int main()
{
Config *config=NULL;
FileManager fm;
FileSet fs;
AdvancedScoreModel model;
EdgeModel edge_model;
PeptideRankScorer drs;
rand_seed(112233);
// train_all();
model.read_model("CID_IT_TRYP");
config = model.get_config();
config->apply_selected_PTMs("C+57:M+16:Q-17");
// fm.init_from_file(config,"C:\\Work\\msms5\\DnvScore\\all_ds\\HEK_98_3_unique_30.mgf");
fs.select_files_in_mz_range(fm,300,2000,3);
fs.randomly_reduce_ssfs(100);
vector<int> cc(4,0);
cc[3]=100;
fs.create_mgf_file(fm,config,"HEK_4_30e.mgf",cc);
exit(0);
// model.get_config()->apply_selected_PTMs("C+57:M+16:Q-17");
PMCSQS_Scorer *pmcsqs = (PMCSQS_Scorer *)model.get_pmcsqs_ptr();
fm.init_from_list_file(config,"C:\\Work\\msms5\\PepNovoHQ\\train3.txt");
pmcsqs->benchmark_pm_selection(config,fm,0.3);
exit(0);
/* benchmark_shew(model,"C:\\Work\\msms5\\PepNovoHQ\\Shew_test_10.mgf");
exit(0);
drs.set_model_type(0);
drs.read_denovo_rank_scorer_model("C:\\Work\\msms5\\PepNovoHQ\\Models\\DBSCORE\\DBSCORE_rank_model.txt");
drs.give_de_novo_and_peak_match_examples("C:\\Work\\msms5\\DnvScore\\all_db_hits",
"C:\\Work\\msms5\\DnvScore\\seq_freqs\\sequences",
"C:\\Work\\msms5\\DnvScore\\dnv_full_parts",
"C:\\Work\\msms5\\DnvScore\\dicty2_all.txt",
2,2);
exit(0);
drs.read_denovo_rank_scorer_model("C:\\Work\\msms5\\PepNovoHQ\\Models\\DBSCORE\\DBSCORE_rank_model.txt");
drs.rescore_inspect_results("C:\\Work\\msms5\\DnvScore\\inspect_res\\H293-40ul-08.mzXML",
"C:\\Work\\msms5\\DnvScore\\inspect_res\\H293-40ul-08.txt",
"C:\\Work\\msms5\\DnvScore\\inspect_res\\H293-40ul-08_new.txt");
exit(0);
// test_denovo_integrity(model,"C:\\Work\\msms5\\DnvScore\\all_ds\\Dicty_98_2_unique_8.mgf", 20000, 8);
// benchmark_ranking_on_denovo("C:\\Work\\msms5\\PepNovoHQ\\Models\\DNVSCORE5\\DNVSCORE5_rank_model.txt",
// "C:\\Work\\msms5\\DnvScore\\test\\DNVSCORE4_test_10.mgf",400,10); //
// benchmark_ranking_on_full_denovo("C:\\Work\\msms5\\PepNovoHQ\\Models\\DNVFULL\\DNVFULL_rank_model.txt",
// "C:\\Work\\msms5\\DnvScore\\test\\FULL_test_10.mgf",1000);
// exit(0);
fm.init_from_list_file(config,//"C:\\Work\\msms5\\DnvScore\\short2_train_mgf_list.txt");
"C:\\Work\\msms5\\DnvScore\\comp2_train_mgf_list.txt");
// "C:\\Work\\msms5\\NewScore\\lists\\Shew_98_3_unique_mgf_list.txt");
fs.select_files(fm,0,2500,-1,-1,2);
find_special_PTM_frags_using_offset_counts("S",fm,fs.get_ssf_pointers(),&model,2);
exit(0);
drs.read_denovo_rank_scorer_model("C:\\Work\\msms5\\PepNovoHQ\\Models\\DNVSC_RANK\\LTQ_DNVRANK_model.txt");
drs.test_model("C:\\Work\\msms5\\DnvScore\\test_sets\\LTQ_DNVRANK_test_10.mgf",2000);
drs.train_denovo_partition_model("C:\\Work\\msms5\\DnvScore\\all_db_hits",
"C:\\Work\\msms5\\DnvScore\\seq_freqs\\sequences",
"C:\\Work\\msms5\\DnvScore\\comp_all_parts",
// "C:\\Work\\msms5\\DnvScore\\short2_train_mgf_list.txt",
"C:\\Work\\msms5\\DnvScore\\comp2_train_mgf_list.txt",
2,
1,
30000,
5);
// model.read_model("ETD");
// config = model.get_config();
// config->apply_selected_PTMs("M+16:Q-17:N+1:C+57");
// fm.init_from_list_file(config,"C:\\Work\\msms5\\PepNovoHQ\\ETD2\\ETD_unique_train.txt");
// model.full_train_model("ETD",fm,0.5);
// model.train_pmc_rank_models("C:\\Work\\msms5\\PepNovoHQ\\ETD2\\ETD_all_train.txt");
// model.write_model();
exit(0);
// train_all();
// create_training_sets();
// exit(0);
// generate_size_reports();
// test_sims();
// data_set_stats();
// convert_list_to_trianing_peptide_file(
// "C:\\Work\\msms5\\NewScore\\lists\\Dicty_98_3_unique_mgf_list.txt",
// "C:\\Work\\msms5\\NewScore\\tps\\Dicty_98_3_unique_tps.txt");
// proline_cleavage_reports("b",2);
// exit(0);
// center_cleavage_reports("y",3);
// n_terminal_cleavage_reports("y",2);
// c_terminal_cleavage_reports("y",-2);
// find_best_similar_pairs("LTQ_LOW_TRYP",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\HEK_pos2.mgf",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\Shew_pos2.mgf",8);
// find_self_similarity("LTQ_LOW_TRYP",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\HEK_pos2.mgf",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\Shew_pos2.mgf");
// find_similar_pairs_ditrib("LTQ_LOW_TRYP",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\HEK_pos2.mgf",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\Shew_pos2.mgf");
// find_homeometric_similarity_distrib("LTQ_LOW_TRYP",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\HEK_pos2.mgf",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\Shew_pos2.mgf");
// find_self_similarity_ranges("LTQ_LOW_TRYP",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\SHEW18.mgf");
// peptide_distances();
// find_matches_similarity_distrib("LTQ_LOW_TRYP",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\HEK_pos2.mgf",
// "C:\\Work\\msms5\\PepNovoHQ\\pairs\\Shew_pos2.mgf");
// match_sim_exp();
// exit(0);
// edge_model.train_all_edge_models("C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt","LTQ",2);
// saa.train_saa_models("C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt","LTQ",2);
// saa.train_saancd_models("C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt","LTQ",2);
// daa.train_daa_models("C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt","LTQ",2,0.25);
// daa.train_daancd_model("C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt","LTQ",2);
// dot_prod_exp();
// qc_exp();
// qc_ann_exp("64068",true);
// exit(0);
config = model.get_config();
config->init_with_defaults();
config->apply_selected_PTMs("M+16:Q-17:N+1:C+57");
fm.init_from_file(config,"C:\\Work\\msms5\\PepNovoHQ\\ETD\\train_etd.mgf");
model.full_train_model("ETD",fm,0.5);
exit(0);
if (1)
{
model.read_model("LTQ_LOW_TRYP");
// model.get_config()->apply_selected_PTMs("C+57:M+16");
// model.get_config()->init_with_defaults();
model.get_config()->apply_selected_PTMs("M+16:C+57:Q-17");
// model.test_pmc("C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\sqs_train_1.mgf",1);
// model.compute_sqs_cum_stats_for_ided("C:\\Work\\msms5\\NewScore\\lists\\all_HEK_mgf_list.txt");
// model.compute_sqs_cum_stats_for_crap("C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\crap_list.txt");
// model.write_model();
model.compute_sqs_cum_stats_for_ided("C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\H40good\\H40good_mgf_list.txt");
/// model.benchmark_sqs("C:\\Work\\msms5\\PepNovoHQ\\small_list.txt",
// "C:\\Work\\msms5\\PepNovoHQ\\small_anns.txt");
// model.benchmark_sqs("C:\\Work\\msms5\\PepNovoHQ\\tmp\\H40ul_0_list.txt",
// "C:\\Work\\msms5\\PepNovoHQ\\H40ul55_missed.txt");
// "C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\H40ul98_anns.txt");
exit(0);
DAT_Converter dat;
dat.create_dat_files_for_anns(model.get_config(),
"C:\\Work\\Data\\Briggs\\HEK293\\40ul_list.txt",
// "C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\H40ul98_anns.txt",
"C:\\Work\\msms5\\PepNovoHQ\\H40ul55_missed.txt",
"C:\\Work\\msms5\\PepNovoHQ\\tmp\\",
"H4055");
//
// model.train_pmc_rank_models(
// "C:\\Work\\msms5\\NewScore\\lists\\HEK_98_1_unique_mgf_list.txt",0);
// "C:\\Work\\msms5\\NewScore\\lists\\all_unique_mgf_list.txt",0);
// "C:\\Work\\msms5\\NewScore\\lists\\all_HEK_mgf_list.txt",0);
// model.write_model();
// make_before_and_after_matrices(model.get_config(),"C:\\Work\\msms5\\lists\\mgf10.txt",3,"y");
exit(0);
FileManager fm;
fm.init_from_list_file(model.get_config(),"C:\\Work\\msms5\\lists\\LTQ_train_list.txt");
model.full_train_model("LTQ_IT_TRYP",fm,0.45);
model.write_model();
// model.train_pmc("C:\\Work\\msms5\\lists\\pos_sqs_list.txt");
vector< vector<float> > weights;
weights.resize(4);
weights[1].resize(3,0);
weights[2].resize(3,0);
weights[3].resize(3,0);
weights[1][0] = 0.1; weights[1][1] = 0.1; weights[1][2] = 0.4;
weights[2][0] = 0.6; weights[2][1] = 0.75; weights[2][2] = 0.5;
weights[3][0] = 0.3; weights[3][1] = 0.15; weights[3][2] = 0.1;
// model.train_sqs("C:\\Work\\msms5\\lists\\pos_sqs_list.txt",
// "C:\\Work\\msms5\\lists\\neg_sqs_list.txt",&weights);
// model.train_sqs("C:\\Work\\msms5\\NewScore\\lists\\all_unique_mgf_list.txt",
// "C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\crap_list.txt",&weights);
// config = model.get_config();
// config->set_tolerance(0.5);
//
// find_pair_similarities(config,"C:/Work/clust_exp/Results/Shew_bm/ShewBM40_0_1.mgf",
// "C:/Work/clust_exp/Results/Shew_bm/ShewBM40_pairs.txt");
exit(0);
}
// make_y_vectors("C:\\Work\\msms5\\PepNovoHQ\\pmcsqs\\sqs10_train_2.mgf",&model);
// create_training_files(config);
// exit(0);
if (0)
{
PMCSQS_Scorer sqs;
// exit(0);
// create_training_files(config);
exit(0);
}
if (1)
{
// fm.init_from_file(model.get_config(),"C:\\Work\\msms5\\PepNovoHQ\\orbi_ann.mgf");
// create_MSB_query_for_file_list(fm,&model);
vector< vector<int> > annotation_idxs;
vector<mzXML_annotation> annotations;
read_mzXML_annotations("C:/Work/Data/Briggs/HEK293_mzxml_list.txt",
"C:/Work/ClusterAnn/mzxml_anns3.txt", annotation_idxs, annotations, 35000);
// read_mzXML_annotations("C:/Work/ClusterAnn/H40ul_mgf_list.txt",
// "C:/Work/ClusterAnn/mgf_anns.txt", annotation_idxs, annotations, 35000);
cout << "Read annotations: " << annotations.size() << endl;
fm.init_from_list_file_and_add_annotations(config,"C:/Work/Data/Briggs/HEK293_mzxml_list.txt",
annotation_idxs, annotations,true);
// fm.init_from_list_file_and_add_annotations(config,"C:/Work/ClusterAnn/H40ul_mgf_list.txt",annotation_idxs,
// annotations,true);
FileSet all_spec_fs;
all_spec_fs.select_all_files(fm,true);
// config->set_need_to_normalize(0);
// all_spec_fs.create_MGF_file(fm,config,"C:/Work/ClusterAnn/mgf_spectra.mgf");
// exit(0);
ofstream mgf_stream("C:/Work/ClusterAnn/mzxml_spectra3.mgf",ios::out);
BasicSpecReader bsr;
const vector<SingleSpectrumFile *>& ssfs = all_spec_fs.get_ssf_pointers();
int i;
for (i=0; i<ssfs.size(); i++)
{
static QCPeak peaks[5000];
BasicSpectrum bs;
MZXML_single *ssf = (MZXML_single *)ssfs[i];
bs.peaks = peaks;
bs.ssf = ssf;
ostringstream oss;
oss << ssf->file_idx << " " << ssf->scan_number;
ssf->single_name = oss.str();
bs.num_peaks = bsr.read_basic_spec(config,fm,ssf,peaks);
if (ssf->scan_number<0)
{
cout << "Error: no scan number read from mzXML!!!" << endl;
exit(1);
}
cout << "scan: " << ssf->scan_number << " " << bs.num_peaks << endl;
bs.output_to_mgf(mgf_stream,config);
// bs.output_to_mgf(cout,&config);
}
//all_spec_fs.create_MGF_file(fm,config,"C:/Work/ClusterAnn/mzxml_spectra.mgf");
// extractMZFromFiles(model.get_config(),,"C:/Work/Data/Briggs/HEK293/H29340ul_mz.txt");
//
exit(0);
}
if (1)
{
model.read_model("LTQ_LOW_TRYP");
config = model.get_config();
config->apply_selected_PTMs("C+57 M+16");
config->set_tolerances(0.5);
config->set_pm_tolerance(2.5);
config->set_digest_type(TRYPSIN_DIGEST);
config->set_max_number_peaks_per_local_window(15);
// fm.init_from_list_file(config,"C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt");
// fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\LTQ_train_list.txt");
// fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\orbi_train.txt");
// edge_model.train_all_edge_models(fm,&model);
// tm.train_models(fm,&model);
// fm.init_from_list_file(config,"C:\\Work\\clust_exp\\ShewMGF\\BM2000_ann_list.txt");
// make_frag_rank_histogram(fm,config);
// exit(0);
// benchmark_k_value(config,"C:\\Work\\clust_exp\\ShewMGF\\BM2000_ann_list.txt");
// make_benchmark_clustering_dataset(config, "C:\\Work\\clust_exp\\ShewMGF\\AnnsPlus_ann_list.txt",
// 600, 750, false, "C:\\Work\\clust_exp\\ShewMGF\\", "BMNEW");
// exit(0);
benchmark_clustering_performance(config,
"C:\\Work\\clust_exp\\ShewMGF\\BM2000_ann_list.txt",15);
// print_dataset_spectra_by_stats(config,"C:\\Work\\clust_exp\\ann_mgf\\Sings_1.mgf");
// benchmark_top7_and_sim_thresh(config,"C:\\Work\\clust_exp\\tmp\\H293_40ul_list.txt",
// "C:\\Work\\clust_exp\\Results\\BM40ul\\BM40ul_anns.txt");
// benchmark_heuristic_filtering(config,"C:\\Work\\clust_exp\\tmp\\H293_40ul_list.txt");
// benchmark_retention_thresh(config,"C:\\Work\\clust_exp\\tmp\\H293_40ul_list.txt",
// "C:\\Work\\clust_exp\\Results\\BM40ul\\BM40ul_anns.txt");
exit(0);
FileManager fm;
// fm.init_from_mgf(config,"C:\\Work\\clust_exp\\ShewMGF\\OnlyAnn_1.mgf");
// make_specified_benchmark_clustering_dataset(config,"C:\\Work\\clust_exp\\ShewMGF\\both_list.txt",400,1000,
// "C:\\Work\\clust_exp\\ShewMGF\\","BM3000",3000,10,0);
make_benchmark_clustering_dataset(config, "C:\\Work\\clust_exp\\ShewMGF\\AnnsPlus_ann_list.txt",
800, 1200, true, "C:\\Work\\clust_exp\\ShewMGF\\", "AnnOnly");
exit(0);
ann_mgf_and_create_mgf_with_sim_masses(config,"K:\\Work\\Data\\Shewenella\\FT_anns.txt",
"K:\\Work\\Data\\Shewenella\\FT_mgf_list.txt",
"K:\\Work\\Data\\Shewenella\\FT_peptides.txt",
"C:\\Work\\clust_exp\\ShewMGF\\",
"AnnsPlus");
exit(0);
ann_mgf_and_create_mgf(config,"C:\\Work\\Data\\FT_mgf\\FT_single_anns.txt",
"C:\\Work\\Data\\FT_mgf\\FT_single_mgf.txt",
"C:\\Work\\clust_exp\\ShewMGF\\",
"Single",true);
exit(0);
ann_mgf_and_create_mgf(config,"C:\\Work\\Data\\FT_mgf\\FT_anns.txt",
"C:\\Work\\Data\\FT_mgf\\FT_mgf_list.txt",
"C:\\Work\\clust_exp\\ShewMGF\\",
"OnlyAnn",true);
exit(0);
// create_16O_18O_dataset("C:\\Work\\msms5\\lists\\p19_list.txt",config);
// exit(0);
// config->set_need_to_estimate_pm(0);
model.clone_charge_model(2,1);
model.clone_charge_model(2,3);
model.clone_charge_model(2,4);
model.clone_charge_model(2,5);
// dataset_eval(&model,"C:\\Work\\msms5\\lists\\CAD_376.txt",0.05);
// dataset_eval(&model,"C:\\Work\\msms5\\lists\\ann_qtof_list.txt",0.1);
// dataset_eval(&model,"C:\\Work\\msms5\\lists\\list280_mgf.txt",0.6);
vector<int> set_sizes;
vector<float> probs;
denovo_sequencing_and_aa_probs(&model,"C:\\Work\\msms5\\lists\\m280_list.txt",
set_sizes,probs,2);
// denovo_sequencing_and_aa_probs(&model,"C:\\Work\\clust_exp\\LTQ_train2_ann_list.txt",
// set_sizes,probs,2);
//
// output_denovo_results(&model,"C:\\Work\\msms5\\lists\\LTQ-FT_mgf_list.txt");
// denovo_sequencing_and_aa_probs(&model,"C:\\Work\\msms5\\lists\\LTQ-FT_mgf_list.txt",
// set_sizes,probs, 2);
exit(0);
// print_specs(model.get_config(), "C:\\Work\\msms5\\lists\\one_mzxml.txt");
// check_m_over_z(&model,"C:\\Work\\msms5\\lists\\CoCl345sann_ann_list.txt");
// calc_parent_mass_tolerance_distribution(&model, "C:\\Work\\msms5\\lists\\ann_mgf_list.txt" , 0.6, 0.98);
// calc_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\ann_mgf_list.txt", 0.6, 0.95);
// perfrom_inital_evalutation("C:\\Work\\msms5\\lists\\ann_mgf_list.txt",0.5,2,0.05);
// denovo_sequencing_results(&model,"C:\\Work\\msms5\\lists\\CAD_376.txt" ,0.0075);
// denovo_sequencing_results(&model,"C:\\Work\\msms5\\lists\\ann_qtof_list.txt",0.1);
// denovo_sequencing_results(&model,"C:\\Work\\msms5\\lists\\ann_orbi_list.txt",0.008);
// perfrom_inital_evalutation("C:\\Work\\msms5\\lists\\ann_qtof_list.txt",0.2,2,0.05);
// perfrom_inital_evalutation("C:\\Work\\msms5\\lists\\ann_orbi_list.txt",0.025,2,0.05);
// calc_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\ann_qtof_list.txt",0.1,0.95);
// calc_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\ann_orbi_list.txt",0.1,0.95);
// calc_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\CAD_376.txt",0.1,0.95);
// calc_tolerance_distribution(&model,"C:\\Work\\Data\\Omics04\\omics_ann_list.txt",0.75,0.95);
// calc_parent_mass_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\ann_qtof_list.txt",0.1,0.975);
// calc_parent_mass_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\ann_orbi_list.txt",0.1,0.975);
// calc_parent_mass_tolerance_distribution(&model,"C:\\Work\\msms5\\lists\\CAD_376.txt",0.1,0.975);
exit(0);
// fm.init_from_mgf(config,"C:\\Work\\msms4\\PepNovo\\test\\m280.mgf");
// fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\good_list2.txt");
// fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\p215.txt");
// fm.init_from_list_file(config,"C:\\Work\\Data\\Omics04\\omics_ann_list.txt");
// fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\omics_mgf_list.txt");
// fm.init_from_mgf(config,"C:\\Work\\msms5\\PepNovoHQ\\Omics04Spectra.mgf");
// fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\omics02_dta.txt");
// FileSet fs;
// fs.select_all_files(fm);
// fs.sort_according_to_m_over_z();
// fs.create_MGF_file(fm,config,"Omics02Spectra.mgf");
// exit(0);
// collect_denovo_statistics(fm,&model);
// denovo_histograms(fm,&model);
// config->set_tolerance(0.0075);
// random_check_homemorphic(config,50000,25);
// create_spectrum_clusters(config,"C:\\Work\\msms5\\lists\\Drosophila_list.txt",".","cc",0,5E6,0,1E6);
// create_spectrum_clusters(config,"C:\\Work\\msms5\\lists\\Dros_short.txt",".","cc",0,1E6,0,1E6);
// create_spectrum_clusters(config,"C:\\Work\\msms5\\lists\\all_clust.txt","clust_out","ikkb",0,5E6,0,1E6);
// create_spectrum_clusters(config,"C:\\Work\\msms5\\lists\\omics_mgf_list.txt","clust_out",
// "Omics04b",0,5E6,0,1E6);
// create_spectrum_clusters(config,"C:\\Work\\msms5\\lists\\omics02_mgf_list.txt","clust_out",
// "Omics02",0,5E6,0,1E6);
// create_spectrum_clusters(config,"C:\\Work\\msms5\\PepNovoHQ\\clust_out2\\h293_dat_list.txt",
// "clust_out2","H293b_2nd_digest_abd3",0,5E6,1938.76,1E6,2);
// create_spectrum_clusters(config,"C:\\Work\\msms5\\PepNovoHQ\\clust_out\\h29s_list.txt","clust_out",
// "xxxx",0,5E6,835.397,1E6,2);
exit(0);
DAT_Converter dat;
dat.init_DAT_Converter(2000,25,1048576);
exit(0);
}
// config->add_selected_PTMs("C+57 M+16 S+80 T+80 Y+80 N+1 Q+1 K+42 D+16 K+16 P+16 N+16");
// config->set_tolerances(0.0075);
// config->set_pm_tolerance(0.011);
// fdb.create_db_from_fasta("C:\\Work\\msms5\\PepNovoHQ\\DB\\contaminants.fasta",config);
// fdb.create_db_from_fasta("C:\\Work\\msms5\\PepNovoHQ\\DB\\Homo_sapiens.NCBI35.dec.pep.fa",config);
// fdb.create_db_from_fasta("C:\\Work\\msms5\\PepNovoHQ\\DB\\fa50mb.fa",config,true,5,6);
// fdb.create_db_from_fasta("C:\\Work\\msms5\\PepNovoHQ\\DB\\homo_pos.fa",config);
// fdb.print_protein_names();
// fdb.write_FastaDB("C:\\Work\\msms5\\PepNovoHQ\\DB\\h**o.dat");
// fdb.read_FastaDB("C:\\Work\\msms5\\PepNovoHQ\\DB\\h**o.dat",config);
// fdb.read_FastaDB("C:\\Work\\msms5\\PepNovoHQ\\DB\\qqq.dat",config);
// fdb.read_FastaDB("C:\\Work\\msms5\\PepNovoHQ\\DB\\fa500k.dat",config);
// fdb.print_protein_names();
// fdb.write_FastaDB("C:\\Work\\msms5\\PepNovoHQ\\DB\\fa5--0mb.dat");
// exit(0);
// fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\CAD_seq_list.txt");
// fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\CAD_u_list.txt");
fm.init_from_list_file(config,"C:\\Work\\msms5\\lists\\CAD_376.txt");
// make_bin_histograms(fm,config);
// calc_avg_rand(fm,config);
// explore_fragment_set(fm,config);
// show_occurences(fm,config,"p-25.0");
// find_internal_offset_counts(fm,config);
// make_frag_rank_histogram(fm,config);
// exit(0);
// internal_fragment_annotation(fm,model.get_config());
// find_internal_offset_counts(fm,model.get_config());
// exit(0);
FileSet fs;
fs.select_all_files(fm);
fstream ofs("true_seq.txt",ios::out);
fs.make_fasta_from_file_seqs(fm,config,45,ofs);
// dbsm.train_regression_models(fm,fdb,12,&model);
// analyze_cad_spec(fm,config);
// make_rank_histograms(fm,&model);
// dbsm.read_model("DBS.txt");
// CAD_histograms(fm,&model,fdb,&dbsm);
// rand_db_stats(fm,&model,&dbsm);
// db_search_stats(fm,&model,&dbsm);
// neg_db_search_stats(fm,&model,&dbsm);
// CAD_edge_stats(fm,&model);
// CAD_denovo_histograms(fm,&model,fdb);
// CAD_edge_stats(fm,&model);
// collect_denovo_statistics(fm,&model);
exit(0);
// int *arr;
// int t_size;
// read_fasta("cshort.fasta",&arr,&t_size,&config);
// read_fasta("C:\\Work\\msms4\\PepNovo\\Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,config);
read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config);
read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config);
read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config);
read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config);
read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config);
read_fasta("Homo_sapiens.NCBI35.dec.pep.fa",&arr,&t_size,&config);
// homeomorphic_levels(&config,arr,t_size,1000.0,1001,"hp_res.txt");
config->set_tolerance(0.0075);
// full_exp(config,0,arr,t_size,"hp_res_dis_a0.txt");
// full_exp(config,1,arr,t_size,"hp_res_dis_a1.txt");
// full_exp(config,2,arr,t_size,"hp_res_dis_a2.txt");
// full_exp(config,3,arr,t_size,"hp_res_dis_a3.txt");
// full_exp(config,4,arr,t_size,"hp_res_dis_a4.txt");
// homeomorphic_exp3(&config,100);
// exit(0);
// config.print_supported_PTMs();
// config.print_session_aas();
string p;
// ifstream fs("D:\\msms4\\PepNovo\\test\\C25A19_IP_01.mgf",ios::in);
// ifstream fs("D:\\msms4\\PepNovo\\test\\m280.mgf",ios::in);
// fm.init_from_mgf(&config,"D:\\msms4\\PepNovo\\test\\m280.mgf");
// fm.init_from_mgf(&config,"D:\\msms4\\PepNovo\\mgf_2600.2.mgf");
// fm.init_from_list_file(&config,"D:\\msms4\\lists\\unique_good2.txt");
// fm.init_from_list_file(&config,"D:\\msms4\\lists\\short2.txt");
// fm.init_from_list_file(&config,"D:\\Data2\\ikkb_unmod_list.txt");
// rand_seed(1111);
rand_seed(1426347);
// model.read_model("ESI_RANKS");
// model.get_config()->add_selected_PTMs("C+57");
// SpectrumScore sqs;
// sqs.learn_score_params(&model,"D:\\msms4\\lists\\sqs2_short.txt",
// "D:\\msms4\\lists\\sqs_neg1.txt");
// exit(0);
// model.set_model_name(string("ESI2"));
// random_peak_match_exp(model.get_config(),fm,800,1200,10000000);
// model.print_joint_scores();
// me_reg_exp();
// me_exp();
// exit(0);
// fm.init_from_mgf(model.get_config(),"c:\\work\\msms4\\PepNovo\\test\\m280.mgf");
// fm.init_from_mgf(model.get_config(),"c:\\work\\msms4\\PepNovo\\hpep.mgf");
fm.init_from_list_file(config,"c:\\Work\\msms4\\lists\\efast2.txt");
// fm.init_from_list_file(&config,"D:\\msms4\\lists\\charge2.txt");
//m.init_from_list_file(model.get_config(),"C:\\Work\\msms4\\PepNovo\\lll.txt");
//m.init_from_list_file(model.get_config(),"D:\\msms4\\lists\\l1.txt");
*/
return 0;
}
