fr.profi.mzdb.model

Class SpectrumData

java.lang.Object

fr.profi.mzdb.model.SpectrumData

public class SpectrumData
extends Object

The Class SpectrumData.

Author:

David Bouyssie

Field Summary

Fields

Modifier and Type	Field and Description
protected float[]	intensityList The intensity list.
protected float[]	leftHwhmList The left hwhm list.
protected double[]	mzList The mz list.
protected int	peaksCount
protected float[]	rightHwhmList The right hwhm list.

Constructor Summary

Constructors

Constructor and Description
SpectrumData(double[] mzList, float[] intensityList) Instantiates a new spectrum data.
SpectrumData(double[] mzList, float[] intensityList, float[] lHwhmList, float[] rHwhmList) Instantiates a new spectrum data.

Method Summary

Modifier and Type	Method and Description
void	addSpectrumData(SpectrumData spectrumData) Adds the spectrum data.
float[]	getIntensityList() Gets the intensity list.
float[]	getLeftHwhmList() Gets the left hwhm list.
double	getMaxMz() Gets the max mz.
double	getMinMz() Gets the min mz.
double[]	getMzList() Gets the mz list.
Peak	getNearestPeak(double mz, double mzTolPPM, ILcContext lcContext) assuming mzList is sorted
int	getNearestPeakIndex(double value)
int	getPeakIndex(double value, double ppmTol)
int	getPeaksCount() Gets the peaks count.
float[]	getRightHwhmList() Gets the right hwhm list.
boolean	isEmpty() Checks if is empty.
SpectrumData	mzRangeFilter(double mzMin, double mzMax) Mz range filter.
void	resizeDataArrays(int newLength) Resize data arrays.
Peak[]	toPeaks(ILcContext lcContext) To peaks.

Methods inherited from class java.lang.Object

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

Field Detail

mzList

protected double[] mzList

The mz list.

intensityList

protected float[] intensityList

The intensity list.

leftHwhmList

protected float[] leftHwhmList

The left hwhm list.

rightHwhmList

protected float[] rightHwhmList

The right hwhm list.

peaksCount

protected int peaksCount

Constructor Detail

SpectrumData

public SpectrumData(double[] mzList,
                    float[] intensityList,
                    float[] lHwhmList,
                    float[] rHwhmList)

Instantiates a new spectrum data.

Parameters:

mzList - the mz list

intensityList - the intensity list

lHwhmList - the l hwhm list

rHwhmList - the r hwhm list

SpectrumData

public SpectrumData(double[] mzList,
                    float[] intensityList)

Instantiates a new spectrum data.

Parameters:

mzList - the mz list

intensityList - the intensity list

Method Detail

getPeaksCount

public int getPeaksCount()

Gets the peaks count.

Returns:

the peaks list

getMzList

public double[] getMzList()

Gets the mz list.

Returns:

the mz list

getIntensityList

public float[] getIntensityList()

Gets the intensity list.

Returns:

the intensity list

getLeftHwhmList

public float[] getLeftHwhmList()

Gets the left hwhm list.

Returns:

the left hwhm list

getRightHwhmList

public float[] getRightHwhmList()

Gets the right hwhm list.

Returns:

the right hwhm list

toPeaks

public Peak[] toPeaks(ILcContext lcContext)

To peaks. A new peaks tab is instantiated at each call

Returns:

the peak[]

addSpectrumData

public void addSpectrumData(SpectrumData spectrumData)

Adds the spectrum data.

Parameters:

spectrumData - the spectrum data

resizeDataArrays

public void resizeDataArrays(int newLength)

Resize data arrays.

Parameters:

newLength - the new length

getMinMz

public double getMinMz()

Gets the min mz.

Returns:

the min mz

getMaxMz

public double getMaxMz()

Gets the max mz.

Returns:

the max mz

isEmpty

public boolean isEmpty()

Checks if is empty.

Returns:

true, if is empty

getNearestPeak

public Peak getNearestPeak(double mz,
                           double mzTolPPM,
                           ILcContext lcContext)

assuming mzList is sorted

getNearestPeakIndex

public int getNearestPeakIndex(double value)

getPeakIndex

public int getPeakIndex(double value,
                        double ppmTol)

mzRangeFilter

public SpectrumData mzRangeFilter(double mzMin,
                                  double mzMax)

Mz range filter.

Parameters:

mzMin - the mz min

mzMax - the mz max

Returns:

the spectrum data