Class ProteinInferenceParameters

java.lang.Object
com.compomics.util.experiment.personalization.ExperimentObject
com.compomics.util.parameters.identification.advanced.ProteinInferenceParameters
All Implemented Interfaces:
Serializable

public class ProteinInferenceParameters
extends ExperimentObject
Generic class grouping the protein inference preferences.
Author:
Marc Vaudel, Harald Barsnes
See Also:
Serialized Form
  • Constructor Details

  • Method Details

    • getShortDescription

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

      public boolean equals​(ProteinInferenceParameters otherProteinInferencePreferences)
      Returns true if the objects have identical settings.
      Parameters:
      otherProteinInferencePreferences - the ProteinInferencePreferences to compare to
      Returns:
      true if the objects have identical settings
    • getSimplifyGroups

      public boolean getSimplifyGroups()
      Returns a boolean indicating whether the protein groups should be simplified.
      Returns:
      a boolean indicating whether the protein groups should be simplified
    • setSimplifyGroups

      public void setSimplifyGroups​(boolean simplifyProteinGroups)
      Sets whether the protein groups should be simplified based on the PeptideShaker confidence.
      Parameters:
      simplifyProteinGroups - whether the protein groups should be simplified
    • getSimplifyGroupsEvidence

      public boolean getSimplifyGroupsEvidence()
      Returns a boolean indicating whether the protein groups should be simplified based on the Uniprot evidence level.
      Returns:
      a boolean indicating whether the protein groups should be simplified based on the Uniprot evidence level
    • setSimplifyGroupsEvidence

      public void setSimplifyGroupsEvidence​(boolean simplifyGroupsEvidence)
      Sets whether the protein groups should be simplified based on the Uniprot evidence level.
      Parameters:
      simplifyGroupsEvidence - whether the protein groups should be simplified based on the Uniprot evidence level
    • getSimplifyGroupsConfidence

      public boolean getSimplifyGroupsConfidence()
      Returns a boolean indicating whether the protein groups should be simplified based on the peptide confidence.
      Returns:
      a boolean indicating whether the protein groups should be simplified based on the peptide confidence
    • setSimplifyGroupsConfidence

      public void setSimplifyGroupsConfidence​(boolean simplifyGroupsConfidence)
      Sets whether the protein groups should be simplified based on the peptide confidence level.
      Parameters:
      simplifyGroupsConfidence - whether the protein groups should be simplified based on the peptide confidence level
    • getConfidenceThreshold

      public double getConfidenceThreshold()
      Returns the confidence below which a peptide is considered absent.
      Returns:
      the confidence below which a peptide is considered absent
    • setConfidenceThreshold

      public void setConfidenceThreshold​(double confidenceThreshold)
      Sets the confidence below which a peptide is considered absent.
      Parameters:
      confidenceThreshold - the confidence below which a peptide is considered absent
    • getSimplifyGroupsEnzymaticity

      public boolean getSimplifyGroupsEnzymaticity()
      Returns a boolean indicating whether the protein groups should be simplified based on the peptide enzymaticity.
      Returns:
      a boolean indicating whether the protein groups should be simplified based on the peptide enzymaticity
    • setSimplifyGroupsEnzymaticity

      public void setSimplifyGroupsEnzymaticity​(boolean simplifyGroupsEnzymaticity)
      Sets whether the protein groups should be simplified based on the peptide enzymaticity.
      Parameters:
      simplifyGroupsEnzymaticity - whether the protein groups should be simplified based on the peptide enzymaticity
    • getSimplifyGroupsVariants

      public boolean getSimplifyGroupsVariants()
      Returns a boolean indicating whether the protein groups should be simplified based on the peptide variant matching.
      Returns:
      a boolean indicating whether the protein groups should be simplified based on the peptide variant matching
    • setSimplifyGroupsVariants

      public void setSimplifyGroupsVariants​(boolean simplifyGroupsVariants)
      Sets whether the protein groups should be simplified based on the peptide variant matching.
      Parameters:
      simplifyGroupsVariants - whether the protein groups should be simplified based on the peptide variant matching
    • isModificationRefinement

      public boolean isModificationRefinement()
      Returns whether the protein mapping should be refined based on terminal and pattern modifications.
      Returns:
      a boolean indicating whether the protein mapping should be refined based on terminal and pattern modifications
    • setModificationRefinement

      public void setModificationRefinement​(boolean modificationRefinement)
      Sets whether the protein mapping should be refined based on terminal and pattern modifications.
      Parameters:
      modificationRefinement - a boolean indicating whether the protein mapping should be refined based on terminal and pattern modifications