org.expasy.mzjava.core.ms.consensus

Class AbstractConsensusSpectrumBuilder<A extends LibPeakAnnotation,B extends AbstractConsensusSpectrumBuilder<A,B,C>,C extends ConsensusSpectrum<A>>

java.lang.Object

org.expasy.mzjava.core.ms.consensus.AbstractConsensusSpectrumBuilder<A,B,C>

Direct Known Subclasses:

ConsensusSpectrum.Builder, PeptideConsensusSpectrum.BuilderOld

public abstract class AbstractConsensusSpectrumBuilder<A extends LibPeakAnnotation,B extends AbstractConsensusSpectrumBuilder<A,B,C>,C extends ConsensusSpectrum<A>>
extends Object

Version:

0.0

Author:

Markus Muller

Field Summary

Fields

Modifier and Type	Field and Description
protected double	fragMzTolerance
protected int	initialCapacity
protected AbstractMergePeakFilter.IntensityMode	intCombMeth
protected double	maxMzClusterWidth
protected int	minPeakCount
protected int	msLevel
protected double	peakFraction
protected List<PeakList<PeakAnnotation>>	spectra

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractConsensusSpectrumBuilder()

Method Summary

Methods

Modifier and Type	Method and Description
abstract C	build()
protected abstract void	calculatePrecursor(ConsensusSpectrum<? extends LibPeakAnnotation> consensus)
B	fragMzTolerance(double fragMzTolerance)
B	initialCapacity(int initialCapacity)
B	intensityCombMethod(AbstractMergePeakFilter.IntensityMode intCombMethod)
B	maxMzClusterWidth(double maxMzClusterWidth)
B	msLevel(int msLevel)
B	setPeakFilterParams(double peakFraction, int minPeakCount)
B	spectra(Collection<? extends PeakList<PeakAnnotation>> spectra)

Methods inherited from class java.lang.Object

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

Field Detail

spectra

protected final List<PeakList<PeakAnnotation>> spectra

peakFraction

protected double peakFraction

minPeakCount

protected int minPeakCount

fragMzTolerance

protected double fragMzTolerance

maxMzClusterWidth

protected double maxMzClusterWidth

intCombMeth

protected AbstractMergePeakFilter.IntensityMode intCombMeth

initialCapacity

protected int initialCapacity

msLevel

protected int msLevel

Constructor Detail

AbstractConsensusSpectrumBuilder

protected AbstractConsensusSpectrumBuilder()

Method Detail

spectra

public B spectra(Collection<? extends PeakList<PeakAnnotation>> spectra)

initialCapacity

public B initialCapacity(int initialCapacity)

fragMzTolerance

public B fragMzTolerance(double fragMzTolerance)

intensityCombMethod

public B intensityCombMethod(AbstractMergePeakFilter.IntensityMode intCombMethod)

maxMzClusterWidth

public B maxMzClusterWidth(double maxMzClusterWidth)

setPeakFilterParams

public B setPeakFilterParams(double peakFraction,
                    int minPeakCount)

msLevel

public B msLevel(int msLevel)

calculatePrecursor

protected abstract void calculatePrecursor(ConsensusSpectrum<? extends LibPeakAnnotation> consensus)

build

public abstract C build()