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 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 |
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 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.
|
Pattern |
AminoAcidPattern.getAsStringPattern(SequenceMatchingParameters sequenceMatchingParameters,
boolean includeMutations)
Returns the amino acid pattern as case insensitive pattern for String
matching.
|
String[] |
AminoAcidSequence.getFixedModifications(boolean nTerm,
boolean cTerm,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the fixed modifications for this sequence based on the given
modification parameters.
|
ArrayList<Integer> |
AminoAcidPattern.getIndexes(AminoAcidPattern input,
SequenceMatchingParameters sequenceMatchingParameters)
Returns the indexes where the amino acid pattern was found in the input.
|
int[] |
AminoAcidPattern.getIndexes(String input,
SequenceMatchingParameters sequenceMatchingParameters)
Returns the indexes where the amino acid pattern was found in the input.
|
boolean |
AminoAcidPattern.isEnding(AminoAcidPattern aminoAcidPattern,
SequenceMatchingParameters sequenceMatchingParameters)
Indicates whether the given amino acid sequence ends with the pattern.
|
boolean |
AminoAcidPattern.isEnding(String aminoAcidSequence,
SequenceMatchingParameters sequenceMatchingParameters)
Indicates whether the given amino acid sequence ends with the pattern.
|
boolean |
AminoAcidPattern.isSameAs(AminoAcidPattern anotherPattern,
SequenceMatchingParameters sequenceMatchingParameters)
Indicates whether another AminoAcidPattern targets the same pattern.
|
boolean |
AminoAcidSequence.isSameAs(AminoAcidSequence anotherSequence,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another sequence has a matching sequence.
|
boolean |
AminoAcidSequence.isSameAs(TagComponent anotherCompontent,
SequenceMatchingParameters sequenceMatchingPreferences) |
boolean |
AminoAcidSequence.isSameSequenceAndModificationStatusAs(AminoAcidSequence anotherSequence,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another sequence targets the same sequence without
accounting for PTM localization.
|
boolean |
AminoAcidSequence.isSameSequenceAndModificationStatusAs(TagComponent anotherCompontent,
SequenceMatchingParameters sequenceMatchingPreferences) |
boolean |
AminoAcidPattern.isStarting(AminoAcidPattern aminoAcidPattern,
SequenceMatchingParameters sequenceMatchingParameters)
Indicates whether the given amino acid sequence starts with the pattern.
|
boolean |
AminoAcidPattern.isStarting(String aminoAcidSequence,
SequenceMatchingParameters sequenceMatchingParameters)
Indicates whether the given amino acid sequence starts with the pattern.
|
boolean |
AminoAcidPattern.isTargeted(Character aa,
int index,
SequenceMatchingParameters sequenceMatchingParameters)
Indicates whether the given amino acid at the given index of the pattern
is targeted without accounting for mutations.
|
boolean |
AminoAcidPattern.matches(AminoAcidPattern aminoAcidPattern,
SequenceMatchingParameters sequenceMatchingParameters)
Indicates whether the pattern matches the given amino acid sequence
|
boolean |
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 sequenceMatchingParameters)
Indicates whether the pattern matches the given amino acid sequence.
|
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 |
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 sequenceMatchingParameters)
Indicates whether the pattern is found in the given amino acid sequence.
|
Modifier and Type | Method and Description |
---|---|
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(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(Tag tag,
ModificationParameters modificationParameters,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
This method returns the theoretic ions expected from a tag.
|
Modifier and Type | Method and Description |
---|---|
void |
Peptide.estimateTheoreticMass(ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Estimates the theoretic mass of the peptide.
|
String[] |
Peptide.getFixedModifications(ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the fixed modifications for this peptide based on the given
modification parameters.
|
double |
Peptide.getMass(ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Returns the mass, estimates it if not done before.
|
long |
Peptide.getMatchingKey(SequenceMatchingParameters sequenceMatchingPreferences)
Returns a unique key for the peptide when considering the given matching
preferences.
|
String |
Peptide.getTaggedModifiedSequence(ModificationParameters modificationProfile,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useHtmlColorCoding,
boolean includeHtmlStartEndTags,
boolean useShortName,
HashSet<String> displayedModifications)
Returns the modified sequence as an tagged string with potential
modification sites color coded or with Modification tags, e.g,
<mox>.
|
boolean |
Peptide.isSameSequence(Peptide anotherPeptide,
SequenceMatchingParameters sequenceMatchingPreferences)
Returns a boolean indicating whether another peptide has the same
sequence as the given peptide
|
boolean |
Peptide.isSameSequenceAndModificationStatus(Peptide anotherPeptide,
SequenceMatchingParameters sequenceMatchingPreferences)
Indicates whether another peptide has the same sequence and modification
status without accounting for modification localization.
|
Modifier and Type | Method and 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 |
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 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.
|
Modifier and Type | Method and 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.
|
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,
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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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(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 |
---|---|
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.
|
Modifier and Type | Method and Description |
---|---|
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.
|
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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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[] |
TagSpectrumAnnotator.getCurrentAnnotation(String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter) |
IonMatch[] |
PeptideSpectrumAnnotator.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[] |
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.
|
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.
|
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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and 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.
|
Modifier and Type | Method and Description |
---|---|
ArrayList<SpectrumMatch> |
XTandemIdfileReader.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> |
PNovoIdfileReader.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> |
PepNovoIdfileReader.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> |
NovorIdfileReader.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> |
MsAmandaIdfileReader.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> |
DirecTagIdfileReader.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> |
AndromedaIdfileReader.getAllSpectrumMatches(SpectrumProvider spectrumProvider,
WaitingHandler waitingHandler,
SearchParameters searchParameters,
SequenceMatchingParameters sequenceMatchingPreferences,
boolean expandAaCombinations) |
Constructor and Description |
---|
ModificationTable(Identification identification,
AnnotationParameters annotationParameters,
PeptideMatch peptideMatch,
Modification modification,
boolean areaChart,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SpectrumProvider spectrumProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Constructor.
|
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 |
---|---|
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,
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,
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.
|
Constructor and 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.
|
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,
FastaParameters fastaParameters)
Constructor.
|
Modifier and Type | Field and Description |
---|---|
static SequenceMatchingParameters |
SequenceMatchingParameters.DEFAULT_STRING_MATCHING
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
modifications 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 modifications
on amino acid sequences.
|
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