Class SpecificAnnotationParameters

java.lang.Object
com.compomics.util.experiment.identification.spectrum_annotation.SpecificAnnotationParameters

public class SpecificAnnotationParameters
extends Object
The spectrum annotation preferences specific to a spectrum and an identification assumption.
Author:
Marc Vaudel
  • Constructor Details

  • Method Details

    • setPrecursorCharge

      public void setPrecursorCharge​(int precursorCharge)
      Sets the precursor charge.
      Parameters:
      precursorCharge - The precursor charge.
    • getPrecursorCharge

      public int getPrecursorCharge()
      Returns the charge of the precursor.
      Returns:
      the charge of the precursor
    • getIonTypes

      public HashMap<Ion.IonType,​HashSet<Integer>> getIonTypes()
      Returns the map of ions to annotate.
      Returns:
      the map of ions to annotate
    • getFragmentIonTypes

      public HashSet<Integer> getFragmentIonTypes()
      Returns the type of peptide fragment ions annotated.
      Returns:
      the type of peptide fragment ions annotated
    • setSelectedIonsMap

      public void setSelectedIonsMap​(HashMap<Ion.IonType,​HashSet<Integer>> selectedIonsMap)
      Sets the map of ions to annotate.
      Parameters:
      selectedIonsMap - the map of ions to annotate
    • clearIonTypes

      public void clearIonTypes()
      Clears the ion types annotated.
    • addIonType

      public void addIonType​(Ion.IonType ionType, int subType)
      Adds a new ion type and subtype to annotate.
      Parameters:
      ionType - a new ion type to annotate
      subType - the ion sub type
    • addIonType

      public void addIonType​(Ion.IonType ionType)
      Adds a new ion type to annotate. All subtypes will be annotated.
      Parameters:
      ionType - a new ion type to annotate
    • getNeutralLossesMap

      public NeutralLossesMap getNeutralLossesMap()
      Returns the map of neutral losses to annotate.
      Returns:
      the map of neutral losses to annotate
    • setNeutralLossesMap

      public void setNeutralLossesMap​(NeutralLossesMap neutralLossesMap)
      Sets the map of neutral losses to annotate.
      Parameters:
      neutralLossesMap - the map of neutral losses to annotate
    • clearNeutralLosses

      public void clearNeutralLosses()
      Clears the considered neutral losses.
    • addNeutralLoss

      public void addNeutralLoss​(NeutralLoss neutralLoss)
      Adds a neutral loss.
      Parameters:
      neutralLoss - a new neutral loss
    • getSelectedCharges

      public HashSet<Integer> getSelectedCharges()
      Returns the charges selected for annotation.
      Returns:
      the charges selected for annotation
    • setSelectedCharges

      public void setSelectedCharges​(HashSet<Integer> selectedCharges)
      Sets the charges selected for annotation.
      Parameters:
      selectedCharges - the charges selected for annotation
    • clearCharges

      public void clearCharges()
      Clears the selected charges.
    • addSelectedCharge

      public void addSelectedCharge​(int selectedCharge)
      Add a charge to take into account when annotating the spectrum.
      Parameters:
      selectedCharge - a charge to take into account when annotating the spectrum
    • getFragmentIonAccuracy

      public double getFragmentIonAccuracy()
      Returns the fragment ion accuracy.
      Returns:
      the fragment ion accuracy
    • getFragmentIonAccuracyInDa

      public double getFragmentIonAccuracyInDa​(double refMass)
      Returns the fragment ion accuracy in Da. If the tolerance is in ppm it will be converted using the given reference mass.
      Parameters:
      refMass - the reference mass to use for the ppm to Da conversion
      Returns:
      the fragment ion accuracy
    • setFragmentIonAccuracy

      public void setFragmentIonAccuracy​(double fragmentIonAccuracy)
      Sets the fragment ion accuracy.
      Parameters:
      fragmentIonAccuracy - the fragment ion accuracy
    • isFragmentIonPpm

      public boolean isFragmentIonPpm()
      Indicates whether the fragment ion accuracy is in ppm.
      Returns:
      a boolean indicating whether the fragment ion accuracy is in ppm
    • setFragmentIonPpm

      public void setFragmentIonPpm​(boolean fragmentIonPpm)
      Sets whether the fragment ion accuracy is in ppm.
      Parameters:
      fragmentIonPpm - a boolean indicating whether the fragment ion accuracy is in ppm
    • isNeutralLossesAuto

      public boolean isNeutralLossesAuto()
      Indicates whether neutral losses should be automatically selected.
      Returns:
      a boolean indicating whether neutral losses should be automatically selected
    • setNeutralLossesAuto

      public void setNeutralLossesAuto​(boolean neutralLossesAuto)
      Sets whether neutral losses should be automatically selected.
      Parameters:
      neutralLossesAuto - a boolean indicating whether neutral losses should be automatically selected
    • clone

      Overrides:
      clone in class Object