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

Packages that use ModAttachment

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

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

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

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

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

Modifier and Type	Method and Description
protected double	PepXmlReader.adjustMass(Double mass, ModAttachment modAttachment)

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

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

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

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

Modifier and Type	Method and Description
void	LibrarySpectrumBuilder.addMod(ModAttachment modAttachment, String mod)

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

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

Modifier and Type	Method and Description
PeptideBuilder	PeptideBuilder.addModification(ModAttachment modAttachment, Modification modification) Add a the modification to either end of the the peptide.
ModifiedPeptideFactory.Builder	ModifiedPeptideFactory.Builder.addTarget(ModAttachment attachment, Modification mod)
ModifiedPeptideFactory.Builder	ModifiedPeptideFactory.Builder.addTarget(Set<AminoAcid> aas, ModAttachment attachment, Modification mod)
int	AminoAcidSequence.getModificationCount(ModAttachment attachment) Returns the number of modifications that are attached to the given attachment
boolean	AminoAcidSequence.hasModificationAt(ModAttachment modAttachment) Returns true if there are modifications attached via the given modAttachment

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

Modifier and Type	Method and Description
int[]	AminoAcidSequence.getModificationIndexes(Set<ModAttachment> modAttachments) Returns a sorted Array containing the indexes of the modified amino acids
ModificationList	AminoAcidSequence.getModifications(Set<ModAttachment> attachments) Returns a ModificationList containing all the modifications for the given attachments.
ModificationList	AminoAcidSequence.getModificationsAt(int index, Set<ModAttachment> attachments) Returns a ModificationList containing all the modifications for the given index and attachments.
boolean	AminoAcidSequence.hasModificationAt(int index, Set<ModAttachment> modAttachments) Returns true if the residue at index has a modification attached by modAttachment.
boolean	AminoAcidSequence.hasModificationAt(Set<ModAttachment> modAttachments) Returns true if there are modifications attached via any of the ModAttachments in modAttachments

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

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.
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.

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

Fields in org.expasy.mzjava.proteomics.mol.modification with type parameters of type ModAttachment

Modifier and Type	Field and Description
static Set<ModAttachment>	ModAttachment.all
static Set<ModAttachment>	ModAttachment.cTermSet
static Set<ModAttachment>	ModAttachment.nTermSet
static Set<ModAttachment>	ModAttachment.sideChainSet
static Set<ModAttachment>	ModAttachment.termSet

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

Modifier and Type	Method and Description
static ModAttachment	ModAttachment.valueOf(String name) Returns the enum constant of this type with the specified name.
static ModAttachment[]	ModAttachment.values() Returns an array containing the constants of this enum type, in the order they are declared.

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

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

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 ModAttachment in org.expasy.mzjava.proteomics.ms.ident

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

Modifier and Type	Method and Description
ModAttachment	ModificationMatch.getModAttachment()

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

Modifier and Type	Method and Description
ModificationMatch	PeptideMatch.addModificationMatch(ModAttachment modAttachment, double modificationMass) Convenience method for adding a ModificationMatch.
ModificationMatch	PeptideMatch.addModificationMatch(ModAttachment modAttachment, Modification modification) Convenience method for adding a ModificationMatch.
void	PeptideMatch.addModificationMatch(ModAttachment modAttachment, ModificationMatch modificationMatch) Add a the modificationMatch to either end of the this peptide match.

Method parameters in org.expasy.mzjava.proteomics.ms.ident with type arguments of type ModAttachment

Modifier and Type	Method and Description
List<ModificationMatch>	PeptideMatch.getModifications(int index, Set<ModAttachment> attachments) Returns a list containing all ModificationMatch for the residue at index that are attached by a ModAttachment contained in the attachments set.
List<ModificationMatch>	PeptideMatch.getModifications(Set<ModAttachment> attachments) Return a list containing all ModificationMatch for ModAttachment's in the attachments set.

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

Constructor and Description
ModificationMatch(double massShift, AminoAcid residue, Integer position, ModAttachment modAttachment) Create a ModificationMatch given a mass shift
ModificationMatch(Modification modification, AminoAcid residue, int position, ModAttachment modAttachment) Create a ModificationMatch given a modification.