Uses of Class
org.expasy.mzjava.proteomics.mol.modification.Modification

Packages that use Modification

Package	Description
org.expasy.mzjava.proteomics.avro.io
org.expasy.mzjava.proteomics.io.ms.ident
org.expasy.mzjava.proteomics.mol
org.expasy.mzjava.proteomics.mol.digest
org.expasy.mzjava.proteomics.mol.modification
org.expasy.mzjava.proteomics.mol.modification.unimod
org.expasy.mzjava.proteomics.ms.fragment
org.expasy.mzjava.proteomics.ms.ident

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

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

Modifier and Type	Method and Description
Modification	ModificationReader.read(org.apache.avro.io.Decoder in)

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

Modifier and Type	Method and Description
void	ModificationWriter.write(Modification mod, org.apache.avro.io.Encoder out)

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

Fields in org.expasy.mzjava.proteomics.io.ms.ident with type parameters of type Modification

Modifier and Type	Field and Description
protected com.google.common.collect.Multimap<Integer,Modification>	MODaPsmReader.sideChainFixedModMap
protected com.google.common.collect.Multimap<ModAttachment,Modification>	MODaPsmReader.termFixedModMap

Methods in org.expasy.mzjava.proteomics.io.ms.ident that return types with arguments of type Modification

Modifier and Type	Method and Description
com.google.common.base.Optional<Modification>	ProteinPilotModificationResolver.resolve(String input)

Constructor parameters in org.expasy.mzjava.proteomics.io.ms.ident with type arguments of type Modification

Constructor and Description
MODaPsmReader(List<AminoAcid> fixedModResidues, com.google.common.collect.Multimap<Integer,Modification> sideChainFixedModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termFixedModMap)
MODaPsmReader(List<AminoAcid> fixedModResidues, com.google.common.collect.Multimap<Integer,Modification> sideChainFixedModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termFixedModMap)

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

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

Modifier and Type	Method and Description
PeptideBuilder	PeptideBuilder.addModification(int index, Modification modification) Add a the modification to the side chain of residue at index
PeptideBuilder	PeptideBuilder.addModification(ModAttachment modAttachment, Modification modification) Add a the modification to either end of the the peptide.
PeptideBuilder	PeptideBuilder.addModificationToAll(Modification modification, AminoAcid aminoAcid) Add the modification to all amino acids that are equal to aminoAcid
ModifiedPeptideFactory.Builder	ModifiedPeptideFactory.Builder.addTarget(ModAttachment attachment, Modification mod)
ModifiedPeptideFactory.Builder	ModifiedPeptideFactory.Builder.addTarget(Set<AminoAcid> aas, ModAttachment attachment, Modification mod)
ModifiedPeptideFactory.Builder	ModifiedPeptideFactory.Builder.addTarget(Set<AminoAcid> aas, Modification mod)

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

Modifier and Type	Method and Description
PeptideBuilder	PeptideBuilder.addModificationToAll(Collection<Modification> modifications, AminoAcid aminoAcid) Add all of the Modification's in modifications to all amino acids that are equal to aminoAcid

Constructor parameters in org.expasy.mzjava.proteomics.mol with type arguments of type Modification

Constructor and Description
AminoAcidSequence(List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an AminoAcidSequence from the list of residues with the modifications contained in side chain and term mod map.
AminoAcidSequence(List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an AminoAcidSequence from the list of residues with the modifications contained in side chain and term mod map.
Peptide(List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an Peptide from the list of residues with the modifications contained in side chain and term mod map.
Peptide(List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an Peptide from the list of residues with the modifications contained in side chain and term mod map.
PeptideFragment(FragmentType fragmentType, List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an PeptideFragment from the list of residues with the modifications contained in side chain and term mod map.
PeptideFragment(FragmentType fragmentType, List<AminoAcid> residues, com.google.common.collect.Multimap<Integer,Modification> sideChainModMap, com.google.common.collect.Multimap<ModAttachment,Modification> termModMap) Constructs an PeptideFragment from the list of residues with the modifications contained in side chain and term mod map.

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

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

Modifier and Type	Method and Description
com.google.common.base.Optional<Modification>	CleavageSiteMatcher.getCtermMod()
com.google.common.base.Optional<Modification>	CleavageSiteMatcher.getNtermMod()

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

Modifier and Type	Method and Description
ProteinDigester.Builder	ProteinDigester.Builder.addFixedMod(AminoAcid target, Modification mod)

Constructor parameters in org.expasy.mzjava.proteomics.mol.digest with type arguments of type Modification

Constructor and Description
CleavageSiteMatcher(String cleavageFormat, com.google.common.base.Optional<Modification> nTermMod, com.google.common.base.Optional<Modification> cTermMod)
CleavageSiteMatcher(String cleavageFormat, com.google.common.base.Optional<Modification> nTermMod, com.google.common.base.Optional<Modification> cTermMod)

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

Methods in org.expasy.mzjava.proteomics.mol.modification that return Modification

Modifier and Type	Method and Description
Modification	ModificationList.get(int index)
static Modification	Modification.parseModification(String s) Parse a modification.

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

Modifier and Type	Method and Description
com.google.common.base.Optional<Modification>	CompositeModResolver.resolve(String input)
com.google.common.base.Optional<Modification>	NumericModificationResolver.resolve(String input)
com.google.common.base.Optional<Modification>	ModificationResolver.resolve(String input) Create or fetch a modification for input

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

Subclasses of Modification in org.expasy.mzjava.proteomics.mol.modification.unimod

Modifier and Type	Class and Description
class	UnimodMod A extension of the Modification class to store UniMod specific fields.

Methods in org.expasy.mzjava.proteomics.mol.modification.unimod that return types with arguments of type Modification

Modifier and Type	Method and Description
static List<Modification>	UnimodManager.getModifications(double mass, Tolerance tolerance)
static List<Modification>	UnimodManager.getModifications(double mass, Tolerance tolerance, Set<String> aminoAcids)
com.google.common.base.Optional<Modification>	UnimodModificationResolver.resolve(String input)

Methods in org.expasy.mzjava.proteomics.mol.modification.unimod with parameters of type Modification

Modifier and Type	Method and Description
void	UnimodModificationResolver.putOverrideUnimod(String name, Modification modification) Override the modification that the name is mapped to in Unimod.

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

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

Modifier and Type	Method and Description
static PeptideNeutralLossPeakGenerator	PeptideNeutralLossPeakGenerator.newModificationLossGenerator(Mass loss, Set<AminoAcid> aminoAcids, Set<Modification> modifications, Set<ModAttachment> modAttachments, Set<IonType> ionTypes, double peakIntensity)

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

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

Modifier and Type	Method and Description
Modification	ModificationMatch.getModificationCandidate(int index)

Methods in org.expasy.mzjava.proteomics.ms.ident that return types with arguments of type Modification

Modifier and Type	Method and Description
com.google.common.base.Optional<Modification>	ModificationMatchResolver.resolve(ModificationMatch modificationMatch)
com.google.common.base.Optional<Modification>	ModListModMatchResolver.resolve(ModificationMatch modMatch)

Methods in org.expasy.mzjava.proteomics.ms.ident with parameters of type Modification

Modifier and Type	Method and Description
ModificationMatch	PeptideMatch.addModificationMatch(int index, Modification modification) Convenience method for adding a ModificationMatch.
ModificationMatch	PeptideMatch.addModificationMatch(ModAttachment modAttachment, Modification modification) Convenience method for adding a ModificationMatch.
void	ModificationMatch.addPotentialModification(Modification modification) Add a modification to the list of potential modifications

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

Constructor and Description
ModificationMatch(Modification modification, AminoAcid residue, int position, ModAttachment modAttachment) Create a ModificationMatch given a modification.
ModListModMatchResolver(Tolerance tolerance, Modification... mods)

Constructor parameters in org.expasy.mzjava.proteomics.ms.ident with type arguments of type Modification

Constructor and Description
ModListModMatchResolver(Tolerance tolerance, Collection<Modification> mods)