org.expasy.mzjava.proteomics.ms.spectrum

Class PepFragAnnotation

java.lang.Object

org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

All Implemented Interfaces:

PeakAnnotation, Copyable<PeakAnnotation>

public class PepFragAnnotation
extends Object
implements PeakAnnotation

This class is used to annotate peptide fragment peaks in a PeakList.

PepFragAnnotation can store data on the ionType, charge, peptide fragment, isotpe composition

The annotation

Version:

1.0

Author:

Oliver Horlacher, nikitin

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PepFragAnnotation.Builder PepFragAnnotation Builder

Field Summary

Fields

Modifier and Type	Field and Description
static Composition	EMPTY_COMPOSITION

Constructor Summary

Constructors

Constructor and Description
PepFragAnnotation(IonType ionType, int charge, AminoAcidSequence sequence) Construct a PepFragAnnotation
PepFragAnnotation(PepFragAnnotation src) Copy constructor

Method Summary

Methods

Modifier and Type	Method and Description
PepFragAnnotation	copy() Creates and returns a copy of this object.
boolean	equals(Object o)
int	getCharge() Return this peaks charge
PeptideFragment	getFragment() Return the peptide fragment associated with this annotation
IonType	getIonType() Return the peaks ion type
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
double	getTheoreticalMz() Returns the theoretical m/z for this annotation.
int	hashCode()
boolean	hasNeutralLoss() Returns true if this annotation annotates a peak with a neutral loss, false otherwise
String	toSptxtString() Convert this annotation to a SptxtString
String	toString()

Methods inherited from class java.lang.Object

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

Field Detail

EMPTY_COMPOSITION

public static final Composition EMPTY_COMPOSITION

Constructor Detail

PepFragAnnotation

public PepFragAnnotation(PepFragAnnotation src)

Copy constructor

Parameters:

src - the PepFragAnnotation to copy

PepFragAnnotation

public PepFragAnnotation(IonType ionType,
                 int charge,
                 AminoAcidSequence sequence)

Construct a PepFragAnnotation

Parameters:

ionType - the ion type

charge - the charge

sequence - the sequence of the

Method Detail

getIonType

public IonType getIonType()

Return the peaks ion type

Returns:

the peaks ion type

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 PeptideFragment getFragment()

Return the peptide fragment associated with this annotation

Returns:

the peptide 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()

Description copied from interface: PeakAnnotation

Return this peaks charge

Specified by:

getCharge in interface PeakAnnotation

Returns:

this peaks charge

equals

public boolean equals(Object o)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

copy

public PepFragAnnotation 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.

getTheoreticalMz

public double getTheoreticalMz()

Returns the theoretical m/z for this annotation.

Returns:

the theoretical m/z for this annotation

toSptxtString

public String toSptxtString()

Convert this annotation to a SptxtString

Returns:

a string representation of this annotation in the Sptxt format

toString

public String toString()

Overrides:

toString in class Object