Modifier and Type | Method and Description |
---|---|
void |
PTMFactory.checkFixedModifications(ModificationProfile modificationProfile,
Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Removes the fixed modifications of the peptide and remaps the one
searched for according to the ModificationProfile.
|
void |
PTMFactory.checkFixedModifications(ModificationProfile 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(ModificationProfile modificationProfile,
Peptide peptide,
double modificationMass,
double ptmMassTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the expected modifications based on the modification profile, the
peptide found and the modification details.
|
HashMap<Integer,ArrayList<String>> |
PTMFactory.getExpectedPTMs(ModificationProfile modificationProfile,
Peptide peptide,
String ptmName,
Double ptmMassTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
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 String |
AminoAcid.getMatchingAminoAcid(String aminoAcid,
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(boolean remap,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the parent proteins and eventually remaps the peptide to the
protein using the default protein tree.
|
ArrayList<String> |
Peptide.getParentProteins(boolean remap,
SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Returns the parent proteins and eventually remaps the peptide to the
protein.
|
ArrayList<String> |
Peptide.getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the parent proteins and remaps the peptide to the protein if no
protein mapping was set using the default protein tree of the sequence
factory.
|
ArrayList<String> |
Peptide.getParentProteins(SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
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,
ModificationProfile modificationProfile)
Returns the potential modification sites as an ordered list of string.
|
ArrayList<Integer> |
Peptide.getPotentialModificationSites(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of string.
|
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,
Enzyme enzyme,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns true of the peptide is non-enzymatic, i.e., has one or more end
points that cannot be caused by the enzyme alone.
|
boolean |
Peptide.isModifiable(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given modification can be found on the peptide.
|
boolean |
AminoAcidPattern.isMutationTarget(char aa,
int index,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given amino acid at the given index of the pattern
is targeted when accounting for mutations.
|
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 |
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 |
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(char aa,
int index,
SequenceMatchingPreferences sequenceMatchingPreferences)
Indicates whether the given amino acid at the given index of the pattern
is targeted without accounting for mutations.
|
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 is matches the given amino acid sequence in
.
|
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.
|
int |
AminoAcidSequence.nMutations(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the number of mutations used when matching the given reference
sequence.
|
int |
AminoAcidPattern.nMutations(String aminoAcidSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the number of mutations used to match an 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.
|
static NeutralLossesMap |
SpectrumAnnotator.getDefaultLosses(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the possible neutral losses expected by default for a given
peptide.
|
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.
|
HashMap<Integer,HashMap<String,ArrayList<TagAssumption>>> |
SpectrumMatch.getTagAssumptionsMap(int keySize,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a map containing the tag assumptions of this spectrum assumptions
indexed by the beginning of the longest amino acid sequence.
|
boolean |
ProteinMatch.hasEnzymaticPeptide(String accession,
Enzyme enzyme,
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 |
---|---|
HashMap<String,ArrayList<Integer>> |
ProteinTree.getMatchedPeptideSequences(String peptideSequence,
String proteinAccession,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns a list of peptides matched using the given peptide sequence in
the given protein according the provided matching settings.
|
HashMap<String,HashMap<String,ArrayList<Integer>>> |
Node.getProteinMapping(AminoAcidSequence query,
String currentSequence,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
HashMap<String,HashMap<String,ArrayList<Integer>>> |
ProteinTree.getProteinMapping(String peptideSequence,
SequenceMatchingPreferences proteinInferencePrefeerences)
Returns the protein mapping in the sequence factory for the given peptide
sequence.
|
HashMap<Peptide,HashMap<String,ArrayList<Integer>>> |
ProteinTree.getProteinMapping(Tag tag,
TagMatcher tagMatcher,
SequenceMatchingPreferences sequenceMatchingPreferences,
Double massTolerance)
Returns the protein mappings for the given peptide sequence.
|
Modifier and Type | Method and Description |
---|---|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location without accounting for
neutral losses.
|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location.
|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the A-score for the best PTM location.
|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
Integer rounding)
Returns the A-score for the best PTM location.
|
static HashMap<Integer,Double> |
AScore.getAScore(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the A-score for the best PTM location accounting for neutral
losses.
|
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,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
static HashMap<Integer,Double> |
PhosphoRS.getSequenceProbabilities(Peptide peptide,
ArrayList<PTM> ptms,
MSnSpectrum spectrum,
HashMap<Ion.IonType,HashSet<Integer>> iontypes,
NeutralLossesMap neutralLosses,
ArrayList<Integer> charges,
int precursorCharge,
double mzTolerance,
boolean accountNeutralLosses,
SequenceMatchingPreferences sequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator,
Integer ptmScoreScale)
Returns the PhosphoRS sequence probabilities for the PTM possible
locations.
|
Modifier and Type | Method and Description |
---|---|
static NeutralLossesMap |
PeptideSpectrumAnnotator.getDefaultLosses(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the possible neutral losses expected by default for a given
peptide.
|
static NeutralLossesMap |
TagSpectrumAnnotator.getDefaultLosses(Tag tag,
SequenceMatchingPreferences sequenceMatchingPreferences)
Returns the possible neutral losses expected by default for a given tag.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Integer> |
Tag.getPotentialModificationSites(PTM ptm,
SequenceMatchingPreferences sequenceMatchingPreferences)
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 |
MassGap.isSameAs(TagComponent anotherCompontent,
SequenceMatchingPreferences sequenceMatchingPreferences) |
boolean |
MassGap.isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent,
SequenceMatchingPreferences sequenceMatchingPreferences) |
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> |
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> |
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 | Field and Description |
---|---|
static SequenceMatchingPreferences |
SequenceMatchingPreferences.defaultStringMatching
Default string matching.
|
Modifier and Type | Method and Description |
---|---|
static SequenceMatchingPreferences |
SequenceMatchingPreferences.getDefaultSequenceMatching(SearchParameters searchParameters)
Returns default preferences from amino acid matching.
|
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 proteinInferencePreferences)
Indicates whether another protein inference preferences is the same as
this one.
|
void |
AnnotationPreferences.resetAutomaticAnnotation(SequenceMatchingPreferences sequenceMatchingPreferences)
Updates the neutral losses and charge annotation settings.
|
void |
AnnotationPreferences.setCurrentSettings(SpectrumIdentificationAssumption spectrumIdentificationAssumption,
boolean newSpectrum,
SequenceMatchingPreferences sequenceMatchingPreferences)
Sets the annotation settings for the current peptide and precursor
charge.
|
void |
IdentificationParameters.setSequenceMatchingPreferences(SequenceMatchingPreferences sequenceMatchingPreferences)
Sets the sequence matching preferences.
|
boolean |
IdFilter.validateModifications(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
ModificationProfile modificationProfile)
Validates the modifications of a peptide.
|
boolean |
IdFilter.validatePeptide(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Validates the peptide based on the peptide length and share of X's in the
sequence.
|
boolean |
IdFilter.validateProteins(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences)
Validates a peptide depending on its protein inference status.
|
boolean |
IdFilter.validateProteins(Peptide peptide,
SequenceMatchingPreferences sequenceMatchingPreferences,
ProteinTree proteinTree)
Validates a peptide depending on its protein inference status.
|
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