Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
boolean |
AminoAcidPattern.contains(AminoAcidPattern aminoAcidPattern,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether the pattern contains a subsequence of amino acids.
|
boolean |
AminoAcidPattern.contains(String aminoAcidSequence,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether the pattern contains a subsequence of amino acids.
|
int |
AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns the first index where the amino acid pattern is found.
|
int |
AminoAcidPattern.firstIndex(AminoAcidPattern aminoAcidPattern,
SequenceMatchingParameters sequenceMatchingPreferences,
int startIndex)
Returns the first index where the amino acid pattern is found in the
given pattern.
|
int |
AminoAcidPattern.firstIndex(AminoAcidSequence aminoAcidSequence,
SequenceMatchingParameters sequenceMatchingPreferences)
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.
|
int |
AminoAcidPattern.firstIndex(String aminoAcidSequence,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns the first index where the amino acid pattern is found.
|
int |
AminoAcidPattern.firstIndex(String aminoAcidSequence,
SequenceMatchingParameters sequenceMatchingPreferences,
int startIndex)
Returns the first index where the amino acid pattern is found.
|
Pattern |
AminoAcidPattern.getAsStringPattern(SequenceMatchingParameters sequenceMatchingPreferences,
boolean includeMutations)
Returns the amino acid pattern as case insensitive pattern for String
matching.
|
ArrayList<Integer> |
AminoAcidPattern.getIndexes(AminoAcidPattern input,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns the indexes where the amino acid pattern was found in the input.
|
ArrayList<Integer> |
AminoAcidPattern.getIndexes(String input,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns the indexes where the amino acid pattern was found in the input.
|
boolean |
AminoAcidPattern.isEnding(AminoAcidPattern aminoAcidPattern,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether the given amino acid sequence ends with the pattern.
|
boolean |
AminoAcidPattern.isEnding(String aminoAcidSequence,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether the given amino acid sequence ends with the pattern.
|
boolean |
AminoAcidPattern.isSameAs(AminoAcidPattern anotherPattern,
SequenceMatchingParameters sequenceMatchingPreferences)
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(AminoAcidPattern anotherPattern,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another AminoAcidPattern targets the same sequence
without accounting for PTM localization.
|
boolean |
AminoAcidPattern.isSameSequenceAndModificationStatusAs(AminoAcidPattern anotherPattern,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another AminoAcidPattern targets the same pattern
without accounting for Modification localization.
|
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 sequenceMatchingPreferences)
Indicates whether the given amino acid sequence starts with the pattern.
|
boolean |
AminoAcidPattern.isStarting(String aminoAcidSequence,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether the given amino acid sequence starts with the pattern.
|
boolean |
AminoAcidPattern.isTargeted(Character aa,
int index,
SequenceMatchingParameters 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,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether the pattern is found in 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.matches(String aminoAcidSequence,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether the pattern matches the given amino acid sequence.
|
boolean |
AminoAcidPattern.matchesAt(String aminoAcidSequence,
SequenceMatchingParameters 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,
SequenceMatchingParameters sequenceMatchingPreferences)
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.
|
boolean |
AminoAcidPattern.matchesIn(String aminoAcidSequence,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether the pattern is found in the given amino acid sequence.
|
Modifier and Type | Method and Description |
---|---|
long |
Peptide.getMatchingKey(SequenceMatchingParameters sequenceMatchingPreferences)
Returns a unique key for the peptide when considering the given matching
preferences.
|
HashSet<Integer> |
Peptide.getPotentialModificationSites(Modification modification,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingPreferences)
Returns the potential modification sites as a set.
|
ArrayList<Integer> |
Peptide.getPotentialModificationSites(Modification modification,
String proteinSequence,
int peptideStart,
SequenceMatchingParameters modificationSequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of sites.
|
boolean |
Peptide.isSameSequence(Peptide anotherPeptide,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
|
boolean |
Peptide.isSameSequenceAndModificationStatus(Peptide anotherPeptide,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another peptide has the same sequence and modification
status without accounting for modification localization.
|
Modifier and Type | Method and Description |
---|---|
void |
Identification.buildPeptidesAndProteins(SpectrumMatch spectrumMatch,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceProvider sequenceProvider)
Creates the peptides and protein instances based on the given spectrum
match.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<Integer> |
Tag.getPotentialModificationSites(Modification modification,
SequenceMatchingParameters modificationSequenceMatchingPreferences)
Returns the potential modification sites as an ordered list of string.
|
boolean |
TagComponent.isSameAs(TagComponent anotherCompontent,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another component is the same as the component of
interest.
|
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.isSameSequenceAndModificationStatusAs(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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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,
Spectrum spectrum,
SequenceProvider sequenceProvider,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
boolean accountNeutralLosses,
SequenceMatchingParameters sequenceMatchingPreferences,
SequenceMatchingParameters modificationSequenceMatchingPreferences,
PeptideSpectrumAnnotator spectrumAnnotator)
Returns the PhosphoRS sequence probabilities for the modification
possible locations.
|
Modifier and Type | Method and Description |
---|---|
static Collection<Peptide> |
PeptideProteinMapping.getPeptides(ArrayList<PeptideProteinMapping> peptideProteinMappings,
SequenceMatchingParameters sequenceMatchingPreferences)
Aggregates the given mapping into a list of peptides.
|
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.
|
ArrayList<PeptideProteinMapping> |
FastaMapper.getProteinMapping(Tag tag,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns the protein mappings for the given peptide sequence.
|
Modifier and Type | Method and Description |
---|---|
LinkedList<SpectrumMatch> |
IdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters 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> |
XTandemIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
TideIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PepxmlIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
PepNovoIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
OnyaseIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
NovorIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MzIdentMLIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MsAmandaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
MascotIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
DirecTagIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
LinkedList<SpectrumMatch> |
AndromedaIdfileReader.getAllSpectrumMatches(WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
Modifier and Type | Method and Description |
---|---|
SequenceMatchingParameters |
SequenceMatchingParametersDialog.getSequenceMatchingPreferences()
Returns the sequence matching settings as set by the user.
|
Constructor and 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.
|
Modifier and Type | Method and Description |
---|---|
SequenceMatchingParameters |
IdentificationParameters.getSequenceMatchingParameters()
Returns the sequence matching parameters.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationParameters.setSequenceMatchingParameters(SequenceMatchingParameters sequenceMatchingParameters)
Sets the sequence matching preferences.
|
Constructor and 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)
Constructor.
|
Modifier and Type | Field and Description |
---|---|
static SequenceMatchingParameters |
SequenceMatchingParameters.defaultStringMatching
Default string matching.
|
Modifier and Type | Method and Description |
---|---|
static SequenceMatchingParameters |
SequenceMatchingParameters.getDefaultSequenceMatching()
Returns default preferences from amino acid matching.
|
SequenceMatchingParameters |
ModificationLocalizationParameters.getSequenceMatchingParameters()
Returns the sequence matching preferences to use when mapping PTMs on
amino acid sequences.
|
static SequenceMatchingParameters |
SequenceMatchingParameters.getStringMatching()
Returns preferences for simple string matching.
|
Modifier and Type | Method and 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 PTMs on amino
acid sequences.
|
Copyright © 2018. All rights reserved.