def score_alignment_annotated_ion_peaks(spec1,spec2,pm1,pm2,tolerance,annotation1,annotation2,max_charge_consideration=1):
#filter unannotated peaks
filtered_peaks1 = ming_spectrum_library.attenuate_unannotated_peaks(spec1, 3, tolerance, annotation1)
filtered_peaks2 = ming_spectrum_library.attenuate_unannotated_peaks(spec2, 3, tolerance, annotation2)
total_score, alignment = score_alignment(filtered_peaks1,filtered_peaks2,pm1,pm2,tolerance,max_charge_consideration)
return total_score
def score_alignment_annotated_ion_peaks(spec1,spec2,pm1,pm2,tolerance,annotation1,annotation2,max_charge_consideration=1):
#filter unannotated peaks
filtered_peaks1 = ming_spectrum_library.attenuate_unannotated_peaks(spec1, 3, tolerance, annotation1)
filtered_peaks2 = ming_spectrum_library.attenuate_unannotated_peaks(spec2, 3, tolerance, annotation2)
total_score, alignment = score_alignment(filtered_peaks1,filtered_peaks2,pm1,pm2,tolerance,max_charge_consideration)
return total_score