org.expasy.mzjava.glycomics.ms.spectrum

Class GlycanFragAnnotation

java.lang.Object

org.expasy.mzjava.glycomics.ms.spectrum.GlycanFragAnnotation

All Implemented Interfaces:

PeakAnnotation, Copyable<PeakAnnotation>

public class GlycanFragAnnotation
extends Object
implements PeakAnnotation

Version:

sqrt -1.

Author:

Davide Alocci

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GlycanFragAnnotation.FragBuilder GlycanFragAnnotation Builder

Field Summary

Fields

Modifier and Type	Field and Description
static Composition	EMPTY_COMPOSITION

Constructor Summary

Constructors

Constructor and Description
GlycanFragAnnotation(GlycanFragAnnotation src) Copy constructor
GlycanFragAnnotation(int charge, GlycanFragment fragment) Construct a GlycanFragAnnotation
GlycanFragAnnotation(int charge, GlycanFragment fragment, Composition isotopeComposition, Mass neutralLoss)

Method Summary

Methods

Modifier and Type	Method and Description
double	calcTheoreticalMz() Returns the theoretical m/z for this annotation.
GlycanFragAnnotation	copy() Creates and returns a copy of this object.
boolean	equals(Object o)
int	getCharge() Return the charge for this annotation.
GlycanFragment	getFragment() Return the glycan fragment associated with this annotation
Composition	getIsotopeComposition() Return the Composition that contains the isotopes.
int	getIsotopeCount() Return the number of isotopes
Mass	getNeutralLoss() Return the mass shift that is associated with this annotation
int	hashCode()
boolean	hasNeutralLoss() Returns true if this annotation annotates a peak with a neutral loss, false otherwise

Methods inherited from class java.lang.Object

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

Field Detail

EMPTY_COMPOSITION

public static final Composition EMPTY_COMPOSITION

Constructor Detail

GlycanFragAnnotation

public GlycanFragAnnotation(int charge,
                    GlycanFragment fragment)

Construct a GlycanFragAnnotation

Parameters:

charge - the charge of the fragment.

fragment - the glycan fragment to be annotated.

GlycanFragAnnotation

public GlycanFragAnnotation(int charge,
                    GlycanFragment fragment,
                    Composition isotopeComposition,
                    Mass neutralLoss)

GlycanFragAnnotation

public GlycanFragAnnotation(GlycanFragAnnotation src)

Copy constructor

Parameters:

src - the GlycanFragAnnotation to copy

Method Detail

hasNeutralLoss

public boolean hasNeutralLoss()

Returns true if this annotation annotates a peak with a neutral loss, false otherwise

Returns:

true if this annotation has a neutral loss, false otherwise

getNeutralLoss

public Mass getNeutralLoss()

Return the mass shift that is associated with this annotation

Returns:

the mass shift that is associated with this annotation

getFragment

public GlycanFragment getFragment()

Return the glycan fragment associated with this annotation

Returns:

the glycan fragment associated with this annotation

getIsotopeCount

public int getIsotopeCount()

Return the number of isotopes

Returns:

the number of isotopes

getIsotopeComposition

public Composition getIsotopeComposition()

Return the Composition that contains the isotopes.

Returns:

the Composition that contains the isotopes

getCharge

public int getCharge()

Return the charge for this annotation.

Specified by:

getCharge in interface PeakAnnotation

Returns:

the charge for this annotation.

calcTheoreticalMz

public double calcTheoreticalMz()

Returns the theoretical m/z for this annotation.

Returns:

the theoretical m/z for this annotation.

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

copy

public final GlycanFragAnnotation copy()

Description copied from interface: Copyable

Creates and returns a copy of this object. The precise meaning of "copy" may depend on the class of the object. The general intent is that, for any object x, the expression:

 x.copy() != x

will be true, and that the expression:

 x.copy().getClass() == x.getClass()

will be true, but these are not absolute requirements. While it is typically the case that:

 x.copy().equals(x)

will be true, this is not an absolute requirement.

Specified by:

copy in interface Copyable<PeakAnnotation>

Returns:

a copy of this instance.