org.gersteinlab.tyna.core.io
Class SIFIO

java.lang.Object
  org.gersteinlab.tyna.core.io.SIFIO

All Implemented Interfaces:

GraphReader, GraphWriter

public class SIFIO

extends java.lang.Object

implements GraphReader, GraphWriter

	This class represents the IO unit for the SIF format for directed
	graphs. Each line is of the following form:

	
	...

	Node IDs and relationship types are case-insensitive, and are stored in
	upper case.

	This format does not allow nodes that have no incident edges. Node names
	are case-insensitive. White spaces at the beginning and end of a node
	name are trimmed.
	

Version:

1.0 (November 2, 2005) Change History: 1.0 - Initial version

Author:

Kevin Yuk-Lap Yip

Constructor Summary

SIFIO()

Method Summary

Graph	readGraph(java.io.InputStream in, boolean isDirected, boolean isMultigraph) Read the graph from an input stream.
Graph	readGraph(java.io.Reader in, boolean isDirected, boolean isMultigraph) Read the graph from a reader.
void	writeGraph(Graph graph, java.io.OutputStream out) Write the graph to an output stream.
void	writeGraph(Graph graph, java.io.Writer out) Write the graph to a writer.

Methods inherited from class java.lang.Object

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

Constructor Detail

SIFIO

public SIFIO()

Method Detail

readGraph

public Graph readGraph(java.io.InputStream in,
                       boolean isDirected,
                       boolean isMultigraph)
                throws GraphTypeException,
                       java.io.IOException,
                       InputFormatException

Description copied from interface: GraphReader

Read the graph from an input stream. The class of the returned object depends on the input values of isDirected and isMulti. If isDirected is true, the returned object is an instance of DirectedGraph. Otherwise, it is an instance of UndirectedGraph. If isMulti is true, the returned object is an instance of MultiGraph. Otherwise, it is an instance of SimpleGraph. The method does not close the input stream.

Specified by:

readGraph in interface GraphReader

Parameters:

in - The input stream

isDirected - Whether the graph is to be directed

isMultigraph - Whether the graph is to be a multigraph

Returns:

The graph being read

Throws:

GraphTypeException - When the graph type does not match requirements

java.io.IOException - When there is an IO error

InputFormatException - When the input format is invalid

readGraph

public Graph readGraph(java.io.Reader in,
                       boolean isDirected,
                       boolean isMultigraph)
                throws GraphTypeException,
                       java.io.IOException,
                       InputFormatException

Description copied from interface: GraphReader

Read the graph from a reader. The class of the returned object depends on the input values of isDirected and isMulti. If isDirected is true, the returned object is an instance of DirectedGraph. Otherwise, it is an instance of UndirectedGraph. If isMulti is true, the returned object is an instance of MultiGraph. Otherwise, it is an instance of SimpleGraph. The method does not close the reader.

Specified by:

readGraph in interface GraphReader

Parameters:

in - The reader

isDirected - Whether the graph is to be directed

isMultigraph - Whether the graph is to be a multigraph

Returns:

The graph being read

Throws:

GraphTypeException - When the graph type does not match requirements

InputFormatException - When the input format is invalid

java.io.IOException - When there is an IO error

writeGraph

public void writeGraph(Graph graph,
                       java.io.OutputStream out)
                throws GraphTypeException,
                       java.io.IOException

Description copied from interface: GraphWriter

Write the graph to an output stream. The method does not close the stream.

Specified by:

writeGraph in interface GraphWriter

Parameters:

graph - The graph

out - The output stream

Throws:

java.io.IOException - When there is an IO error

GraphTypeException - When the graph type does not match requirements

writeGraph

public void writeGraph(Graph graph,
                       java.io.Writer out)
                throws GraphTypeException,
                       java.io.IOException

Description copied from interface: GraphWriter

Write the graph to a writer. The method does not close the writer.

Specified by:

writeGraph in interface GraphWriter

Parameters:

graph - The graph

out - The writer

Throws:

java.io.IOException - When there is an IO error

GraphTypeException - When the graph type does not match requirements