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

Class UnimodMod

java.lang.Object

org.expasy.mzjava.proteomics.mol.modification.Modification

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

All Implemented Interfaces:

Weighable

public class UnimodMod
extends Modification

A extension of the Modification class to store UniMod specific fields.

Adds fields for:

• approved
• recordId
• interim name
• full name
• sites
• neutral losses
• precursor neutral losses

Version:

sqrt -1

Author:

Oliver Horlacher

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	UnimodMod.Builder

Field Summary

Fields inherited from class org.expasy.mzjava.proteomics.mol.modification.Modification

parsePattern

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	UnimodMod(int recordId, boolean approved, String psiMsName, String interimName, String fullName, gnu.trove.map.TObjectIntMap<Atom> atomCounterMap, List<String> sites, List<NeutralLoss> neutralLosses, List<NeutralLoss> precursorNeutralLosses)

Method Summary

Methods

Modifier and Type	Method and Description
Composition	getComposition() Returns the Composition associated with this UnimodMod.
String	getFullName() Returns the UniMod full name.
String	getInterimName() Returns the UniMod interim name.
List<NeutralLoss>	getNeutralLosses() Return an unmodifiable list containing the neutral losses.
List<NeutralLoss>	getPrecursorNeutralLosses() Returns an unmodifiable list containing the precursor neutral losses.
String	getPsiMsMsName() Returns the psi ms ms name
int	getRecordId() Returns the UniMod record id.
List<String>	getSites() Return the list of modification sites
boolean	isApproved() Returns the approved flag.

Methods inherited from class org.expasy.mzjava.proteomics.mol.modification.Modification

equals, getLabel, getMass, getMolecularMass, hashCode, parseModification, toString

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

UnimodMod

protected UnimodMod(int recordId,
         boolean approved,
         String psiMsName,
         String interimName,
         String fullName,
         gnu.trove.map.TObjectIntMap<Atom> atomCounterMap,
         List<String> sites,
         List<NeutralLoss> neutralLosses,
         List<NeutralLoss> precursorNeutralLosses)

Method Detail

getSites

public List<String> getSites()

Return the list of modification sites

Returns:

Return the list of modification sites

getNeutralLosses

public List<NeutralLoss> getNeutralLosses()

Return an unmodifiable list containing the neutral losses.

Returns:

an unmodifiable list containing the neutral losses

getPrecursorNeutralLosses

public List<NeutralLoss> getPrecursorNeutralLosses()

Returns an unmodifiable list containing the precursor neutral losses.

Returns:

an unmodifiable list containing the precursor neutral losses

getPsiMsMsName

public String getPsiMsMsName()

Returns the psi ms ms name

Returns:

the psi ms ms name

isApproved

public boolean isApproved()

Returns the approved flag.

Returns:

the approved flag

getRecordId

public int getRecordId()

Returns the UniMod record id.

Returns:

the UniMod record id

getInterimName

public String getInterimName()

Returns the UniMod interim name.

Returns:

the UniMod interim name

getFullName

public String getFullName()

Returns the UniMod full name.

Returns:

the UniMod full name

getComposition

public Composition getComposition()

Returns the Composition associated with this UnimodMod.

Returns:

the Composition associated with this UnimodMod