Uses of Interface
org.expasy.mzjava.proteomics.mol.modification.ModificationResolver

Packages that use ModificationResolver

Package	Description
org.expasy.mzjava.proteomics.io.ms.ident
org.expasy.mzjava.proteomics.io.ms.spectrum
org.expasy.mzjava.proteomics.io.ms.spectrum.sptxt
org.expasy.mzjava.proteomics.mol
org.expasy.mzjava.proteomics.mol.modification
org.expasy.mzjava.proteomics.mol.modification.unimod

Uses of ModificationResolver in org.expasy.mzjava.proteomics.io.ms.ident

Classes in org.expasy.mzjava.proteomics.io.ms.ident that implement ModificationResolver

Modifier and Type	Class and Description
class	ProteinPilotModificationResolver The default ProteinPilot Modification Resolver

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

Constructor and Description
MaxQuantPsmReader(ModificationResolver modResolver)
MzIdentMlReader(ModificationResolver modResolver)
ProteinPilotPsmReader(ModificationResolver modResolver)

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

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

Modifier and Type	Method and Description
MspReader.Builder	MspReader.Builder.useModificationResolver(ModificationResolver modResolver)
SptxtReader.Builder	SptxtReader.Builder.useModificationResolver(ModificationResolver modResolver)

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

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

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

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

Modifier and Type	Method and Description
PeptideConsensusSpectrum	LibrarySpectrumBuilder.build(PeakList.Precision precision, ModificationResolver modificationResolver, AnnotationResolver annotationResolver, boolean acceptUnsortedSpectra)

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

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

Modifier and Type	Method and Description
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
static Peptide	Peptide.parse(String s, ModificationResolver modResolver) Parse s to build a Peptide using the modResolver to convert modification strings to Modification

Uses of ModificationResolver in org.expasy.mzjava.proteomics.mol.modification

Classes in org.expasy.mzjava.proteomics.mol.modification that implement ModificationResolver

Modifier and Type	Class and Description
class	CompositeModResolver
class	NumericModificationResolver

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

Constructor and Description
CompositeModResolver(ModificationResolver first, ModificationResolver... rest)
CompositeModResolver(ModificationResolver first, ModificationResolver... rest)

Uses of ModificationResolver in org.expasy.mzjava.proteomics.mol.modification.unimod

Classes in org.expasy.mzjava.proteomics.mol.modification.unimod that implement ModificationResolver

Modifier and Type	Class and Description
class	UnimodModificationResolver A Modification that converts Strings to modifications.