fern.analysis

Class AutocatalyticNetworkDetection

java.lang.Object

fern.analysis.AnalysisBase

fern.analysis.AutocatalyticNetworkDetection

public class AutocatalyticNetworkDetection
extends AnalysisBase

Detects the autocatalytic set of the given network if there is any. An autocatalytic set is defined as a set of species that are produced by a path of reactions, starting at some food molecules and fully catalyzed by members of the autocatalytic set.

The algorithm iterates over two modified breath first searches until none of them can exclude species / reactions any more. The first bfs removes reactions that are not catalyzed in the remaining network (and molecule species that are only produced by that reactions). The second bfs removes species, that do not have a path from each necessary food molecule.

Author:

Florian Erhard

Constructor Summary

Constructors

Constructor and Description
AutocatalyticNetworkDetection(Network network) Creates the AutocatalyticDetection by using the in the network built in CatalystIterator.
AutocatalyticNetworkDetection(Network network, CatalystIterator cataIt) Creates the AutocatalyticDetection by using the second argument as CatalystIterator.

Method Summary

Modifier and Type	Method and Description
void	annotate(String field, String value) Adds annotations to each autocatalytic reaction / species.
int	detect() Performs the detection algorithm.
cern.colt.bitvector.BitVector	getAutocatalyticReactions() Gets the autocatalytic reactions as BitVector.
cern.colt.bitvector.BitVector	getAutocatalyticSpecies() Gets the autocatalytic species as BitVector.
boolean	isAutocatalyticReaction(int reaction) Returns true if the given reaction is autocatalytic.
boolean	isAutocatalyticSpecies(int species) Returns true if the given species is autocatalytic.

Methods inherited from class fern.analysis.AnalysisBase

bfs, dfs, search

Methods inherited from class java.lang.Object

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

Constructor Detail

AutocatalyticNetworkDetection

public AutocatalyticNetworkDetection(Network network)

Creates the AutocatalyticDetection by using the in the network built in CatalystIterator. The network has to implement CatalystIterator, otherwise an IllegalArgumentException is thrown.

Parameters:

network - the network to detect the autocatalytic set in

AutocatalyticNetworkDetection

public AutocatalyticNetworkDetection(Network network,
                                     CatalystIterator cataIt)

Creates the AutocatalyticDetection by using the second argument as CatalystIterator.

Parameters:

network - network the network to detect the autocatalytic set in

cataIt - a CatalystIterator for the network

Method Detail

detect

public int detect()

Performs the detection algorithm. The results can be retrieved by the methods getAutocatalyticReactions, getAutocatalyticSpecies, isAutocatalyticReaction, isAutocatalyticSpecies, annotate

Returns:

number of iterations

getAutocatalyticReactions

public cern.colt.bitvector.BitVector getAutocatalyticReactions()

Gets the autocatalytic reactions as BitVector. Throws a RuntimeException if the detection algorithms has not been called.

Returns:

autocatalytic reactions

getAutocatalyticSpecies

public cern.colt.bitvector.BitVector getAutocatalyticSpecies()

Gets the autocatalytic species as BitVector. Throws a RuntimeException if the detection algorithms has not been called.

Returns:

autocatalytic species

isAutocatalyticReaction

public boolean isAutocatalyticReaction(int reaction)

Returns true if the given reaction is autocatalytic. Throws a RuntimeException if the detection algorithms has not been called.

Parameters:

reaction - the reaction index

Returns:

if the reaction is autocatalytic

isAutocatalyticSpecies

public boolean isAutocatalyticSpecies(int species)

Returns true if the given species is autocatalytic. Throws a RuntimeException if the detection algorithms has not been called.

Parameters:

species - the species index

Returns:

if the species is autocatalytic

annotate

public void annotate(String field,
                     String value)

Adds annotations to each autocatalytic reaction / species.

Parameters:

field - name of the annotation

value - value of the annotation