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

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:

  • Constructor Details

    • ProteinInferenceParameters

      public ProteinInferenceParameters()
      Empty default constructor

  • 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