Uses of Class
com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters
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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 sequenceboolean
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 peptideboolean
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)
Returns the PhosphoRS sequence probabilities for the modification possible locations. -
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, SpectrumAnnotator spectrumAnnotator)
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. -
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>
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)
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Uses of SequenceMatchingParameters in com.compomics.util.gui.modification
Constructors in com.compomics.util.gui.modification with parameters of type SequenceMatchingParameters 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 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 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 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 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.