/** 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());
}