org.expasy.mzjava.core.ms.consensus

Class ConsensusSpectrum<A extends LibPeakAnnotation>

java.lang.Object

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

org.expasy.mzjava.core.ms.consensus.ConsensusSpectrum<A>

All Implemented Interfaces:

PeakList<A>

Direct Known Subclasses:

PeptideConsensusSpectrum

public class ConsensusSpectrum<A extends LibPeakAnnotation>
extends Spectrum<A>

Version:

sqrt -1

Author:

Oliver Horlacher, Markus Muller

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	ConsensusSpectrum.Builder

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

PeakList.Precision

Field Summary

Fields

Modifier and Type	Field and Description
protected Set<UUID>	memberIds
protected String	name
protected double	precursorMzMean
protected double	precursorMzStdev
protected double	simScoreMean
protected double	simScoreStdev

Constructor Summary

Constructors

Constructor and Description
ConsensusSpectrum(ConsensusSpectrum<A> consensusSpectrum, PeakProcessor<A,A> peakProcessor)
ConsensusSpectrum(ConsensusSpectrum<A> consensusSpectrum, PeakProcessorChain<A> peakProcessorChain)
ConsensusSpectrum(int initialCapacity, PeakList.Precision precision, Set<UUID> memberIds)

Method Summary

Methods

Modifier and Type	Method and Description
void	addMemberIds(Collection<UUID> memberIds)
ConsensusSpectrum<A>	copy(PeakProcessor<A,A> peakProcessor) Return PeakList copy processed with PeakProcessor
ConsensusSpectrum<A>	copy(PeakProcessorChain<A> peakProcessorChain) Return PeakList copy processed with PeakProcessorChain
boolean	equals(Object o)
Set<UUID>	getMemberIds()
String	getName()
double	getPrecursorMzMean()
double	getPrecursorMzStdev()
double	getSimScoreMean()
double	getSimScoreStdev()
int	hashCode()
int	nrOfMembers()
void	setName(String name)
ConsensusSpectrum	setPrecursorStats(double precursorMean, double precursorStdev)
ConsensusSpectrum	setScoreStats(double simScoreMean, double simScoreStdev)

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

Field Detail

name

protected String name

simScoreMean

protected double simScoreMean

simScoreStdev

protected double simScoreStdev

precursorMzMean

protected double precursorMzMean

precursorMzStdev

protected double precursorMzStdev

memberIds

protected Set<UUID> memberIds

Constructor Detail

ConsensusSpectrum

public ConsensusSpectrum(int initialCapacity,
                 PeakList.Precision precision,
                 Set<UUID> memberIds)

ConsensusSpectrum

public ConsensusSpectrum(ConsensusSpectrum<A> consensusSpectrum,
                 PeakProcessor<A,A> peakProcessor)

ConsensusSpectrum

public ConsensusSpectrum(ConsensusSpectrum<A> consensusSpectrum,
                 PeakProcessorChain<A> peakProcessorChain)

Method Detail

addMemberIds

public void addMemberIds(Collection<UUID> memberIds)

getMemberIds

public Set<UUID> getMemberIds()

nrOfMembers

public int nrOfMembers()

setName

public void setName(String name)

getName

public String getName()

setScoreStats

public ConsensusSpectrum setScoreStats(double simScoreMean,
                              double simScoreStdev)

setPrecursorStats

public ConsensusSpectrum setPrecursorStats(double precursorMean,
                                  double precursorStdev)

getSimScoreMean

public double getSimScoreMean()

getSimScoreStdev

public double getSimScoreStdev()

getPrecursorMzMean

public double getPrecursorMzMean()

getPrecursorMzStdev

public double getPrecursorMzStdev()

copy

public ConsensusSpectrum<A> copy(PeakProcessor<A,A> 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 ConsensusSpectrum<A> copy(PeakProcessorChain<A> 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

equals

public boolean equals(Object o)

Overrides:

equals in class Spectrum<A extends LibPeakAnnotation>

hashCode

public int hashCode()

Overrides:

hashCode in class Spectrum<A extends LibPeakAnnotation>