
for the reverse reactionsMethod Detail |
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public AmountManager getAmountManager()
AmountManager
for the modified network.
getAmountManager
in interface Network
getAmountManager
in class ModifierNetwork
AmountManager
for the modified networkpublic int getNumReactions()
getNumReactions
in interface Network
getNumReactions
in class ModifierNetwork
public int[] getProducts(int reaction)
getProducts
in interface Network
getProducts
in class ModifierNetwork
reaction
- index of the reaction
public int[] getReactants(int reaction)
getReactants
in interface Network
getReactants
in class ModifierNetwork
reaction
- index of the reaction
public PropensityCalculator getPropensityCalculator()
PropensityCalculator
for the modified network. If the
original PropensityCalculator
and the one for the reverse reactions
is a AbstractKineticConstantPropensityCalculator
, an AbstractKineticConstantPropensityCalculator
is returned.
getPropensityCalculator
in interface Network
getPropensityCalculator
in class ModifierNetwork
PropensityCalculator
for the modified networkpublic AnnotationManager getAnnotationManager()
AnnotationManager
for the modified network.
getAnnotationManager
in interface Network
getAnnotationManager
in class ModifierNetwork
AnnotationManager
for the modified network.public String getReactionName(int index)
getReactionName
in interface Network
getReactionName
in class ModifierNetwork
index
- index of the reaction
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