Uses of Class
org.expasy.mzjava.proteomics.ms.spectrum.PepFragAnnotation

Packages that use PepFragAnnotation

Package	Description
org.expasy.mzjava.proteomics.avro.io
org.expasy.mzjava.proteomics.hadoop.io
org.expasy.mzjava.proteomics.io.ms.spectrum.msp
org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt
org.expasy.mzjava.proteomics.ms.dbsearch
org.expasy.mzjava.proteomics.ms.fragment
org.expasy.mzjava.proteomics.ms.spectrum

Uses of PepFragAnnotation in org.expasy.mzjava.proteomics.avro.io

Methods in org.expasy.mzjava.proteomics.avro.io that return PepFragAnnotation

Modifier and Type	Method and Description
PepFragAnnotation	PepFragAnnotationReader.read(org.apache.avro.io.Decoder in)

Methods in org.expasy.mzjava.proteomics.avro.io with parameters of type PepFragAnnotation

Modifier and Type	Method and Description
void	PepFragAnnotationWriter.write(PepFragAnnotation annotation, org.apache.avro.io.Encoder out)

Constructor parameters in org.expasy.mzjava.proteomics.avro.io with type arguments of type PepFragAnnotation

Constructor and Description
PeptideSpectrumReader(com.google.common.base.Optional<PeakList.Precision> precisionOverride, List<PeakProcessor<PepFragAnnotation,PepFragAnnotation>> peakProcessors)
PeptideSpectrumReader(com.google.common.base.Optional<PeakList.Precision> precisionOverride, List<PeakProcessor<PepFragAnnotation,PepFragAnnotation>> peakProcessors)

Uses of PepFragAnnotation in org.expasy.mzjava.proteomics.hadoop.io

Constructor parameters in org.expasy.mzjava.proteomics.hadoop.io with type arguments of type PepFragAnnotation

Constructor and Description
PeptideSpectrumValue(com.google.common.base.Optional<PeakList.Precision> precisionOverride, List<PeakProcessor<PepFragAnnotation,PepFragAnnotation>> peakProcessors)
PeptideSpectrumValue(com.google.common.base.Optional<PeakList.Precision> precisionOverride, List<PeakProcessor<PepFragAnnotation,PepFragAnnotation>> peakProcessors)

Uses of PepFragAnnotation in org.expasy.mzjava.proteomics.io.ms.spectrum.msp

Methods in org.expasy.mzjava.proteomics.io.ms.spectrum.msp that return types with arguments of type PepFragAnnotation

Modifier and Type	Method and Description
protected com.google.common.base.Optional<PepFragAnnotation>	MspAnnotationResolver.parseBackboneAnnotation(String value, Peptide peptide) Parses annotations like
protected com.google.common.base.Optional<PepFragAnnotation>	MspAnnotationResolver.parseInternalAnnotation(String value)
protected com.google.common.base.Optional<PepFragAnnotation>	MspAnnotationResolver.parsePrecursorAnnotation(String value, Peptide peptide) Parses annotations like

Uses of PepFragAnnotation in org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt

Methods in org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt that return types with arguments of type PepFragAnnotation

Modifier and Type	Method and Description
protected com.google.common.base.Optional<PepFragAnnotation>	SpectraStAnnotationResolver.parseBackboneAnnotation(String value, Peptide peptide) Parses annotations like
protected com.google.common.base.Optional<PepFragAnnotation>	SpectraStAnnotationResolver.parseInternalAnnotation(String value)
protected com.google.common.base.Optional<PepFragAnnotation>	SpectraStAnnotationResolver.parsePrecursorAnnotation(String value, Peptide peptide) Parses annotations like

Uses of PepFragAnnotation in org.expasy.mzjava.proteomics.ms.dbsearch

Method parameters in org.expasy.mzjava.proteomics.ms.dbsearch with type arguments of type PepFragAnnotation

Modifier and Type	Method and Description
PeptideSpectrumDB.FragmentDSL	PeptideSpectrumDB.FragmentDSL.processGeneratedSpectraWith(PeakProcessorChain<PepFragAnnotation> processorChain) Set the processorChain that is used to process the generated spectra

Constructor parameters in org.expasy.mzjava.proteomics.ms.dbsearch with type arguments of type PepFragAnnotation

Constructor and Description
PeptideSpectrumDB(Tolerance precursorTolerance, PeptideFragmenter fragmenter, DigestDB digestDB, PeptideSpectrumCache peptideSpectrumCache, PeakProcessorChain<PepFragAnnotation> processorChain) Construct a PeptideSpectrumDB backed by the fragmenter, proteinDB and peptideSpectrumCache.

Uses of PepFragAnnotation in org.expasy.mzjava.proteomics.ms.fragment

Methods in org.expasy.mzjava.proteomics.ms.fragment with type parameters of type PepFragAnnotation

Modifier and Type	Method and Description
<S extends PeakList<PepFragAnnotation>> S	PeptideFragmentAnnotator.annotate(S peaklist, Peptide peptide) Annotate peaklist from peptide at precursor charge
<S extends PeakList<PepFragAnnotation>> S	PeptideFragmentAnnotator.annotate(S peaklist, Peptide peptide, int precursorCharge) Annotate peaklist from peptide at specific charge
<S extends PeakList<PepFragAnnotation>> S	PeptideFragmentAnnotator.annotate(S peaklist, Peptide peptide, int precursorCharge, int... fragmentCharges) Annotate peaklist from peptide at specific charge

Methods in org.expasy.mzjava.proteomics.ms.fragment that return types with arguments of type PepFragAnnotation

Modifier and Type	Method and Description
List<AnnotatedPeak<PepFragAnnotation>>	PeptideNeutralLossPeakGenerator.generatePeaks(Peptide precursor, PeptideFragment fragment, int[] charges, List<AnnotatedPeak<PepFragAnnotation>> peaks)
List<AnnotatedPeak<PepFragAnnotation>>	BackbonePeakGenerator.generatePeaks(Peptide precursor, PeptideFragment fragment, int[] charges, List<AnnotatedPeak<PepFragAnnotation>> peaks)

Method parameters in org.expasy.mzjava.proteomics.ms.fragment with type arguments of type PepFragAnnotation

Modifier and Type	Method and Description
List<AnnotatedPeak<PepFragAnnotation>>	PeptideNeutralLossPeakGenerator.generatePeaks(Peptide precursor, PeptideFragment fragment, int[] charges, List<AnnotatedPeak<PepFragAnnotation>> peaks)
List<AnnotatedPeak<PepFragAnnotation>>	BackbonePeakGenerator.generatePeaks(Peptide precursor, PeptideFragment fragment, int[] charges, List<AnnotatedPeak<PepFragAnnotation>> peaks)
protected void	PeptideFragmentAnnotator.reportAnnotations(PeakList<PepFragAnnotation> peakList, int index, List<PepFragAnnotation> fragAnnotations)
protected void	PeptideFragmentAnnotator.reportAnnotations(PeakList<PepFragAnnotation> peakList, int index, List<PepFragAnnotation> fragAnnotations)

Constructor parameters in org.expasy.mzjava.proteomics.ms.fragment with type arguments of type PepFragAnnotation

Constructor and Description
PeptideFragmentAnnotator(PeptideFragmenter fragmenter, PeakListAligner<PepFragAnnotation,PepFragAnnotation> aligner)
PeptideFragmentAnnotator(PeptideFragmenter fragmenter, PeakListAligner<PepFragAnnotation,PepFragAnnotation> aligner)
PeptideFragmenter(List<PeptidePeakGenerator<PepFragAnnotation>> peakGeneratorList, PeakList.Precision precision) Constructs a CID peptide fragmenter that generates peaks using the supplied peak generators

Uses of PepFragAnnotation in org.expasy.mzjava.proteomics.ms.spectrum

Methods in org.expasy.mzjava.proteomics.ms.spectrum that return PepFragAnnotation

Modifier and Type	Method and Description
PepFragAnnotation	PepFragAnnotation.Builder.build() Build the PepFragAnnotation annotation.
PepFragAnnotation	PepFragAnnotation.copy()

Methods in org.expasy.mzjava.proteomics.ms.spectrum that return types with arguments of type PepFragAnnotation

Modifier and Type	Method and Description
com.google.common.base.Optional<PepFragAnnotation>	PepLibPeakAnnotation.getOptFragmentAnnotation()

Method parameters in org.expasy.mzjava.proteomics.ms.spectrum with type arguments of type PepFragAnnotation

Modifier and Type	Method and Description
PeptideSpectrum	PeptideSpectrum.copy(PeakProcessor<PepFragAnnotation,PepFragAnnotation> peakProcessor)
PeptideSpectrum	PeptideSpectrum.copy(PeakProcessor<PepFragAnnotation,PepFragAnnotation> peakProcessor)
PeptideSpectrum	PeptideSpectrum.copy(PeakProcessorChain<PepFragAnnotation> peakProcessorChain)

Constructors in org.expasy.mzjava.proteomics.ms.spectrum with parameters of type PepFragAnnotation

Constructor and Description
PepFragAnnotation.Builder(PepFragAnnotation src) Copy constructor
PepFragAnnotation(PepFragAnnotation src) Copy constructor

Constructor parameters in org.expasy.mzjava.proteomics.ms.spectrum with type arguments of type PepFragAnnotation

Constructor and Description
PepLibPeakAnnotation(int mergedPeakCount, double mzStd, double intensityStd, com.google.common.base.Optional<PepFragAnnotation> optFragmentAnnotation)
PeptideSpectrum(PeptideSpectrum src, PeakProcessor<PepFragAnnotation,PepFragAnnotation> peakProcessor)
PeptideSpectrum(PeptideSpectrum src, PeakProcessor<PepFragAnnotation,PepFragAnnotation> peakProcessor)
PeptideSpectrum(PeptideSpectrum src, PeakProcessorChain<PepFragAnnotation> peakProcessorChain)
PeptideSpectrum(Spectrum<PepFragAnnotation> src, Peptide peptide, int charge)