org.biopax.paxtools.pattern.miner

Interface Miner

All Known Subinterfaces:

SIFMiner

All Known Implementing Classes:

AbstractSIFMiner, CatalysisPrecedesMiner, ChemicalAffectsThroughBindingMiner, ChemicalAffectsThroughControlMiner, ConsumptionControlledByMiner, ControlsDegradationIndirectMiner, ControlsExpressionMiner, ControlsExpressionWithConvMiner, ControlsPhosphorylationMiner, ControlsProductionOfMiner, ControlsStateChangeDetailedMiner, ControlsStateChangeOfMiner, ControlsTransportMiner, ControlsTransportOfChemicalMiner, CSCOBothControllerAndParticipantMiner, CSCOButIsParticipantMiner, CSCOThroughBindingSmallMoleculeMiner, CSCOThroughControllingSmallMoleculeMiner, CSCOThroughDegradationMiner, DirectedRelationMiner, InComplexWithMiner, InteractsWithMiner, MinerAdapter, NeighborOfMiner, ReactsWithMiner, RelatedGenesOfInteractionsMiner, UbiquitousIDMiner, UsedToProduceMiner

public interface Miner

A miner provides a pattern to mine, and knows how to use the result set to prepare the text output.

Author:

Ozgun Babur

Method Summary

Modifier and Type	Method and Description
String	getDescription() Gets description of the miner.
String	getName() Gets name of the miner.
Pattern	getPattern() Gets the pattern to use for mining the graph.
void	writeResult(Map<BioPAXElement,List<Match>> matches, OutputStream out) Writes the text output to the given stream.

Method Detail

getName

String getName()

Gets name of the miner.

Returns:

name

getDescription

String getDescription()

Gets description of the miner.

Returns:

description

getPattern

Pattern getPattern()

Gets the pattern to use for mining the graph.

Returns:

the pattern

writeResult

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

Writes the text output to the given stream.

Parameters:

matches - pattern search result

out - output stream

Throws:

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