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

Packages that use PeptideFragment

Package	Description
org.expasy.mzjava.proteomics.avro.io
org.expasy.mzjava.proteomics.mol
org.expasy.mzjava.proteomics.ms.fragment
org.expasy.mzjava.proteomics.ms.spectrum

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

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

Modifier and Type	Method and Description
PeptideFragment	PeptideFragmentReader.read(org.apache.avro.io.Decoder in)

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

Modifier and Type	Method and Description
void	PeptideFragmentWriter.write(PeptideFragment fragment, org.apache.avro.io.Encoder out)

Uses of PeptideFragment in org.expasy.mzjava.proteomics.mol

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

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

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

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

Modifier and Type	Method and Description
boolean	PeptideNeutralLossPeakGenerator.ModifiedAaPresencePredicate.apply(PeptideFragment fragment)
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)

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

Modifier and Type	Method and Description
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)
protected void	PeptideFragmenter.generateReverse(Peptide peptide, List<PeptideFragment> fragments)

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

Constructor and Description
PeptideNeutralLossPeakGenerator(Mass massShift, com.google.common.base.Predicate<PeptideFragment> modificationPredicate, Set<IonType> ionTypes, double peakIntensity)

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

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

Modifier and Type	Method and Description
PeptideFragment	PepFragAnnotation.getFragment() Return the peptide fragment associated with this annotation