org.biopax.paxtools.pattern.miner

Class ReactsWithMiner

java.lang.Object

org.biopax.paxtools.pattern.miner.MinerAdapter

org.biopax.paxtools.pattern.miner.AbstractSIFMiner

org.biopax.paxtools.pattern.miner.ReactsWithMiner

All Implemented Interfaces:

Miner, SIFMiner

public class ReactsWithMiner
extends AbstractSIFMiner

Miner for the "reacts-with" relation.

Author:

Ozgun Babur

Field Summary

Fields inherited from class org.biopax.paxtools.pattern.miner.MinerAdapter

blacklist, description, idFetcher, idMap, name

Constructor Summary

Constructors

Constructor and Description
ReactsWithMiner() Constructor that sets sif type.

Method Summary

Modifier and Type	Method and Description
Pattern	constructPattern() Constructs the pattern.
String[]	getMediatorLabels() If a SIF miner wants to tell which essential BioPAX elements mediated this relation, then they need to override this method and pass the labels of elements.
String	getSourceLabel() Gets the label of the source node.
String[]	getSourcePELabels() If a SIF miner wants to tell which PhysicalEntity objects acted as source of the relation, they need to override this method and pass the labels of elements.
String	getTargetLabel() Gets the label of the target node.
String[]	getTargetPELabels() If a SIF miner wants to tell which PhysicalEntity objects acted as source of the relation, they need to override this method and pass the labels of elements.

Methods inherited from class org.biopax.paxtools.pattern.miner.AbstractSIFMiner

getSIFType, setType, writeResult

Methods inherited from class org.biopax.paxtools.pattern.miner.MinerAdapter

concat, createSIFInteraction, fetchIDs, getCellularLocations, getChain, getCompoundName, getDeltaCompartments, getDeltaModifications, getDescription, getGeneSymbol, getGeneSymbol, getHeader, getIdentifiers, getIdMap, getModifications, getModifications, getModificationTerm, getName, getPattern, getPositionInString, getPositionStart, getRelationType, getUniprotNameForHuman, getUniprotNameForHuman, getValue, isInhibition, labeledInactive, removeCommon, setBlacklist, setDescription, setIDFetcher, setIdMap, setName, sign, sign, toString, toStringSet, writeResultAsSIF, writeResultDetailed, writeSIFsUsingSIFFramework

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

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

createSIFInteraction, setBlacklist, setIDFetcher

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

getDescription, getName, getPattern

Constructor Detail

ReactsWithMiner

public ReactsWithMiner()

Constructor that sets sif type.

Method Detail

constructPattern

public Pattern constructPattern()

Constructs the pattern.

Specified by:

constructPattern in class MinerAdapter

Returns:

pattern

getSourceLabel

public String getSourceLabel()

Description copied from interface: SIFMiner

Gets the label of the source node.

Returns:

source label

getTargetLabel

public String getTargetLabel()

Description copied from interface: SIFMiner

Gets the label of the target node.

Returns:

target label

getMediatorLabels

public String[] getMediatorLabels()

Description copied from class: MinerAdapter

If a SIF miner wants to tell which essential BioPAX elements mediated this relation, then they need to override this method and pass the labels of elements.

Overrides:

getMediatorLabels in class MinerAdapter

Returns:

labels of elements to collect publication refs

getSourcePELabels

public String[] getSourcePELabels()

Description copied from class: MinerAdapter

If a SIF miner wants to tell which PhysicalEntity objects acted as source of the relation, they need to override this method and pass the labels of elements.

Overrides:

getSourcePELabels in class MinerAdapter

Returns:

labels of elements

getTargetPELabels

public String[] getTargetPELabels()

Description copied from class: MinerAdapter

If a SIF miner wants to tell which PhysicalEntity objects acted as source of the relation, they need to override this method and pass the labels of elements.

Overrides:

getTargetPELabels in class MinerAdapter

Returns:

labels of elements