*/
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());