fern.analysis

Interface NetworkSearchAction

public interface NetworkSearchAction

Implementing classes of NetworkSearchAction are able to control/watch searches in AnalysisBase. On the one hand they control by using checkReaction, checkSpecies (control if a network node should be visited) and getAdditionalSpeciesNeighbors, getAdditionalSpeciesNeighbors (if there are other neighbors to visit e.g. catalysts of reactions). On the other hand they can watch the searches by implementing reactionDiscovered, reactionFinished and speciesDiscovered, speciesFinished.

Author:

Florian Erhard

Nested Class Summary

Nested Classes

Modifier and Type	Interface and Description
static class	NetworkSearchAction.NeighborType Defines different types of neighborhoods in a Network.

Method Summary

Modifier and Type	Method and Description
boolean	checkReaction(int reaction, NetworkSearchAction.NeighborType neighborType) Gets called, before the reaction is inserted into the search structure.
boolean	checkSpecies(int species, NetworkSearchAction.NeighborType neighborType) Gets called, before the species is inserted into the search structure.
void	finished() Gets called, when the search is done.
Iterable<Integer>	getAdditionalReactionNeighbors(int index) Returns an iterator for additional neighbors of this species
Iterable<Integer>	getAdditionalSpeciesNeighbors(int index) Returns an iterator for additional neighbors of this reaction
void	initialize(Network net) Gets called before anything is inserted into the search structure.
void	reactionDiscovered(int reaction) Gets called when a reaction is inserted into the search structure.
void	reactionFinished(int reaction) Gets called when a reaction gets out of the search structure.
void	speciesDiscovered(int species) Gets called when a species is inserted into the search structure.
void	speciesFinished(int species) Gets called when a species gets out of the search structure.

Method Detail

reactionDiscovered

void reactionDiscovered(int reaction)

Gets called when a reaction is inserted into the search structure.

Parameters:

reaction - index of the inserted reaction

speciesDiscovered

void speciesDiscovered(int species)

Gets called when a species is inserted into the search structure.

Parameters:

species - index of the inserted species

reactionFinished

void reactionFinished(int reaction)

Gets called when a reaction gets out of the search structure.

Parameters:

reaction - index of the reactions

speciesFinished

void speciesFinished(int species)

Gets called when a species gets out of the search structure.

Parameters:

species - index of the species

checkSpecies

boolean checkSpecies(int species,
                     NetworkSearchAction.NeighborType neighborType)

Gets called, before the species is inserted into the search structure. If the implementing instance returns false, the species is not inserted.

Parameters:

species - species index

neighborType - one of the NeighborTypes

Returns:

true if the species should be inserted

checkReaction

boolean checkReaction(int reaction,
                      NetworkSearchAction.NeighborType neighborType)

Gets called, before the reaction is inserted into the search structure. If the implementing instance returns false, the reaction is not inserted.

Parameters:

reaction - reaction index

neighborType - one of the NeighborTypes

Returns:

true if the reaction should be inserted

initialize

void initialize(Network net)

Gets called before anything is inserted into the search structure.

Parameters:

net - the network where the search is going to be performed

finished

void finished()

Gets called, when the search is done.

getAdditionalSpeciesNeighbors

Iterable<Integer> getAdditionalSpeciesNeighbors(int index)

Returns an iterator for additional neighbors of this reaction

Parameters:

index - reaction index

Returns:

iterator of additional neighbors

getAdditionalReactionNeighbors

Iterable<Integer> getAdditionalReactionNeighbors(int index)

Returns an iterator for additional neighbors of this species

Parameters:

index - species index

Returns:

iterator of additional neighbors