org.proteios.io
Class SpectrumImpl

java.lang.Object
  org.proteios.io.SpectrumImpl

All Implemented Interfaces:

SpectrumInterface

public class SpectrumImpl
extends Object
implements SpectrumInterface

This class implements the SpectrumInterface that defines methods to access an array of mass or intensity values for mass spectrometry peak lists.

Author:

olle

Constructor Summary

SpectrumImpl()

Method Summary

void	addExtraData(StringPairInterface extraData) Add spectrum extra data.
void	addPrecursor(SpectrumPrecursor precursor)
List<StringPairInterface>	getExtraDataList() Get the spectrum extra data list.
List<SpectrumPrecursor>	getPrecursors()
Double	getRetentionTimeInMinutes() Get the retention time in minutes.
double[]	listIntensities() Get the intensity array.
double[]	listMass() Get the mass array.
void	setExtraDataList(List<StringPairInterface> extraDataList) Set the spectrum extra data list.
void	setIntensities(double[] dataIntensityArray) Set the intensity array.
void	setMass(double[] dataMassArray) Set the mass array.
void	setPrecursors(List<SpectrumPrecursor> precursors)
void	setRetentionTimeInMinutes(Double retentionTimeInMinutes) Set the retention time in minutes.

Methods inherited from class java.lang.Object

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

Constructor Detail

SpectrumImpl

public SpectrumImpl()

Method Detail

setMass

public void setMass(double[] dataMassArray)

Set the mass array.

Parameters:

dataMassArray - double[] array of mass values to set

setIntensities

public void setIntensities(double[] dataIntensityArray)

Set the intensity array.

Parameters:

dataIntensityArray - double[] array of intensity values to set

setRetentionTimeInMinutes

public void setRetentionTimeInMinutes(Double retentionTimeInMinutes)

Set the retention time in minutes.

Parameters:

retentionTimeInMinutes - Double

setPrecursors

public void setPrecursors(List<SpectrumPrecursor> precursors)

addPrecursor

public void addPrecursor(SpectrumPrecursor precursor)

setExtraDataList

public void setExtraDataList(List<StringPairInterface> extraDataList)

Set the spectrum extra data list.

Parameters:

extraDataList - List The spectrum extra data list to set.

addExtraData

public void addExtraData(StringPairInterface extraData)

Add spectrum extra data.

Parameters:

extraData - StringPairInterface The spectrum extra data to add.

listMass

public double[] listMass()

Get the mass array.

Specified by:

listMass in interface SpectrumInterface

Returns:

dataMassArray double[] array of mass values

listIntensities

public double[] listIntensities()

Get the intensity array.

Specified by:

listIntensities in interface SpectrumInterface

Returns:

dataIntensityArray double[] array of intensity values

getRetentionTimeInMinutes

public Double getRetentionTimeInMinutes()

Get the retention time in minutes.

Specified by:

getRetentionTimeInMinutes in interface SpectrumInterface

Returns:

retentionTimeInMinutes Double

getPrecursors

public List<SpectrumPrecursor> getPrecursors()

Specified by:

getPrecursors in interface SpectrumInterface

Returns:

a list of precursor or null if there are none associated with the spectrum

getExtraDataList

public List<StringPairInterface> getExtraDataList()

Get the spectrum extra data list.

Specified by:

getExtraDataList in interface SpectrumInterface

Returns:

List The spectrum extra data list.