Package org.biopax.paxtools.pattern.miner

Class SIFSearcher

java.lang.Object
org.biopax.paxtools.pattern.miner.SIFSearcher
public class SIFSearcher extends Object
Searches a model and generates SIF network using the pattern matches.
Author:
Ozgun Babur

  • Constructor Details

    • SIFSearcher

      public SIFSearcher(SIFType... types)
      Constructor with binary interaction types.
      Parameters:
      types - sif types

    • SIFSearcher

      public SIFSearcher(SIFMiner... miners)
      Constructor with miners.
      Parameters:
      miners - sif miners

    • SIFSearcher

      public SIFSearcher(IDFetcher idFetcher, SIFType... types)
      Constructor with ID fetcher and binary interaction types.
      Parameters:
      idFetcher - ID fetcher
      types - sif types

    • SIFSearcher

      public SIFSearcher(IDFetcher idFetcher, SIFMiner... miners)
      Constructor with ID fetcher and miners.
      Parameters:
      idFetcher - ID fetcher
      miners - sif miners

  • Method Details

    • setBlacklist

      public void setBlacklist(Blacklist blacklist)
      Sets the blacklist that manages IDs of ubique molecules. This is not mandatory but need if ubiquitous small molecules are needed to be handled.
      Parameters:
      blacklist - for identifying ubiquitous small molecules

    • searchSIFGetMatrix

      public AdjacencyMatrix searchSIFGetMatrix(Model model)
      Searches the given model with the contained miners.
      Parameters:
      model - model to search
      Returns:
      sif interactions

    • searchSIF

      public Set<SIFInteraction> searchSIF(Model model)
      Searches the given model with the contained miners.
      Parameters:
      model - model to search
      Returns:
      sif interactions

    • searchSIF

      public boolean searchSIF(Model model, OutputStream out)
      Searches the given model with the contained miners. Writes the textual result to the given output stream. Closes the stream at the end. Produces the simplest version of SIF format.
      Parameters:
      model - model to search
      out - stream to write
      Returns:
      true if any output produced successfully

    • searchSIF

      public boolean searchSIF(Model model, OutputStream out, SIFToText stt)
      Searches the given model with the contained miners. Writes the textual result to the given output stream. Closes the stream at the end.
      Parameters:
      model - model to search
      out - stream to write
      stt - sif to text converter
      Returns:
      true if any output produced successfully