Cytoscape 2.8.0 API

cytoscape.cruft.obo
Class OboOntologyReader

java.lang.Object
  extended by java.io.Reader
      extended by cytoscape.cruft.obo.OboOntologyReader
All Implemented Interfaces:
Closeable, Readable

public final class OboOntologyReader
extends Reader

The purpose of this class is to convert a 'gene_ontology.obo' file to a crufty old 'go.onto' file that Cytoscape's BioDataServer understands. The parameter passed to the constructor is the 'gene_ontology.obo' file and the content read from this reader is the crufty old 'go.onto' 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
OboOntologyReader(Reader oboFile)
          Creates a new OboOntologyReader object.
 
Method Summary
 void close()
          Closes the underlying obo 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

OboOntologyReader

public OboOntologyReader(Reader oboFile)
Creates a new OboOntologyReader object.

Parameters:
oboFile - 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 obo file stream as well.

Specified by:
close in interface Closeable
Specified by:
close in class Reader
Throws:
IOException

Cytoscape 2.8.0 API

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