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.quantification.spectrumcounting |
Experiment classes related to spectrum counting.
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Modifier and Type | Method and Description |
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Metrics |
IdentificationFeaturesGenerator.getMetrics()
Returns the metrics.
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Modifier and Type | Method and Description |
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double |
IdentificationFeaturesGenerator.getNormalizedSpectrumCounting(long proteinMatchKey,
Metrics metrics,
UnitOfMeasurement unit,
Double referenceMass,
SpectrumCountingMethod method)
Returns the spectrum counting metric of the protein match of interest
using the preference settings normalized to the injected protein amount.
|
double |
IdentificationFeaturesGenerator.getNormalizedSpectrumCounting(long proteinMatchKey,
SpectrumCountingParameters spectrumCountingPreferences,
Metrics metrics)
Returns the spectrum counting metric of the protein match of interest
using the preference settings normalized to the injected protein amount
using the given spectrum counting preferences.
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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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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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