Package com.compomics.util.experiment.quantification.reporterion

Class ReporterIonQuantification

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.experiment.quantification.Quantification
com.compomics.util.experiment.quantification.reporterion.ReporterIonQuantification
All Implemented Interfaces:
Serializable
public class ReporterIonQuantification extends Quantification
This class contains quantification parameters.
Author:
Marc Vaudel
See Also:

  • Constructor Details

    • ReporterIonQuantification

      public ReporterIonQuantification()
      Empty default constructor

    • ReporterIonQuantification

      public ReporterIonQuantification(Quantification.QuantificationMethod methodUsed)
      Constructor for the reporter ion quantification.
      Parameters:
      methodUsed - the method used for this quantification

  • 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