org.expasy.mzjava.glycomics.mol

Class DefaultGlycanMassCalculator

java.lang.Object

org.expasy.mzjava.glycomics.mol.DefaultGlycanMassCalculator

All Implemented Interfaces:

GlycanMassCalculator

public class DefaultGlycanMassCalculator
extends Object
implements GlycanMassCalculator

Version:

sqrt -1.

Author:

Davide Alocci

Constructor Summary

Constructors

Constructor and Description
DefaultGlycanMassCalculator()

Method Summary

Methods

Modifier and Type	Method and Description
double	calculateMz(double molecularMass, int charge, FragmentType fragmentType) Return the value of the mass over charge.
CutIndexes[]	getAllInternalTypeCleavage(Monosaccharide monosaccharide) Return all possible type of internal cleavage for the monosaccharide of interest Before call this method be sure that the molecularMass it is correct.
double	getCrossRingLossMass(IonType ionType, int attachCarbon, Monosaccharide cleavedMonosaccaride, CutIndexes cutIndexes) Return the value of mass that the glycan have lost during the crossring fragmentation depending on the ion type.
Composition	getGlycosidicDeltaComposition(IonType ionType) Return the value of mass that the glycan have lost during the glycosidic fragmentation depending on the ion type.
double	getGlycosidicDeltaMass(IonType ionType) Return the value of mass that the glycan have lost during the glycosidic fragmentation depending on the ion type.

Methods inherited from class java.lang.Object

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

Constructor Detail

DefaultGlycanMassCalculator

public DefaultGlycanMassCalculator()

Method Detail

getCrossRingLossMass

public final double getCrossRingLossMass(IonType ionType,
                          int attachCarbon,
                          Monosaccharide cleavedMonosaccaride,
                          CutIndexes cutIndexes)

Return the value of mass that the glycan have lost during the crossring fragmentation depending on the ion type. It does not take into account the charge of the ion.

Specified by:

getCrossRingLossMass in interface GlycanMassCalculator

Parameters:

ionType - the type of ion taken into account.

attachCarbon - is the number of a carbon that is attached to the remaining part of the ring.

cleavedMonosaccaride - the cleaved monosaccharide in the crossring fragment.

cutIndexes - if is a x or a ion, this paramenter specify the positions of the cut in the monosaccharide ring.

Returns:

the value of mass.

getGlycosidicDeltaMass

public final double getGlycosidicDeltaMass(IonType ionType)

Return the value of mass that the glycan have lost during the glycosidic fragmentation depending on the ion type. It does not take into account the charge of the ion.

Specified by:

getGlycosidicDeltaMass in interface GlycanMassCalculator

Parameters:

ionType - the type of ion taken into account.

Returns:

the value of mass.

getGlycosidicDeltaComposition

public final Composition getGlycosidicDeltaComposition(IonType ionType)

Return the value of mass that the glycan have lost during the glycosidic fragmentation depending on the ion type.

Specified by:

getGlycosidicDeltaComposition in interface GlycanMassCalculator

Parameters:

ionType - the type of ion taken into account.

Returns:

the value of mass.

calculateMz

public final double calculateMz(double molecularMass,
                 int charge,
                 FragmentType fragmentType)

Return the value of the mass over charge. Specify FragmentType.INTACT if you are dealing with precursor. Before call this method be sure that the molecularMass it is correct.

Specified by:

calculateMz in interface GlycanMassCalculator

Parameters:

molecularMass - the molecular mass.

charge - the charge of which calculate.

fragmentType - the fragment type of interest.

Returns:

the value of mass over charge.

getAllInternalTypeCleavage

public final CutIndexes[] getAllInternalTypeCleavage(Monosaccharide monosaccharide)

Return all possible type of internal cleavage for the monosaccharide of interest Before call this method be sure that the molecularMass it is correct.

Specified by:

getAllInternalTypeCleavage in interface GlycanMassCalculator

Parameters:

monosaccharide - the monosaccharide of interest.

Returns:

an array