Package com.compomics.util.parameters.identification.advanced

Class IdMatchValidationParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.IdMatchValidationParameters
All Implemented Interfaces:
Serializable
public class IdMatchValidationParameters extends ExperimentObject
Generic class grouping the identification matches validation preferences.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • IdMatchValidationParameters

      public IdMatchValidationParameters()
      Constructor for default settings.

    • IdMatchValidationParameters

      public IdMatchValidationParameters(IdMatchValidationParameters idMatchValidationPreferences)
      Creates a new IdMatchValidationPreferences based on the values of the given IdMatchValidationPreferences.
      Parameters:
      idMatchValidationPreferences - an IdMatchValidationPreferences to take default values from.

  • Method Details

    • getDefaultProteinFDR

      public double getDefaultProteinFDR()
      Returns the default protein FDR.
      Returns:
      the default protein FDR

    • setDefaultProteinFDR

      public void setDefaultProteinFDR(double defaultProteinFDR)
      Sets the default protein FDR.
      Parameters:
      defaultProteinFDR - the default protein FDR

    • getDefaultPeptideFDR

      public double getDefaultPeptideFDR()
      Returns the default peptide FDR.
      Returns:
      the default peptide FDR

    • setDefaultPeptideFDR

      public void setDefaultPeptideFDR(double defaultPeptideFDR)
      Sets the default peptide FDR.
      Parameters:
      defaultPeptideFDR - the default peptide FDR

    • getDefaultPsmFDR

      public double getDefaultPsmFDR()
      Returns the default PSM FDR.
      Returns:
      the default PSM FDR

    • setDefaultPsmFDR

      public void setDefaultPsmFDR(double defaultPsmFDR)
      Sets the default PSM FDR.
      Parameters:
      defaultPsmFDR - the default PSM FDR

    • getValidationQCParameters

      public ValidationQcParameters getValidationQCParameters()
      Returns the validation QC preferences.
      Returns:
      the validation QC preferences

    • setValidationQCParameters

      public void setValidationQCParameters(ValidationQcParameters validationQCPreferences)
      Sets the validation QC preferences.
      Parameters:
      validationQCPreferences - the validation QC preferences

    • getShortDescription

      public String getShortDescription()
      Returns a short description of the parameters.
      Returns:
      a short description of the parameters

    • equals

      public boolean equals(IdMatchValidationParameters otherIdMatchValidationPreferences)
      Returns true if the objects have identical settings.
      Parameters:
      otherIdMatchValidationPreferences - the IdMatchValidationPreferences to compare to
      Returns:
      true if the objects have identical settings