org.biopax.paxtools.pattern.miner

Class ControlsExpressionWithConvMiner

java.lang.Object

org.biopax.paxtools.pattern.miner.MinerAdapter

org.biopax.paxtools.pattern.miner.AbstractSIFMiner

org.biopax.paxtools.pattern.miner.ControlsExpressionMiner

org.biopax.paxtools.pattern.miner.ControlsExpressionWithConvMiner

All Implemented Interfaces:

Miner, SIFMiner

public class ControlsExpressionWithConvMiner
extends ControlsExpressionMiner

Miner for the transcriptional regulation pattern, modeled using Conversion.

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
ControlsExpressionWithConvMiner() Constructor that sets name and description.

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[]	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[]	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.ControlsExpressionMiner

getSourceLabel, getTargetLabel

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

ControlsExpressionWithConvMiner

public ControlsExpressionWithConvMiner()

Constructor that sets name and description.

Method Detail

constructPattern

public Pattern constructPattern()

Constructs the pattern.

Overrides:

constructPattern in class ControlsExpressionMiner

Returns:

pattern

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 ControlsExpressionMiner

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 ControlsExpressionMiner

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 ControlsExpressionMiner

Returns:

labels of elements