Uses of Class
com.compomics.util.experiment.identification.matches.ModificationMatch

Packages that use ModificationMatch

Package	Description
com.compomics.util.experiment.biology.aminoacids.sequence	Classes related to the handling of protein sequences.
com.compomics.util.experiment.biology.proteins	Classes related to proteins.
com.compomics.util.experiment.identification.features	Classes for the generation of identification features.
com.compomics.util.experiment.identification.matches	Experiment classes related to matches.
com.compomics.util.experiment.identification.modification.mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.search_engine_mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.protein_inference	Classes related to protein inference.
com.compomics.util.experiment.identification.protein_inference.fm_index	Protein sequence database indexing classes based on Burrows-Wheeler transform.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.

Uses of ModificationMatch in com.compomics.util.experiment.biology.aminoacids.sequence

Methods in com.compomics.util.experiment.biology.aminoacids.sequence that return ModificationMatch

Modifier and Type	Method	Description
ModificationMatch[]	AminoAcidSequence.getVariableModifications()	Getter for the modifications carried by this sequence in a map: aa number > modification matches.

Methods in com.compomics.util.experiment.biology.aminoacids.sequence with parameters of type ModificationMatch

Modifier and Type	Method	Description
void	AminoAcidSequence.addVariableModification(ModificationMatch modificationMatch)	Adds a modification to one of the amino acid sequence.
void	AminoAcidSequence.setVariableModifications(ModificationMatch[] variableModifications)	Sets the variable modifications.

Constructors in com.compomics.util.experiment.biology.aminoacids.sequence with parameters of type ModificationMatch

Modifier	Constructor	Description
	AminoAcidSequence(String sequence, ModificationMatch[] variableModifications)	Constructor taking a sequence of amino acids as input.

Uses of ModificationMatch in com.compomics.util.experiment.biology.proteins

Methods in com.compomics.util.experiment.biology.proteins that return ModificationMatch

Modifier and Type	Method	Description
ModificationMatch[]	Peptide.getVariableModifications()	Returns the variable modifications.

Methods in com.compomics.util.experiment.biology.proteins with parameters of type ModificationMatch

Modifier and Type	Method	Description
void	Peptide.addVariableModification(ModificationMatch modificationMatch)	Adds a modification match.
static long	Peptide.getKey(String sequence, ModificationMatch[] variableModifications)	Returns the reference key of a peptide.
void	Peptide.setVariableModifications(ModificationMatch[] variableModifications)	Sets the variable modifications.

Constructors in com.compomics.util.experiment.biology.proteins with parameters of type ModificationMatch

Modifier	Constructor	Description
	Peptide(String aSequence, ModificationMatch[] variableModifications)	Constructor.
	Peptide(String aSequence, ModificationMatch[] variableModifications, boolean sanityCheck)	Constructor.
	Peptide(String aSequence, ModificationMatch[] variableModifications, boolean sanityCheck, double mass)	Constructor.
	Peptide(String aSequence, ModificationMatch[] variableModifications, HashMap<String,HashMap<Integer,PeptideVariantMatches>> variantMatches, boolean sanityCheck)	Constructor for the peptide.
	Peptide(String aSequence, ModificationMatch[] variableModifications, HashMap<String,HashMap<Integer,PeptideVariantMatches>> variantMatches, boolean sanityCheck, double mass)	Constructor.

Uses of ModificationMatch in com.compomics.util.experiment.identification.features

Methods in com.compomics.util.experiment.identification.features with parameters of type ModificationMatch

Modifier and Type	Method	Description
String	IdentificationFeaturesGenerator.getModificationSites(String sequence, ModificationMatch[] modificationMatches, boolean confident)	Returns a summary of the modifications present on the sequence.
String	IdentificationFeaturesGenerator.getModificationSites(String sequence, ModificationMatch[] modificationMatches, boolean confident, HashSet<String> targetedModifications)	Returns a summary of the modifications present on the peptide sequence confidently assigned to an amino acid with focus on given list of modifications.
String	IdentificationFeaturesGenerator.getModificationSitesNumber(ModificationMatch[] modificationMatches, boolean confident)	Returns the number of confidently localized variable modifications.
int	IdentificationFeaturesGenerator.getModificationSitesNumber(ModificationMatch[] modificationMatches, boolean confident, HashSet<String> targetedModifications)	Returns the number of confidently localized variable modifications.
String	IdentificationFeaturesGenerator.getModifiedSequence(ModificationMatch[] modificationMatches, String sequence)	Returns the match sequence annotated with modifications.

Uses of ModificationMatch in com.compomics.util.experiment.identification.matches

Fields in com.compomics.util.experiment.identification.matches declared as ModificationMatch

Modifier and Type	Field	Description
static final ModificationMatch[]	ModificationMatch.NO_MOD	Convenience array for no modifications.

Methods in com.compomics.util.experiment.identification.matches that return ModificationMatch

Modifier and Type	Method	Description
ModificationMatch	ModificationMatch.clone()	Clones the modification match into a new match with the same attributes.
ModificationMatch[]	ProteinMatch.getVariableModifications()	Returns the variable modifications.

Methods in com.compomics.util.experiment.identification.matches with parameters of type ModificationMatch

Modifier and Type	Method	Description
boolean	ModificationMatch.isSameAs(ModificationMatch anotherModificationMatch)	Indicates whether this modification match is the same of another one.
void	ProteinMatch.setVariableModifications(ModificationMatch[] variableModifications)	Sets the variable modifications.

Uses of ModificationMatch in com.compomics.util.experiment.identification.modification.mapping

Methods in com.compomics.util.experiment.identification.modification.mapping with parameters of type ModificationMatch

Modifier and Type	Method	Description
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNames(Peptide peptide, ModificationMatch modificationMatch, IdfileReader idfileReader, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modification names.
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNamesAndromeda(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible Andromeda modification names.
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNamesByMass(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modifications names by mass.
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNamesByName(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modifications by name.
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNamesOmssa(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible OMSSA modification names.

Uses of ModificationMatch in com.compomics.util.experiment.identification.modification.search_engine_mapping

Methods in com.compomics.util.experiment.identification.modification.search_engine_mapping with parameters of type ModificationMatch

Modifier and Type	Method	Description
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNames(Peptide peptide, ModificationMatch modificationMatch, IdfileReader idfileReader, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modification names from a search engine modification indexed by site.
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNamesAndromeda(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible Andromeda modification names.
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNamesByMass(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modifications names by mass.
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNamesByName(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible modifications by name.
static HashMap<Integer,HashSet<String>>	ModificationNameMapper.getPossibleModificationNamesOmssa(Peptide peptide, ModificationMatch modificationMatch, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider)	Returns the possible OMSSA modification names.

Uses of ModificationMatch in com.compomics.util.experiment.identification.protein_inference

Methods in com.compomics.util.experiment.identification.protein_inference that return ModificationMatch

Modifier and Type	Method	Description
ModificationMatch[]	PeptideProteinMapping.getVariableModifications()	Returns eventual modifications found.

Constructors in com.compomics.util.experiment.identification.protein_inference with parameters of type ModificationMatch

Modifier	Constructor	Description
	PeptideProteinMapping(String proteinAccession, String peptideSequence, int index, ModificationMatch[] modificationMatches)	Constructor.
	PeptideProteinMapping(String proteinAccession, String peptideSequence, int index, ModificationMatch[] modificationMatches, PeptideVariantMatches peptideVariantMatches)	Constructor.

Uses of ModificationMatch in com.compomics.util.experiment.identification.protein_inference.fm_index

Fields in com.compomics.util.experiment.identification.protein_inference.fm_index declared as ModificationMatch

Modifier and Type	Field	Description
ModificationMatch	MatrixContent.modification	Index to the modifications list.

Fields in com.compomics.util.experiment.identification.protein_inference.fm_index with type parameters of type ModificationMatch

Modifier and Type	Field	Description
ArrayList<ModificationMatch>	MatrixContent.modifications	List of all modifications.

Constructors in com.compomics.util.experiment.identification.protein_inference.fm_index with parameters of type ModificationMatch

Modifier	Constructor	Description
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, int length, int numX, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos, int[] numSpecificVariants, char variant, String allVariants)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, int length, int numX, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos, int numVariants, char variant, String allVariants)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, String peptideSequenceSearch, int length, int numX, int tagComponent, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, String peptideSequenceSearch, int length, int numX, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos, int ambiguousChar)	Constructor.

Constructor parameters in com.compomics.util.experiment.identification.protein_inference.fm_index with type arguments of type ModificationMatch

Modifier	Constructor	Description
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, int length, int numX, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos, int[] numSpecificVariants, char variant, String allVariants)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, int length, int numX, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos, int numVariants, char variant, String allVariants)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, String peptideSequenceSearch, int length, int numX, int tagComponent, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos)	Constructor.
	MatrixContent(int left, int right, int character, MatrixContent previousContent, double mass, String peptideSequence, String peptideSequenceSearch, int length, int numX, ModificationMatch modification, ArrayList<ModificationMatch> modifications, int modifictationPos, int ambiguousChar)	Constructor.

Uses of ModificationMatch in com.compomics.util.experiment.identification.utils

Methods in com.compomics.util.experiment.identification.utils with parameters of type ModificationMatch

Modifier and Type	Method	Description
static String	PeptideUtils.getVariableModificationsAsString(ModificationMatch[] modificationMatches)	Returns the peptide modifications as a string.