Uses of Class
org.expasy.mzjava.proteomics.mol.Peptide

Packages that use Peptide

Package	Description
org.expasy.mzjava.proteomics.avro.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.mol
org.expasy.mzjava.proteomics.mol.digest
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 Peptide in org.expasy.mzjava.proteomics.avro.io

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

Modifier and Type	Method and Description
Peptide	PeptideReader.read(org.apache.avro.io.Decoder in)

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

Modifier and Type	Method and Description
void	PeptideWriter.write(Peptide value, org.apache.avro.io.Encoder out)

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

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

Modifier and Type	Method and Description
void	AbstractSptxtWriter.write(PeakList<? extends PeakAnnotation> peakList, Peptide peptide, Collection<String> proteinAccessionNumbers)
protected void	AbstractSptxtWriter.writeComment(PeakList peakList, Peptide peptide, Writer writer, Collection<String> proteinAccessionNumbers)
protected abstract void	AbstractSptxtWriter.writeLibId(PeakList peakList, Peptide peptide, Writer writer)
protected void	SptxtWriter.writeLibId(PeakList peakList, Peptide peptide, Writer writer)
protected void	AbstractSptxtWriter.writeName(PeakList peakList, Peptide peptide, Writer writer)

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

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

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.parsePrecursorAnnotation(String value, Peptide peptide) Parses annotations like
List<PepLibPeakAnnotation>	MspAnnotationResolver.resolveAnnotations(String value, Peptide peptide)

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

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

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.parsePrecursorAnnotation(String value, Peptide peptide) Parses annotations like
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 Peptide in org.expasy.mzjava.proteomics.mol

Methods in org.expasy.mzjava.proteomics.mol that return Peptide

Modifier and Type	Method and Description
Peptide	PeptideBuilder.build() Build a Peptide
static Peptide	Peptide.parse(String s) Parse s to build a Peptide.
static Peptide	Peptide.parse(String s, ModificationResolver modResolver) Parse s to build a Peptide using the modResolver to convert modification strings to Modification
Peptide	Peptide.replace(Set<AminoAcid> oldAAs, AminoAcid newAa)
Peptide	Peptide.subSequence(int beginIndex, int endIndex) Returns a new peptide that is a sub sequence of this peptide.
Peptide	Peptide.subSequence(IonType ionType, int residueNumber) Create a sub sequence for the give ion type and residue number Given peptide CERVILAS subSequence(y, 1) will return S, subSequence(b, 1) will return C subSequence(b, 3) will return CER.

Methods in org.expasy.mzjava.proteomics.mol that return types with arguments of type Peptide

Modifier and Type	Method and Description
List<Peptide>	ModifiedPeptideFactory.createVarModPeptides(Peptide peptide)

Methods in org.expasy.mzjava.proteomics.mol with parameters of type Peptide

Modifier and Type	Method and Description
List<Peptide>	ModifiedPeptideFactory.createVarModPeptides(Peptide peptide)

Constructors in org.expasy.mzjava.proteomics.mol with parameters of type Peptide

Constructor and Description
Peptide(Peptide peptide, Set<AminoAcid> oldAAs, AminoAcid newAa)
PeptideBuilder(Peptide peptide) Construct a PeptideBuilder initialised to contain the amino acids sequence and modifications copied from the peptide

Uses of Peptide in org.expasy.mzjava.proteomics.mol.digest

Methods in org.expasy.mzjava.proteomics.mol.digest that return types with arguments of type Peptide

Modifier and Type	Method and Description
List<Peptide>	ProteinDigester.digest(Protein protein) Digest protein
Collection<Peptide>	ProteinDigester.digest(Protein protein, Collection<Peptide> digests) Digest protein given a container for digests

Methods in org.expasy.mzjava.proteomics.mol.digest with parameters of type Peptide

Modifier and Type	Method and Description
boolean	DigestionController.retainDigest(Protein protein, Peptide digest, int digestIndex) Process DigestedPeptide with/without missed cleavages
boolean	LengthDigestionController.retainDigest(Protein protein, Peptide digest, int digestIndex)
boolean	AcceptAllDigestionController.retainDigest(Protein protein, Peptide digest, int digestIndex) Process DigestedPeptide with/without missed cleavages
boolean	DigestionController.retainSemiDigest(Peptide digest) Process Semi digested products.
boolean	LengthDigestionController.retainSemiDigest(Peptide digest)
boolean	AcceptAllDigestionController.retainSemiDigest(Peptide digest) Process Semi digested products.

Method parameters in org.expasy.mzjava.proteomics.mol.digest with type arguments of type Peptide

Modifier and Type	Method and Description
Collection<Peptide>	ProteinDigester.digest(Protein protein, Collection<Peptide> digests) Digest protein given a container for digests

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

Methods in org.expasy.mzjava.proteomics.ms.consensus that return Peptide

Modifier and Type	Method and Description
Peptide	PeptideConsensusSpectrum.getPeptide() Return the peptide

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

Modifier and Type	Method and Description
<A extends PeakAnnotation,S extends PeakList<A>> PeptideConsensusSpectrum	PeptideConsensusSpectrum.Builder.buildConsensus(int charge, Peptide peptide, Collection<S> spectra, Set<String> proteinAccessionNumbers)
<A extends PeakAnnotation,S extends PeakList<A>> PeptideConsensusSpectrum	PeptideConsensusSpectrum.Builder.buildConsensus(int charge, Peptide peptide, Collection<S> spectra, Set<String> proteinAccessionNumbers, RetentionTimeList retentionTimes)
PeptideConsensusSpectrum.BuilderOld	PeptideConsensusSpectrum.BuilderOld.peptide(Peptide peptide)
void	PeptideConsensusSpectrum.setPeptide(Peptide peptide)

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

Constructor and Description
PeptideConsensusSpectrum(Peptide peptide) Construct a LibrarySpectrum for the peptide
PeptideConsensusSpectrum(Peptide peptide, int initialCapacity, PeakList.Precision precision) Construct a Spectrum that has an initial capacity of initialCapacity and a precision of precision
PeptideConsensusSpectrum(Peptide peptide, int initialCapacity, PeakList.Precision precision, Set<UUID> memberIds) Construct a Spectrum that has an initial capacity of initialCapacity and a precision of precision
PeptideConsensusSpectrum(Peptide peptide, PeakList.Precision precision) Construct a Spectrum that has a precision of precision
PeptideConsensusSpectrum(Peptide peptide, PeakList.Precision precision, Set<UUID> memberIds) Construct a Spectrum that has a precision of precision
PeptideConsensusSpectrum(Peptide peptide, PeakList.Precision precision, Set<UUID> memberIDs, Set<String> proteinAccessionNumbers)
PeptideConsensusSpectrum(Peptide peptide, PeakList.Precision precision, Set<UUID> memberIDs, Set<String> proteinAccessionNumbers, RetentionTimeDiscrete retentionTimeDiscrete)
PeptideConsensusSpectrum(Peptide peptide, Set<UUID> memberIds) Construct a LibrarySpectrum for the peptide

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

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

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 Peptide

Modifier and Type	Method and Description
Peptide	Digest.getPeptide() Return the peptide.

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

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)

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

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

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
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)
protected void	PeptideFragmenter.generateForward(Peptide peptide, List<PeptideFragment> fragments)
protected void	PeptideFragmenter.generateImmonium(Peptide peptide, List<PeptideFragment> fragments)
List<AnnotatedPeak<A>>	PeptidePeakGenerator.generatePeaks(Peptide precursor, PeptideFragment fragment, int[] charges, List<AnnotatedPeak<A>> peaks) Generate peaks that are observed for the fragment at the supplied charge states.
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	PeptideFragmenter.generateReverse(Peptide peptide, List<PeptideFragment> fragments)

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

Methods in org.expasy.mzjava.proteomics.ms.ident that return Peptide

Modifier and Type	Method and Description
Peptide	PeptideMatch.toBarePeptide() Convert this PeptideMatch to a peptide containing only the bare peptide sequence.
Peptide	PeptideMatch.toPeptide() Convert this PeptideMatch to a peptide
Peptide	PeptideMatch.toPeptide(ModificationMatchResolver modMatchResolver) Convert this PeptideMatch to a peptide using the supplied modificationMatchResolver to convert ModificationMatch instances to Modifications.

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

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

Modifier and Type	Method and Description
Peptide	PeptideSpectrum.getPeptide()

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

Constructor and Description
PeptideSpectrum(Peptide peptide, int charge)
PeptideSpectrum(Peptide peptide, int charge, int initialCapacity, double constantIntensity, PeakList.Precision precision)
PeptideSpectrum(Peptide peptide, int charge, int initialCapacity, PeakList.Precision precision)
PeptideSpectrum(Peptide peptide, int charge, PeakList.Precision precision)
PeptideSpectrum(Spectrum<PepFragAnnotation> src, Peptide peptide, int charge)