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

Packages that use PepLibPeakAnnotation

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

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

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

Modifier and Type	Method and Description
PepLibPeakAnnotation	PepLibPeakAnnotationReader.read(org.apache.avro.io.Decoder in)

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

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

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

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

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

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

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

Uses of PepLibPeakAnnotation in org.expasy.mzjava.proteomics.io.ms.spectrum

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

Modifier and Type	Method and Description
MspReader.Builder	MspReader.Builder.usePeakProcessorChain(PeakProcessorChain<PepLibPeakAnnotation> processorChain)
SptxtReader.Builder	SptxtReader.Builder.usePeakProcessorChain(PeakProcessorChain<PepLibPeakAnnotation> processorChain)

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

Constructor and Description
MsLibReader(Reader reader, URI spectraSource, PeakList.Precision precision, SpectraLibCommentParser commentParser, AnnotationResolver annotationResolver, PeakProcessorChain<PepLibPeakAnnotation> processorChain, ModificationResolver modResolver)

Uses of PepLibPeakAnnotation 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 PepLibPeakAnnotation

Modifier and Type	Method and Description
List<PepLibPeakAnnotation>	MspAnnotationResolver.resolveAnnotations(String value, Peptide peptide)

Uses of PepLibPeakAnnotation 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 PepLibPeakAnnotation

Modifier and Type	Method and Description
List<PepLibPeakAnnotation>	AnnotationResolver.resolveAnnotations(String annotations, Peptide peptide)
List<PepLibPeakAnnotation>	SkipAnnotationResolver.resolveAnnotations(String annotations, Peptide peptide)
List<PepLibPeakAnnotation>	SpectraStAnnotationResolver.resolveAnnotations(String value, Peptide peptide)

Uses of PepLibPeakAnnotation in org.expasy.mzjava.proteomics.ms.consensus

Method parameters in org.expasy.mzjava.proteomics.ms.consensus with type arguments of type PepLibPeakAnnotation

Modifier and Type	Method and Description
PeptideConsensusSpectrum	PeptideConsensusSpectrum.copy(PeakProcessor<PepLibPeakAnnotation,PepLibPeakAnnotation> peakProcessor)
PeptideConsensusSpectrum	PeptideConsensusSpectrum.copy(PeakProcessor<PepLibPeakAnnotation,PepLibPeakAnnotation> peakProcessor)
PeptideConsensusSpectrum	PeptideConsensusSpectrum.copy(PeakProcessorChain<PepLibPeakAnnotation> peakProcessorChain)
void	PeptideConsensusPeakSink.processPeak(double mz, double intensity, List<PepLibPeakAnnotation> annotations)
void	PeptideFragmentAnnotator.processPeak(double mz, double intensity, List<PepLibPeakAnnotation> annotations)

Constructor parameters in org.expasy.mzjava.proteomics.ms.consensus with type arguments of type PepLibPeakAnnotation

Constructor and Description
PeptideConsensusSpectrum(PeptideConsensusSpectrum src, PeakProcessor<PepLibPeakAnnotation,PepLibPeakAnnotation> peakProcessor) Copy constructor
PeptideConsensusSpectrum(PeptideConsensusSpectrum src, PeakProcessor<PepLibPeakAnnotation,PepLibPeakAnnotation> peakProcessor) Copy constructor
PeptideConsensusSpectrum(PeptideConsensusSpectrum src, PeakProcessorChain<PepLibPeakAnnotation> peakProcessorChain)

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

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

Modifier and Type	Method and Description
PepLibPeakAnnotation	PepLibPeakAnnotation.copy()

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

Constructor and Description
PepLibPeakAnnotation(PepLibPeakAnnotation src) Copy constructor