cytoscape.cruft.obo
Class MolecularFunctionAnnotationReader

java.lang.Object
  java.io.Reader
      cytoscape.cruft.obo.MolecularFunctionAnnotationReader

All Implemented Interfaces:

Closeable, Readable

public final class MolecularFunctionAnnotationReader
extends Reader

The purpose of this class is to convert a 'gene_association.*' file (for example 'gene_association.sgd') into a crufty old 'molfunc.anno' file that Cytoscape's BioDataServer understands. The parameter passed to the constructor is the 'gene_association.*' file and the content read from this reader is the crufty old 'molfunc.anno' file.

Please note that this code was not written with performance in mind. Therefore, evaluating this code will not give a good indication of the author's programming ability.

Field Summary

Fields inherited from class java.io.Reader

lock

Constructor Summary

MolecularFunctionAnnotationReader(String speciesName, Map ontologyTypeMap, Reader geneAssociationFile)
Creates a new MolecularFunctionAnnotationReader object.

MolecularFunctionAnnotationReader(String speciesName, Reader geneAssociationFile)
Creates a new MolecularFunctionAnnotationReader object.

Method Summary

void	close() Closes the underlying gene_association file stream as well.
int	read(char[] cbuf, int off, int len) DOCUMENT ME!

Methods inherited from class java.io.Reader

mark, markSupported, read, read, read, ready, reset, skip

Methods inherited from class java.lang.Object

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

Constructor Detail

MolecularFunctionAnnotationReader

public MolecularFunctionAnnotationReader(String speciesName,
                                         Reader geneAssociationFile)

Creates a new MolecularFunctionAnnotationReader object.

Parameters:

speciesName - DOCUMENT ME!

geneAssociationFile - DOCUMENT ME!

MolecularFunctionAnnotationReader

public MolecularFunctionAnnotationReader(String speciesName,
                                         Map ontologyTypeMap,
                                         Reader geneAssociationFile)

Creates a new MolecularFunctionAnnotationReader object.

Parameters:

speciesName - DOCUMENT ME!

ontologyTypeMap - DOCUMENT ME!

geneAssociationFile - DOCUMENT ME!

Method Detail

read

public final int read(char[] cbuf,
                      int off,
                      int len)
               throws IOException

DOCUMENT ME!

Specified by:

read in class Reader

Parameters:

cbuf - DOCUMENT ME!

off - DOCUMENT ME!

len - DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

close

public final void close()
                 throws IOException

Closes the underlying gene_association file stream as well.

Specified by:

close in interface Closeable

Specified by:

close in class Reader

Throws:

IOException