Cytoscape 2.8.0 API

cytoscape.cruft.obo
Class SynonymReader

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

public final class SynonymReader
extends Reader

The purpose of this class is to convert a 'gene_association.*' file (for example 'gene_association.sgd') into a crufty old '*.syno' 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 '*.syno' 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
SynonymReader(String speciesName, Reader geneAssociationFile)
          Creates a new SynonymReader 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

SynonymReader

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

Parameters:
speciesName - 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

Cytoscape 2.8.0 API

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