org.expasy.mzjava.core.ms.spectrum

Class MsnSpectrum

java.lang.Object

org.expasy.mzjava.core.ms.spectrum.Spectrum<PeakAnnotation>

org.expasy.mzjava.core.ms.spectrum.MsnSpectrum

All Implemented Interfaces:

PeakList<PeakAnnotation>

public class MsnSpectrum
extends Spectrum<PeakAnnotation>

Version:

1.0

Author:

Oliver Horlacher

Nested Class Summary

Nested classes/interfaces inherited from interface org.expasy.mzjava.core.ms.peaklist.PeakList

PeakList.Precision

Constructor Summary

Constructors

Modifier	Constructor and Description
	MsnSpectrum() Default constructor
	MsnSpectrum(int initialCapacity, double constantIntensity, PeakList.Precision precision) Construct a MsnSpectrum that has a constant intensity.
	MsnSpectrum(int initialCapacity, PeakList.Precision precision) Construct a MsnSpectrum that stores the peak list at the given precision and has an initial capacity equal to initialCapacity
protected	MsnSpectrum(MsnSpectrum src, PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor) Copy constructor
protected	MsnSpectrum(MsnSpectrum src, PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor, com.google.common.base.Function<Double,Double> rtCorrFct) Copy constructor
protected	MsnSpectrum(MsnSpectrum src, PeakProcessorChain<PeakAnnotation> peakProcessorChain) Copy constructor
protected	MsnSpectrum(MsnSpectrum src, PeakProcessorChain<PeakAnnotation> peakProcessorChain, com.google.common.base.Function<Double,Double> rtCorrFct) Copy constructor
	MsnSpectrum(PeakList.Precision precision) Construct a MsnSpectrum that stores the peak list at the given precision

Method Summary

Methods

Modifier and Type	Method and Description
void	addRetentionTime(RetentionTime retentionTime) Add the retentionTime to this MsnSpectrum's retention time list
void	addRetentionTimes(RetentionTimeList retentionTimes) Add all retention times from the retentionTimes to this MsnSpectrum's retention times.
void	addScanNumber(int scanNumber) Add scanNumber to this MsnSpectrum
void	addScanNumber(ScanNumber scanNumber) Add scanNumber to this MsnSpectrum
void	addScanNumbers(Collection<? extends ScanNumber> scanNumbers) Add a all scan numbers from scanNumbers to this MsnSpectrum
MsnSpectrum	copy(com.google.common.base.Function<Double,Double> rtCorrFct)
MsnSpectrum	copy(PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor) Return PeakList copy processed with PeakProcessor
MsnSpectrum	copy(PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor, com.google.common.base.Function<Double,Double> rtCorrFct)
MsnSpectrum	copy(PeakProcessorChain<PeakAnnotation> peakProcessorChain) Return PeakList copy processed with PeakProcessorChain
MsnSpectrum	copy(PeakProcessorChain<PeakAnnotation> peakProcessorChain, com.google.common.base.Function<Double,Double> rtCorrFct)
boolean	equals(Object o)
String	getComment() Return the comment associated with this MsnSpectrum.
String	getFragMethod() Return the fragmentation method
ScanNumber	getParentScanNumber() Returns the scan number of the parent scan.
RetentionTimeList	getRetentionTimes() Return this MsnSpectrum's retention time list.
ScanNumberList	getScanNumbers() Returns the scan number of this MsnSpectrum
int	getSpectrumIndex() Return the index of this MsnSpectrum.
URI	getSpectrumSource() Return the URI that describes the source of this MsnSpectrum.
int	hashCode()
void	setComment(String comment) Set the comment
void	setFragMethod(String fragMethod) Set the fragmentation method
void	setParentScanNumber(ScanNumber parentScanNumber) Set the parent scan number
void	setSpectrumIndex(int spectrumIndex) Set the spectrum index
void	setSpectrumSource(URI spectrumSource) Set the URI that describes the source of this MsnSpectrum

Methods inherited from class org.expasy.mzjava.core.ms.spectrum.Spectrum

add, add, add, addAnnotation, addAnnotations, addPeaks, addPeaks, addPeaksNoAnnotations, addSorted, addSorted, apply, apply, calcVectorLength, clear, clearAnnotations, clearAnnotationsAt, cursor, ensureCapacity, getAnnotationIndexes, getAnnotations, getBasePeakIntensity, getBasePeakMz, getClosestIndex, getFirstAnnotation, getId, getIntensities, getIntensities, getIntensities, getIntensity, getMostIntenseIndex, getMostIntenseIndex, getMsLevel, getMz, getMzs, getMzs, getMzs, getPrecision, getPrecursor, getTotalIonCurrent, hasAnnotations, hasAnnotationsAt, indexOf, indexOf, isEmpty, removeAnnotation, setId, setIntensityAt, setMsLevel, setPrecursor, size, sortAnnotations, trimToSize

Methods inherited from class java.lang.Object

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

Constructor Detail

MsnSpectrum

public MsnSpectrum()

Default constructor

MsnSpectrum

public MsnSpectrum(PeakList.Precision precision)

Construct a MsnSpectrum that stores the peak list at the given precision

Parameters:

precision - the precision that the peak list is stored at

MsnSpectrum

public MsnSpectrum(int initialCapacity,
           PeakList.Precision precision)

Construct a MsnSpectrum that stores the peak list at the given precision and has an initial capacity equal to initialCapacity

Parameters:

initialCapacity - the initial capacity of the peak list

precision - the precision that the peak list is stored at

MsnSpectrum

public MsnSpectrum(int initialCapacity,
           double constantIntensity,
           PeakList.Precision precision)

Construct a MsnSpectrum that has a constant intensity. The precision needs to be either PeakList.Precision.DOUBLE_CONSTANT or PeakList.Precision.FLOAT_CONSTANT. The peak lists initial capacity is set to initialCapacity

Parameters:

initialCapacity - the initial capacity of the peak list

constantIntensity - the constant intensity if

precision - the precision that the peak list is stored at

MsnSpectrum

protected MsnSpectrum(MsnSpectrum src,
           PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor)

Copy constructor

Parameters:

src - the MsnSpectrum to copy

MsnSpectrum

protected MsnSpectrum(MsnSpectrum src,
           PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor,
           com.google.common.base.Function<Double,Double> rtCorrFct)

Copy constructor

Parameters:

src - the MsnSpectrum to copy

MsnSpectrum

protected MsnSpectrum(MsnSpectrum src,
           PeakProcessorChain<PeakAnnotation> peakProcessorChain)

Copy constructor

Parameters:

src - the MsnSpectrum to copy

MsnSpectrum

protected MsnSpectrum(MsnSpectrum src,
           PeakProcessorChain<PeakAnnotation> peakProcessorChain,
           com.google.common.base.Function<Double,Double> rtCorrFct)

Copy constructor

Parameters:

src - the MsnSpectrum to copy

Method Detail

copy

public MsnSpectrum copy(PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor)

Description copied from interface: PeakList

Return PeakList copy processed with PeakProcessor

Parameters:

peakProcessor - the processor to process the peaks

Returns:

the copy of this with the peaks processed by peakProcessor

copy

public MsnSpectrum copy(PeakProcessorChain<PeakAnnotation> peakProcessorChain)

Description copied from interface: PeakList

Return PeakList copy processed with PeakProcessorChain

Parameters:

peakProcessorChain - the processor chain to process the peaks

Returns:

the copy of this with the peaks processed by peakProcessorChain

copy

public MsnSpectrum copy(PeakProcessor<PeakAnnotation,PeakAnnotation> peakProcessor,
               com.google.common.base.Function<Double,Double> rtCorrFct)

copy

public MsnSpectrum copy(PeakProcessorChain<PeakAnnotation> peakProcessorChain,
               com.google.common.base.Function<Double,Double> rtCorrFct)

copy

public MsnSpectrum copy(com.google.common.base.Function<Double,Double> rtCorrFct)

getFragMethod

public String getFragMethod()

Return the fragmentation method

Returns:

the fragmentation method

setFragMethod

public void setFragMethod(String fragMethod)

Set the fragmentation method

Parameters:

fragMethod - the fragmentation method

getParentScanNumber

public ScanNumber getParentScanNumber()

Returns the scan number of the parent scan.

Returns:

the scan number of the parent scan

setParentScanNumber

public void setParentScanNumber(ScanNumber parentScanNumber)

Set the parent scan number

Parameters:

parentScanNumber - the new value for the parent scan number

getScanNumbers

public ScanNumberList getScanNumbers()

Returns the scan number of this MsnSpectrum

Returns:

the scan number of this MsnSpectrum

addScanNumbers

public void addScanNumbers(Collection<? extends ScanNumber> scanNumbers)

Add a all scan numbers from scanNumbers to this MsnSpectrum

Parameters:

scanNumbers - the scan numbers to add

addScanNumber

public void addScanNumber(ScanNumber scanNumber)

Add scanNumber to this MsnSpectrum

Parameters:

scanNumber - the scan number to add

addScanNumber

public void addScanNumber(int scanNumber)

Add scanNumber to this MsnSpectrum

Parameters:

scanNumber - the scan number to add

getRetentionTimes

public RetentionTimeList getRetentionTimes()

Return this MsnSpectrum's retention time list.

Returns:

this MsnSpectrum's retention time list

addRetentionTimes

public void addRetentionTimes(RetentionTimeList retentionTimes)

Add all retention times from the retentionTimes to this MsnSpectrum's retention times.

Parameters:

retentionTimes - the retention times to add

addRetentionTime

public void addRetentionTime(RetentionTime retentionTime)

Add the retentionTime to this MsnSpectrum's retention time list

Parameters:

retentionTime - the retention time to add

getSpectrumIndex

public int getSpectrumIndex()

Return the index of this MsnSpectrum.

Returns:

the index of this MsnSpectrum

setSpectrumIndex

public void setSpectrumIndex(int spectrumIndex)

Set the spectrum index

Parameters:

spectrumIndex - the new spectrum index

getComment

public String getComment()

Return the comment associated with this MsnSpectrum.

Returns:

the comment associated with this MsnSpectrum

setComment

public void setComment(String comment)

Set the comment

Parameters:

comment - the new value of the comment

getSpectrumSource

public URI getSpectrumSource()

Return the URI that describes the source of this MsnSpectrum.

Returns:

the URI that describes the source of this MsnSpectrum

setSpectrumSource

public void setSpectrumSource(URI spectrumSource)

Set the URI that describes the source of this MsnSpectrum

Parameters:

spectrumSource - the new spectrum source URI

equals

public boolean equals(Object o)

Overrides:

equals in class Spectrum<PeakAnnotation>

hashCode

public int hashCode()

Overrides:

hashCode in class Spectrum<PeakAnnotation>