void SeedListGenerator::convertSeedList(const SeedList& seeds,
FeatureMap& features)
{
features.clear(true); // "true" should really be a default value here...
Size counter = 0;
for (SeedList::const_iterator seed_it = seeds.begin();
seed_it != seeds.end(); ++seed_it, ++counter)
{
Feature feature;
feature.setRT(seed_it->getX());
feature.setMZ(seed_it->getY());
feature.setUniqueId(counter);
features.push_back(feature);
}
// // assign unique ids:
// features.applyMemberFunction(&UniqueIdInterface::setUniqueId);
}
void FeatureFinder::run(const String& algorithm_name, PeakMap& input_map, FeatureMap& features, const Param& param, const FeatureMap& seeds)
{
// Nothing to do if there is no data
if ((algorithm_name != "mrm" && input_map.empty()) || (algorithm_name == "mrm" && input_map.getChromatograms().empty()))
{
features.clear(true);
return;
}
// check input
{
// We need updated ranges => check number of peaks
if (algorithm_name != "mrm" && input_map.getSize() == 0)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "FeatureFinder needs updated ranges on input map. Aborting.");
}
// We need MS1 data only => check levels
if (algorithm_name != "mrm" && (input_map.getMSLevels().size() != 1 || input_map.getMSLevels()[0] != 1))
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "FeatureFinder can only operate on MS level 1 data. Please do not use MS/MS data. Aborting.");
}
//Check if the peaks are sorted according to m/z
if (!input_map.isSorted(true))
{
LOG_WARN << "Input map is not sorted by RT and m/z! This is done now, before applying the algorithm!" << std::endl;
input_map.sortSpectra(true);
input_map.sortChromatograms(true);
}
for (Size s = 0; s < input_map.size(); ++s)
{
if (input_map[s].empty())
continue;
if (input_map[s][0].getMZ() < 0)
{
throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "FeatureFinder can only operate on spectra that contain peaks with positive m/z values. Filter the data accordingly beforehand! Aborting.");
}
}
}
// initialize
if (algorithm_name != "mrm" && algorithm_name != "centroided")
{
// Resize peak flag vector
flags_.resize(input_map.size());
for (Size i = 0; i < input_map.size(); ++i)
{
flags_[i].assign(input_map[i].size(), UNUSED);
}
}
// do the work
if (algorithm_name != "none")
{
FeatureFinderAlgorithm* algorithm = Factory<FeatureFinderAlgorithm>::create(algorithm_name);
algorithm->setParameters(param);
algorithm->setData(input_map, features, *this);
algorithm->setSeeds(seeds);
algorithm->run();
delete(algorithm);
}
if (algorithm_name != "mrm") // mrm works on chromatograms; the next section is only for conventional data
{
//report RT apex spectrum index and native ID for each feature
for (Size i = 0; i < features.size(); ++i)
{
//index
Size spectrum_index = input_map.RTBegin(features[i].getRT()) - input_map.begin();
features[i].setMetaValue("spectrum_index", spectrum_index);
//native id
if (spectrum_index < input_map.size())
{
String native_id = input_map[spectrum_index].getNativeID();
features[i].setMetaValue("spectrum_native_id", native_id);
}
else
{
/// @todo that happens sometimes using IsotopeWaveletFeatureFinder (Rene, Marc, Andreas, Clemens)
std::cerr << "FeatureFinderAlgorithm_impl, line=" << __LINE__ << "; FixMe this cannot be, but happens" << std::endl;
}
}
}
}