org.expasy.mzjava.proteomics.ms.spectrum

Class PeptideSpectrum

java.lang.Object

org.expasy.mzjava.core.ms.spectrum.Spectrum<PepFragAnnotation>

org.expasy.mzjava.proteomics.ms.spectrum.PeptideSpectrum

All Implemented Interfaces:

PeakList<PepFragAnnotation>

public class PeptideSpectrum
extends Spectrum<PepFragAnnotation>

Version:

1.0

Author:

Oliver Horlacher

Nested Class Summary

Nested classes/interfaces inherited from interface org.expasy.mzjava.core.ms.peaklist.PeakList

PeakList.Precision

Constructor Summary

Constructors

Modifier	Constructor and Description
	PeptideSpectrum(Peptide peptide, int charge)
	PeptideSpectrum(Peptide peptide, int charge, int initialCapacity, double constantIntensity, PeakList.Precision precision)
	PeptideSpectrum(Peptide peptide, int charge, int initialCapacity, PeakList.Precision precision)
	PeptideSpectrum(Peptide peptide, int charge, PeakList.Precision precision)
protected	PeptideSpectrum(PeptideSpectrum src, PeakProcessor<PepFragAnnotation,PepFragAnnotation> peakProcessor)
protected	PeptideSpectrum(PeptideSpectrum src, PeakProcessorChain<PepFragAnnotation> peakProcessorChain)
	PeptideSpectrum(Spectrum<PepFragAnnotation> src, Peptide peptide, int charge)

Method Summary

Methods

Modifier and Type	Method and Description
void	addProteinAccessionNumbers(Collection<String> accessionNumbers)
void	addProteinAccessionNumbers(String... acc)
PeptideSpectrum	copy(PeakProcessor<PepFragAnnotation,PepFragAnnotation> peakProcessor) Return PeakList copy processed with PeakProcessor
PeptideSpectrum	copy(PeakProcessorChain<PepFragAnnotation> peakProcessorChain) Return PeakList copy processed with PeakProcessorChain
boolean	equals(Object o)
int	getCharge()
Peptide	getPeptide()
List<String>	getProteinAccessionNumbers()
int	hashCode()

Methods inherited from class org.expasy.mzjava.core.ms.spectrum.Spectrum

add, add, add, addAnnotation, addAnnotations, addPeaks, addPeaks, addPeaksNoAnnotations, addSorted, addSorted, apply, apply, calcVectorLength, clear, clearAnnotations, clearAnnotationsAt, cursor, ensureCapacity, getAnnotationIndexes, getAnnotations, getBasePeakIntensity, getBasePeakMz, getClosestIndex, getFirstAnnotation, getId, getIntensities, getIntensities, getIntensities, getIntensity, getMostIntenseIndex, getMostIntenseIndex, getMsLevel, getMz, getMzs, getMzs, getMzs, getPrecision, getPrecursor, getTotalIonCurrent, hasAnnotations, hasAnnotationsAt, indexOf, indexOf, isEmpty, removeAnnotation, setId, setIntensityAt, setMsLevel, setPrecursor, size, sortAnnotations, trimToSize

Methods inherited from class java.lang.Object

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

Constructor Detail

PeptideSpectrum

public PeptideSpectrum(Peptide peptide,
               int charge)

PeptideSpectrum

public PeptideSpectrum(Peptide peptide,
               int charge,
               PeakList.Precision precision)

PeptideSpectrum

public PeptideSpectrum(Peptide peptide,
               int charge,
               int initialCapacity,
               PeakList.Precision precision)

PeptideSpectrum

public PeptideSpectrum(Peptide peptide,
               int charge,
               int initialCapacity,
               double constantIntensity,
               PeakList.Precision precision)

PeptideSpectrum

protected PeptideSpectrum(PeptideSpectrum src,
               PeakProcessor<PepFragAnnotation,PepFragAnnotation> peakProcessor)

PeptideSpectrum

protected PeptideSpectrum(PeptideSpectrum src,
               PeakProcessorChain<PepFragAnnotation> peakProcessorChain)

PeptideSpectrum

public PeptideSpectrum(Spectrum<PepFragAnnotation> src,
               Peptide peptide,
               int charge)

Method Detail

equals

public boolean equals(Object o)

Overrides:

equals in class Spectrum<PepFragAnnotation>

hashCode

public int hashCode()

Overrides:

hashCode in class Spectrum<PepFragAnnotation>

copy

public PeptideSpectrum copy(PeakProcessor<PepFragAnnotation,PepFragAnnotation> peakProcessor)

Description copied from interface: PeakList

Return PeakList copy processed with PeakProcessor

Parameters:

peakProcessor - the processor to process the peaks

Returns:

the copy of this with the peaks processed by peakProcessor

copy

public PeptideSpectrum copy(PeakProcessorChain<PepFragAnnotation> peakProcessorChain)

Description copied from interface: PeakList

Return PeakList copy processed with PeakProcessorChain

Parameters:

peakProcessorChain - the processor chain to process the peaks

Returns:

the copy of this with the peaks processed by peakProcessorChain

getPeptide

public Peptide getPeptide()

getCharge

public int getCharge()

addProteinAccessionNumbers

public void addProteinAccessionNumbers(String... acc)

addProteinAccessionNumbers

public void addProteinAccessionNumbers(Collection<String> accessionNumbers)

getProteinAccessionNumbers

public List<String> getProteinAccessionNumbers()