ExitCodes main_(int , const char**)
{
String in = getStringOption_("in");
String out_meta = getStringOption_("out");
String in_cached = in + ".cached";
String out_cached = out_meta + ".cached";
bool convert_back = getFlag_("convert_back");
if (!convert_back)
{
MapType exp;
CachedmzML cacher;
MzMLFile f;
cacher.setLogType(log_type_);
f.setLogType(log_type_);
f.load(in,exp);
cacher.writeMemdump(exp, out_cached);
DataProcessing dp;
std::set<DataProcessing::ProcessingAction> actions;
actions.insert(DataProcessing::FORMAT_CONVERSION);
dp.setProcessingActions(actions);
dp.setMetaValue("cached_data", "true");
for (Size i=0; i<exp.size(); ++i)
{
exp[i].getDataProcessing().push_back(dp);
}
std::vector<MSChromatogram<ChromatogramPeak> > chromatograms = exp.getChromatograms();
for (Size i=0; i<chromatograms.size(); ++i)
{
chromatograms[i].getDataProcessing().push_back(dp);
}
exp.setChromatograms(chromatograms);
cacher.writeMetadata(exp, out_meta);
}
else
{
MzMLFile f;
MapType meta_exp;
CachedmzML cacher;
MapType exp_reading;
cacher.setLogType(log_type_);
f.setLogType(log_type_);
f.load(in,meta_exp);
cacher.readMemdump(exp_reading, in_cached);
std::cout << " read back, got " << exp_reading.size() << " spectra " << exp_reading.getChromatograms().size() << " chromats " << std::endl;
{
for (Size i=0; i<meta_exp.size(); ++i)
{
for (Size j = 0; j < meta_exp[i].getDataProcessing().size(); j++)
{
DataProcessing& dp = meta_exp[i].getDataProcessing()[j];
if (dp.metaValueExists("cached_data"))
{
dp.removeMetaValue("cached_data");
}
}
}
std::vector<MSChromatogram<ChromatogramPeak> > chromatograms = meta_exp.getChromatograms();
for (Size i=0; i<chromatograms.size(); ++i)
{
for (Size j = 0; j < chromatograms[i].getDataProcessing().size(); j++)
{
DataProcessing& dp = chromatograms[i].getDataProcessing()[j];
if (dp.metaValueExists("cached_data"))
{
dp.removeMetaValue("cached_data");
}
}
}
}
if (meta_exp.size() != exp_reading.size())
{
std::cerr << " Both experiments need to have the same size!";
}
for (Size i=0; i<exp_reading.size(); ++i)
{
for (Size j = 0; j < exp_reading[i].size(); j++)
{
meta_exp[i].push_back(exp_reading[i][j]);
}
}
std::vector<MSChromatogram<ChromatogramPeak> > chromatograms = exp_reading.getChromatograms();
std::vector<MSChromatogram<ChromatogramPeak> > old_chromatograms = meta_exp.getChromatograms();
for (Size i=0; i<chromatograms.size(); ++i)
{
for (Size j = 0; j < chromatograms[i].size(); j++)
{
old_chromatograms[i].push_back(chromatograms[i][j]);
}
}
meta_exp.setChromatograms(old_chromatograms);
f.store(out_meta,meta_exp);
}
return EXECUTION_OK;
}
void ChromatogramExtractor::return_chromatogram(std::vector< OpenSwath::ChromatogramPtr > & chromatograms,
std::vector< ChromatogramExtractor::ExtractionCoordinates > & coordinates,
OpenMS::TargetedExperiment & transition_exp_used, SpectrumSettings settings,
std::vector<OpenMS::MSChromatogram<> > & output_chromatograms, bool ms1) const
{
typedef std::map<String, const ReactionMonitoringTransition* > TransitionMapType;
TransitionMapType trans_map;
for (Size i = 0; i < transition_exp_used.getTransitions().size(); i++)
{
trans_map[transition_exp_used.getTransitions()[i].getNativeID()] = &transition_exp_used.getTransitions()[i];
}
for (Size i = 0; i < chromatograms.size(); i++)
{
const OpenSwath::ChromatogramPtr & chromptr = chromatograms[i];
const ChromatogramExtractor::ExtractionCoordinates & coord = coordinates[i];
TargetedExperiment::Peptide pep;
OpenMS::ReactionMonitoringTransition transition;
OpenMS::MSChromatogram<> chrom;
// copy data
OpenSwathDataAccessHelper::convertToOpenMSChromatogram(chrom, chromptr);
chrom.setNativeID(coord.id);
// Create precursor and set
// 1) the target m/z
// 2) the isolation window (upper/lower)
// 3) the peptide sequence
Precursor prec;
if (ms1)
{
pep = transition_exp_used.getPeptideByRef(coord.id);
prec.setMZ(coord.mz);
chrom.setChromatogramType(ChromatogramSettings::BASEPEAK_CHROMATOGRAM);
}
else
{
transition = (*trans_map[coord.id]);
pep = transition_exp_used.getPeptideByRef(transition.getPeptideRef());
prec.setMZ(transition.getPrecursorMZ());
if (settings.getPrecursors().size() > 0)
{
prec.setIsolationWindowLowerOffset(settings.getPrecursors()[0].getIsolationWindowLowerOffset());
prec.setIsolationWindowUpperOffset(settings.getPrecursors()[0].getIsolationWindowUpperOffset());
}
// Create product and set its m/z
Product prod;
prod.setMZ(transition.getProductMZ());
chrom.setProduct(prod);
chrom.setChromatogramType(ChromatogramSettings::SELECTED_REACTION_MONITORING_CHROMATOGRAM);
}
prec.setMetaValue("peptide_sequence", pep.sequence);
chrom.setPrecursor(prec);
// Set the rest of the meta-data
chrom.setInstrumentSettings(settings.getInstrumentSettings());
chrom.setAcquisitionInfo(settings.getAcquisitionInfo());
chrom.setSourceFile(settings.getSourceFile());
for (Size i = 0; i < settings.getDataProcessing().size(); ++i)
{
DataProcessing dp = settings.getDataProcessing()[i];
dp.setMetaValue("performed_on_spectra", "true");
chrom.getDataProcessing().push_back(dp);
}
output_chromatograms.push_back(chrom);
}
}
