Package edu.claflin.finder.io.graph

Class NOABatchIO

  • All Implemented Interfaces:
    GraphWriter
    public final class NOABatchIO
extends java.lang.Object
implements GraphWriter
    A class for writing graphs in the NOA batch format. NOA batch format is similar to the SIF format except that multiple graphs are contained within a single file for batch processing by the NOA plugin for Cytoscape. An example batch graph is here:
    Version:
    3.1 May 28, 2015
    Author:
    Charles Allen Schultz II

    • Field Summary

      Fields 
      Modifier and Type Field Description
      private java.lang.String defaultRelationship
      Contains the String representation of the default relationship to use.

    • Constructor Summary

      Constructors 
      Constructor Description
      NOABatchIO​(java.lang.String defaultRelationship)
      Constructs the NOABatchIO object.

    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      private java.lang.String verifyRelationship​(java.lang.Object edgeData)
      Verifies the relationship between edges.
      void writeGraph​(Graph toWrite)
      Writes graphs to memory.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • defaultRelationship

        private final java.lang.String defaultRelationship
        Contains the String representation of the default relationship to use. The default relationship value is used when writing a graph and the graph being read does not use String objects to represent edges. Currently, String objects are being used for simplicity.

    • Constructor Detail

      • NOABatchIO

        public NOABatchIO​(java.lang.String defaultRelationship)
        Constructs the NOABatchIO object.
        Parameters:
        defaultRelationship - the String representing the default edge relationship.

    • Method Detail

      • writeGraph

        public void writeGraph​(Graph toWrite)
        Writes graphs to memory. Writes NOA batch files.
        Specified by:
        writeGraph in interface GraphWriter
        Parameters:
        toWrite - the Graph object to write to memory.

      • verifyRelationship

        private java.lang.String verifyRelationship​(java.lang.Object edgeData)
        Verifies the relationship between edges. Checks to see that the Object used in the Graph for representing an edge is a String. If it not, the default relationship is used instead.
        Parameters:
        edgeData -
        Returns: