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

Class ValidationQcParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.ValidationQcParameters
All Implemented Interfaces:
Serializable
public class ValidationQcParameters extends ExperimentObject
This class lists the criteria used for quality control of the validated matches.
Author:
Marc Vaudel, Harald Barsnes
See Also:

  • Constructor Details

    • ValidationQcParameters

      public ValidationQcParameters()
      Creates a validation quality control preferences object with default settings.

    • ValidationQcParameters

      public ValidationQcParameters(ValidationQcParameters validationQCPreferences)
      Creates a validation quality control preferences object based on an other ValidationQCPreferences.
      Parameters:
      validationQCPreferences - an other ValidationQCPreferences

  • Method Details

    • isDbSize

      public boolean isDbSize()
      Indicates whether the database size should be checked.
      Returns:
      true if the database size should be checked

    • setDbSize

      public void setDbSize(boolean dbSize)
      Sets whether the database size should be checked.
      Parameters:
      dbSize - a boolean indicating whether the database size should be checked

    • isFirstDecoy

      public boolean isFirstDecoy()
      Indicates whether the number of hits before the first decoy should be checked.
      Returns:
      true if the number of hits before the first decoy should be checked

    • setFirstDecoy

      public void setFirstDecoy(boolean firstDecoy)
      Sets whether the number of hits before the first decoy should be checked.
      Parameters:
      firstDecoy - a boolean indicating whether the number of hits before the first decoy should be checked.

    • getConfidenceMargin

      public Double getConfidenceMargin()
      Returns the margin to the threshold to use as factor of the resolution. e.g. for a threshold of 10% and a resolution of 1%, with a factor of 1 the threshold will be 11%, with a factor of 2.5 the threshold will be 12.5%.
      Returns:
      the margin to the threshold to use as factor of the resolution

    • setConfidenceMargin

      public void setConfidenceMargin(Double confidenceMargin)
      Sets the margin to the threshold to use as factor of the resolution. e.g. for a threshold of 10% and a resolution of 1%, with a factor of 1 the threshold will be 11%, with a factor of 2.5 the threshold will be 12.5%.
      Parameters:
      confidenceMargin - the margin to the threshold to use as factor of the resolution

    • getPsmFilters

      public ArrayList<Filter> getPsmFilters()
      Returns the list of PSM quality filters.
      Returns:
      the list of PSM quality filters

    • setPsmFilters

      public void setPsmFilters(ArrayList<Filter> psmFilters)
      Sets the list of PSM quality filters.
      Parameters:
      psmFilters - the list of PSM quality filters

    • getPeptideFilters

      public ArrayList<Filter> getPeptideFilters()
      Returns the list of peptide quality filters.
      Returns:
      the list of peptide quality filters

    • setPeptideFilters

      public void setPeptideFilters(ArrayList<Filter> peptideFilters)
      Sets the list of peptide quality filters.
      Parameters:
      peptideFilters - the list of peptide quality filters

    • getProteinFilters

      public ArrayList<Filter> getProteinFilters()
      Returns the list of protein quality filters.
      Returns:
      the list of peptide quality filters

    • setProteinFilters

      public void setProteinFilters(ArrayList<Filter> proteinFilters)
      Sets the list of protein quality filters.
      Parameters:
      proteinFilters - the list of protein quality filters

    • isSameAs

      public boolean isSameAs(ValidationQcParameters validationQCPreferences)
      Returns true if the two ValidationQCPreferences are the same.
      Parameters:
      validationQCPreferences - the ValidationQCPreferences to compare to
      Returns:
      true if the two ValidationQCPreferences are the same

    • getShortDescription

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