base_dir = /dir/for/alignment
conf_dir = /dir/for/alignment/conf
out_dir  = /dir/for/alignment/results
aligned_file_simple = /path/to/aligned_summary.txt

mode_rt = fwhm                  // "static" or "fwhm"
method_regression = false       // use of regression for best match peaks.
output_type = ids               // "ids" or "details"
method_both_best_match = true   // do or do not both directional best matching.
margin_rt_ref = 5               // second
margin_rt_target = 5            // second
margin_mass_resolution_high = 5 // ppm
margin_mass_resolution_low = 15 // ppm
factor_fwhm = 3                 // times
min_fwhm = 3                    // second
max_fwhm = 10                   // second


database_search.margin_mass = 5.0  // ppm

job.auto_make_files = true
job.merge_adduct_ini = true

job.alignment = true
job.alignment.new_alignment_calc = true
job.alignment.check_neighbor_alignments = true
job.alignment.check_isotope_alignments = true
job.alignment.check_34S_peaks = true
job.flavonoid_search = true
job.database_search = true
job.output_aligned_file_simple = true


find_best_msn.ms_level_to_top_ions.add_new = 3, 2
