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

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and 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: