fern.network

Class AbstractNetworkImpl

java.lang.Object

fern.network.AbstractNetworkImpl

All Implemented Interfaces:

Network

Direct Known Subclasses:

AutocatalyticNetwork, FernMLNetwork, SBMLNetwork

public abstract class AbstractNetworkImpl
extends Object
implements Network

Base implementation for the Network interface. Implementing class only have to create all the protected fields.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
AbstractNetworkImpl(String name) Create the network and give it an identifier.

Method Summary

Modifier and Type	Method and Description
AmountManager	getAmountManager() Gets the AmountManager for this network.
AnnotationManager	getAnnotationManager() Gets the AnnotationManager for this network.
String	getName() Gets an identifier of the network.
int	getNumReactions() Gets the number of reaction within the network.
int	getNumSpecies() Gets the number of species within the network.
int[]	getProducts(int reaction) Gets the products of the specified reaction.
PropensityCalculator	getPropensityCalculator() Gets the PropensityCalculator for this network.
int[]	getReactants(int reaction) Gets the reactants of the specified reaction.
String	getReactionName(int index) Gets a string representation of the reaction.
int	getSpeciesByName(String name) Gets the species index by name.
Map<String,Integer>	getSpeciesMapping() Gets the mapping from species names to their indices.
String	getSpeciesName(int index) Gets the species name by index.

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface fern.network.Network

getInitialAmount, setInitialAmount

Constructor Detail

AbstractNetworkImpl

public AbstractNetworkImpl(String name)

Create the network and give it an identifier.

Parameters:

name - identifier for the network

Method Detail

getAmountManager

public AmountManager getAmountManager()

Description copied from interface: Network

Gets the AmountManager for this network.

Specified by:

getAmountManager in interface Network

Returns:

the AmountManager

getPropensityCalculator

public PropensityCalculator getPropensityCalculator()

Description copied from interface: Network

Gets the PropensityCalculator for this network.

Specified by:

getPropensityCalculator in interface Network

Returns:

the PropensityCalculator

getAnnotationManager

public AnnotationManager getAnnotationManager()

Description copied from interface: Network

Gets the AnnotationManager for this network.

Specified by:

getAnnotationManager in interface Network

Returns:

the AnnotationManager

getNumReactions

public int getNumReactions()

Description copied from interface: Network

Gets the number of reaction within the network.

Specified by:

getNumReactions in interface Network

Returns:

number of reactions

getNumSpecies

public int getNumSpecies()

Description copied from interface: Network

Gets the number of species within the network.

Specified by:

getNumSpecies in interface Network

Returns:

number of species

getProducts

public int[] getProducts(int reaction)

Description copied from interface: Network

Gets the products of the specified reaction.

Specified by:

getProducts in interface Network

Parameters:

reaction - index of the reaction

Returns:

indices of the products

getReactants

public int[] getReactants(int reaction)

Description copied from interface: Network

Gets the reactants of the specified reaction.

Specified by:

getReactants in interface Network

Parameters:

reaction - index of the reaction

Returns:

indices of the reactants

getSpeciesByName

public int getSpeciesByName(String name)

Description copied from interface: Network

Gets the species index by name. If the argument is no valid species, -1 is returned.

Specified by:

getSpeciesByName in interface Network

Parameters:

name - name of the species

Returns:

index of the species

getSpeciesMapping

public Map<String,Integer> getSpeciesMapping()

Gets the mapping from species names to their indices.

Returns:

species mapping

getSpeciesName

public String getSpeciesName(int index)

Description copied from interface: Network

Gets the species name by index.

Specified by:

getSpeciesName in interface Network

Parameters:

index - index of the species

Returns:

name of the species

getReactionName

public String getReactionName(int index)

Description copied from interface: Network

Gets a string representation of the reaction.

Specified by:

getReactionName in interface Network

Parameters:

index - reaction index

Returns:

string representation

getName

public String getName()

Description copied from interface: Network

Gets an identifier of the network.

Specified by:

getName in interface Network

Returns:

identifier of the network