Uses of Class
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters

Packages that use SequenceMatchingParameters

Package	Description
com.compomics.util.experiment.biology.aminoacids	The amino acid classes.
com.compomics.util.experiment.biology.aminoacids.sequence	Classes related to the handling of protein sequences.
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.amino_acid_tags	Amino Acid Tag classes.
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.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.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	Experiment identification classes.
com.compomics.util.experiment.io.identification.idfilereaders	Experiment classes related to reading search engine files.
com.compomics.util.gui.modification	PTM GUI dialogs.
com.compomics.util.gui.parameters.identification.advanced	Dialogs for advanced identification parameters.
com.compomics.util.gui.spectrum	Spectrum and Chromatogram visualization GUI classes.
com.compomics.util.parameters.identification	Identification parameters.
com.compomics.util.parameters.identification.advanced	Advanced Identification parameters.

Uses of SequenceMatchingParameters in com.compomics.util.experiment.biology.aminoacids

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

Modifier and Type	Method	Description
static char	AminoAcid.getMatchingAminoAcid(char aa, SequenceMatchingParameters sequenceMatchingPreferences)	Returns a matching amino acid using the given preferences.
static String	AminoAcid.getMatchingSequence(String sequence, SequenceMatchingParameters sequenceMatchingPreferences)	Returns the matching sequence of a given sequence.

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

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

Modifier and Type	Method	Description
boolean	AminoAcidPattern.contains(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the pattern contains a subsequence of amino acids.
boolean	AminoAcidPattern.contains(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the pattern contains a subsequence of amino acids.
int	AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Returns the first index where the amino acid pattern is found.
int	AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters, int startIndex)	Returns the first index where the amino acid pattern is found in the given pattern.
int	AminoAcidPattern.firstIndex(AminoAcidSequence aminoAcidSequence, SequenceMatchingParameters sequenceMatchingParameters)	Returns the first index where the amino acid pattern is found.
int	AminoAcidPattern.firstIndex(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingParameters)	Returns the first index where the amino acid pattern is found.
int	AminoAcidPattern.firstIndex(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingParameters, int startIndex)	Returns the first index where the amino acid pattern is found.
int	AminoAcidSequence.firstIndex(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Returns the first index where the amino acid sequence is found in the given sequence.
Pattern	AminoAcidPattern.getAsStringPattern(SequenceMatchingParameters sequenceMatchingParameters, boolean includeMutations)	Returns the amino acid pattern as case insensitive pattern for String matching.
String[]	AminoAcidSequence.getFixedModifications(boolean nTerm, boolean cTerm, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the fixed modifications for this sequence based on the given modification parameters.
ArrayList<Integer>	AminoAcidPattern.getIndexes(AminoAcidPattern input, SequenceMatchingParameters sequenceMatchingParameters)	Returns the indexes where the amino acid pattern was found in the input.
int[]	AminoAcidPattern.getIndexes(String input, SequenceMatchingParameters sequenceMatchingParameters)	Returns the indexes where the amino acid pattern was found in the input.
boolean	AminoAcidPattern.isEnding(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the given amino acid sequence ends with the pattern.
boolean	AminoAcidPattern.isEnding(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the given amino acid sequence ends with the pattern.
boolean	AminoAcidPattern.isSameAs(AminoAcidPattern anotherPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether another AminoAcidPattern targets the same pattern.
boolean	AminoAcidSequence.isSameAs(AminoAcidSequence anotherSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether another sequence has a matching sequence.
boolean	AminoAcidSequence.isSameAs(TagComponent anotherCompontent, SequenceMatchingParameters sequenceMatchingPreferences)
boolean	AminoAcidSequence.isSameSequenceAndModificationStatusAs(AminoAcidSequence anotherSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether another sequence targets the same sequence without accounting for PTM localization.
boolean	AminoAcidSequence.isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent, SequenceMatchingParameters sequenceMatchingPreferences)
boolean	AminoAcidPattern.isStarting(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the given amino acid sequence starts with the pattern.
boolean	AminoAcidPattern.isStarting(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the given amino acid sequence starts with the pattern.
boolean	AminoAcidPattern.isTargeted(Character aa, int index, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the given amino acid at the given index of the pattern is targeted without accounting for mutations.
boolean	AminoAcidPattern.matches(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the pattern matches the given amino acid sequence
boolean	AminoAcidPattern.matches(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the pattern matches the given amino acid sequence.
boolean	AminoAcidSequence.matches(AminoAcidSequence aminoAcidSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
boolean	AminoAcidSequence.matches(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether the sequence matches the given amino acid sequence in size and according to the given matching preferences.
boolean	AminoAcidPattern.matchesAt(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingParameters, int index)	Indicates whether the pattern is found in the given amino acid sequence at the given index, where 0 is the first amino acid.
boolean	AminoAcidPattern.matchesIn(AminoAcidPattern aminoAcidPattern, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the pattern is found in the given amino acid sequence.
boolean	AminoAcidPattern.matchesIn(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingParameters)	Indicates whether the pattern is found in the given amino acid sequence.
boolean	AminoAcidSequence.matchesIn(AminoAcidSequence aminoAcidSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether the sequence is found in the given amino acid sequence.
boolean	AminoAcidSequence.matchesIn(String aminoAcidSequence, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether the sequence is found in the given amino acid sequence.

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

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

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.
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>>	IonFactory.getFragmentIons(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	This method returns the theoretic ions expected from a tag.

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

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

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.
long	Peptide.getMatchingKey(SequenceMatchingParameters sequenceMatchingPreferences)	Returns a unique key for the peptide when considering the given matching preferences.
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>.
boolean	Peptide.isSameSequence(Peptide anotherPeptide, SequenceMatchingParameters sequenceMatchingPreferences)	Returns a boolean indicating whether another peptide has the same sequence as the given peptide
boolean	Peptide.isSameSequenceAndModificationStatus(Peptide anotherPeptide, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether another peptide has the same sequence and modification status without accounting for modification localization.

Uses of SequenceMatchingParameters in com.compomics.util.experiment.identification.amino_acid_tags

Methods in com.compomics.util.experiment.identification.amino_acid_tags with parameters of type SequenceMatchingParameters

Modifier and Type	Method	Description
String	Tag.getCTerminal(boolean includeTerminalGaps, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the C-terminal tag of this tag as a string for sequence display.
String	Tag.getNTerminal(boolean includeTerminalGaps, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the N-terminal tag of this tag as a string for sequence display.
ArrayList<Integer>	Tag.getPotentialModificationSites(Modification modification, SequenceMatchingParameters modificationSequenceMatchingPreferences)	Returns the potential modification sites as an ordered list of string.
String	Tag.getTaggedModifiedSequence(ModificationParameters modificationProfile, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName, boolean includeTerminalGaps, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashSet<String> displayedModifications)	Returns the modified sequence as an tagged string with potential modification sites color coded or with modification tags, e.g, <mox>.
static String	Tag.getTaggedModifiedSequence(ModificationParameters modificationParameters, Tag tag, boolean useHtmlColorCoding, boolean includeHtmlStartEndTags, boolean useShortName, boolean includeTerminalGaps, SequenceMatchingParameters modificationsSequenceMatchingParameters, HashSet<String> displayedModifications)	Returns the modified sequence as an tagged string with potential modification sites color coded or with modification tags, e.g, <mox>.
boolean	MassGap.isSameAs(TagComponent anotherCompontent, SequenceMatchingParameters sequenceMatchingPreferences)
boolean	Tag.isSameAs(Tag anotherTag, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether this tag is the same as another tag.
boolean	TagComponent.isSameAs(TagComponent anotherCompontent, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether another component is the same as the component of interest.
boolean	MassGap.isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent, SequenceMatchingParameters sequenceMatchingPreferences)
boolean	Tag.isSameSequenceAndModificationStatusAs(Tag anotherTag, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether this tag is the same as another tag without accounting for modification localization.
boolean	TagComponent.isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent, SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether another component is the same as the component of interest.

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

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

Modifier and Type	Method	Description
boolean	PeptideAssumptionFilter.validateModifications(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceMatchingParameters modificationSequenceMatchingPreferences, ModificationParameters modificationProfile)	Verifies that the definition of every modification name is available.
boolean	PeptideAssumptionFilter.validatePeptide(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, DigestionParameters digestionPreferences)	Validates the peptide based on the peptide length, the share of X's in the sequence and the allowed number of missed cleavages.
boolean	PeptideAssumptionFilter.validateProteins(Peptide peptide, SequenceMatchingParameters sequenceMatchingPreferences, SequenceProvider sequenceProvider)	Validates a peptide depending on its protein inference status.

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

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

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 SequenceMatchingParameters in com.compomics.util.experiment.identification.modification.mapping

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

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

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

Modifier and Type	Method	Description
static Double	MDScore.getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions, Peptide peptideCandidate, ArrayList<String> ptms, SequenceMatchingParameters sequenceMatchingPreferences, Integer rounding)	Returns the MD score for the given peptide in a spectrum match.
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 SequenceMatchingParameters 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 SequenceMatchingParameters

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 SequenceMatchingParameters 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 SequenceMatchingParameters

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 SequenceMatchingParameters in com.compomics.util.experiment.identification.protein_inference

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

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.
static Collection<Peptide>	PeptideProteinMapping.getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings, SequenceMatchingParameters sequenceMatchingPreferences)	Aggregates the given mapping into a list of peptides.
ArrayList<PeptideProteinMapping>	FastaMapper.getProteinMapping(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences)	Returns the protein mappings for the given peptide sequence.
ArrayList<PeptideProteinMapping>	FastaMapper.getProteinMapping(String peptideSequence, SequenceMatchingParameters proteinInferencePreferences)	Returns the protein mapping in the FASTA file loaded in the sequence factory for the given peptide sequence in a map: peptide sequence found in the FASTA file | protein accession | list of indexes of the peptide sequence on the protein sequence.

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

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

Modifier and Type	Method	Description
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMapping(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences)
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMapping(String peptide, SequenceMatchingParameters sequenceMatchingParameters)
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithoutVariants(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences, int indexPart)	Mapping tags against proteome without variants.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithoutVariants(String peptide, SequenceMatchingParameters seqMatchPref, int indexPart)	Exact mapping peptides against the proteome.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithVariants(Tag tag, SequenceMatchingParameters sequenceMatchingPreferences, int indexPart)	Mapping tags against proteome with variants.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithVariantsFixed(String peptide, SequenceMatchingParameters seqMatchPref, int indexPart)	Variant tolerant mapping peptides against the proteome.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithVariantsGeneric(String peptide, SequenceMatchingParameters seqMatchPref, int indexPart)	Variant tolerant mapping peptides against the proteome.
ArrayList<PeptideProteinMapping>	FMIndex.getProteinMappingWithVariantsSpecific(String peptide, SequenceMatchingParameters seqMatchPref, int indexPart)	Variant tolerant mapping peptides against the proteome

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

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

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 SequenceMatchingParameters 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 SequenceMatchingParameters

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 SequenceMatchingParameters in com.compomics.util.experiment.identification.spectrum_annotation

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

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 SequenceMatchingParameters 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 SequenceMatchingParameters

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.
static NeutralLossesMap	TagSpectrumAnnotator.getDefaultLosses(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters)	Returns the possible neutral losses expected by default for a given tag.
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.
IonMatch[]	TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Tag tag)	Returns the spectrum annotations of a spectrum in a list of IonMatches using an intensity filter.
IonMatch[]	TagSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, SpecificAnnotationParameters specificAnnotationSettings, String spectrumFile, String spectrumTitle, Spectrum spectrum, Tag tag, 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)	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.
void	TagSpectrumAnnotator.setTag(Tag newTag, ModificationParameters modificationParameters, SequenceMatchingParameters modificationsSequenceMatchingParameters, int precursorCharge)	Sets a new tag to match.

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

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

Modifier and Type	Method	Description
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 HashSet<String>	ModificationUtils.getAllModifications(Tag tag, ModificationParameters modificationParameters, SequenceMatchingParameters sequenceMatchingParameters)	Returns a set of the names of all modifications found on a tag.
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(AminoAcidSequence aminoAcidSequence, boolean nTerm, boolean cTerm, Modification modification, 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)	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.

Uses of SequenceMatchingParameters in com.compomics.util.experiment.io.identification

Methods in com.compomics.util.experiment.io.identification with parameters of type SequenceMatchingParameters

Modifier and Type	Method	Description
ArrayList<SpectrumMatch>	IdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)	Retrieves all the spectrum matches from an identification file as a list of spectrum matches, one spectrum match per spectrum.It is very important to close the file reader after creation.

Uses of SequenceMatchingParameters in com.compomics.util.experiment.io.identification.idfilereaders

Methods in com.compomics.util.experiment.io.identification.idfilereaders with parameters of type SequenceMatchingParameters

Modifier and Type	Method	Description
ArrayList<SpectrumMatch>	AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	CossIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	DirecTagIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MascotIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MsAmandaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	MzIdentMLIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	NovorIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	OnyaseIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PepNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PepxmlIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	PNovoIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	SageIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	TideIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)
ArrayList<SpectrumMatch>	XTandemIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider, WaitingHandler waitingHandler, SearchParameters searchParameters, SequenceMatchingParameters sequenceMatchingPreferences, boolean expandAaCombinations)

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

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

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 SequenceMatchingParameters in com.compomics.util.gui.parameters.identification.advanced

Methods in com.compomics.util.gui.parameters.identification.advanced that return SequenceMatchingParameters

Modifier and Type	Method	Description
SequenceMatchingParameters	SequenceMatchingParametersDialog.getSequenceMatchingPreferences()	Returns the sequence matching settings as set by the user.

Constructors in com.compomics.util.gui.parameters.identification.advanced with parameters of type SequenceMatchingParameters

Modifier	Constructor	Description
	SequenceMatchingParametersDialog(Dialog owner, Frame parentFrame, SequenceMatchingParameters sequenceMatchingPreferences, boolean editable)	Creates a new SequenceMatchingSettingsDialog with a dialog as owner.
	SequenceMatchingParametersDialog(Frame parentFrame, SequenceMatchingParameters sequenceMatchingPreferences, boolean editable)	Creates a new SequenceMatchingSettingsDialog with a frame as owner.

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

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

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 SequenceMatchingParameters

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.

Uses of SequenceMatchingParameters in com.compomics.util.parameters.identification

Methods in com.compomics.util.parameters.identification that return SequenceMatchingParameters

Modifier and Type	Method	Description
SequenceMatchingParameters	IdentificationParameters.getSequenceMatchingParameters()	Returns the sequence matching parameters.

Methods in com.compomics.util.parameters.identification with parameters of type SequenceMatchingParameters

Modifier and Type	Method	Description
void	IdentificationParameters.setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)	Sets the sequence matching preferences.

Constructors in com.compomics.util.parameters.identification with parameters of type SequenceMatchingParameters

Modifier	Constructor	Description
	IdentificationParameters(String name, String description, SearchParameters searchParameters, AnnotationParameters annotationParameters, SequenceMatchingParameters sequenceMatchingParameters, PeptideVariantsParameters peptideVariantsParameters, GeneParameters geneParameters, PsmScoringParameters psmScoringParameters, PeptideAssumptionFilter peptideAssumptionFilter, ModificationLocalizationParameters ModificationLocalizationParameters, ProteinInferenceParameters proteinInferenceParameters, IdMatchValidationParameters idValidationParameters, FractionParameters fractionParameters, FastaParameters fastaParameters)	Constructor.

Uses of SequenceMatchingParameters in com.compomics.util.parameters.identification.advanced

Fields in com.compomics.util.parameters.identification.advanced declared as SequenceMatchingParameters

Modifier and Type	Field	Description
static final SequenceMatchingParameters	SequenceMatchingParameters.DEFAULT_STRING_MATCHING	Default string matching.

Methods in com.compomics.util.parameters.identification.advanced that return SequenceMatchingParameters

Modifier and Type	Method	Description
static SequenceMatchingParameters	SequenceMatchingParameters.getDefaultSequenceMatching()	Returns default preferences from amino acid matching.
SequenceMatchingParameters	ModificationLocalizationParameters.getSequenceMatchingParameters()	Returns the sequence matching preferences to use when mapping modifications on amino acid sequences.
static SequenceMatchingParameters	SequenceMatchingParameters.getStringMatching()	Returns preferences for simple string matching.

Methods in com.compomics.util.parameters.identification.advanced with parameters of type SequenceMatchingParameters

Modifier and Type	Method	Description
boolean	SequenceMatchingParameters.isSameAs(SequenceMatchingParameters sequenceMatchingPreferences)	Indicates whether another sequence matching preferences is the same as this one.
void	ModificationLocalizationParameters.setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)	Sets the sequence matching preferences to use when mapping modifications on amino acid sequences.