Class ReporterIonQuantification

All Implemented Interfaces:
Serializable

public class ReporterIonQuantification
extends Quantification
This class contains quantification parameters.
Author:
Marc Vaudel
See Also:
Serialized Form
  • Constructor Details

  • Method Details

    • assignSample

      public void assignSample​(String reporterName, String sample)
      Assign a sample to an ion referenced by its static index.
      Parameters:
      reporterName - the name of the reporter ion
      sample - the sample
    • getSampleIndex

      public Integer getSampleIndex​(String sampleReference)
      Returns the sample index for the given sample.
      Parameters:
      sampleReference - the sample reference
      Returns:
      the sample index for the given sample
    • setSampleIndex

      public void setSampleIndex​(String sampleReference, Integer index)
      Set the sample index for the given sample.
      Parameters:
      sampleReference - the sample reference
      index - the index
    • getSample

      public String getSample​(String reporterIonName)
      This method returns the sample associated to the given ion.
      Parameters:
      reporterIonName - the static index of the reporter ion
      Returns:
      the corresponding sample
    • getReporterIndex

      public String getReporterIndex​(String aSample)
      This method returns the reporter ion name associated to the given sample. Null if not found.
      Parameters:
      aSample - the sample
      Returns:
      the static index of the associated ion
    • getReporterMethod

      public ReporterMethod getReporterMethod()
      Returns the reporter method used.
      Returns:
      the method used
    • setMethod

      public void setMethod​(ReporterMethod reporterMethod)
      Sets the reporter method used.
      Parameters:
      reporterMethod - the reporter method used
    • getDefaultReference

      public static String getDefaultReference​(String experimentReference, String sampleReference, int replicateNumber)
      Returns the default reference for an identification.
      Parameters:
      experimentReference - the experiment reference
      sampleReference - the sample reference
      replicateNumber - the replicate number
      Returns:
      the default reference
    • getControlSamples

      public ArrayList<String> getControlSamples()
      Returns the indexes of the samples labeled as control.
      Returns:
      the indexes of the samples labeled as control
    • setControlSamples

      public void setControlSamples​(ArrayList<String> controlSamples)
      Sets the indexes of the samples labeled as control.
      Parameters:
      controlSamples - the indexes of the samples to label as control
    • getSampleIndexes

      public Set<String> getSampleIndexes()
      Returns a set containing the indexes of every sample.
      Returns:
      a set containing the indexes of every sample
    • getNormalizationFactors

      public NormalizationFactors getNormalizationFactors()
      Returns the normalization factors.
      Returns:
      the normalization factors
    • setNormalizationFactors

      public void setNormalizationFactors​(NormalizationFactors normalizationFactors)
      Sets the normalization factors.
      Parameters:
      normalizationFactors - the normalization factors