Package eu.isas.reporter.calculation.normalization

Class Normalizer

java.lang.Object
eu.isas.reporter.calculation.normalization.Normalizer
public class Normalizer extends Object
Normalizes the ratios according to the NormalizationSettings.
Author:
Marc Vaudel, Harald Barsnes

  • Constructor Summary

    Constructors
    Constructor
    Description
    Normalizer()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    void
    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
    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
    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.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • Normalizer

      public Normalizer()

  • Method Details

    • setPsmNormalizationFactors

      public void 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) throws SQLException, IOException, ClassNotFoundException, InterruptedException
      Sets the PSM normalization factors in the ReporterIonQuantification object.
      Parameters:
      reporterIonQuantification - the reporter ion quantification
      ratioEstimationSettings - the ratio estimation settings
      normalizationSettings - the normalization settings
      sequenceMatchingParameters - the peptide to protein sequence matching preferences
      identification - the identification
      spectrumProvider - the spectrum provider
      quantificationFeaturesGenerator - the quantification features generator
      processingParameters - the processing preferences
      searchParameters - the search parameters
      fastaParameters - the FASTA parameters
      peptideVariantsPreferences - the peptide variants parameters
      exceptionHandler - handler in case exception occur
      waitingHandler - waiting handler displaying progress to the user
      Throws:
      SQLException - exception thrown whenever an error occurred while interacting with the database
      IOException - exception thrown whenever an error occurred while interacting with a file
      ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object
      InterruptedException - exception thrown whenever a threading error occurred

    • setPeptideNormalizationFactors

      public void 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) throws SQLException, IOException, ClassNotFoundException, InterruptedException
      Sets the peptide normalization factors in the ReporterIonQuantification object.
      Parameters:
      reporterIonQuantification - the reporter ion quantification
      ratioEstimationSettings - the ratio estimation settings
      normalizationSettings - the normalization settings
      sequenceMatchingParameters - the peptide to protein sequence matching preferences
      identification - the identification
      spectrumProvider - the spectrum provider
      quantificationFeaturesGenerator - the quantification features generator
      processingParameters - the processing preferences
      searchParameters - the search parameters
      fastaParameters - the FASTA parameters
      peptideVariantsPreferences - the peptide variants parameters
      exceptionHandler - handler in case exception occur
      waitingHandler - waiting handler displaying progress to the user
      Throws:
      SQLException - exception thrown whenever an error occurred while interacting with the database
      IOException - exception thrown whenever an error occurred while interacting with a file
      ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object
      InterruptedException - exception thrown whenever a threading error occurred

    • setProteinNormalizationFactors

      public void 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) throws SQLException, IOException, ClassNotFoundException, InterruptedException
      Sets the protein normalization factors in the ReporterIonQuantification object.
      Parameters:
      reporterIonQuantification - the reporter ion quantification
      ratioEstimationSettings - the ratio estimation settings
      normalizationSettings - the normalization settings
      identification - the identification
      spectrumProvider - the spectrum provider
      metrics - the identification metrics
      quantificationFeaturesGenerator - the quantification features generator
      processingParameters - the processing parameters
      searchParameters - the search parameters
      fastaParameters - the FASTA parameters
      peptideVariantsPreferences - the peptide variants parameters
      exceptionHandler - handler in case exception occur
      waitingHandler - waiting handler displaying progress to the user
      Throws:
      SQLException - exception thrown whenever an error occurred while interacting with the database
      IOException - exception thrown whenever an error occurred while interacting with a file
      ClassNotFoundException - exception thrown whenever an error occurred while deserializing an object
      InterruptedException - exception thrown whenever a threading error occurred