org.biopax.paxtools.pattern.miner

Class DirectedRelationMiner

java.lang.Object

org.biopax.paxtools.pattern.miner.MinerAdapter

org.biopax.paxtools.pattern.miner.DirectedRelationMiner

All Implemented Interfaces:

Miner

public class DirectedRelationMiner
extends MinerAdapter

Miner for the directed relations between proteins.

Author:

Ozgun Babur

Field Summary

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

blacklist, description, idFetcher, idMap, name, pattern

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
Pattern	constructPattern() Constructs the pattern.
String	getHeader() Sets header of the output.
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()
String	getTargetLabel()
void	writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.

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

concat, createSIFInteraction, fetchIDs, getCellularLocations, getChain, getCompoundName, getDeltaCompartments, getDeltaModifications, getDescription, getGeneSymbol, getGeneSymbol, getIdentifiers, getIdMap, getModifications, getModifications, getModificationTerm, getName, getPattern, getPositionInString, getPositionStart, getRelationType, getSourcePELabels, getTargetPELabels, 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

Constructor Detail

DirectedRelationMiner

public DirectedRelationMiner()

Constructor that sets name and description.

Method Detail

constructPattern

public Pattern constructPattern()

Constructs the pattern.

Specified by:

constructPattern in class MinerAdapter

Returns:

pattern

writeResult

public void writeResult(Map<BioPAXElement,List<Match>> matches,
                        OutputStream out)
                 throws IOException

Writes the result as "A B", where A and B are gene symbols, and whitespace is tab.

Parameters:

matches - pattern search result

out - output stream

Throws:

IOException - when there's a problem writing to the output stream

getHeader

public String getHeader()

Sets header of the output.

Overrides:

getHeader in class MinerAdapter

Returns:

header

getSourceLabel

public String getSourceLabel()

getTargetLabel

public String getTargetLabel()

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