fern.network.modification

Class ExtractSubNetwork

java.lang.Object

fern.network.modification.ModifierNetwork

fern.network.modification.ExtractSubNetwork

All Implemented Interfaces:

Network

public class ExtractSubNetwork
extends ModifierNetwork

Extracts some reactions / species from a given net to form a new network. As proposed by ModifierNetwork, the network is not copied but the indices are redirected.

The subnet to be extracted has to be given by BitVectors containing a 1 for an index to be in the extracted subnet.

This class can be used e.g. to extract only the autocatalytic set of an evolved network.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
ExtractSubNetwork(Network originalNet, cern.colt.bitvector.BitVector reactions, cern.colt.bitvector.BitVector species) Extracts a given subnet from a network.

Method Summary

Modifier and Type	Method and Description
AmountManager	getAmountManager() Gets the AmountManager for the extracted subnet.
AnnotationManager	getAnnotationManager() Gets an AnnotationManager for the redirected index space.
long	getInitialAmount(int species) Gets the initial amount of the specified molecule species.
int	getNumReactions() Gets the number of reactions in the extracted subnet.
int	getNumSpecies() Gets the number of species in the extracted subnet.
int[]	getProducts(int reaction) Gets the products of a reaction.
PropensityCalculator	getPropensityCalculator() Gets the PropensityCalculator for the extracted subnet.
int[]	getReactants(int reaction) Gets the reactants of a reaction.
String	getReactionName(int index) Gets a string representation of the reaction
int	getSpeciesByName(String name) Gets the index of the species by its name.
String	getSpeciesName(int index) Gets the name of the species with given index.
void	setInitialAmount(int species, long value) Sets the initial amount of the specified molecule species.

Methods inherited from class fern.network.modification.ModifierNetwork

getName, getOriginalNetwork, getParentNetwork

Methods inherited from class java.lang.Object

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

Constructor Detail

ExtractSubNetwork

public ExtractSubNetwork(Network originalNet,
                         cern.colt.bitvector.BitVector reactions,
                         cern.colt.bitvector.BitVector species)

Extracts a given subnet from a network. The subnet has to be given by BitVectors containing a 1 for each index which has to be in the extracted subnet.

Parameters:

originalNet - network containing the subnet

reactions - reactions of the subnet

species - species of the subnet

Method Detail

getAnnotationManager

public AnnotationManager getAnnotationManager()

Gets an AnnotationManager for the redirected index space.

Specified by:

getAnnotationManager in interface Network

Overrides:

getAnnotationManager in class ModifierNetwork

Returns:

the AnnotationManager object

getNumReactions

public int getNumReactions()

Gets the number of reactions in the extracted subnet.

Specified by:

getNumReactions in interface Network

Overrides:

getNumReactions in class ModifierNetwork

Returns:

number of reactions

getNumSpecies

public int getNumSpecies()

Gets the number of species in the extracted subnet.

Specified by:

getNumSpecies in interface Network

Overrides:

getNumSpecies in class ModifierNetwork

Returns:

number of species

getProducts

public int[] getProducts(int reaction)

Gets the products of a reaction.

Specified by:

getProducts in interface Network

Overrides:

getProducts in class ModifierNetwork

Parameters:

reaction - the index of the reaction

Returns:

indices of the products

getReactants

public int[] getReactants(int reaction)

Gets the reactants of a reaction.

Specified by:

getReactants in interface Network

Overrides:

getReactants in class ModifierNetwork

Parameters:

reaction - the index of the reaction

Returns:

indices of the reactants

getInitialAmount

public long getInitialAmount(int species)

Description copied from interface: Network

Gets the initial amount of the specified molecule species.

Specified by:

getInitialAmount in interface Network

Overrides:

getInitialAmount in class ModifierNetwork

Parameters:

species - index of the species

Returns:

initial amount of the species

setInitialAmount

public void setInitialAmount(int species,
                             long value)

Description copied from interface: Network

Sets the initial amount of the specified molecule species.

Specified by:

setInitialAmount in interface Network

Overrides:

setInitialAmount in class ModifierNetwork

Parameters:

species - index of the species

value - initial amount of the species

getSpeciesName

public String getSpeciesName(int index)

Gets the name of the species with given index.

Specified by:

getSpeciesName in interface Network

Overrides:

getSpeciesName in class ModifierNetwork

Parameters:

index - index of the species

Returns:

name of the species

getSpeciesByName

public int getSpeciesByName(String name)

Gets the index of the species by its name.

Specified by:

getSpeciesByName in interface Network

Overrides:

getSpeciesByName in class ModifierNetwork

Parameters:

name - name of the species

Returns:

index of the species

getAmountManager

public AmountManager getAmountManager()

Gets the AmountManager for the extracted subnet.

Specified by:

getAmountManager in interface Network

Overrides:

getAmountManager in class ModifierNetwork

Returns:

the amount manager

getPropensityCalculator

public PropensityCalculator getPropensityCalculator()

Gets the PropensityCalculator for the extracted subnet.

Specified by:

getPropensityCalculator in interface Network

Overrides:

getPropensityCalculator in class ModifierNetwork

Returns:

the propensity calculator

getReactionName

public String getReactionName(int index)

Gets a string representation of the reaction

Specified by:

getReactionName in interface Network

Overrides:

getReactionName in class ModifierNetwork

Parameters:

index - index of the reaction

Returns:

string representation of the reaction