com.compomics.util.experiment.massspectrometry

Class MSnSpectrum

java.lang.Object

com.compomics.util.experiment.personalization.ExperimentObject

com.compomics.util.experiment.massspectrometry.Spectrum

com.compomics.util.experiment.massspectrometry.MSnSpectrum

All Implemented Interfaces:

Serializable, Cloneable

public class MSnSpectrum
extends Spectrum

This class models an MSn spectrum.

Author:

Marc Vaudel

See Also:

Serialized Form

Field Summary

Fields inherited from class com.compomics.util.experiment.massspectrometry.Spectrum

fileName, intensityPeakMap, level, peakList, scanNumber, scanStartTime, SPECTRUM_KEY_SPLITTER, spectrumTitle

Constructor Summary

Constructors

Constructor and Description
MSnSpectrum() Constructor for the spectrum.
MSnSpectrum(int level, Precursor precursor, String spectrumTitle, HashMap<Double,Peak> peakMap, String fileName) Constructor for the spectrum.
MSnSpectrum(int level, Precursor precursor, String spectrumTitle, HashMap<Double,Peak> peakMap, String fileName, double scanStartTime) Constructor for the spectrum.
MSnSpectrum(int level, Precursor precursor, String spectrumTitle, String fileName) Minimal constructor for the spectrum.

Method Summary

Modifier and Type	Method and Description
String	asMgf() Returns the peak list as an mgf bloc.
String	asMgf(HashMap<String,String> additionalTags) Returns the peak list as an mgf bloc.
Precursor	getPrecursor() Returns the precursor.
void	setPrecursor(Precursor precursor) Set the precursor.
void	writeMgf(BufferedWriter writer1) Writes the spectrum in the mgf format using the given writer.
void	writeMgf(BufferedWriter mgfWriter, HashMap<String,String> additionalTags) Writes the spectrum in the mgf format using the given writer.

Methods inherited from class com.compomics.util.experiment.massspectrometry.Spectrum

addPeak, getDesignaledPeakList, getFileName, getIntensityLimit, getIntensityMap, getIntensityValuesAsArray, getIntensityValuesNormalizedAsArray, getJFreePeakList, getLevel, getMaxIntensity, getMaxMz, getMinMz, getMzAndIntensityAsArray, getMzValuesAsArray, getNPeaks, getOrderedMzValues, getPeakList, getPeakMap, getPeaksAboveIntensityThreshold, getRecalibratedPeakList, getScanNumber, getScanStartTime, getSpectrumFile, getSpectrumKey, getSpectrumKey, getSpectrumTitle, getSpectrumTitle, getSubSpectrum, getTotalIntensity, removePeakList, setIntensityValuesAsArray, setMzOrdered, setPeakList, setPeaks, setScanNumber, setScanStartTime, setSpectrumTitle

Methods inherited from class com.compomics.util.experiment.personalization.ExperimentObject

addUrParam, getParameterKey, getUrParam

Methods inherited from class java.lang.Object

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

Constructor Detail

MSnSpectrum

public MSnSpectrum()

Constructor for the spectrum.

MSnSpectrum

public MSnSpectrum(int level,
                   Precursor precursor,
                   String spectrumTitle,
                   String fileName)

Minimal constructor for the spectrum. The peak list is not loaded in order to reduce memory consumption.

Parameters:

level - MS level

precursor - precursor

spectrumTitle - spectrum title

fileName - file name

MSnSpectrum

public MSnSpectrum(int level,
                   Precursor precursor,
                   String spectrumTitle,
                   HashMap<Double,Peak> peakMap,
                   String fileName)

Constructor for the spectrum.

Parameters:

level - MS level

precursor - precursor

spectrumTitle - spectrum title

peakMap - set of peaks

fileName - file name

MSnSpectrum

public MSnSpectrum(int level,
                   Precursor precursor,
                   String spectrumTitle,
                   HashMap<Double,Peak> peakMap,
                   String fileName,
                   double scanStartTime)

Constructor for the spectrum.

Parameters:

level - MS level

precursor - precursor

spectrumTitle - spectrum title

peakMap - set of peaks

fileName - file name

scanStartTime - The time point when the spectrum was recorded

Method Detail

getPrecursor

public Precursor getPrecursor()

Returns the precursor.

Returns:

precursor charge

setPrecursor

public void setPrecursor(Precursor precursor)

Set the precursor.

Parameters:

precursor - the precursor to set

asMgf

public String asMgf()

Returns the peak list as an mgf bloc.

Returns:

the peak list as an mgf bloc

asMgf

public String asMgf(HashMap<String,String> additionalTags)

Returns the peak list as an mgf bloc. @TODO: move this to the massspectrometry.export package

Parameters:

additionalTags - additional tags which will be added after the BEGIN IONS tag in alphabetic order

Returns:

the peak list as an mgf bloc

writeMgf

public void writeMgf(BufferedWriter writer1)
              throws IOException

Writes the spectrum in the mgf format using the given writer.

Parameters:

writer1 - a buffered writer where the spectrum will be written

Throws:

IOException - if an IOException occurs

writeMgf

public void writeMgf(BufferedWriter mgfWriter,
                     HashMap<String,String> additionalTags)
              throws IOException

Writes the spectrum in the mgf format using the given writer.

Parameters:

mgfWriter - a buffered writer where the spectrum will be written

additionalTags - additional tags which will be added after the BEGIN IONS tag in alphabetic order

Throws:

IOException - if an IOException occurs