Modifier and Type | Method and Description |
---|---|
void |
PTMFactory.checkFixedModifications(PtmSettings modificationProfile,
Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Removes the fixed modifications of the peptide and remaps the one
searched for according to the ModificationProfile.
|
void |
PTMFactory.checkFixedModifications(PtmSettings modificationProfile,
Tag tag,
SequenceMatchingPreferences sequenceMatchingPreferences)
Removes the fixed modifications of the given tag and remaps the one
searched for according to the ModificationProfile.
|
boolean |
AminoAcidPattern.contains(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the pattern contains a subsequence of amino acids.
|
boolean |
AminoAcidPattern.contains(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the pattern contains a subsequence of amino acids.
|
int |
AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the first index where the amino acid pattern is found.
|
int |
AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences,
int startIndex)
Returns the first index where the amino acid pattern is found in the
given pattern.
|
int |
AminoAcidPattern.firstIndex(AminoAcidSequence aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the first index where the amino acid pattern is found.
|
int |
AminoAcidSequence.firstIndex(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the first index where the amino acid sequence is found in the
given sequence.
|
int |
AminoAcidPattern.firstIndex(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the first index where the amino acid pattern is found.
|
int |
AminoAcidPattern.firstIndex(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences,
int startIndex)
Returns the first index where the amino acid pattern is found.
|
Pattern |
AminoAcidPattern.getAsStringPattern(SequenceMatchingPreferences sequenceMatchingPreferences,
boolean includeMutations)
Returns the amino acid pattern as case insensitive pattern for String
matching.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(PtmSettings modificationProfile,
Peptide peptide,
double modificationMass,
double ptmMassTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the expected modifications based on the modification profile, the
peptide found and the modification details.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(PtmSettings modificationProfile,
Peptide peptide,
String ptmName,
Double ptmMassTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the names of the possibly expected modification based on the name
of the expected modification in a map where the PTM names are indexed by
their potential site on the sequence.
|
ArrayList<Integer> |
AminoAcidPattern.getIndexes(AminoAcidPattern input,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the indexes where the amino acid pattern was found in the input.
|
ArrayList<Integer> |
AminoAcidPattern.getIndexes(String input,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the indexes where the amino acid pattern was found in the input.
|
static char |
AminoAcid.getMatchingAminoAcid(char aa,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a matching amino acid using the given preferences.
|
String |
Peptide.getMatchingKey(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a unique key for the peptide when considering the given matching
preferences.
|
static String |
AminoAcid.getMatchingSequence(String sequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the matching sequence of a given sequence.
|
ArrayList<String> |
Peptide.getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the parent proteins and remaps the peptide to the protein in the
sequence factory if no protein mapping was set using the default mapper
of the sequence factory.
|
ArrayList<String> |
Peptide.getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences,
boolean remap)
Returns the parent proteins and eventually remaps the peptide to the
protein using the default protein tree.
|
ArrayList<String> |
Peptide.getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideMapper peptideMapper)
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set.
|
ArrayList<Integer> |
Protein.getPeptideStart(String peptideSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the list of indexes where a peptide can be found in the protein
sequence.
|
ArrayList<Integer> |
Peptide.getPotentialModificationSites(Double ptmMass,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PtmSettings modificationProfile)
Returns the potential modification sites as an ordered list of sites.
|
ArrayList<Integer> |
Peptide.getPotentialModificationSites(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of sites.
|
HashMap<Integer,String[]> |
Protein.getSurroundingAA(String peptide,
int nAA,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the amino acids surrounding a peptide in the sequence of the
given protein in a map: peptide start index > (amino acids before,
amino acids after).
|
ArrayList<String> |
Peptide.isCterm(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a list of proteins where this peptide can be found in the
C-terminus.
|
boolean |
Protein.isCTerm(String peptideSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a boolean indicating whether the protein ends with the given
peptide.
|
boolean |
Peptide.isDecoy(SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether a peptide can be derived from a decoy protein.
|
boolean |
AminoAcidPattern.isEnding(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given amino acid sequence ends with the pattern.
|
boolean |
AminoAcidPattern.isEnding(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given amino acid sequence ends with the pattern.
|
boolean |
Protein.isEnzymaticPeptide(String peptideSequence,
ArrayList<Enzyme> enzymes,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns true if the peptide is enzymatic, i.e., both termini can be
generated by one of the enzymes used.
|
boolean |
Protein.isEnzymaticPeptide(String peptideSequence,
Enzyme enzyme,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns true if the peptide is enzymatic, i.e., both termini can be
generated by the enzyme used.
|
boolean |
Peptide.isModifiable(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given modification can be found on the peptide.
|
ArrayList<String> |
Peptide.isNterm(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a list of proteins where this peptide can be found in the
N-terminus.
|
boolean |
Protein.isNTerm(String peptideSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a boolean indicating whether the protein starts with the given
peptide.
|
boolean |
AminoAcidPattern.isSameAs(AminoAcidPattern anotherPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another AminoAcidPattern targets the same pattern.
|
boolean |
AminoAcidSequence.isSameAs(AminoAcidSequence anotherSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another sequence has a matching sequence.
|
boolean |
MassGap.isSameAs(TagComponent anotherCompontent,
SequenceMatchingPreferences sequenceMatchingPreferences) |
boolean |
AminoAcidSequence.isSameAs(TagComponent anotherCompontent,
SequenceMatchingPreferences sequenceMatchingPreferences) |
boolean |
AminoAcidPattern.isSameAs(TagComponent anotherCompontent,
SequenceMatchingPreferences sequenceMatchingPreferences) |
boolean |
Peptide.isSameSequence(Peptide anotherPeptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
|
boolean |
Peptide.isSameSequenceAndModificationStatus(Peptide anotherPeptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another peptide has the same sequence and modification
status without accounting for modification localization.
|
boolean |
AminoAcidSequence.isSameSequenceAndModificationStatusAs(AminoAcidPattern anotherPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another AminoAcidPattern targets the same sequence
without accounting for PTM localization.
|
boolean |
AminoAcidPattern.isSameSequenceAndModificationStatusAs(AminoAcidPattern anotherPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another AminoAcidPattern targets the same pattern
without accounting for PTM localization.
|
boolean |
AminoAcidSequence.isSameSequenceAndModificationStatusAs(AminoAcidSequence anotherSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another sequence targets the same sequence without
accounting for PTM localization.
|
boolean |
MassGap.isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent,
SequenceMatchingPreferences sequenceMatchingPreferences) |
boolean |
AminoAcidSequence.isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent,
SequenceMatchingPreferences sequenceMatchingPreferences) |
boolean |
AminoAcidPattern.isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent,
SequenceMatchingPreferences sequenceMatchingPreferences) |
boolean |
AminoAcidPattern.isStarting(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given amino acid sequence starts with the pattern.
|
boolean |
AminoAcidPattern.isStarting(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given amino acid sequence starts with the pattern.
|
boolean |
AminoAcidPattern.isTargeted(Character aa,
int index,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given amino acid at the given index of the pattern
is targeted without accounting for mutations.
|
void |
Peptide.mapParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideMapper peptideMapper)
Maps the peptides to the proteins in the sequence database loaded in the
sequence factory.
|
boolean |
AminoAcidPattern.matches(AminoAcidPattern aminoAcidPattern,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the pattern is found in the given amino acid sequence.
|
boolean |
AminoAcidSequence.matches(AminoAcidSequence aminoAcidSequence,
SequenceMatchingPreferences 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,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the sequence matches the given amino acid sequence in
size and according to the given matching preferences.
|
boolean |
AminoAcidPattern.matches(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the pattern matches the given amino acid sequence.
|
boolean |
AminoAcidPattern.matchesAt(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences,
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,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the pattern is found in the given amino acid sequence.
|
boolean |
AminoAcidSequence.matchesIn(AminoAcidSequence aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the sequence is found in the given amino acid sequence.
|
boolean |
AminoAcidSequence.matchesIn(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the sequence is found in the given amino acid sequence.
|
boolean |
AminoAcidPattern.matchesIn(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the pattern is found in the given amino acid sequence.
|
Modifier and Type | Method and Description |
---|---|
void |
Identification.buildPeptidesAndProteins(String spectrumMatchKey,
SequenceMatchingPreferences sequenceMatchingPreferences)
Creates the peptides and protein instances based on the given spectrum
match.
|
void |
Identification.buildPeptidesAndProteins(WaitingHandler waitingHandler,
SequenceMatchingPreferences sequenceMatchingPreferences)
Creates the peptides and protein instances based on the spectrum matches.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Integer> |
Tag.getPotentialModificationSites(PTM ptm,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of string.
|
boolean |
TagComponent.isSameAs(TagComponent anotherCompontent,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another component is the same as the component of
interest.
|
boolean |
Tag.isSameAs(Tag anotherTag,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether this tag is the same as another tag.
|
boolean |
TagComponent.isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another component is the same as the component of
interest.
|
boolean |
Tag.isSameSequenceAndModificationStatusAs(Tag anotherTag,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether this tag is the same as another tag without accounting
for modification localization.
|
Constructor and Description |
---|
TagMatcher(ArrayList<String> fixedModifications,
ArrayList<String> variableModifications,
SequenceMatchingPreferences sequenceMatchingPreferences)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
boolean |
PeptideAssumptionFilter.validateModifications(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PtmSettings modificationProfile)
Validates the modifications of a peptide.
|
boolean |
PeptideAssumptionFilter.validatePeptide(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
DigestionPreferences 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,
SequenceMatchingPreferences sequenceMatchingPreferences)
Validates a peptide depending on its protein inference status.
|
boolean |
PeptideAssumptionFilter.validateProteins(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideMapper peptideMapper)
Validates a peptide depending on its protein inference status.
|
Modifier and Type | Method and Description |
---|---|
SpectrumMatch |
SpectrumMatch.getPeptidesFromTags(ProteinTree proteinTree,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance,
boolean scoreInAscendingOrder,
boolean ascendingScore)
Creates a peptide based spectrum match where peptide assumptions are
deduced from tag assumptions.
|
boolean |
ProteinMatch.hasEnzymaticPeptide(String accession,
ArrayList<Enzyme> enzymes,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the protein group has an enzymatic peptide when
considering the given accession as main accession.
|
Modifier and Type | Method and Description |
---|---|
static Collection<Peptide> |
PeptideProteinMapping.getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings,
SequenceMatchingPreferences sequenceMatchingPreferences)
Aggregates the given mapping into a list of peptides.
|
ArrayList<PeptideProteinMapping> |
PeptideMapper.getProteinMapping(String peptideSequence,
SequenceMatchingPreferences 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.
|
ArrayList<PeptideProteinMapping> |
PeptideMapper.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
ArrayList<PeptideProteinMapping> |
PeptideMapper.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance)
Returns the protein mappings for the given peptide sequence.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(String peptide,
SequenceMatchingPreferences seqMatchPref)
Main method for mapping a peptide with all variants against all
registered proteins in the experiment.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences)
Mapping tags against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance)
Mapping tags against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithoutVariants(String peptide,
SequenceMatchingPreferences seqMatchPref,
int indexPart)
Exact mapping peptides against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithoutVariants(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
int indexPart)
Mapping tags against proteome without variants.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithVariants(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
int indexPart)
Mapping tags against proteome with variants.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithVariantsGeneric(String peptide,
SequenceMatchingPreferences seqMatchPref,
int indexPart)
Variant tolerant mapping peptides against the proteome.
|
ArrayList<PeptideProteinMapping> |
FMIndex.getProteinMappingWithVariantsSpecific(String peptide,
SequenceMatchingPreferences seqMatchPref,
int indexPart)
Variant tolerant mapping peptides against the proteome.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<PeptideProteinMapping> |
Node.getProteinMapping(AminoAcidSequence query,
String currentSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
ArrayList<PeptideProteinMapping> |
ProteinTree.getProteinMapping(String peptideSequence,
SequenceMatchingPreferences proteinInferencePreferences) |
ArrayList<PeptideProteinMapping> |
ProteinTree.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences) |
ArrayList<PeptideProteinMapping> |
ProteinTree.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance) |
Modifier and Type | Method and Description |
---|---|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(SequenceMatchingPreferences sequenceMatchingPreferences,
SearchParameters searchParameters,
PeptideVariantsPreferences peptideVariantsPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
PeptideMapper |
SequenceFactory.getDefaultPeptideMapper(SequenceMatchingPreferences sequenceMatchingPreferences,
SearchParameters searchParameters,
PeptideVariantsPreferences peptideVariantsPreferences,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
boolean displayProgress,
int nThreads)
Returns the default peptide to protein mapper for the database loaded in
factory according to the sequence matching preferences.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
AnnotationSettings annotationPreferences,
SpecificAnnotationSettings specificAnnotationPreferences,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the A-score for the best PTM location.
|
static Double |
MDScore.getMDScore(ArrayList<SpectrumIdentificationAssumption> mascotAssumptions,
Peptide peptideCandidate,
ArrayList<String> ptms,
SequenceMatchingPreferences sequenceMatchingPreferences,
Integer rounding)
Returns the MD score for the given peptide in a spectrum match.
|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
AnnotationSettings annotationSettings,
SpecificAnnotationSettings specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
Modifier and Type | Method and Description |
---|---|
static NeutralLossesMap |
SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the possible neutral losses expected by default for a given
peptide.
|
SpecificAnnotationSettings |
AnnotationSettings.getSpecificAnnotationPreferences(String spectrumKey,
SpectrumIdentificationAssumption spectrumIdentificationAssumption,
SequenceMatchingPreferences sequenceMatchingPreferences,
SequenceMatchingPreferences ptmSequenceMatchingPreferences)
Returns the annotation preferences specific to a spectrum and an
identification assumption.
|
Modifier and Type | Method and Description |
---|---|
static NeutralLossesMap |
PeptideSpectrumAnnotator.getDefaultLosses(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingSettings,
SequenceMatchingPreferences ptmSequenceMatchingSettings)
Returns the possible neutral losses expected by default for a given
peptide.
|
static NeutralLossesMap |
TagSpectrumAnnotator.getDefaultLosses(Tag tag,
SequenceMatchingPreferences ptmSequenceMatchingSettings)
Returns the possible neutral losses expected by default for a given tag.
|
Modifier and Type | Method and Description |
---|---|
LinkedList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations)
Retrieves all the identifications from an identification file as a list
of spectrum matches It is very important to close the file reader after
creation.
|
Modifier and Type | Method and Description |
---|---|
LinkedList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean expandAaCombinations) |
Modifier and Type | Method and Description |
---|---|
SequenceMatchingPreferences |
SequenceMatchingSettingsDialog.getSequenceMatchingPreferences()
Returns the sequence matching settings as set by the user.
|
Constructor and Description |
---|
SequenceMatchingSettingsDialog(Dialog owner,
Frame parentFrame,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean editable)
Creates a new SequenceMatchingSettingsDialog with a dialog as owner.
|
SequenceMatchingSettingsDialog(Frame parentFrame,
SequenceMatchingPreferences sequenceMatchingPreferences,
boolean editable)
Creates a new SequenceMatchingSettingsDialog with a frame as owner.
|
Modifier and Type | Field and Description |
---|---|
static SequenceMatchingPreferences |
SequenceMatchingPreferences.defaultStringMatching
Default string matching.
|
Modifier and Type | Method and Description |
---|---|
static SequenceMatchingPreferences |
SequenceMatchingPreferences.getDefaultSequenceMatching()
Returns default preferences from amino acid matching.
|
SequenceMatchingPreferences |
PTMScoringPreferences.getSequenceMatchingPreferences()
Returns the sequence matching preferences to use when mapping PTMs on
amino acid sequences.
|
SequenceMatchingPreferences |
IdentificationParameters.getSequenceMatchingPreferences()
Returns the sequence matching preferences.
|
static SequenceMatchingPreferences |
SequenceMatchingPreferences.getStringMatching()
Returns preferences for simple string matching.
|
Modifier and Type | Method and Description |
---|---|
boolean |
SequenceMatchingPreferences.isSameAs(SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether another sequence matching preferences is the same as
this one.
|
void |
PTMScoringPreferences.setSequenceMatchingPreferences(SequenceMatchingPreferences sequenceMatchingPreferences)
Sets the sequence matching preferences to use when mapping PTMs on amino
acid sequences.
|
void |
IdentificationParameters.setSequenceMatchingPreferences(SequenceMatchingPreferences sequenceMatchingPreferences)
Sets the sequence matching preferences.
|
Constructor and Description |
---|
IdentificationParameters(String name,
String description,
SearchParameters searchParameters,
AnnotationSettings annotationSettings,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideVariantsPreferences peptideVariantsPreferences,
GenePreferences genePreferences,
PsmScoringPreferences psmScoringPreferences,
PeptideAssumptionFilter peptideAssumptionFilter,
PTMScoringPreferences ptmScoringPreferences,
ProteinInferencePreferences proteinInferencePreferences,
IdMatchValidationPreferences idValidationPreferences,
FractionSettings fractionSettings)
Constructor.
|
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