Package org.biopax.paxtools.pattern.miner

Class ControlsStateChangeOfMiner

java.lang.Object

org.biopax.paxtools.pattern.miner.MinerAdapter

org.biopax.paxtools.pattern.miner.AbstractSIFMiner

org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner

All Implemented Interfaces:

Miner, SIFMiner

Direct Known Subclasses:

ControlsPhosphorylationMiner, ControlsTransportMiner, CSCOButIsParticipantMiner, CSCOThroughBindingSmallMoleculeMiner, CSCOThroughControllingSmallMoleculeMiner

public class ControlsStateChangeOfMiner
extends AbstractSIFMiner

Miner for the controls-state-change pattern.

Author:

Ozgun Babur

Field Summary

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

blacklist, description, idFetcher, idMap, name

Constructor Summary

Constructors

Modifier	Constructor	Description
	ControlsStateChangeOfMiner()	Empty constructor.
protected	ControlsStateChangeOfMiner(String name, String description)	Constructor for extension purposes.
protected	ControlsStateChangeOfMiner(SIFType type)	Constructor for extension purposes.

Method Summary

Modifier and Type	Method	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.Miner

getDescription, getName, getPattern

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

createSIFInteraction, setBlacklist, setIDFetcher

Constructor Details

ControlsStateChangeOfMiner

protected ControlsStateChangeOfMiner(String name,
 String description)

Constructor for extension purposes.

Parameters:

name - name of the miner

description - description of the miner

ControlsStateChangeOfMiner

public ControlsStateChangeOfMiner()

Empty constructor.

ControlsStateChangeOfMiner

protected ControlsStateChangeOfMiner(SIFType type)

Constructor for extension purposes.

Parameters:

type - relation type

Method Details

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