Package org.biopax.paxtools.pattern.miner

Class CSCOThroughBindingSmallMoleculeMiner

java.lang.Object

org.biopax.paxtools.pattern.miner.MinerAdapter

org.biopax.paxtools.pattern.miner.AbstractSIFMiner

org.biopax.paxtools.pattern.miner.ControlsStateChangeOfMiner

org.biopax.paxtools.pattern.miner.CSCOThroughBindingSmallMoleculeMiner

All Implemented Interfaces:

Miner, SIFMiner

public class CSCOThroughBindingSmallMoleculeMiner
extends ControlsStateChangeOfMiner

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

Constructor	Description
CSCOThroughBindingSmallMoleculeMiner()	Constructor that sets name and description.

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

CSCOThroughBindingSmallMoleculeMiner

public CSCOThroughBindingSmallMoleculeMiner()

Constructor that sets name and description.

Method Details

constructPattern

public Pattern constructPattern()

Constructs the pattern.

Overrides:

constructPattern in class ControlsStateChangeOfMiner

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 ControlsStateChangeOfMiner

Returns:

labels of elements to collect publication refs

getSourceLabel

public String getSourceLabel()

Description copied from interface: SIFMiner

Gets the label of the source node.

Specified by:

getSourceLabel in interface SIFMiner

Overrides:

getSourceLabel in class ControlsStateChangeOfMiner

Returns:

source label

getTargetLabel

public String getTargetLabel()

Description copied from interface: SIFMiner

Gets the label of the target node.

Specified by:

getTargetLabel in interface SIFMiner

Overrides:

getTargetLabel in class ControlsStateChangeOfMiner

Returns:

target label

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 ControlsStateChangeOfMiner

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 ControlsStateChangeOfMiner

Returns:

labels of elements