Modifier and Type | Method and Description |
---|---|
GeneMaps |
ProteinGeneDetailsProvider.getGeneMaps(GeneParameters genePreferences,
FastaSummary fastaSummary,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
WaitingHandler waitingHandler)
Returns the gene maps for the given proteins.
|
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.
|
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.
|
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>.
|
Modifier and Type | Method and Description |
---|---|
static double |
IdentificationFeaturesGenerator.estimateSpectrumCounting(Identification identification,
SequenceProvider sequenceProvider,
long proteinMatchKey,
SpectrumCountingParameters spectrumCountingPreferences,
int maxPepLength,
IdentificationParameters identificationParameters)
Returns the spectrum counting index based on the project settings.
|
Constructor and Description |
---|
IdentificationFeaturesGenerator(Identification identification,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
SpectrumProvider spectrumProvider,
Metrics metrics,
SpectrumCountingParameters spectrumCountingPreferences)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
boolean |
MatchFilter.isValidated(long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider)
Tests whether a match is validated by this filter.
|
boolean |
AssumptionFilter.isValidated(long spectrumMatchKey,
String spectrumFile,
String spectrumTitle,
PeptideAssumption peptideAssumption,
Identification identification,
SequenceProvider sequenceProvider,
SpectrumProvider spectrumProvider,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters)
Tests whether a match is validated by this filter.
|
boolean |
PsmFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider) |
boolean |
ProteinFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider) |
boolean |
PeptideFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider) |
abstract boolean |
MatchFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long matchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider)
Indicates whether the match designated by the match key validates the
given item using the given comparator and value threshold.
|
boolean |
AssumptionFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long spectrumMatchKey,
Identification identification,
GeneMaps geneMaps,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider) |
boolean |
AssumptionFilter.isValidated(String itemName,
FilterItemComparator filterItemComparator,
Object value,
long spectrumMatchKey,
String spectrumFile,
String spectrumTitle,
PeptideAssumption peptideAssumption,
Identification identification,
SequenceProvider sequenceProvider,
SpectrumProvider spectrumProvider,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
IdentificationParameters identificationParameters)
Indicates whether the match designated by the match key validates the
given item using the given comparator and value threshold.
|
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 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 |
PeptideInference.peptideInference(Identification identification,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ModificationProvider modificationProvider,
WaitingHandler waitingHandler)
Infers the PTM localization and its confidence for the best match of
every spectrum.
|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
FMIndex
The FM index.
|
Modifier and Type | Class and Description |
---|---|
class |
SingleProteinSequenceProvider
Sequence provider for a single protein.
|
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.
|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the expected ions in a map indexed by the possible charges.
|
HashMap<Integer,ArrayList<Ion>> |
PeptideSpectrumAnnotator.getExpectedIons(SpecificAnnotationParameters specificAnnotationSettings,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possibleFragmentIons)
Returns the expected ions in a map indexed by the possible charges.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters)
Returns the spectrum annotations of a spectrum in a list of IonMatches
using the intensity filter.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in a list of IonMatches.
|
IonMatch[] |
PeptideSpectrumAnnotator.getSpectrumAnnotation(AnnotationParameters annotationSettings,
SpecificAnnotationParameters specificAnnotationSettings,
String spectrumFile,
String spectrumTitle,
Spectrum spectrum,
Peptide peptide,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SequenceMatchingParameters modificationsSequenceMatchingParameters,
HashMap<Integer,HashMap<Integer,ArrayList<Ion>>> possiblePeptideFragments,
boolean useIntensityFilter)
Returns the spectrum annotations of a spectrum in an array of IonMatches.
|
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.
|
Modifier and Type | Method and Description |
---|---|
static TreeMap<String,String[]> |
PeptideUtils.getAaAfter(Peptide peptide,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
|
static String |
PeptideUtils.getAaAfter(Peptide peptide,
String accession,
int index,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string.
|
static TreeMap<String,String[]> |
PeptideUtils.getAaBefore(Peptide peptide,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
|
static String |
PeptideUtils.getAaBefore(Peptide peptide,
String accession,
int index,
int nAa,
SequenceProvider sequenceProvider)
Returns the amino acids before the given peptide as a string in a map
based on the peptide protein mapping.
|
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 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(Peptide peptide,
Modification modification,
SequenceProvider sequenceProvider,
SequenceMatchingParameters sequenceMatchingParameters)
Returns an array of the possible modification sites for the given
modification on the given peptide.
|
static boolean |
PeptideUtils.isCterm(Peptide peptide,
SequenceProvider sequenceProvider)
Indicates whether a peptide is at the C-terminus of a protein.
|
static boolean |
PeptideUtils.isCterm(Peptide peptide,
String proteinAccession,
SequenceProvider sequenceProvider)
Indicates whether a peptide is at the C-terminus of a given protein.
|
static boolean |
PeptideUtils.isDecoy(Peptide peptide,
SequenceProvider sequenceProvider)
Returns a boolean indicating whether the peptide matches a decoy
sequence.
|
static boolean |
ProteinUtils.isDecoy(String accession,
SequenceProvider sequenceProvider)
Returns a boolean indicating whether the given accession corresponds to a
decoy sequence according to the given sequence provider.
|
static boolean |
PeptideUtils.isEnzymatic(Peptide peptide,
SequenceProvider sequenceProvider,
ArrayList<Enzyme> enzymes)
Returns a boolean indicating whether the peptide is enzymatic in at least
one protein using one of the given enzymes.
|
static boolean |
PeptideUtils.isNterm(Peptide peptide,
SequenceProvider sequenceProvider)
Indicates whether a peptide is at the N-terminus of a protein.
|
static boolean |
PeptideUtils.isNterm(Peptide peptide,
String proteinAccession,
SequenceProvider sequenceProvider)
Indicates whether a peptide is at the N-terminus of a given protein.
|
Constructor and Description |
---|
SimpleMzIdentMLExporter(String softwareName,
String softwareVersion,
String softwareUrl,
File tempFolder,
File destinationFile,
ArrayList<File> spectrumFiles,
File searchEngineFile,
HashMap<String,ArrayList<String>> searchEngines,
File fastaFile,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
ProteinDetailsProvider proteinDetailsProvider,
SpectrumProvider spectrumProvider,
ModificationProvider modificationProvider,
FastaSummary fastaSummary,
String contactFirstName,
String contactLastName,
String contactAddress,
String contactEmail,
String contactOrganizationName,
String contactOrganizationAddress,
String contactOrganizationEmail,
boolean peptideInference)
Constructor.
|
Modifier and Type | Method and Description |
---|---|
void |
ScalingFactorsEstimators.estimateScalingFactors(Identification identification,
Metrics metrics,
SequenceProvider sequenceProvider,
IdentificationFeaturesGenerator identificationFeaturesGenerator,
WaitingHandler waitingHandler,
ExceptionHandler exceptionHandler,
ProcessingParameters processingParameters)
Estimates the scaling factors and stores them in the given metrics.
|
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 |
---|---|
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.
|
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