io.github.msdk.spectra.peakinvestigator

Class PeakInvestigatorMsSpectrum

java.lang.Object

io.github.msdk.spectra.peakinvestigator.PeakInvestigatorMsSpectrum

All Implemented Interfaces:

MsSpectrum

public class PeakInvestigatorMsSpectrum
extends Object
implements MsSpectrum

This class is used provide m/z-dependent mass tolerances from PeakInvestigator by decorating an existing instance of MsSpectrum.

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	PeakInvestigatorMsSpectrum.Error

Constructor Summary

Constructors

Constructor and Description
PeakInvestigatorMsSpectrum(MsSpectrum spectrum, TreeMap<Double,PeakInvestigatorMsSpectrum.Error> errors) Constructor for PeakInvestigatorMsSpectrum.

Method Summary

Modifier and Type	Method and Description
PeakInvestigatorMsSpectrum.Error	getError(Double mzValue) getError.
float[]	getIntensityValues(float[] array) Returns the intensity values of this spectrum.
double	getMultiplier() Getter for the field multiplier.
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() Returns the sum of intensities of all data points (total ion current or TIC).
com.google.common.collect.Range<Double>	getToleranceRange(Double mzValue) getToleranceRange.
void	setMultiplier(double multiplier) Setter for the field multiplier.

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

PeakInvestigatorMsSpectrum

public PeakInvestigatorMsSpectrum(MsSpectrum spectrum,
                                  TreeMap<Double,PeakInvestigatorMsSpectrum.Error> errors)

Constructor for PeakInvestigatorMsSpectrum.

Parameters:

spectrum - a MsSpectrum object.

errors - a TreeMap object.

Method Detail

getMultiplier

public double getMultiplier()

Getter for the field multiplier.

Returns:

a double.

setMultiplier

public void setMultiplier(double multiplier)

Setter for the field multiplier.

Parameters:

multiplier - a double.

getSpectrumType

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)

getNumberOfDataPoints

public Integer getNumberOfDataPoints()

getNumberOfDataPoints.

Specified by:

getNumberOfDataPoints in interface MsSpectrum

Returns:

a Integer object.

getMzValues

public 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.

Specified by:

getMzValues in interface MsSpectrum

Returns:

an array of double.

getIntensityValues

public 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.

Specified by:

getIntensityValues in interface MsSpectrum

Returns:

an array of float.

getTIC

public Float getTIC()

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

Specified by:

getTIC in interface MsSpectrum

Returns:

total ion current

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

getToleranceRange

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

getToleranceRange.

Parameters:

mzValue - a Double object.

Returns:

a Range object.

getError

public PeakInvestigatorMsSpectrum.Error getError(Double mzValue)

getError.

Parameters:

mzValue - a Double object.

Returns:

a PeakInvestigatorMsSpectrum.Error object.

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