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.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.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.
|
Modifier and Type | Method and Description |
---|---|
ModificationMatch[] |
AminoAcidSequence.getVariableModifications()
Getter for the modifications carried by this sequence in a map: aa number
> modification matches.
|
Modifier and Type | Method and 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.
|
Constructor and Description |
---|
AminoAcidSequence(String sequence,
ModificationMatch[] variableModifications)
Constructor taking a sequence of amino acids as input.
|
Modifier and Type | Method and Description |
---|---|
ModificationMatch[] |
Peptide.getVariableModifications()
Returns the variable modifications.
|
Modifier and Type | Method and 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.
|
Constructor and 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.
|
Modifier and Type | Method and Description |
---|---|
ModificationMatch |
ModificationMatch.clone()
Clones the modification match into a new match with the same attributes.
|
Modifier and Type | Method and Description |
---|---|
boolean |
ModificationMatch.isSameAs(ModificationMatch anotherModificationMatch)
Indicates whether this modification match is the same of another one.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
static void |
ModificationLocalizationMapper.modificationLocalization(Peptide peptide,
HashMap<Integer,ArrayList<String>> expectedNames,
HashMap<ModificationMatch,ArrayList<String>> modNames,
IdentificationParameters identificationParameters,
IdfileReader idfileReader,
ModificationProvider modificationProvider)
Makes an initial modification mapping based on the search engine results
and the compatibility to the searched modifications.
|
Modifier and Type | Method and Description |
---|---|
ModificationMatch[] |
PeptideProteinMapping.getVariableModifications()
Returns eventual modifications found.
|
Constructor and Description |
---|
PeptideProteinMapping(String proteinAccession,
String peptideSequence,
int index,
ModificationMatch[] modificationMatches)
Constructor.
|
PeptideProteinMapping(String proteinAccession,
String peptideSequence,
int index,
ModificationMatch[] modificationMatches,
PeptideVariantMatches peptideVariantMatches)
Constructor.
|
Modifier and Type | Field and Description |
---|---|
ModificationMatch |
MatrixContent.modification
Index to the modifications list.
|
Modifier and Type | Field and Description |
---|---|
ArrayList<ModificationMatch> |
MatrixContent.modifications
List of all modifications.
|
Constructor and 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 and 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.
|
Modifier and Type | Method and Description |
---|---|
static String |
PeptideUtils.getVariableModificationsAsString(ModificationMatch[] modificationMatches)
Returns the peptide modifications as a string.
|
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