ExitCodes main_(int, const char **)
{
String in = getStringOption_("in");
String out = getStringOption_("out");
String tr_file = getStringOption_("tr");
bool force = getFlag_("force");
boost::shared_ptr<PeakMap > exp ( new PeakMap );
MzMLFile mzmlfile;
mzmlfile.setLogType(log_type_);
mzmlfile.load(in, *exp);
TargetedExpType transition_exp;
TraMLFile().load(tr_file, transition_exp);
FeatureMap output;
OpenSwath::SpectrumAccessPtr input = SimpleOpenMSSpectraFactory::getSpectrumAccessOpenMSPtr(exp);
run_(input, output, transition_exp, force);
output.ensureUniqueId();
StringList ms_runs;
exp->getPrimaryMSRunPath(ms_runs);
output.setPrimaryMSRunPath(ms_runs);
FeatureXMLFile().store(out, output);
return EXECUTION_OK;
}
ExitCodes main_(int, const char**) override
{
//input file names
String in = getStringOption_("in");
String out = getStringOption_("out");
String out_mzq = getStringOption_("out_mzq");
//prevent loading of fragment spectra
PeakFileOptions options;
options.setMSLevels(vector<Int>(1, 1));
//reading input data
MzMLFile f;
f.getOptions() = options;
f.setLogType(log_type_);
PeakMap exp;
f.load(in, exp);
exp.updateRanges();
if (exp.getSpectra().empty())
{
throw OpenMS::Exception::FileEmpty(__FILE__, __LINE__, __FUNCTION__, "Error: No MS1 spectra in input file.");
}
// determine type of spectral data (profile or centroided)
SpectrumSettings::SpectrumType spectrum_type = exp[0].getType();
if (spectrum_type == SpectrumSettings::PROFILE)
{
if (!getFlag_("force"))
{
throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, __FUNCTION__, "Error: Profile data provided but centroided spectra expected. To enforce processing of the data set the -force flag.");
}
}
//load seeds
FeatureMap seeds;
if (getStringOption_("seeds") != "")
{
FeatureXMLFile().load(getStringOption_("seeds"), seeds);
}
//setup of FeatureFinder
FeatureFinder ff;
ff.setLogType(log_type_);
// A map for the resulting features
FeatureMap features;
StringList ms_runs;
exp.getPrimaryMSRunPath(ms_runs);
features.setPrimaryMSRunPath(ms_runs);
// get parameters specific for the feature finder
Param feafi_param = getParam_().copy("algorithm:", true);
writeDebug_("Parameters passed to FeatureFinder", feafi_param, 3);
// Apply the feature finder
ff.run(FeatureFinderAlgorithmPicked::getProductName(), exp, features, feafi_param, seeds);
features.applyMemberFunction(&UniqueIdInterface::setUniqueId);
// DEBUG
if (debug_level_ > 10)
{
FeatureMap::Iterator it;
for (it = features.begin(); it != features.end(); ++it)
{
if (!it->isMetaEmpty())
{
vector<String> keys;
it->getKeys(keys);
LOG_INFO << "Feature " << it->getUniqueId() << endl;
for (Size i = 0; i < keys.size(); i++)
{
LOG_INFO << " " << keys[i] << " = " << it->getMetaValue(keys[i]) << endl;
}
}
}
}
//-------------------------------------------------------------
// writing files
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(features, getProcessingInfo_(DataProcessing::QUANTITATION));
// write features to user specified output file
FeatureXMLFile map_file;
// Remove detailed convex hull information and subordinate features
// (unless requested otherwise) to reduce file size of feature files
// unless debugging is turned on.
if (debug_level_ < 5)
{
FeatureMap::Iterator it;
for (it = features.begin(); it != features.end(); ++it)
{
it->getConvexHull().expandToBoundingBox();
for (Size i = 0; i < it->getConvexHulls().size(); ++i)
{
it->getConvexHulls()[i].expandToBoundingBox();
}
it->getSubordinates().clear();
}
}
map_file.store(out, features);
if (!out_mzq.trim().empty())
{
std::vector<DataProcessing> tmp;
for (Size i = 0; i < exp[0].getDataProcessing().size(); i++)
{
tmp.push_back(*exp[0].getDataProcessing()[i].get());
}
MSQuantifications msq(features, exp.getExperimentalSettings(), tmp );
msq.assignUIDs();
MzQuantMLFile file;
file.store(out_mzq, msq);
}
return EXECUTION_OK;
}