Package com.compomics.util.experiment.normalization

Class NormalizationFactors

java.lang.Object
com.compomics.util.experiment.normalization.NormalizationFactors
public class NormalizationFactors extends Object
Class grouping the normalization factors used to normalize quantification results.
Author:
Marc Vaudel

  • Constructor Details

    • NormalizationFactors

      public NormalizationFactors()
      Constructor.

  • Method Details

    • hasNormalizationFactors

      public boolean hasNormalizationFactors()
      Indicates whether normalization factors are set.
      Returns:
      a boolean indicating whether the protein normalization factors are set

    • hasProteinNormalisationFactors

      public boolean hasProteinNormalisationFactors()
      Indicates whether the protein normalization factors are set.
      Returns:
      a boolean indicating whether the protein normalization factors are set

    • hasPeptideNormalisationFactors

      public boolean hasPeptideNormalisationFactors()
      Indicates whether the peptide normalization factors are set.
      Returns:
      a boolean indicating whether the peptide normalization factors are set

    • hasPsmNormalisationFactors

      public boolean hasPsmNormalisationFactors()
      Indicates whether the PSM normalization factors are set.
      Returns:
      a boolean indicating whether the PSM normalization factors are set

    • resetProteinNormalisationFactors

      public void resetProteinNormalisationFactors()
      Resets the protein normalization factors.

    • resetPeptideNormalisationFactors

      public void resetPeptideNormalisationFactors()
      Resets the peptide normalization factors.

    • resetPsmNormalisationFactors

      public void resetPsmNormalisationFactors()
      Resets the PSM normalization factors.

    • addProteinNormalisationFactor

      public void addProteinNormalisationFactor(String sampleName, double normalisationFactor)
      Adds a protein normalization factor.
      Parameters:
      sampleName - the index of the sample
      normalisationFactor - the normalization factor

    • addPeptideNormalisationFactor

      public void addPeptideNormalisationFactor(String sampleName, double normalisationFactor)
      Adds a peptide normalization factor.
      Parameters:
      sampleName - the index of the sample
      normalisationFactor - the normalization factor

    • addPsmNormalisationFactor

      public void addPsmNormalisationFactor(String sampleName, double normalisationFactor)
      Adds a PSM normalization factor.
      Parameters:
      sampleName - the index of the sample
      normalisationFactor - the normalization factor

    • getProteinNormalisationFactor

      public double getProteinNormalisationFactor(String sampleName)
      Returns the protein normalization factor for the given sample, 1.0 if not set.
      Parameters:
      sampleName - the index of the sample
      Returns:
      the normalization factor

    • getPeptideNormalisationFactor

      public double getPeptideNormalisationFactor(String sampleName)
      Returns the peptide normalization factor for the given sample, 1.0 if not set.
      Parameters:
      sampleName - the index of the sample
      Returns:
      the normalization factor

    • getPsmNormalisationFactor

      public double getPsmNormalisationFactor(String sampleName)
      Returns the PSM normalization factor for the given sample, 1.0 if not set.
      Parameters:
      sampleName - the index of the sample
      Returns:
      the normalization factor