Uses of Class
org.expasy.mzjava.proteomics.ms.fragment.PeptideFragmenter

Packages that use PeptideFragmenter

Package	Description
org.expasy.mzjava.proteomics.ms.consensus
org.expasy.mzjava.proteomics.ms.dbsearch
org.expasy.mzjava.proteomics.ms.fragment

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

Fields in org.expasy.mzjava.proteomics.ms.consensus declared as PeptideFragmenter

Modifier and Type	Field and Description
protected PeptideFragmenter	PeptideConsensusSpectrum.Builder.fragmenter

Methods in org.expasy.mzjava.proteomics.ms.consensus with parameters of type PeptideFragmenter

Modifier and Type	Method and Description
PeptideConsensusSpectrum.BuilderOld	PeptideConsensusSpectrum.BuilderOld.fragmenter(PeptideFragmenter fragmenter)
PeptideConsensusSpectrum.FilterParametersSetter	PeptideConsensusSpectrum.AnnotationParametersSetter.setAnnotationParameters(Tolerance fragmentTolerance, PeptideFragmenter fragmenter)
PeptideConsensusSpectrum.FilterParametersSetter	PeptideConsensusSpectrum.Builder.setAnnotationParameters(Tolerance fragmentTolerance, PeptideFragmenter fragmenter)

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

Methods in org.expasy.mzjava.proteomics.ms.dbsearch with parameters of type PeptideFragmenter

Modifier and Type	Method and Description
PeptideSpectrumDB.EndDSL	PeptideSpectrumDB.FragmentDSL.generateSpectraWith(PeptideFragmenter peptideFragmenter) Set the PeptideFragmenter that is used to generate the theoretical spectra.

Constructors in org.expasy.mzjava.proteomics.ms.dbsearch with parameters of type PeptideFragmenter

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 PeptideFragmenter in org.expasy.mzjava.proteomics.ms.fragment

Methods in org.expasy.mzjava.proteomics.ms.fragment that return PeptideFragmenter

Modifier and Type	Method and Description
static PeptideFragmenter	PeptideFragmenterFactory.newSequestPeptideFragmenter(PeakList.Precision precision)

Constructors in org.expasy.mzjava.proteomics.ms.fragment with parameters of type PeptideFragmenter

Constructor and Description
PeptideFragmentAnnotator(PeptideFragmenter fragmenter, PeakListAligner<PepFragAnnotation,PepFragAnnotation> aligner)
PeptideFragmentAnnotator(PeptideFragmenter fragmenter, Tolerance tolerance)