/** Set the default preferences. */ private void setDefaultPreferences() { searchParameters = new SearchParameters(); annotationPreferences.setAnnotationLevel(0.75); annotationPreferences.useAutomaticAnnotation(true); spectrumCountingPreferences.setSelectedMethod(SpectralCountingMethod.NSAF); spectrumCountingPreferences.setValidatedHits(true); IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.NH3); IonFactory.getInstance().addDefaultNeutralLoss(NeutralLoss.H2O); processingPreferences = new ProcessingPreferences(); ptmScoringPreferences = new PTMScoringPreferences(); }
/** Updates the ions used for fragment annotation. */ public void updateAnnotationPreferencesFromSearchSettings() { annotationPreferences.setPreferencesFromSearchParamaers(searchParameters); }
public ArrayList<IonMatch> getIonsCurrentlyMatched() throws MzMLUnmarshallerException { return spectrumAnnotator.getCurrentAnnotation( annotationPreferences.getIonTypes(), annotationPreferences.getNeutralLosses(), annotationPreferences.getValidatedCharges()); }