io.github.msdk.datamodel

Class AbstractMsSpectrum

java.lang.Object

io.github.msdk.datamodel.AbstractMsSpectrum

All Implemented Interfaces:

MsSpectrum

Direct Known Subclasses:

MgfMsSpectrum, MspSpectrum, SimpleMsScan, SimpleMsSpectrum

public abstract class AbstractMsSpectrum
extends Object
implements MsSpectrum

Simple implementation of the MsSpectrum interface

Constructor Summary

Constructors

Constructor and Description
AbstractMsSpectrum()

Method Summary

Modifier and Type	Method and Description
float[]	getIntensityValues(float[] array) Returns the intensity values of this spectrum.
com.google.common.collect.Range<Double>	getMzRange() Returns the range of m/z values for the current spectrum.
MzTolerance	getMzTolerance() Returns an object that implements the MzTolerance interface.
double[]	getMzValues(double[] array) Returns the m/z values of this spectrum.
Integer	getNumberOfDataPoints() getNumberOfDataPoints.
MsSpectrumType	getSpectrumType() Returns the type of this mass spectrum.
Float	getTIC() getTIC.
void	setDataPoints(double[] mzValues, float[] intensityValues, Integer size)
void	setMzTolerance(MzTolerance mzTolerance) Setter for the field mzTolerance.
void	setSpectrumType(MsSpectrumType spectrumType)

Methods inherited from class java.lang.Object

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

Methods inherited from interface io.github.msdk.datamodel.MsSpectrum

getIntensityValues, getMzValues

Constructor Detail

AbstractMsSpectrum

public AbstractMsSpectrum()

Method Detail

getNumberOfDataPoints

@Nonnull
public Integer getNumberOfDataPoints()

getNumberOfDataPoints.

Specified by:

getNumberOfDataPoints in interface MsSpectrum

Returns:

a Integer object.

getMzValues

@Nonnull
public double[] getMzValues(@Nullable
                                     double[] array)

Returns the m/z values of this spectrum. Note: this method may need to read data from disk, therefore it may be quite slow.

Specified by:

getMzValues in interface MsSpectrum

Returns:

an array of double.

getIntensityValues

@Nonnull
public float[] getIntensityValues(@Nullable
                                           float[] array)

Returns the intensity values of this spectrum. Note: this method may need to read data from disk, therefore it may be quite slow.

Specified by:

getIntensityValues in interface MsSpectrum

Returns:

an array of float.

setDataPoints

public void setDataPoints(@Nonnull
                          double[] mzValues,
                          @Nonnull
                          float[] intensityValues,
                          @Nonnull
                          Integer size)

Parameters:

mzValues - an array of double.

intensityValues - an array of float.

size - a Integer object.

getSpectrumType

@Nonnull
public MsSpectrumType getSpectrumType()

Returns the type of this mass spectrum. For spectra that are loaded from raw data files, the type is detected automatically. For calculated spectra, the type depends on the method of calculation.

Specified by:

getSpectrumType in interface MsSpectrum

Returns:

spectrum type (profile, centroided, thresholded)

setSpectrumType

public void setSpectrumType(@Nonnull
                            MsSpectrumType spectrumType)

Parameters:

spectrumType - a MsSpectrumType object.

getTIC

@Nonnull
public Float getTIC()

getTIC.

Specified by:

getTIC in interface MsSpectrum

Returns:

a Float object.

getMzRange

public com.google.common.collect.Range<Double> getMzRange()

Returns the range of m/z values for the current spectrum. This can return null if the spectrum has no data points.

Specified by:

getMzRange in interface MsSpectrum

Returns:

m/z range

getMzTolerance

public MzTolerance getMzTolerance()

Returns an object that implements the MzTolerance interface. If not MzTolernace is available, then null is returned.

Specified by:

getMzTolerance in interface MsSpectrum

Returns:

m/z tolerance for the scan

setMzTolerance

public void setMzTolerance(MzTolerance mzTolerance)

Setter for the field mzTolerance.

Parameters:

mzTolerance - a MzTolerance object.