net.sf.ciccgrid.pws
Class Synonyms

java.lang.Object
  net.sf.ciccgrid.pws.Synonyms

public class Synonyms
extends java.lang.Object

Methods to get synonyms from ID's and SMILES and vice versa.

Author:

rguha

Constructor Summary

Synonyms()

Method Summary

java.lang.String[]	getCompoundSynonyms(java.lang.String identifier, boolean isCID) Get the synonyms for a compound.
java.lang.String[]	getSmilesBySynonym(java.lang.String synonym) Returns the SMILES corresponding to a given synonym.
java.lang.String[]	getSubstanceSynonyms(java.lang.String identifier) Get the synonyms for a substance.

Methods inherited from class java.lang.Object

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

Constructor Detail

Synonyms

public Synonyms()
         throws java.sql.SQLException,
                java.lang.ClassNotFoundException

Throws:

java.sql.SQLException

java.lang.ClassNotFoundException

Method Detail

getCompoundSynonyms

public java.lang.String[] getCompoundSynonyms(java.lang.String identifier,
                                              boolean isCID)
                                       throws java.sql.SQLException,
                                              java.lang.ClassNotFoundException

Get the synonyms for a compound.

The compound can be specified via its CID or as a SMILES string

Parameters:

identifier - The CID or SMILES string

isCID - true if the identifier is a CID, false if it is a SMILES string

Returns:

An array of synonyms if any are found, or else an array with the single element None

Throws:

java.sql.SQLException

java.lang.ClassNotFoundException

getSubstanceSynonyms

public java.lang.String[] getSubstanceSynonyms(java.lang.String identifier)
                                        throws java.sql.SQLException,
                                               java.lang.ClassNotFoundException

Get the synonyms for a substance.

Parameters:

identifier - The substance identifier

Returns:

An array of synonyms if found, else an array with the single element None

Throws:

java.sql.SQLException

java.lang.ClassNotFoundException

getSmilesBySynonym

public java.lang.String[] getSmilesBySynonym(java.lang.String synonym)
                                      throws java.lang.Exception

Returns the SMILES corresponding to a given synonym.

Parameters:

synonym - The synonym of interest

Returns:

An array of SMILES if found, else an array with the single string equal to None

Throws:

java.lang.Exception