org.biopax.paxtools.pattern.util

Class ChemicalNameNormalizer

java.lang.Object

org.biopax.paxtools.pattern.util.ChemicalNameNormalizer

public class ChemicalNameNormalizer
extends Object

This class is used for finding a standard name for a small molecule. During detection of ubiquitous small molecules, we map the duplicated small molecules to one standard name, otherwise their degree would be divided and this would spoil the detection method.

Author:

Ozgun Babur

Constructor Summary

Constructors

Constructor and Description
ChemicalNameNormalizer(Model model) Constructor that also infers all the mapping.

Method Summary

Modifier and Type	Method and Description
String	getName(SmallMoleculeReference smr) Gets the standard name of the small molecule.
static void	main(String[] args)

Methods inherited from class java.lang.Object

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

Constructor Detail

ChemicalNameNormalizer

public ChemicalNameNormalizer(Model model)

Constructor that also infers all the mapping.

Parameters:

model - the big picture

Method Detail

main

public static void main(String[] args)
                 throws FileNotFoundException

Throws:

FileNotFoundException

getName

public String getName(SmallMoleculeReference smr)

Gets the standard name of the small molecule.

Parameters:

smr - the molecule to check standard name

Returns:

standard name