Uses of Interface
com.compomics.util.experiment.io.biology.protein.SequenceProvider

Packages that use SequenceProvider

Package	Description
com.compomics.util.experiment.biology.genes	Classes related to genes.
com.compomics.util.experiment.biology.ions	Experiment classes related to ions.
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.filtering	Classes for the filtering of identification objects.
com.compomics.util.experiment.identification.modification	Modification mapping and localization.
com.compomics.util.experiment.identification.modification.mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.modification.scores	PTM scores.
com.compomics.util.experiment.identification.modification.search_engine_mapping	Mapping between search engine and Utilities modifications.
com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation	This package contains the classes needed to generate ms2pip features.
com.compomics.util.experiment.identification.peptide_inference	Classes related to peptide inference.
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.protein_sequences	Protein sequence handling related classes.
com.compomics.util.experiment.identification.psm_scoring	Main PSM scoring class.
com.compomics.util.experiment.identification.psm_scoring.psm_scores	Main PTM scoring classes.
com.compomics.util.experiment.identification.spectrum_annotation	Classes used for ms2 spectrum annotation.
com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators	This package contains implementations of the SpectrumAnnotator allowing the annotation of all ions.
com.compomics.util.experiment.identification.utils	This package contains utilities classes to handle identification objects.
com.compomics.util.experiment.io.identification.writers	Writer for identification results.
com.compomics.util.experiment.quantification.spectrumcounting	Experiment classes related to spectrum counting.
com.compomics.util.gui.modification	PTM GUI dialogs.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.

Uses of SequenceProvider in com.compomics.util.experiment.biology.genes

Methods in com.compomics.util.experiment.biology.genes with parameters of type SequenceProvider

Modifier and Type	Method	Description
GeneMaps	ProteinGeneDetailsProvider.getGeneMaps(GeneParameters genePreferences, FastaSummary fastaSummary, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, WaitingHandler waitingHandler)	Returns the gene maps for the given proteins.

Uses of SequenceProvider in com.compomics.util.experiment.biology.ions

Methods in com.compomics.util.experiment.biology.ions with parameters of type SequenceProvider

Modifier and Type	Method	Description
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	IonFactory.getFragmentIons(Peptide peptide, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	This method returns the theoretic ions expected from a peptide.
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	IonFactory.getFragmentIons(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	This method returns all the theoretic ions expected from a peptide.

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

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

Modifier and Type	Method	Description
void	Peptide.estimateTheoreticMass(ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Estimates the theoretic mass of the peptide.
String[]	Peptide.getFixedModifications(ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the fixed modifications for this peptide based on the given modification parameters.
double	Peptide.getMass(ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Returns the mass, estimates it if not done before.
String	Peptide.getTaggedModifiedSequence(ModificationParameters modificationProfile, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName, HashSet<String> displayedModifications)	Returns the modified sequence as an tagged string with potential modification sites color coded or with Modification tags, e.g, <mox>.

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

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

Modifier and Type	Method	Description
static double	IdentificationFeaturesGenerator.estimateSpectrumCounting(Identification identification, SequenceProvider sequenceProvider, long proteinMatchKey, SpectrumCountingParameters spectrumCountingPreferences, int maxPepLength, IdentificationParameters identificationParameters)	Returns the spectrum counting index based on the project settings.

Constructors in com.compomics.util.experiment.identification.features with parameters of type SequenceProvider

Modifier	Constructor	Description
	IdentificationFeaturesGenerator(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, Metrics metrics, SpectrumCountingParameters spectrumCountingPreferences)	Constructor.

Uses of SequenceProvider in com.compomics.util.experiment.identification.filtering

Methods in com.compomics.util.experiment.identification.filtering with parameters of type SequenceProvider

Modifier and Type	Method	Description
boolean	AssumptionFilter.isValidated(long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)	Tests whether a match is validated by this filter.
boolean	AssumptionFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean	AssumptionFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long spectrumMatchKey, String spectrumFile, String spectrumTitle, PeptideAssumption peptideAssumption, Identification identification, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters)	Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.
boolean	MatchFilter.isValidated(long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)	Tests whether a match is validated by this filter.
abstract boolean	MatchFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)	Indicates whether the match designated by the match key validates the given item using the given comparator and value threshold.
boolean	PeptideFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean	ProteinFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean	PsmFilter.isValidated(String itemName, FilterItemComparator filterItemComparator, Object value, long matchKey, Identification identification, GeneMaps geneMaps, IdentificationFeaturesGenerator identificationFeaturesGenerator, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider)
boolean	PeptideAssumptionFilter.validateProteins(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider)	Validates a peptide depending on its protein inference status.

Uses of SequenceProvider in com.compomics.util.experiment.identification.modification

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

Modifier and Type	Method	Description
static HashMap<PeptideFragmentIon,ArrayList<IonMatch>>	ModificationtableContent.getModificationPlotData(Peptide peptide, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Returns the modification plot series in the JFreechart format for one PSM.
static ModificationtableContent	ModificationtableContent.getModificationTableContent(PeptideAssumption peptideAssumption, Modification modification, int nMod, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Get the table content.

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

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

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 SequenceProvider in com.compomics.util.experiment.identification.modification.scores

Methods in com.compomics.util.experiment.identification.modification.scores with parameters of type SequenceProvider

Modifier and Type	Method	Description
static HashMap<Integer,Double>	PhosphoRS.getSequenceProbabilities(Peptide peptide, ArrayList<Modification> modifications, ModificationParameters modificationParameters, Spectrum spectrum, SequenceProvider sequenceProvider, AnnotationParameters annotationParameters, SpecificAnnotationParameters specificAnnotationSettings, boolean accountNeutralLosses, SequenceMatchingParameters sequenceMatchingParameters, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator spectrumAnnotator, ModificationProvider modificationProvider)	Returns the PhosphoRS sequence probabilities for the modification possible locations.

Uses of SequenceProvider 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 SequenceProvider

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.
static void	ModificationLocalizationMapper.modificationLocalization(Peptide peptide, IdentificationParameters identificationParameters, IdfileReader idfileReader, ModificationProvider modificationProvider, SequenceProvider sequenceProvider)	Makes an initial modification mapping based on the search engine results and the compatibility to the searched modifications.

Uses of SequenceProvider in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation

Methods in com.compomics.util.experiment.identification.peptide_fragmentation.models.ms2pip.features_generation with parameters of type SequenceProvider

Modifier and Type	Method	Description
int[]	FeaturesGenerator.getComplementaryIonsFeatures(Peptide peptide, int charge, int ionIndex, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingPreferences)	Returns the ms2pip features for the complementary ions of the given peptide at the given charge.
int[]	FeaturesGenerator.getForwardIonsFeatures(Peptide peptide, int charge, int ionIndex, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingPreferences)	Returns the ms2pip features for the forward ions of the given peptide at the given charge.

Uses of SequenceProvider in com.compomics.util.experiment.identification.peptide_inference

Methods in com.compomics.util.experiment.identification.peptide_inference with parameters of type SequenceProvider

Modifier and Type	Method	Description
void	PeptideInference.peptideInference(Identification identification, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ModificationProvider modificationProvider, WaitingHandler waitingHandler)	Infers the PTM localization and its confidence for the best match of every spectrum.

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

Methods in com.compomics.util.experiment.identification.protein_inference with parameters of type SequenceProvider

Modifier and Type	Method	Description
void	PeptideAndProteinBuilder.buildPeptidesAndProteins(SpectrumMatch spectrumMatch, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider, boolean protein)	Creates the peptides and protein instances based on the given spectrum match.

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

Classes in com.compomics.util.experiment.identification.protein_inference.fm_index that implement SequenceProvider

Modifier and Type	Class	Description
class	FMIndex	The FM index.

Uses of SequenceProvider in com.compomics.util.experiment.identification.protein_sequences

Classes in com.compomics.util.experiment.identification.protein_sequences that implement SequenceProvider

Modifier and Type	Class	Description
class	SingleProteinSequenceProvider	Sequence provider for a single protein.

Uses of SequenceProvider in com.compomics.util.experiment.identification.psm_scoring

Methods in com.compomics.util.experiment.identification.psm_scoring with parameters of type SequenceProvider

Modifier and Type	Method	Description
double	PsmScoresEstimator.getDecreasingScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)	Scores the match between the given peptide and spectrum using the given score.
double	PsmScoresEstimator.getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, int scoreIndex)	Scores the match between the given peptide and spectrum using the given score.
double	PsmScoresEstimator.getScore(Peptide peptide, int peptideCharge, String spectrumFile, String spectrumTitle, Spectrum spectrum, IdentificationParameters identificationParameters, SpecificAnnotationParameters specificAnnotationParameters, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, PeptideSpectrumAnnotator peptideSpectrumAnnotator, PsmScore psmScore)	Scores the match between the given peptide and spectrum using the given score.

Uses of SequenceProvider in com.compomics.util.experiment.identification.psm_scoring.psm_scores

Methods in com.compomics.util.experiment.identification.psm_scoring.psm_scores with parameters of type SequenceProvider

Modifier and Type	Method	Description
double	HyperScore.getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Returns the hyperscore.
double	SnrScore.getScore(Peptide peptide, String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, PeptideSpectrumAnnotator peptideSpectrumAnnotator, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Returns the score.

Uses of SequenceProvider in com.compomics.util.experiment.identification.spectrum_annotation

Methods in com.compomics.util.experiment.identification.spectrum_annotation with parameters of type SequenceProvider

Modifier and Type	Method	Description
IonMatch[]	SpectrumAnnotator.getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the currently matched ions with the given settings using the intensity filter.
abstract IonMatch[]	SpectrumAnnotator.getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)	Returns the currently matched ions with the given settings.
static NeutralLossesMap	SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the possible neutral losses expected by default for a given peptide.
SpecificAnnotationParameters	AnnotationParameters.getSpecificAnnotationParameters(String spectrumFile, String spectrumTitle, SpectrumIdentificationAssumption spectrumIdentificationAssumption, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters, SpectrumAnnotator spectrumAnnotator)	Returns the annotation preferences specific to a spectrum and an identification assumption.

Uses of SequenceProvider in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators

Methods in com.compomics.util.experiment.identification.spectrum_annotation.spectrum_annotators with parameters of type SequenceProvider

Modifier and Type	Method	Description
Map<Integer,ArrayList<IonMatch>>	PeptideSpectrumAnnotator.getCoveredAminoAcids(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)	Returns the ion matches corresponding to fragment ions indexed by amino acid number in the sequence.
IonMatch[]	PeptideSpectrumAnnotator.getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
IonMatch[]	TagSpectrumAnnotator.getCurrentAnnotation(String spectrumFile, String spectrumTitle, Spectrum spectrum, AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)
static NeutralLossesMap	PeptideSpectrumAnnotator.getDefaultLosses(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the possible neutral losses expected by default for a given peptide.
HashMap<Integer,ArrayList<Ion>>	PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the expected ions in a map indexed by the possible charges.
HashMap<Integer,ArrayList<Ion>>	PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)	Returns the expected ions in a map indexed by the possible charges.
IonMatch[]	PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the spectrum annotations of a spectrum in a list of IonMatches using the intensity filter.
IonMatch[]	PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in a list of IonMatches.
IonMatch[]	PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in an array of IonMatches.
java.util.stream.Stream<IonMatch>	PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the spectrum annotations of a spectrum in a list of IonMatches using the intensity filter.
java.util.stream.Stream<IonMatch>	PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in a list of IonMatches.
java.util.stream.Stream<IonMatch>	PeptideSpectrumAnnotator.getSpectrumAnnotationStream(AnnotationParameters annotationSettings, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments, boolean useIntensityFilter)	Returns the spectrum annotations of a spectrum in a stream of IonMatches.
ArrayList<IonMatch>	PeptideSpectrumAnnotator.matchPeak(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, double peakMz, double peakIntensity)	This method matches the potential fragment ions of a given peptide with a given peak according to the annotation settings.
void	PeptideSpectrumAnnotator.setPeptide(Peptide peptide, int precursorCharge, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings)	Sets a new peptide to annotate.
void	PeptideSpectrumAnnotator.setPeptide(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons, int precursorCharge, SpecificAnnotationParameters specificAnnotationSettings)	Sets a new peptide to annotate.

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

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

Modifier and Type	Method	Description
static TreeMap<String,String[]>	PeptideUtils.getAaAfter(Peptide peptide, int nAa, SequenceProvider sequenceProvider)	Returns the amino acids before the given peptide as a string in a map based on the peptide protein mapping.
static String	PeptideUtils.getAaAfter(Peptide peptide, String accession, int index, int nAa, SequenceProvider sequenceProvider)	Returns the amino acids before the given peptide as a string.
static TreeMap<String,String[]>	PeptideUtils.getAaBefore(Peptide peptide, int nAa, SequenceProvider sequenceProvider)	Returns the amino acids before the given peptide as a string in a map based on the peptide protein mapping.
static String	PeptideUtils.getAaBefore(Peptide peptide, String accession, int index, int nAa, SequenceProvider sequenceProvider)	Returns the amino acids before the given peptide as a string in a map based on the peptide protein mapping.
static HashSet<String>	ModificationUtils.getAllModifications(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters)	Returns a set of the names of all modifications found on a peptide.
static HashMap<Integer,HashSet<String>>	ModificationUtils.getExpectedModifications(double modMass, ModificationParameters modificationParameters, Peptide peptide, double massTolerance, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters, SearchParameters searchParameters)	Returns the expected modifications for a given modification mass indexed by site.
static String	PeptideUtils.getFixedModificationsAsString(Peptide peptide, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Returns the peptide modifications as a string.
static int[]	ModificationUtils.getPossibleModificationSites(Peptide peptide, Modification modification, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters)	Returns an array of the possible modification sites for the given modification on the given peptide.
static int[]	ModificationUtils.getPossibleModificationSites(Peptide peptide, Modification modification, SequenceProvider sequenceProvider, SequenceMatchingParameters sequenceMatchingParameters, ModificationProvider modificationProvider, boolean avoidOverlap)	Returns an array of the possible modification sites for the given modification on the given peptide.
static boolean	PeptideUtils.isCterm(Peptide peptide, SequenceProvider sequenceProvider)	Indicates whether a peptide is at the C-terminus of a protein.
static boolean	PeptideUtils.isCterm(Peptide peptide, String proteinAccession, SequenceProvider sequenceProvider)	Indicates whether a peptide is at the C-terminus of a given protein.
static boolean	PeptideUtils.isDecoy(Peptide peptide, SequenceProvider sequenceProvider)	Returns a boolean indicating whether the peptide matches a decoy sequence.
static boolean	ProteinUtils.isDecoy(String accession, SequenceProvider sequenceProvider)	Returns a boolean indicating whether the given accession corresponds to a decoy sequence according to the given sequence provider.
static boolean	PeptideUtils.isEnzymatic(Peptide peptide, SequenceProvider sequenceProvider, ArrayList<Enzyme> enzymes)	Returns a boolean indicating whether the peptide is enzymatic in at least one protein using one of the given enzymes.
static boolean	PeptideUtils.isNterm(Peptide peptide, SequenceProvider sequenceProvider)	Indicates whether a peptide is at the N-terminus of a protein.
static boolean	PeptideUtils.isNterm(Peptide peptide, String proteinAccession, SequenceProvider sequenceProvider)	Indicates whether a peptide is at the N-terminus of a given protein.

Uses of SequenceProvider in com.compomics.util.experiment.io.identification.writers

Constructors in com.compomics.util.experiment.io.identification.writers with parameters of type SequenceProvider

Modifier	Constructor	Description
	SimpleMzIdentMLExporter(String softwareName, String softwareVersion, String softwareUrl, File tempFolder, File destinationFile, ArrayList<File> spectrumFiles, File searchEngineFile, HashMap<String,ArrayList<String>> searchEngines, File fastaFile, IdentificationParameters identificationParameters, SequenceProvider sequenceProvider, ProteinDetailsProvider proteinDetailsProvider, SpectrumProvider spectrumProvider, ModificationProvider modificationProvider, FastaSummary fastaSummary, String contactFirstName, String contactLastName, String contactAddress, String contactEmail, String contactOrganizationName, String contactOrganizationAddress, String contactOrganizationEmail, boolean peptideInference)	Constructor.

Uses of SequenceProvider in com.compomics.util.experiment.quantification.spectrumcounting

Methods in com.compomics.util.experiment.quantification.spectrumcounting with parameters of type SequenceProvider

Modifier and Type	Method	Description
void	ScalingFactorsEstimators.estimateScalingFactors(Identification identification, Metrics metrics, SequenceProvider sequenceProvider, IdentificationFeaturesGenerator identificationFeaturesGenerator, WaitingHandler waitingHandler, ExceptionHandler exceptionHandler, ProcessingParameters processingParameters)	Estimates the scaling factors and stores them in the given metrics.

Uses of SequenceProvider in com.compomics.util.gui.modification

Constructors in com.compomics.util.gui.modification with parameters of type SequenceProvider

Modifier	Constructor	Description
	ModificationTable(Identification identification, AnnotationParameters annotationParameters, PeptideMatch peptideMatch, Modification modification, boolean areaChart, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SpectrumProvider spectrumProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Constructor.

Uses of SequenceProvider in com.compomics.util.gui.spectrum

Methods in com.compomics.util.gui.spectrum with parameters of type SequenceProvider

Modifier and Type	Method	Description
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags, using default percent height of 0.9 for the forward ions and 1.0 for the reverse ions default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags, using default alpha levels of 0.2.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, float forwardIonAlphaLevel, float rewindIonAlphaLevel, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags.
void	SpectrumPanel.addAutomaticDeNovoSequencing(Peptide currentPeptide, IonMatch[] annotations, int aForwardIon, int aRewindIon, int aDeNovoCharge, boolean showForwardTags, boolean showRewindTags, double forwardIonPercentHeight, double rewindIonPercentHeight, ArrayList<float[]> alphaLevels, boolean excludeFixedModifications, boolean mirrored, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Add reference areas annotating the de novo tags.

Constructors in com.compomics.util.gui.spectrum with parameters of type SequenceProvider

Modifier	Constructor	Description
	FragmentIonTable(Peptide currentPeptide, ArrayList<IonMatch[]> allAnnotations, ArrayList<Spectrum> allSpectra, HashSet<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Creates a novel fragment ion table displaying bar charts with the intensity of each fragment ion type.
	FragmentIonTable(Peptide currentPeptide, ArrayList<IonMatch[]> allAnnotations, HashSet<Integer> currentFragmentIonTypes, NeutralLossesMap neutralLosses, boolean singleCharge, boolean twoCharges, ModificationParameters modificationParameters, SequenceProvider sequenceProvider, SequenceMatchingParameters modificationSequenceMatchingParameters)	Creates a traditional fragment ion table with the theoretical mz values and the detected fragment ions highlighted.