org.expasy.mzjava.proteomics.mol.modification.unimod

Class UnimodManager

java.lang.Object

org.expasy.mzjava.proteomics.mol.modification.unimod.UnimodManager

public class UnimodManager
extends Object

This manager handles modifications registering and look ups from many points of view: the names, the masses and the modified sites (AA + terms).

Version:

1.0

Author:

nikitin

Method Summary

Methods

Modifier and Type	Method and Description
static UnimodManager	getInstance()
static com.google.common.base.Optional<UnimodMod>	getModification(String modName)
List<UnimodMod>	getModificationList() Return an unmodifiable list containing all the modifications that are managed by this
static List<Modification>	getModifications(double mass, Tolerance tolerance)
static List<Modification>	getModifications(double mass, Tolerance tolerance, Set<String> aminoAcids)
static void	setUnimodPath(String unimodPath) Set static variable unimodPath to your local unimod.xml file version
static int	size()
String	toString()

Methods inherited from class java.lang.Object

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

Method Detail

getInstance

public static UnimodManager getInstance()

getModifications

public static List<Modification> getModifications(double mass,
                                  Tolerance tolerance)

getModifications

public static List<Modification> getModifications(double mass,
                                  Tolerance tolerance,
                                  Set<String> aminoAcids)

toString

public String toString()

Overrides:

toString in class Object

getModification

public static com.google.common.base.Optional<UnimodMod> getModification(String modName)

size

public static int size()

getModificationList

public List<UnimodMod> getModificationList()

Return an unmodifiable list containing all the modifications that are managed by this

Returns:

an unmodifiable list containing all the modifications that are managed by this

setUnimodPath

public static void setUnimodPath(String unimodPath)

Set static variable unimodPath to your local unimod.xml file version

Parameters:

unimodPath - path to an unimod.xml file