org.expasy.mzjava.glycomics.mol

Interface GlycanMassCalculator

All Known Implementing Classes:

DefaultGlycanMassCalculator

public interface GlycanMassCalculator

Version:

sqrt -1.

Author:

Davide Alocci

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 anomericCarbon, 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 composition 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.

Method Detail

getCrossRingLossMass

double getCrossRingLossMass(IonType ionType,
                          int anomericCarbon,
                          Monosaccharide cleavedMonosaccaride,
                          CutIndexes cutIndexes)

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

Parameters:

ionType - the type of ion taken into account.

anomericCarbon - the carbon linked to the parent.

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

double getGlycosidicDeltaMass(IonType ionType)

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

Parameters:

ionType - the type of ion taken into account.

Returns:

the value of mass.

getGlycosidicDeltaComposition

Composition getGlycosidicDeltaComposition(IonType ionType)

Return the composition that the glycan have lost during the glycosidic fragmentation depending on the ion type.

Parameters:

ionType - the type of ion taken into account.

Returns:

the composition.

calculateMz

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.

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

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.

Parameters:

monosaccharide - the monosaccharide of interest.

Returns:

an array