fern.network

Interface Network

All Known Implementing Classes:

AbstractNetworkImpl, AutocatalyticNetwork, CatalysedNetwork, ExtractSubNetwork, FernMLNetwork, ModifierNetwork, ReversibleNetwork, SBMLNetwork

public interface Network

The central interface of the whole framework. Each Simulator takes a Network for simulation, as well as each analysis algorithm takes one. Additionally Networks can be modified or saved as FernML-Files.

Basically only the networks structure is stored here, other things like management of the species populations (amounts), propensities or annotations is sourced out to separate classes. The advantage is that you can reuse existing AmountManagers,... when you are implementing your own network (reader, wrapper, evolver,...) when you think, one of the existing ones is suitable.

Author:

Florian Erhard

See Also:

AnalysisBase, FernMLNetwork.FernMLNetwork(Network), FernMLNetwork.saveToFile(java.io.File), ModifierNetwork

Method Summary

Modifier and Type	Method and Description
AmountManager	getAmountManager() Gets the AmountManager for this network.
AnnotationManager	getAnnotationManager() Gets the AnnotationManager for this network.
long	getInitialAmount(int species) Gets the initial amount of the specified molecule species.
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.
String	getSpeciesName(int index) Gets the species name by index.
void	setInitialAmount(int species, long value) Sets the initial amount of the specified molecule species.

Method Detail

getAmountManager

AmountManager getAmountManager()

Gets the AmountManager for this network.

Returns:

the AmountManager

getPropensityCalculator

PropensityCalculator getPropensityCalculator()

Gets the PropensityCalculator for this network.

Returns:

the PropensityCalculator

getAnnotationManager

AnnotationManager getAnnotationManager()

Gets the AnnotationManager for this network.

Returns:

the AnnotationManager

getNumSpecies

int getNumSpecies()

Gets the number of species within the network.

Returns:

number of species

getNumReactions

int getNumReactions()

Gets the number of reaction within the network.

Returns:

number of reactions

getReactants

int[] getReactants(int reaction)

Gets the reactants of the specified reaction.

Parameters:

reaction - index of the reaction

Returns:

indices of the reactants

getProducts

int[] getProducts(int reaction)

Gets the products of the specified reaction.

Parameters:

reaction - index of the reaction

Returns:

indices of the products

getSpeciesByName

int getSpeciesByName(String name)

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

Parameters:

name - name of the species

Returns:

index of the species

getSpeciesName

String getSpeciesName(int index)

Gets the species name by index.

Parameters:

index - index of the species

Returns:

name of the species

getReactionName

String getReactionName(int index)

Gets a string representation of the reaction.

Parameters:

index - reaction index

Returns:

string representation

getName

String getName()

Gets an identifier of the network.

Returns:

identifier of the network

getInitialAmount

long getInitialAmount(int species)

Gets the initial amount of the specified molecule species.

Parameters:

species - index of the species

Returns:

initial amount of the species

setInitialAmount

void setInitialAmount(int species,
                      long value)

Sets the initial amount of the specified molecule species.

Parameters:

species - index of the species

value - initial amount of the species