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Methods in com.compomics.util.experiment.identification.filtering with parameters of type IdentificationParameters
Modifier and Type |
Method |
Description |
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.
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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) |
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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.
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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.
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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.
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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) |
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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) |
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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) |
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Methods in com.compomics.util.experiment.identification.psm_scoring with parameters of type IdentificationParameters
Modifier and Type |
Method |
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.
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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.
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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.
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Constructors in com.compomics.util.experiment.io.identification.writers with parameters of type IdentificationParameters
Constructor |
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.
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Constructors in com.compomics.util.gui.parameters.identification with parameters of type IdentificationParameters
Constructor |
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.
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IdentificationParametersEditionDialog(Frame parentFrame,
IdentificationParameters identificationParameters,
Image normalIcon,
Image waitingIcon,
LastSelectedFolder lastSelectedFolder,
boolean editable) |
Creates a new IdentificationParametersEditionDialog with a frame as
owner.
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IdentificationParametersNameDialog(Dialog owner,
Frame parentFrame,
IdentificationParameters identificationParameters,
boolean editable) |
Creates a new IdentificationParametersNameDialog with a dialog as owner.
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IdentificationParametersNameDialog(Frame parentFrame,
IdentificationParameters identificationParameters,
boolean editable) |
Creates a new IdentificationParametersNameDialog with a frame as owner.
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