org.expasy.mzjava.glycomics.ms.spectrum

Class GlycanSpectrum

java.lang.Object

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

org.expasy.mzjava.glycomics.ms.spectrum.GlycanSpectrum

All Implemented Interfaces:

PeakList<GlycanFragAnnotation>

public class GlycanSpectrum
extends Spectrum<GlycanFragAnnotation>

Version:

sqrt -1.

Author:

Davide Alocci

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
	GlycanSpectrum(Glycan glycan, int charge) Constructor for GlycanSpectrum.
	GlycanSpectrum(Glycan glycan, int charge, int initialCapacity, double constantIntensity, PeakList.Precision precision) Constructor for GlycanSpectrum.
	GlycanSpectrum(Glycan glycan, int charge, int initialCapacity, PeakList.Precision precision) Constructor for GlycanSpectrum.
	GlycanSpectrum(Glycan glycan, int charge, PeakList.Precision precision) Constructor for GlycanSpectrum.
protected	GlycanSpectrum(GlycanSpectrum src, PeakProcessor<GlycanFragAnnotation,GlycanFragAnnotation> peakProcessor) Copy constructor
protected	GlycanSpectrum(GlycanSpectrum src, PeakProcessorChain<GlycanFragAnnotation> peakProcessorChain) Copy constructor
	GlycanSpectrum(Spectrum<GlycanFragAnnotation> src, Glycan glycan, int charge) Constructor for GlycanSpectrum.

Method Summary

Methods

Modifier and Type	Method and Description
GlycanSpectrum	copy(PeakProcessor<GlycanFragAnnotation,GlycanFragAnnotation> peakProcessor) Return PeakList copy processed with PeakProcessor
GlycanSpectrum	copy(PeakProcessorChain<GlycanFragAnnotation> peakProcessorChain) Return PeakList copy processed with PeakProcessorChain
boolean	equals(Object o)
int	getCharge() Returns the charge of the peaks in the spectrum.
Glycan	getGlycan() Returns the glycan used for creating the spectrum.
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

GlycanSpectrum

public GlycanSpectrum(Glycan glycan,
              int charge)

Constructor for GlycanSpectrum. The mass spectrum level is already set at two.

Parameters:

glycan - the glycan for creating the spectrum.

charge - the charge of the peaks in the spectrum.

GlycanSpectrum

public GlycanSpectrum(Spectrum<GlycanFragAnnotation> src,
              Glycan glycan,
              int charge)

Constructor for GlycanSpectrum.

Parameters:

src - the spectrum that belong to the glycan

glycan - the glycan used for creating the specturm.

charge - the charge of the peaks in the spectrum.

GlycanSpectrum

public GlycanSpectrum(Glycan glycan,
              int charge,
              PeakList.Precision precision)

Constructor for GlycanSpectrum. The mass spectrum level is already set at two.

Parameters:

glycan - the glycan for creating the spectrum.

charge - the charge of the peaks in the spectrum.

precision - the precision of the peaklist.

GlycanSpectrum

public GlycanSpectrum(Glycan glycan,
              int charge,
              int initialCapacity,
              PeakList.Precision precision)

Constructor for GlycanSpectrum. The mass spectrum level is already set at two.

Parameters:

glycan - the glycan for creating the spectrum.

charge - the charge of the peaks in the spectrum.

initialCapacity - the initial capacity of the peaklist.

precision - the precision of the peaklist.

GlycanSpectrum

public GlycanSpectrum(Glycan glycan,
              int charge,
              int initialCapacity,
              double constantIntensity,
              PeakList.Precision precision)

Constructor for GlycanSpectrum. The mass spectrum level is already set at two.

Parameters:

glycan - the glycan for creating the spectrum.

charge - the charge of the peaks in the spectrum.

initialCapacity - the initial capacity of the peaklist.

constantIntensity - the fixed intensity of each peak.

precision - the precision of the peaklist, in this case you can choose only DOUBLE_CONSTANT or FLOAT_CONSTANT.

GlycanSpectrum

protected GlycanSpectrum(GlycanSpectrum src,
              PeakProcessor<GlycanFragAnnotation,GlycanFragAnnotation> peakProcessor)

Copy constructor

Parameters:

src - the GlycanSpectrum to copy.

GlycanSpectrum

protected GlycanSpectrum(GlycanSpectrum src,
              PeakProcessorChain<GlycanFragAnnotation> peakProcessorChain)

Copy constructor

Parameters:

src - the GlycanSpectrum to copy.

Method Detail

getGlycan

public Glycan getGlycan()

Returns the glycan used for creating the spectrum.

Returns:

the glycan

getCharge

public int getCharge()

Returns the charge of the peaks in the spectrum.

Returns:

the charge.

copy

public GlycanSpectrum copy(PeakProcessor<GlycanFragAnnotation,GlycanFragAnnotation> 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 GlycanSpectrum copy(PeakProcessorChain<GlycanFragAnnotation> 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

equals

public boolean equals(Object o)

Overrides:

equals in class Spectrum<GlycanFragAnnotation>

hashCode

public int hashCode()

Overrides:

hashCode in class Spectrum<GlycanFragAnnotation>