Uses of Class
eu.isas.reporter.settings.NormalizationSettings

Packages that use NormalizationSettings

Package	Description
eu.isas.reporter.calculation.normalization	Package containing classes used for the quantification.
eu.isas.reporter.gui.settings.quantification	Package containing GUI classes used for the edition of the quantification settings.
eu.isas.reporter.settings	Package containing the different settings.

Uses of NormalizationSettings in eu.isas.reporter.calculation.normalization

Methods in eu.isas.reporter.calculation.normalization with parameters of type NormalizationSettings

Modifier and Type	Method	Description
void	Normalizer.setPeptideNormalizationFactors(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, RatioEstimationSettings ratioEstimationSettings, NormalizationSettings normalizationSettings, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.waiting.WaitingHandler waitingHandler)	Sets the peptide normalization factors in the ReporterIonQuantification object.
void	Normalizer.setProteinNormalizationFactors(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, RatioEstimationSettings ratioEstimationSettings, NormalizationSettings normalizationSettings, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, com.compomics.util.experiment.identification.peptide_shaker.Metrics metrics, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.waiting.WaitingHandler waitingHandler)	Sets the protein normalization factors in the ReporterIonQuantification object.
void	Normalizer.setPsmNormalizationFactors(com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification reporterIonQuantification, RatioEstimationSettings ratioEstimationSettings, NormalizationSettings normalizationSettings, com.compomics.util.parameters.identification.advanced.SequenceMatchingParameters sequenceMatchingParameters, com.compomics.util.experiment.identification.Identification identification, com.compomics.util.experiment.mass_spectrometry.SpectrumProvider spectrumProvider, QuantificationFeaturesGenerator quantificationFeaturesGenerator, com.compomics.util.parameters.tools.ProcessingParameters processingParameters, com.compomics.util.parameters.identification.search.SearchParameters searchParameters, com.compomics.util.experiment.io.biology.protein.FastaParameters fastaParameters, com.compomics.util.parameters.identification.advanced.PeptideVariantsParameters peptideVariantsPreferences, com.compomics.util.exceptions.ExceptionHandler exceptionHandler, com.compomics.util.waiting.WaitingHandler waitingHandler)	Sets the PSM normalization factors in the ReporterIonQuantification object.

Uses of NormalizationSettings in eu.isas.reporter.gui.settings.quantification

Methods in eu.isas.reporter.gui.settings.quantification that return NormalizationSettings

Modifier and Type	Method	Description
NormalizationSettings	NormalizationSettingsDialog.getNormalizationSettings()	Returns the settings as set by the user.

Constructors in eu.isas.reporter.gui.settings.quantification with parameters of type NormalizationSettings

Modifier	Constructor	Description
	NormalizationSettingsDialog(JDialog parentDialog, NormalizationSettings normalizationSettings, boolean editable)	Creates a new NormalizationSettingsDialog.

Uses of NormalizationSettings in eu.isas.reporter.settings

Methods in eu.isas.reporter.settings that return NormalizationSettings

Modifier and Type	Method	Description
NormalizationSettings	NormalizationSettings.clone()
NormalizationSettings	ReporterSettings.getNormalizationSettings()	Returns the normalization settings.

Methods in eu.isas.reporter.settings with parameters of type NormalizationSettings

Modifier and Type	Method	Description
boolean	NormalizationSettings.isSameAs(NormalizationSettings anotherSetting)	Indicates whether another setting is the same as this one.
void	ReporterSettings.setNormalizationSettings(NormalizationSettings normalizationSettings)	Sets the normalization settings.