cytoscape.util
Class BioDataServerUtil

java.lang.Object
  cytoscape.util.BioDataServerUtil

public class BioDataServerUtil
extends Object

Constructor Summary

BioDataServerUtil()

Method Summary

String	checkSpecies(BufferedReader gaReader, BufferedReader taxonFileReader) DOCUMENT ME!
String	getSpecies(BufferedReader taxRd, BufferedReader gaRd) DOCUMENT ME!
protected String	getTaxonFromNCBI(String id)
HashMap	getTaxonMap(BufferedReader taxonFileReader) DOCUMENT ME!
HashMap	getTaxonMap(File taxonFile) DOCUMENT ME!
String	taxIdToName(String taxId, BufferedReader taxRd) DOCUMENT ME!

Methods inherited from class java.lang.Object

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

Constructor Detail

BioDataServerUtil

public BioDataServerUtil()

Method Detail

getSpecies

public String getSpecies(BufferedReader taxRd,
                         BufferedReader gaRd)
                  throws IOException

DOCUMENT ME!

Parameters:

taxRd - DOCUMENT ME!

gaRd - DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

taxIdToName

public String taxIdToName(String taxId,
                          BufferedReader taxRd)
                   throws IOException

DOCUMENT ME!

Parameters:

taxId - DOCUMENT ME!

taxRd - DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

checkSpecies

public String checkSpecies(BufferedReader gaReader,
                           BufferedReader taxonFileReader)
                    throws IOException

DOCUMENT ME!

Parameters:

gaReader - DOCUMENT ME!

taxonFileReader - DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

getTaxonMap

public HashMap getTaxonMap(File taxonFile)
                    throws IOException

DOCUMENT ME!

Parameters:

taxonFile - DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

getTaxonMap

public HashMap getTaxonMap(BufferedReader taxonFileReader)
                    throws IOException

DOCUMENT ME!

Parameters:

taxonFileReader - DOCUMENT ME!

Returns:

DOCUMENT ME!

Throws:

IOException - DOCUMENT ME!

getTaxonFromNCBI

protected String getTaxonFromNCBI(String id)
                           throws MalformedURLException

Throws:

MalformedURLException