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

Packages that use PeptideSpectrum

Package	Description
org.expasy.mzjava.proteomics.avro.io
org.expasy.mzjava.proteomics.io.ms.spectrum
org.expasy.mzjava.proteomics.ms.consensus
org.expasy.mzjava.proteomics.ms.dbsearch
org.expasy.mzjava.proteomics.ms.fragment
org.expasy.mzjava.proteomics.ms.ident
org.expasy.mzjava.proteomics.ms.spectrum

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

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

Modifier and Type	Method and Description
protected PeptideSpectrum	PeptideSpectrumReader.newPeakList(PeakList.Precision precision, double constantIntensity)
PeptideSpectrum	PeptideSpectrumReader.read(org.apache.avro.io.Decoder in)

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

Modifier and Type	Method and Description
void	PeptideSpectrumWriter.write(PeptideSpectrum spectrum, org.apache.avro.io.Encoder out)

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

Methods in org.expasy.mzjava.proteomics.io.ms.spectrum with parameters of type PeptideSpectrum

Modifier and Type	Method and Description
void	SptxtWriter.write(PeptideSpectrum spectrum)

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

Constructors in org.expasy.mzjava.proteomics.ms.consensus with parameters of type PeptideSpectrum

Constructor and Description
PeptideFragmentAnnotator(Tolerance tolerance, PeptideSpectrum theoreticalSpectrum)

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

Fields in org.expasy.mzjava.proteomics.ms.dbsearch with type parameters of type PeptideSpectrum

Modifier and Type	Field and Description
protected gnu.trove.map.TIntObjectMap<Map<Peptide,SoftReference<PeptideSpectrum>>>	SoftRefPepSpectrumCache.cache

Methods in org.expasy.mzjava.proteomics.ms.dbsearch that return types with arguments of type PeptideSpectrum

Modifier and Type	Method and Description
com.google.common.base.Optional<PeptideSpectrum>	SoftRefPepSpectrumCache.get(Peptide peptide, int charge)
com.google.common.base.Optional<PeptideSpectrum>	PeptideSpectrumCache.get(Peptide peptide, int charge)
List<PeptideSpectrum>	PeptideSpectrumDB.getSpectra(Peak precursor) Collect all peptide spectra with mass closed to the given precursor peak

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

Modifier and Type	Method and Description
void	SoftRefPepSpectrumCache.put(PeptideSpectrum peptideSpectrum)
void	PeptideSpectrumCache.put(PeptideSpectrum peptideSpectrum)

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

Modifier and Type	Method and Description
void	PeptideSpectrumDB.getSpectra(Peak precursor, Collection<PeptideSpectrum> spectrumCollection) Add all peptide spectra contained in this database that are within tolerance of the precursor to spectrumCollection

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

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

Modifier and Type	Method and Description
PeptideSpectrum	PeptideFragmenter.fragment(Peptide peptide, int precursorCharge)
protected PeptideSpectrum	PeptideFragmentAnnotator.fragment(Peptide peptidePrecursor, int precursorCharge)
protected PeptideSpectrum	PeptideFragmentAnnotator.fragment(Peptide peptidePrecursor, int precursorCharge, int... fragmentCharges)
PeptideSpectrum	PeptideFragmenter.fragment(Peptide peptide, int precursorCharge, int[] fragmentCharges)
PeptideSpectrum	PeptideFragmenter.fragment(Peptide peptide, int precursorCharge, List<PeptideFragment> fragmentList, int[] fragmentCharges)

Uses of PeptideSpectrum in org.expasy.mzjava.proteomics.ms.ident

Constructors in org.expasy.mzjava.proteomics.ms.ident with parameters of type PeptideSpectrum

Constructor and Description
PeptideMatch(PeptideSpectrum peptideSpectrum, String scoreName, double score) Construct a PeptideMatch from a peptide spectrum and score.

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

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

Modifier and Type	Method and Description
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 PeptideSpectrum

Constructor and Description
PeptideSpectrum(PeptideSpectrum src, PeakProcessor<PepFragAnnotation,PepFragAnnotation> peakProcessor)
PeptideSpectrum(PeptideSpectrum src, PeakProcessorChain<PepFragAnnotation> peakProcessorChain)