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java.lang.Objectfern.network.modification.ModifierNetwork
public abstract class ModifierNetwork
Base class for modified networks, which implements the full Network
interface.
Extending classes should override each method which is
different in the modified network (e.g. in the ReversibleNetwork
only reactions are
virtually doubled, so each method concerning the species do not change).
Note: An extending class should definitely not copy the whole network but should rather redirect indices to the original network when possible in order to minimize the necessary memory.
Constructor Summary | |
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ModifierNetwork(Network originalNet)
Creates a ModifierNetwork from an original network. |
Method Summary | |
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AmountManager |
getAmountManager()
Gets the AmountManager of the original network. |
AnnotationManager |
getAnnotationManager()
Gets the AnnotationManager of the original network |
long |
getInitialAmount(int species)
Gets the initial amount of the specified molecule species. |
String |
getName()
Gets the name of the original network |
int |
getNumReactions()
Gets the number of reaction in the original network. |
int |
getNumSpecies()
Gets the number of species in the original network. |
Network |
getOriginalNetwork()
Gets the original network. |
Network |
getParentNetwork()
Gets the parent 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. |
int |
getSpeciesByName(String name)
Gets the index of the species by its name in the original network. |
String |
getSpeciesName(int index)
Gets the name of the species by index in the original network. |
void |
setInitialAmount(int species,
long value)
Sets the initial amount of the specified molecule species. |
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 ModifierNetwork(Network originalNet)
ModifierNetwork
from an original network.
originalNet
- the network to modifyMethod Detail |
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public String getName()
getName
in interface Network
public AnnotationManager getAnnotationManager()
AnnotationManager
of the original network
getAnnotationManager
in interface Network
AnnotationManager
of the original networkpublic int getNumReactions()
getNumReactions
in interface Network
public int getNumSpecies()
getNumSpecies
in interface Network
public int[] getProducts(int reaction)
getProducts
in interface Network
reaction
- index of the reaction in the original network
public int[] getReactants(int reaction)
getReactants
in interface Network
reaction
- index of the reaction in the original network
public String getSpeciesName(int index)
getSpeciesName
in interface Network
index
- index of the species the original network
public int getSpeciesByName(String name)
getSpeciesByName
in interface Network
name
- name of the species
public AmountManager getAmountManager()
AmountManager
of the original network.
getAmountManager
in interface Network
AmountManager
of the the original networkpublic PropensityCalculator getPropensityCalculator()
PropensityCalculator
of the original network.
getPropensityCalculator
in interface Network
PropensityCalculator
of the the original networkpublic String getReactionName(int index)
getReactionName
in interface Network
index
- index of the reaction in the original network
public long getInitialAmount(int species)
Network
getInitialAmount
in interface Network
species
- index of the species
public void setInitialAmount(int species, long value)
Network
setInitialAmount
in interface Network
species
- index of the speciesvalue
- initial amount of the speciespublic Network getOriginalNetwork()
ExtractSubNetwork
of a ReversibleNetwork
of a
AutocatalyticNetworkExample
), the highest network (here the AutocatalyticNetworkExample
is returned.
public Network getParentNetwork()
ExtractSubNetwork
of a ReversibleNetwork
of a
AutocatalyticNetworkExample
), the parental network (here the ReversibleNetwork
is returned.
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