io.github.msdk.datamodel

Interface MsSpectrum

All Known Subinterfaces:

MsScan

All Known Implementing Classes:

AbstractMsSpectrum, MgfMsSpectrum, MspSpectrum, MzMLMsScan, NetCDFMsScan, PeakInvestigatorMsSpectrum, SimpleMsScan, SimpleMsSpectrum

public interface MsSpectrum

A mass spectrum. This is a base interface typically extended by other, more specialized interfaces. It may represent a single scan in raw MS data, a calculated isotope pattern, a predicted fragmentation spectrum of a molecule, etc.

Method Summary

Modifier and Type	Method and Description
default float[]	getIntensityValues() Returns the intensity values of this spectrum.
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.
default double[]	getMzValues() Returns the m/z values of this spectrum.
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() Returns the sum of intensities of all data points (total ion current or TIC).

Method Detail

getSpectrumType

@Nonnull
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.

Returns:

spectrum type (profile, centroided, thresholded)

getNumberOfDataPoints

@Nonnull
Integer getNumberOfDataPoints()

getNumberOfDataPoints.

Returns:

a Integer object.

getMzValues

@Nonnull
default double[] getMzValues()

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

Returns:

an array of double.

getMzValues

@Nonnull
double[] getMzValues(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.

Returns:

an array of double.

getIntensityValues

@Nonnull
default float[] getIntensityValues()

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

Returns:

an array of float.

getIntensityValues

@Nonnull
float[] getIntensityValues(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.

Returns:

an array of float.

getTIC

@Nonnull
Float getTIC()

Returns the sum of intensities of all data points (total ion current or TIC).

Returns:

total ion current

getMzRange

@Nullable
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.

Returns:

m/z range

getMzTolerance

@Nullable
MzTolerance getMzTolerance()

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

Returns:

m/z tolerance for the scan