Package eu.isas.reporter.quantificationdetails

Class ProteinQuantificationDetails

java.lang.Object
eu.isas.reporter.quantificationdetails.ProteinQuantificationDetails
public class ProteinQuantificationDetails extends Object
This class contains the quantitative information at the protein level.
Author:
Marc Vaudel

  • Constructor Summary

    Constructors
    Constructor
    Description
    ProteinQuantificationDetails()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    Double
    getRatio(String reporterIonName, com.compomics.util.experiment.normalization.NormalizationFactors normalizationFactors)
    Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors.
    Double
    getRawRatio(String reporterIonName)
    Returns the raw (not normalized) ratio of a given sample.
    Double
    getSharedRatio(String reporterIonName, com.compomics.util.experiment.normalization.NormalizationFactors normalizationFactors)
    Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors.
    Double
    getSharedRawRatio(String reporterIonName)
    Returns the shared raw (not normalized) ratio of a given sample.
    Double
    getUniqueRatio(String reporterIonName, com.compomics.util.experiment.normalization.NormalizationFactors normalizationFactors)
    Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors.
    Double
    getUniqueRawRatio(String reporterIonName)
    Returns the unique raw (not normalized) ratio of a given sample.
    void
    setRawRatio(String reporterIonName, double value)
    Sets a raw (not normalized) normalized ratio.
    void
    setSharedRawRatio(String reporterIonName, double value)
    Sets a shared raw (not normalized) normalized ratio.
    void
    setUniqueRawRatio(String reporterIonName, double value)
    Sets a unique raw (not normalized) normalized ratio.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • ProteinQuantificationDetails

      public ProteinQuantificationDetails()

  • Method Details

    • getRatio

      public Double getRatio(String reporterIonName, com.compomics.util.experiment.normalization.NormalizationFactors normalizationFactors)
      Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors. null if not found.
      Parameters:
      reporterIonName - the index of sample of interest
      normalizationFactors - the normalization factors
      Returns:
      the ratio for this sample, null if not set

    • getUniqueRatio

      public Double getUniqueRatio(String reporterIonName, com.compomics.util.experiment.normalization.NormalizationFactors normalizationFactors)
      Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors. null if not found.
      Parameters:
      reporterIonName - the index of sample of interest
      normalizationFactors - the normalization factors
      Returns:
      the ratio for this sample, null if not set

    • getSharedRatio

      public Double getSharedRatio(String reporterIonName, com.compomics.util.experiment.normalization.NormalizationFactors normalizationFactors)
      Returns the ratio of a given sample normalized if the given reporter ion quantification has normalization factors. null if not found.
      Parameters:
      reporterIonName - the index of sample of interest
      normalizationFactors - the normalization factors
      Returns:
      the ratio for this sample, null if not set

    • setRawRatio

      public void setRawRatio(String reporterIonName, double value)
      Sets a raw (not normalized) normalized ratio.
      Parameters:
      reporterIonName - the index of the sample
      value - the value of the raw (not normalized) ratio

    • getRawRatio

      public Double getRawRatio(String reporterIonName)
      Returns the raw (not normalized) ratio of a given sample. null if not found.
      Parameters:
      reporterIonName - the index of sample of interest
      Returns:
      the raw (not normalized) ratio for this sample, null if not set

    • setUniqueRawRatio

      public void setUniqueRawRatio(String reporterIonName, double value)
      Sets a unique raw (not normalized) normalized ratio.
      Parameters:
      reporterIonName - the index of the sample
      value - the value of the raw (not normalized) ratio

    • getUniqueRawRatio

      public Double getUniqueRawRatio(String reporterIonName)
      Returns the unique raw (not normalized) ratio of a given sample. null if not found.
      Parameters:
      reporterIonName - the index of sample of interest
      Returns:
      the raw (not normalized) ratio for this sample, null if not set

    • setSharedRawRatio

      public void setSharedRawRatio(String reporterIonName, double value)
      Sets a shared raw (not normalized) normalized ratio.
      Parameters:
      reporterIonName - the index of the sample
      value - the value of the raw (not normalized) ratio

    • getSharedRawRatio

      public Double getSharedRawRatio(String reporterIonName)
      Returns the shared raw (not normalized) ratio of a given sample. null if not found.
      Parameters:
      reporterIonName - the index of sample of interest
      Returns:
      the raw (not normalized) ratio for this sample, null if not set