Package org.biopax.paxtools.pattern.miner

Class ExtendedSIFWriter

java.lang.Object
org.biopax.paxtools.pattern.miner.ExtendedSIFWriter
public class ExtendedSIFWriter extends Object
This class is used for writing the binary interactions to a text output stream in the so-called Pathway Commons EXTENDED_BINARY_SIF format.
Author:
Ozgun Babur

  • Constructor Details

    • ExtendedSIFWriter

      public ExtendedSIFWriter()

  • Method Details

    • write

      public static boolean write(Set<SIFInteraction> inters, OutputStream out)
      Writes down the given inferred binary interactions into the output stream using the Pathway Commons one-file EXTENDED_BINARY_SIF format, where edges (interactions) are written first, followed by a single blank line, followed by the nodes section (participant details and annotations). Closes the output stream at the end.
      Parameters:
      inters - binary interactions
      out - stream to write
      Returns:
      true if any output produced successfully

    • writeInteractions

      public static boolean writeInteractions(Set<SIFInteraction> inters, OutputStream out)
      Writes down the given interactions into the given "edges" output stream. Closes the stream at the end.
      Parameters:
      inters - binary interactions
      out - stream to write
      Returns:
      true if any output produced successfully

    • writeParticipants

      public static boolean writeParticipants(Set<SIFInteraction> inters, OutputStream out)
      Writes down the interaction participants' (nodes) details to the given output stream. Closes the stream at the end.
      Parameters:
      inters - binary interactions
      out - stream to write
      Returns:
      true if any output produced successfully