Package edu.claflin.finder.io.graph

Class NOABatchIO

java.lang.Object
edu.claflin.finder.io.graph.NOABatchIO
All Implemented Interfaces:
GraphWriter
public final class NOABatchIO extends 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 Details

    • defaultRelationship

      private final 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 Details

    • NOABatchIO

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

  • Method Details

    • 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 String verifyRelationship(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 - the Edge Data
      Returns:
      the relationship in the edge