void OfflinePrecursorIonSelection::createProteinSequenceBasedLPInclusionList(String include, String rt_model_file, String pt_model_file,
FeatureMap & precursors)
{
PrecursorIonSelectionPreprocessing pisp;
Param pisp_param = pisp.getParameters();
pisp_param.setValue("store_peptide_sequences", "true");
pisp.setParameters(pisp_param);
pisp.dbPreprocessing(include, rt_model_file, pt_model_file, false);
// std::cout << "now learn rt probabilities"<<std::endl;
//pisp.learnRTProbabilities(f_map,rt_model,0.5);
// pisp.setGaussianParameters(3,-1);
PSLPFormulation ilp_wrapper;
Param opis_param = param_.copy("ProteinBasedInclusion:", true);
opis_param.remove("max_list_size");
ilp_wrapper.setParameters(opis_param);
ilp_wrapper.setLPSolver(solver_);
// std::cout << "nun die inclusion liste erstellen"<<std::endl;
// std::cout << param_.getValue("ms2_spectra_per_rt_bin") <<std::endl;
// std::cout << param_.getValue("ProteinBasedInclusion:max_list_size") <<std::endl;
ilp_wrapper.createAndSolveILPForInclusionListCreation(pisp, param_.getValue("ms2_spectra_per_rt_bin"),
param_.getValue("ProteinBasedInclusion:max_list_size"), precursors, true); //,960.,3840.,30.);
}
PrecursorIonSelectionPreprocessing* ptr = nullptr;
PrecursorIonSelectionPreprocessing* nullPointer = nullptr;
START_SECTION(PrecursorIonSelectionPreprocessing())
ptr = new PrecursorIonSelectionPreprocessing();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION(~PrecursorIonSelectionPreprocessing())
delete ptr;
END_SECTION
ptr = new PrecursorIonSelectionPreprocessing();
START_SECTION(PrecursorIonSelectionPreprocessing(const PrecursorIonSelectionPreprocessing &source))
PrecursorIonSelectionPreprocessing copy(*ptr);
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
END_SECTION
START_SECTION(PrecursorIonSelectionPreprocessing& operator=(const PrecursorIonSelectionPreprocessing &source))
PrecursorIonSelectionPreprocessing copy;
copy = *ptr;
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
END_SECTION
Param param;
param.setValue("precursor_mass_tolerance",0.9);
param.setValue("precursor_mass_tolerance_unit","Da");
param.setValue("missed_cleavages",0);
std::string tmp_filename;
NEW_TMP_FILE(tmp_filename);
param.setValue("preprocessed_db_path",tmp_filename);