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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com.compomics.util.parameters.quantification.spectrum_counting |
Spectrum counting parameters.
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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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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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void |
IdentificationFeaturesGenerator.setSpectrumCountingPreferences(SpectrumCountingParameters spectrumCountingPreferences)
Sets the 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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Constructor and Description |
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ScalingFactorsEstimators(SpectrumCountingParameters spectrumCountingParameters)
Constructor.
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Modifier and Type | Method and Description |
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boolean |
SpectrumCountingParameters.isSameAs(SpectrumCountingParameters anotherSpectrumCountingPreferences)
Compares two spectrum counting preferences.
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Constructor and Description |
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SpectrumCountingParameters(SpectrumCountingParameters otherSpectrumCountingPreferences)
Creates new preferences based on other spectrum counting preferences.
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