PILISScoring* ptr = 0;
PILISScoring* nullPointer = 0;
String filename(OPENMS_GET_TEST_DATA_PATH("IDFilter_test2.idXML"));
START_SECTION(PILISScoring())
ptr = new PILISScoring();
TEST_NOT_EQUAL(ptr, nullPointer)
END_SECTION
START_SECTION(~PILISScoring())
delete ptr;
END_SECTION
ptr = new PILISScoring();
START_SECTION(PILISScoring(const PILISScoring& source))
PILISScoring copy(*ptr);
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
END_SECTION
START_SECTION(PILISScoring& operator = (const PILISScoring& source))
PILISScoring copy;
copy = *ptr;
TEST_EQUAL(copy.getParameters(), ptr->getParameters())
END_SECTION
START_SECTION(void getScores(std::vector<PeptideIdentification>& ids))
vector<PeptideIdentification> ids;
vector<ProteinIdentification> prot_ids;
String document_id;
IdXMLFile().load(filename, prot_ids, ids, document_id);
ptr->getScores(ids);
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
//input/output files
String in(getStringOption_("in"));
String out(getStringOption_("out"));
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
RichPeakMap exp;
MzMLFile f;
f.setLogType(log_type_);
f.load(in, exp);
writeDebug_("Data set contains " + String(exp.size()) + " spectra", 1);
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
writeDebug_("Reading model file", 2);
// create model an set the given options
PILISModel * model = new PILISModel();
model->readFromFile(getStringOption_("model_file"));
Param model_param(model->getParameters());
model_param.setValue("upper_mz", getDoubleOption_("model:upper_mz"));
model_param.setValue("lower_mz", getDoubleOption_("model:lower_mz"));
model_param.setValue("charge_directed_threshold", getDoubleOption_("model:charge_directed_threshold"));
model_param.setValue("charge_remote_threshold", getDoubleOption_("model:charge_remote_threshold"));
//model_param.setValue("min_main_ion_intensity", getDoubleOption_("model:min_main_ion_intensity"));
//model_param.setValue("min_loss_ion_intensity", getDoubleOption_("model:min_loss_ion_intensity"));
model_param.setValue("min_y_ion_intensity", getDoubleOption_("model:min_y_ion_intensity"));
model_param.setValue("min_b_ion_intensity", getDoubleOption_("model:min_b_ion_intensity"));
model_param.setValue("min_a_ion_intensity", getDoubleOption_("model:min_a_ion_intensity"));
model_param.setValue("min_y_loss_intensity", getDoubleOption_("model:min_y_loss_intensity"));
model_param.setValue("min_b_loss_intensity", getDoubleOption_("model:min_b_loss_intensity"));
model_param.setValue("charge_loss_factor", getDoubleOption_("model:charge_loss_factor"));
model_param.setValue("visible_model_depth", getIntOption_("model:visible_model_depth"));
model_param.setValue("model_depth", getIntOption_("model:model_depth"));
model_param.setValue("fixed_modifications", getStringOption_("fixed_modifications"));
model->setParameters(model_param);
writeDebug_("Reading sequence db", 2);
// create sequence db
SuffixArrayPeptideFinder * sapf = new SuffixArrayPeptideFinder(getStringOption_("peptide_db_file"), "trypticCompressed");
sapf->setTolerance(getDoubleOption_("precursor_mass_tolerance"));
sapf->setNumberOfModifications(0);
sapf->setUseTags(false);
//exp.resize(50); // TODO
UInt max_charge(3), min_charge(1); // TODO
vector<double> pre_weights;
for (RichPeakMap::Iterator it = exp.begin(); it != exp.end(); ++it)
{
double pre_weight(it->getPrecursors()[0].getMZ());
for (Size z = min_charge; z <= max_charge; ++z)
{
pre_weights.push_back((pre_weight * (double)z) - (double)z);
}
}
sort(pre_weights.begin(), pre_weights.end());
cerr << "Getting candidates from SA...";
vector<vector<pair<pair<String, String>, String> > > candidates;
sapf->getCandidates(candidates, pre_weights);
cerr << "done" << endl;
delete sapf;
map<double, vector<pair<pair<String, String>, String> > > sorted_candidates;
UInt count(0);
for (Size count = 0; count != candidates.size(); ++count)
{
sorted_candidates[pre_weights[count]] = candidates[count];
}
candidates.clear();
// create ProteinIdentification and set the options
PILISIdentification PILIS_id;
PILIS_id.setModel(model);
Param id_param(PILIS_id.getParameters());
id_param.setValue("precursor_mass_tolerance", getDoubleOption_("precursor_mass_tolerance"));
id_param.setValue("max_candidates", getIntOption_("max_pre_candidates"));
// disable evalue scoring, this is done separately to allow for a single id per spectrum
id_param.setValue("use_evalue_scoring", 0);
id_param.setValue("fixed_modifications", getStringOption_("fixed_modifications"));
PILIS_id.setParameters(id_param);
vector<PeptideIdentification> ids;
// perform the ProteinIdentification of the given spectra
UInt no(0);
for (RichPeakMap::Iterator it = exp.begin(); it != exp.end(); ++it, ++no)
{
if (it->getMSLevel() == 0)
{
writeLog_("Warning: MSLevel is 0, assuming MSLevel 2");
it->setMSLevel(2);
}
if (it->getMSLevel() == 2)
{
writeDebug_(String(no) + "/" + String(exp.size()), 1);
PeptideIdentification id;
map<String, UInt> cand;
for (UInt z = min_charge; z <= max_charge; ++z)
{
double pre_weight = (it->getPrecursors()[0].getMZ() * (double)z) - (double)z;
for (vector<pair<pair<String, String>, String> >::const_iterator cit = sorted_candidates[pre_weight].begin(); cit != sorted_candidates[pre_weight].end(); ++cit)
{
String seq = cit->first.second;
if (seq.size() > 39)
{
continue;
}
UInt num_cleavages_sites(0);
for (Size k = 0; k != seq.size(); ++k)
{
if (k != seq.size() - 1)
{
if ((seq[k] == 'K' || seq[k] == 'R') && seq[k + 1] != 'P')
{
++num_cleavages_sites;
}
}
}
if (num_cleavages_sites > 1)
{
continue;
}
cand[seq] = z;
}
}
cerr << "#cand=" << cand.size() << endl;
PILIS_id.getIdentification(cand, id, *it);
id.setMetaValue("RT", it->getRT());
id.setMetaValue("MZ", it->getPrecursors()[0].getMZ());
ids.push_back(id);
if (!id.getHits().empty())
{
cerr << it->getPrecursors()[0].getMZ() << " " << AASequence(id.getHits().begin()->getSequence()).getAverageWeight() << endl;
writeDebug_(id.getHits().begin()->getSequence().toString() + " (z=" + id.getHits().begin()->getCharge() + "), score=" + String(id.getHits().begin()->getScore()), 10);
}
}
}
// perform the PILIS scoring to the spectra
if (!getFlag_("scoring:do_not_use_evalue_scoring"))
{
PILISScoring scoring;
Param scoring_param(scoring.getParameters());
scoring_param.setValue("use_local_scoring", (int)getFlag_("scoring:use_local_scoring"));
scoring_param.setValue("survival_function_bin_size", getIntOption_("scoring:survival_function_bin_size"));
scoring_param.setValue("global_linear_fitting_threshold", getDoubleOption_("scoring:global_linear_fitting_threshold"));
scoring_param.setValue("local_linear_fitting_threshold", getDoubleOption_("scoring:local_linear_fitting_threshold"));
scoring.setParameters(scoring_param);
scoring.getScores(ids);
}
// write the result to the IdentificationData structure for the storing
UInt max_candidates = getIntOption_("max_candidates");
for (Size i = 0; i != ids.size(); ++i)
{
if (ids[i].getHits().size() > max_candidates)
{
vector<PeptideHit> hits = ids[i].getHits();
hits.resize(max_candidates);
ids[i].setHits(hits);
}
}
delete model;
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
DateTime now;
now.now();
String date_string;
//now.get(date_string); // @todo Fix it (Andreas)
String identifier("PILIS_" + date_string);
//UInt count(0);
count = 0;
for (RichPeakMap::ConstIterator it = exp.begin(); it != exp.end(); ++it)
{
if (it->getMSLevel() == 2)
{
ids[count].setMetaValue("RT", it->getRT());
ids[count].setMetaValue("MZ", it->getPrecursors()[0].getMZ());
ids[count].setIdentifier(identifier);
ids[count++].setHigherScoreBetter(false);
}
}
// search parameters
ProteinIdentification::SearchParameters search_parameters;
search_parameters.db = getStringOption_("peptide_db_file");
search_parameters.db_version = "";
search_parameters.taxonomy = "";
//search_parameters.charges = getStringOption_("charges");
search_parameters.mass_type = ProteinIdentification::MONOISOTOPIC;
vector<String> fixed_mods;
getStringOption_("fixed_modifications").split(',', fixed_mods);
search_parameters.fixed_modifications = fixed_mods;
search_parameters.enzyme = ProteinIdentification::TRYPSIN;
search_parameters.missed_cleavages = 1;
search_parameters.peak_mass_tolerance = getDoubleOption_("peak_mass_tolerance");
search_parameters.precursor_tolerance = getDoubleOption_("precursor_mass_tolerance");
ProteinIdentification protein_identification;
protein_identification.setDateTime(now);
protein_identification.setSearchEngine("PILIS");
protein_identification.setSearchEngineVersion("beta");
protein_identification.setSearchParameters(search_parameters);
protein_identification.setIdentifier(identifier);
vector<ProteinIdentification> protein_identifications;
protein_identifications.push_back(protein_identification);
IdXMLFile().store(out, protein_identifications, ids);
return EXECUTION_OK;
}