Package org.biopax.paxtools.pattern.miner

Interface SIFMiner

All Superinterfaces:

Miner

All Known Implementing Classes:

AbstractSIFMiner, CatalysisPrecedesMiner, ChemicalAffectsThroughBindingMiner, ChemicalAffectsThroughControlMiner, ConsumptionControlledByMiner, ControlsDegradationIndirectMiner, ControlsExpressionMiner, ControlsExpressionWithConvMiner, ControlsPhosphorylationMiner, ControlsProductionOfMiner, ControlsStateChangeOfMiner, ControlsTransportMiner, ControlsTransportOfChemicalMiner, CSCOBothControllerAndParticipantMiner, CSCOButIsParticipantMiner, CSCOThroughBindingSmallMoleculeMiner, CSCOThroughControllingSmallMoleculeMiner, CSCOThroughDegradationMiner, InComplexWithMiner, InteractsWithMiner, NeighborOfMiner, ReactsWithMiner, UsedToProduceMiner

public interface SIFMiner
extends Miner

This interface tells that the miner supports SIF output.

Author:

Ozgun Babur

Method Summary

Modifier and Type	Method	Description
Set<SIFInteraction>	createSIFInteraction(Match m, IDFetcher fetcher)	Creates SIF interactions for the given match.
SIFType	getSIFType()	Gets the type of the interaction.
String	getSourceLabel()	Gets the label of the source node.
String	getTargetLabel()	Gets the label of the target node.
void	setBlacklist(Blacklist blacklist)	Sets the blacklist that can be used during the search.
void	setIDFetcher(IDFetcher idFetcher)	Sets the idFetcher that helps to fasten the search.

Methods inherited from interface org.biopax.paxtools.pattern.miner.Miner

getDescription, getName, getPattern, writeResult

Method Details

getSourceLabel

String getSourceLabel()

Gets the label of the source node.

Returns:

source label

getTargetLabel

String getTargetLabel()

Gets the label of the target node.

Returns:

target label

getSIFType

SIFType getSIFType()

Gets the type of the interaction.

Returns:

interaction type

createSIFInteraction

Set<SIFInteraction> createSIFInteraction(Match m,
 IDFetcher fetcher)

Creates SIF interactions for the given match.

Parameters:

m - match to use for SIF creation

fetcher - ID generator from BioPAX object

Returns:

SIF interaction

setBlacklist

void setBlacklist(Blacklist blacklist)

Sets the blacklist that can be used during the search.

Parameters:

blacklist - the blacklist

setIDFetcher

void setIDFetcher(IDFetcher idFetcher)

Sets the idFetcher that helps to fasten the search.

Parameters:

idFetcher - ID generator from BioPAX object