Modifier and Type | Method and Description |
---|---|
IdentificationParameters |
IdentificationParametersInputBean.getIdentificationParameters()
Returns the identification parameters.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationParametersInputBean.setIdentificationParameters(IdentificationParameters identificationParameters)
Sets the identification parameters.
|
Modifier and Type | Method and Description |
---|---|
static void |
PeptideMapperCLI.runMapping(File fastaFile,
WaitingHandlerCLIImpl waitingHandlerCLIImpl,
IdentificationParameters identificationParameters,
String inputFileName,
String outputFileName,
int nCores,
boolean peptideMapping) |
Constructor and Description |
---|
MappingWorker(WaitingHandlerCLIImpl waitingHandlerCLIImpl,
FastaMapper peptideMapper,
IdentificationParameters identificationParameters,
BufferedReader br,
PrintWriter writer,
boolean peptideMapping) |
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.
|
Modifier and Type | Method and Description |
---|---|
IdentificationParameters |
IdentificationParametersFactory.getIdentificationParameters(String name)
Returns the identification parameters corresponding to the given name.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationParametersFactory.addIdentificationParameters(IdentificationParameters identificationParameters)
Adds the given identification parameters to the factory.
|
void |
IdentificationParametersFactory.updateIdentificationParameters(IdentificationParameters oldParameters,
IdentificationParameters newParameters)
Replaces old parameters by new.
|
Modifier and Type | Method and Description |
---|---|
static void |
ModificationLocalizationMapper.modificationLocalization(Peptide peptide,
HashMap<Integer,ArrayList<String>> expectedNames,
HashMap<ModificationMatch,ArrayList<String>> modNames,
IdentificationParameters identificationParameters,
IdfileReader idfileReader,
ModificationProvider modificationProvider)
Makes an initial modification mapping based on the search engine results
and the compatibility to the searched modifications.
|
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.
|
Constructor and Description |
---|
FMIndex(File fastaFile,
FastaParameters fastaParameters,
WaitingHandler waitingHandler,
boolean displayProgress,
IdentificationParameters identificationParameters)
Constructor.
|
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.
|
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 |
---|---|
IdentificationParameters |
IdentificationParametersOverviewDialog.getIdentificationParameters()
Returns the selected identification parameters.
|
IdentificationParameters |
IdentificationParametersEditionDialog.getIdentificationParameters()
Returns the identification parameters as set by the user.
|
Modifier and Type | Method and Description |
---|---|
void |
IdentificationParametersNameDialog.updateParameters(IdentificationParameters identificationParameters)
Updates the given identification parameters attributes.
|
Constructor and Description |
---|
IdentificationParametersEditionDialog(Dialog owner,
Frame parentFrame,
IdentificationParameters identificationParameters,
Image normalIcon,
Image waitingIcon,
LastSelectedFolder lastSelectedFolder,
boolean editable)
Creates a new IdentificationParametersEditionDialog with a dialog as
owner.
|
IdentificationParametersEditionDialog(Frame parentFrame,
IdentificationParameters identificationParameters,
Image normalIcon,
Image waitingIcon,
LastSelectedFolder lastSelectedFolder,
boolean editable)
Creates a new IdentificationParametersEditionDialog with a frame as
owner.
|
IdentificationParametersNameDialog(Dialog owner,
Frame parentFrame,
IdentificationParameters identificationParameters,
boolean editable)
Creates a new IdentificationParametersNameDialog with a dialog as owner.
|
IdentificationParametersNameDialog(Frame parentFrame,
IdentificationParameters identificationParameters,
boolean editable)
Creates a new IdentificationParametersNameDialog with a frame as owner.
|
Modifier and Type | Method and Description |
---|---|
static IdentificationParameters |
IdentificationParameters.getIdentificationParameters(File identificationParametersFile)
Loads the identification parameters from a file.
|
Modifier and Type | Method and Description |
---|---|
boolean |
IdentificationParameters.equals(IdentificationParameters otherIdentificationParameters)
Returns true if the identification parameter objects have identical
settings.
|
static void |
IdentificationParameters.saveIdentificationParameters(IdentificationParameters identificationParameters,
File identificationParametersFile)
Saves the identification parameters to a file.
|
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