org.expasy.mzjava.proteomics.ms.consensus

Class PeptideConsensusSpectrum.Builder

java.lang.Object

org.expasy.mzjava.proteomics.ms.consensus.PeptideConsensusSpectrum.Builder

All Implemented Interfaces:

PeptideConsensusSpectrum.AnnotationParametersSetter, PeptideConsensusSpectrum.ConsensusParametersSetter, PeptideConsensusSpectrum.FilterParametersSetter

Enclosing class:

PeptideConsensusSpectrum

public static class PeptideConsensusSpectrum.Builder
extends Object
implements PeptideConsensusSpectrum.ConsensusParametersSetter, PeptideConsensusSpectrum.AnnotationParametersSetter, PeptideConsensusSpectrum.FilterParametersSetter

Field Summary

Fields

Modifier and Type	Field and Description
protected PeptideFragmenter	fragmenter
protected Tolerance	fragmentTolerance
protected AbstractMergePeakFilter.IntensityMode	intensityMode
protected double	maxMzClusterWidth
protected double	maxMzDiff
protected int	minPeakCount
protected double	peakFraction
protected PeakList.Precision	precision
protected URI	spectrumSource

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	PeptideConsensusSpectrum.Builder(PeakList.Precision precision, URI spectrumSource)

Method Summary

Methods

Modifier and Type	Method and Description
<A extends PeakAnnotation,S extends PeakList<A>> PeptideConsensusSpectrum	buildConsensus(int charge, Peptide peptide, Collection<S> spectra, Set<String> proteinAccessionNumbers)
<A extends PeakAnnotation,S extends PeakList<A>> PeptideConsensusSpectrum	buildConsensus(int charge, Peptide peptide, Collection<S> spectra, Set<String> proteinAccessionNumbers, RetentionTimeList retentionTimes)
PeptideConsensusSpectrum.FilterParametersSetter	setAnnotationParameters(Tolerance fragmentTolerance, PeptideFragmenter fragmenter)
PeptideConsensusSpectrum.AnnotationParametersSetter	setConsensusParameters(double maxMzDiff, double maxMzClusterWidth, AbstractMergePeakFilter.IntensityMode intensityMode)
PeptideConsensusSpectrum.Builder	setFilterParameters(double peakFraction, int minPeakCount)

Methods inherited from class java.lang.Object

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

Field Detail

precision

protected final PeakList.Precision precision

spectrumSource

protected final URI spectrumSource

maxMzDiff

protected double maxMzDiff

maxMzClusterWidth

protected double maxMzClusterWidth

intensityMode

protected AbstractMergePeakFilter.IntensityMode intensityMode

fragmentTolerance

protected Tolerance fragmentTolerance

fragmenter

protected PeptideFragmenter fragmenter

minPeakCount

protected int minPeakCount

peakFraction

protected double peakFraction

Constructor Detail

PeptideConsensusSpectrum.Builder

protected PeptideConsensusSpectrum.Builder(PeakList.Precision precision,
                                URI spectrumSource)

Method Detail

setAnnotationParameters

public PeptideConsensusSpectrum.FilterParametersSetter setAnnotationParameters(Tolerance fragmentTolerance,
                                                                      PeptideFragmenter fragmenter)

Specified by:

setAnnotationParameters in interface PeptideConsensusSpectrum.AnnotationParametersSetter

setConsensusParameters

public PeptideConsensusSpectrum.AnnotationParametersSetter setConsensusParameters(double maxMzDiff,
                                                                         double maxMzClusterWidth,
                                                                         AbstractMergePeakFilter.IntensityMode intensityMode)

Specified by:

setConsensusParameters in interface PeptideConsensusSpectrum.ConsensusParametersSetter

setFilterParameters

public PeptideConsensusSpectrum.Builder setFilterParameters(double peakFraction,
                                                   int minPeakCount)

Specified by:

setFilterParameters in interface PeptideConsensusSpectrum.FilterParametersSetter

buildConsensus

public <A extends PeakAnnotation,S extends PeakList<A>> PeptideConsensusSpectrum buildConsensus(int charge,
                                                                                       Peptide peptide,
                                                                                       Collection<S> spectra,
                                                                                       Set<String> proteinAccessionNumbers,
                                                                                       RetentionTimeList retentionTimes)

buildConsensus

public <A extends PeakAnnotation,S extends PeakList<A>> PeptideConsensusSpectrum buildConsensus(int charge,
                                                                                       Peptide peptide,
                                                                                       Collection<S> spectra,
                                                                                       Set<String> proteinAccessionNumbers)