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)
String	getSpecies(BufferedReader taxRd, BufferedReader gaRd)
protected String	getTaxonFromNCBI(String id)
HashMap	getTaxonMap(BufferedReader taxonFileReader)
HashMap	getTaxonMap(File taxonFile)
String	taxIdToName(String taxId, BufferedReader taxRd)

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

Throws:

IOException

taxIdToName

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

Throws:

IOException

checkSpecies

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

Throws:

IOException

getTaxonMap

public HashMap getTaxonMap(File taxonFile)
                    throws IOException

Throws:

IOException

getTaxonMap

public HashMap getTaxonMap(BufferedReader taxonFileReader)
                    throws IOException

Throws:

IOException

getTaxonFromNCBI

protected String getTaxonFromNCBI(String id)
                           throws MalformedURLException

Throws:

MalformedURLException