Package com.compomics.util.experiment.identification.spectrum_annotation

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

    • SpecificAnnotationParameters

      public SpecificAnnotationParameters()
      Empty default constructor

  • 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

      public SpecificAnnotationParameters clone()
      Overrides:
      clone in class Object