org.biopax.paxtools.pattern.miner

Class AbstractSIFMiner

java.lang.Object

org.biopax.paxtools.pattern.miner.MinerAdapter

org.biopax.paxtools.pattern.miner.AbstractSIFMiner

All Implemented Interfaces:

Miner, SIFMiner

Direct Known Subclasses:

CatalysisPrecedesMiner, ChemicalAffectsThroughBindingMiner, ChemicalAffectsThroughControlMiner, ConsumptionControlledByMiner, ControlsDegradationIndirectMiner, ControlsExpressionMiner, ControlsStateChangeOfMiner, ControlsTransportOfChemicalMiner, CSCOBothControllerAndParticipantMiner, CSCOThroughDegradationMiner, InComplexWithMiner, InteractsWithMiner, NeighborOfMiner, ReactsWithMiner, UsedToProduceMiner

public abstract class AbstractSIFMiner
extends MinerAdapter
implements SIFMiner

Base class for SIF Miners.

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
AbstractSIFMiner(SIFType type) Constructor with interaction type.
AbstractSIFMiner(SIFType type, String supplName, String supplDesc) Constructor with interaction type, supplementary name, supplementary description, and ubiquitous IDs.

Method Summary

Modifier and Type	Method and Description
SIFType	getSIFType() Gets the type of the interaction.
protected void	setType(SIFType type) Sets the SIF type
void	writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) Writes the result as "A used-for-production-of B", where A and B are small molecule names, and whitespace is tab.

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

concat, constructPattern, createSIFInteraction, fetchIDs, getCellularLocations, getChain, getCompoundName, getDeltaCompartments, getDeltaModifications, getDescription, getGeneSymbol, getGeneSymbol, getHeader, getIdentifiers, getIdMap, getMediatorLabels, 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

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

createSIFInteraction, getSourceLabel, getTargetLabel, setBlacklist, setIDFetcher

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

getDescription, getName, getPattern

Constructor Detail

AbstractSIFMiner

public AbstractSIFMiner(SIFType type)

Constructor with interaction type.

Parameters:

type - SIF type

AbstractSIFMiner

public AbstractSIFMiner(SIFType type,
                        String supplName,
                        String supplDesc)

Constructor with interaction type, supplementary name, supplementary description, and ubiquitous IDs. Supplementary name and description are sometimes needed, because there can be multiple miners for the same binary interaction type. In that case these supplementary data is augmented to the name and description of the interaction type.

Parameters:

type - SIF type

supplName - supplementary name

supplDesc - supplemantary description

Method Detail

writeResult

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

Writes the result as "A used-for-production-of B", where A and B are small molecule names, and whitespace is tab.

Specified by:

writeResult in interface Miner

Parameters:

matches - pattern search result

out - output stream

Throws:

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

getSIFType

public SIFType getSIFType()

Description copied from interface: SIFMiner

Gets the type of the interaction.

Specified by:

getSIFType in interface SIFMiner

Returns:

interaction type

setType

protected void setType(SIFType type)

Sets the SIF type

Parameters:

type - interaction type