Class SpectrumCountingParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.quantification.spectrum_counting.SpectrumCountingParameters
All Implemented Interfaces:
Serializable

public class SpectrumCountingParameters
extends ExperimentObject
This class contains the spectrum counting parameters.
Author:
Marc Vaudel, Harald Barsnes
See Also:
Serialized Form
  • Constructor Details

  • Method Details

    • getSelectedMethod

      public SpectrumCountingMethod getSelectedMethod()
      Returns the current spectrum counting method.
      Returns:
      the current spectrum counting method
    • setSelectedMethod

      public void setSelectedMethod​(SpectrumCountingMethod selectedMethod)
      Set the current spectrum counting method.
      Parameters:
      selectedMethod - the spectral counting method
    • getMatchValidationLevel

      public Integer getMatchValidationLevel()
      Returns the lowest validation level considered as an integer as indexed in the MatchValidationLevel enum.
      Returns:
      the lowest validation level considered
    • setMatchValidationLevel

      public void setMatchValidationLevel​(Integer matchValidationLevel)
      Sets the lowest validation level to consider as an integer as indexed in the MatchValidationLevel enum.
      Parameters:
      matchValidationLevel - the lowest validation level to consider
    • isSameAs

      public boolean isSameAs​(SpectrumCountingParameters anotherSpectrumCountingPreferences)
      Compares two spectrum counting preferences.
      Parameters:
      anotherSpectrumCountingPreferences - another spectrum counting preferences
      Returns:
      a boolean indicating whether the other spectrum counting preferences is the same as this one
    • getReferenceMass

      public Double getReferenceMass()
      Returns the reference total mass to use for normalization.
      Returns:
      the reference total mass to use for normalization in μg
    • setReferenceMass

      public void setReferenceMass​(Double referenceMass)
      Sets the reference total mass to use for normalization.
      Parameters:
      referenceMass - the reference total mass to use for normalization in μg
    • getUnit

      public UnitOfMeasurement getUnit()
      Returns the unit used for normalization.
      Returns:
      the unit used for normalization
    • setUnit

      public void setUnit​(UnitOfMeasurement unit)
      Sets the unit used for normalization.
      Parameters:
      unit - the unit used for normalization
    • getNormalize

      public Boolean getNormalize()
      Indicates whether the spectrum counting index should be normalized.
      Returns:
      true if the spectrum counting index should be normalized
    • setNormalize

      public void setNormalize​(Boolean normalize)
      Sets whether the spectrum counting index should be normalized.
      Parameters:
      normalize - a boolean indicating whether the spectrum counting index should be normalized