Examples of NeutralLossesMap

     */
    public void estimateIntermediateScores(Identification identification, InputMap inputMap, ProcessingPreferences processingPreferences, AnnotationPreferences annotationPreferences,
            SearchParameters searchParameters, SequenceMatchingPreferences sequenceMatchingPreferences, WaitingHandler waitingHandler) throws SQLException, IOException, InterruptedException, ClassNotFoundException, MzMLUnmarshallerException {


        HashMap<Ion.IonType, HashSet<Integer>> iontypes = annotationPreferences.getIonTypes();
        NeutralLossesMap neutralLosses = annotationPreferences.getNeutralLosses();
        ArrayList<Integer> charges = annotationPreferences.getValidatedCharges();


        waitingHandler.setSecondaryProgressCounterIndeterminate(false);
        waitingHandler.setMaxSecondaryProgressCounter(identification.getSpectrumIdentificationSize());

Examples of com.compomics.util.experiment.identification.NeutralLossesMap

                    if (!inspectedTags.contains(tagSequence)) {
                        mapPtmsForTag(tagAssumption.getTag(), advocateId);
                        ArrayList<TagAssumption> extendedTagList = new ArrayList<TagAssumption>();
                        extendedTagList.add(tagAssumption);
                        ArrayList<IonMatch> annotations = spectrumAnnotator.getSpectrumAnnotation(annotationPreferences.getIonTypes(),
                                new NeutralLossesMap(),
                                charges,
                                tagAssumption.getIdentificationCharge().value,
                                spectrum, tagAssumption.getTag(),
                                0,
                                annotationPreferences.getFragmentIonAccuracy(),

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