Package com.compomics.util.parameters.quantification.spectrum_counting

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:

  • Constructor Details

    • SpectrumCountingParameters

      public SpectrumCountingParameters()
      Default constructor.

    • SpectrumCountingParameters

      public SpectrumCountingParameters(SpectrumCountingParameters otherSpectrumCountingPreferences)
      Creates new preferences based on other spectrum counting preferences.
      Parameters:
      otherSpectrumCountingPreferences - the other spectrum counting preferences

  • 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