Package | Description |
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com.compomics.util.experiment.identification.features |
Classes for the generation of identification features.
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com.compomics.util.experiment.identification.filtering |
Classes for the filtering of identification objects.
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com.compomics.util.experiment.identification.matches_iterators |
Identification match iterators.
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com.compomics.util.experiment.identification.peptide_inference |
Classes related to peptide inference.
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com.compomics.util.experiment.identification.protein_inference |
Classes related to protein inference.
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com.compomics.util.experiment.quantification.spectrumcounting |
Experiment classes related to spectrum counting.
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com.compomics.util.gui.modification |
PTM GUI dialogs.
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Modifier and Type | Method and Description |
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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.
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Constructor and Description |
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IdentificationFeaturesGenerator(Identification identification,
IdentificationParameters identificationParameters,
SequenceProvider sequenceProvider,
SpectrumProvider spectrumProvider,
Metrics metrics,
SpectrumCountingParameters spectrumCountingPreferences)
Constructor.
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Modifier and Type | Method and Description |
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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.
|
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.
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Constructor and Description |
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MatchesIterator(Class className,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
MatchesIterator(long[] keys,
Class className,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress,
String filters)
Constructor.
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PeptideMatchesIterator(Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
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PeptideMatchesIterator(long[] keys,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
ProteinMatchesIterator(Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
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ProteinMatchesIterator(long[] keys,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
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SpectrumMatchesIterator(Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
|
SpectrumMatchesIterator(long[] keys,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress)
Constructor.
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SpectrumMatchesIterator(long[] keys,
Identification identification,
WaitingHandler waitingHandler,
boolean displayProgress,
String filters)
Constructor.
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Modifier and Type | Method and Description |
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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.
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Constructor and Description |
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PeptideAndProteinBuilder(Identification identification)
Constructor.
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Modifier and Type | Method and Description |
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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.
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Constructor and Description |
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ModificationTable(Identification identification,
AnnotationParameters annotationParameters,
PeptideMatch peptideMatch,
Modification modification,
boolean areaChart,
ModificationParameters modificationParameters,
SequenceProvider sequenceProvider,
SpectrumProvider spectrumProvider,
SequenceMatchingParameters modificationSequenceMatchingParameters)
Constructor.
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