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