Package 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 Details

    • 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