org.expasy.mzjava.proteomics.ms.spectrum

Class PepFragAnnotation.Builder

java.lang.Object

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

Enclosing class:

PepFragAnnotation

public static class PepFragAnnotation.Builder
extends Object

PepFragAnnotation Builder

Constructor Summary

Constructors

Constructor and Description
PepFragAnnotation.Builder(IonType ionType, int charge, AminoAcidSequence fragment) Construct a new Builder
PepFragAnnotation.Builder(PepFragAnnotation src) Copy constructor

Method Summary

Methods

Modifier and Type	Method and Description
PepFragAnnotation.Builder	addC13(int count) Add count C13 isotopes
PepFragAnnotation.Builder	addH2(int count) Add count H2 isotpes
PepFragAnnotation.Builder	addIsotope(Atom isotope) Add the isotope
PepFragAnnotation.Builder	addIsotopeComposition(Composition isotopeComposition) Add all the atoms from isotopeComposition
PepFragAnnotation	build() Build the PepFragAnnotation annotation.
int	getCharge()
void	setCharge(int charge)
PepFragAnnotation.Builder	setFragment(AminoAcidSequence fragment) Set the fragment
PepFragAnnotation.Builder	setNeutralLoss(Mass neutralLoss) Set the neutral loss

Methods inherited from class java.lang.Object

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

Constructor Detail

PepFragAnnotation.Builder

public PepFragAnnotation.Builder(IonType ionType,
                         int charge,
                         AminoAcidSequence fragment)

Construct a new Builder

Parameters:

ionType - the ion type

charge - the charge

fragment - the amino acid sequence of the fragment

PepFragAnnotation.Builder

public PepFragAnnotation.Builder(PepFragAnnotation src)

Copy constructor

Parameters:

src - the PepFragAnnotation from which to copy the values

Method Detail

setFragment

public PepFragAnnotation.Builder setFragment(AminoAcidSequence fragment)

Set the fragment

Parameters:

fragment - the fragment

Returns:

this builder

setNeutralLoss

public PepFragAnnotation.Builder setNeutralLoss(Mass neutralLoss)

Set the neutral loss

Parameters:

neutralLoss - the neutral loss

Returns:

this builder

addC13

public PepFragAnnotation.Builder addC13(int count)

Add count C13 isotopes

Parameters:

count - the number of C13 isotopes

Returns:

this builder

addH2

public PepFragAnnotation.Builder addH2(int count)

Add count H2 isotpes

Parameters:

count - the number of H2 to add

Returns:

this builder

addIsotope

public PepFragAnnotation.Builder addIsotope(Atom isotope)

Add the isotope

Parameters:

isotope - the isotope to add

Returns:

this builder

addIsotopeComposition

public PepFragAnnotation.Builder addIsotopeComposition(Composition isotopeComposition)

Add all the atoms from isotopeComposition

Parameters:

isotopeComposition - the atoms to add

Returns:

this builder

build

public PepFragAnnotation build()

Build the PepFragAnnotation annotation.

Returns:

the new PepFragAnnotation

setCharge

public void setCharge(int charge)

getCharge

public int getCharge()