void MapAlignmentTransformer::transformRetentionTimes(
MSExperiment<>& msexp, const TransformationDescription& trafo,
bool store_original_rt)
{
msexp.clearRanges();
// Transform spectra
for (MSExperiment<>::iterator mse_iter = msexp.begin();
mse_iter != msexp.end(); ++mse_iter)
{
double rt = mse_iter->getRT();
if (store_original_rt) storeOriginalRT_(*mse_iter, rt);
mse_iter->setRT(trafo.apply(rt));
}
// Also transform chromatograms
for (Size i = 0; i < msexp.getNrChromatograms(); ++i)
{
MSChromatogram<ChromatogramPeak>& chromatogram = msexp.getChromatogram(i);
vector<double> original_rts;
if (store_original_rt) original_rts.reserve(chromatogram.size());
for (Size j = 0; j < chromatogram.size(); j++)
{
double rt = chromatogram[j].getRT();
if (store_original_rt) original_rts.push_back(rt);
chromatogram[j].setRT(trafo.apply(rt));
}
if (store_original_rt && !chromatogram.metaValueExists("original_rt"))
{
chromatogram.setMetaValue("original_rt", original_rts);
}
}
msexp.updateRanges();
}
ExitCodes main_(int, const char **)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
in = getStringOption_("in");
out = getStringOption_("out");
String process_option = getStringOption_("processOption");
Param filter_param = getParam_().copy("algorithm:", true);
writeDebug_("Parameters passed to filter", filter_param, 3);
SavitzkyGolayFilter sgolay;
sgolay.setLogType(log_type_);
sgolay.setParameters(filter_param);
if (process_option == "lowmemory")
{
return doLowMemAlgorithm(sgolay);
}
//-------------------------------------------------------------
// loading input
//-------------------------------------------------------------
MzMLFile mz_data_file;
mz_data_file.setLogType(log_type_);
MSExperiment<Peak1D> exp;
mz_data_file.load(in, exp);
if (exp.empty() && exp.getChromatograms().size() == 0)
{
LOG_WARN << "The given file does not contain any conventional peak data, but might"
" contain chromatograms. This tool currently cannot handle them, sorry.";
return INCOMPATIBLE_INPUT_DATA;
}
//check for peak type (profile data required)
if (!exp.empty() && PeakTypeEstimator().estimateType(exp[0].begin(), exp[0].end()) == SpectrumSettings::PEAKS)
{
writeLog_("Warning: OpenMS peak type estimation indicates that this is not profile data!");
}
//check if spectra are sorted
for (Size i = 0; i < exp.size(); ++i)
{
if (!exp[i].isSorted())
{
writeLog_("Error: Not all spectra are sorted according to peak m/z positions. Use FileFilter to sort the input!");
return INCOMPATIBLE_INPUT_DATA;
}
}
//check if chromatograms are sorted
for (Size i = 0; i < exp.getChromatograms().size(); ++i)
{
if (!exp.getChromatogram(i).isSorted())
{
writeLog_("Error: Not all chromatograms are sorted according to peak m/z positions. Use FileFilter to sort the input!");
return INCOMPATIBLE_INPUT_DATA;
}
}
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
sgolay.filterExperiment(exp);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(exp, getProcessingInfo_(DataProcessing::SMOOTHING));
mz_data_file.store(out, exp);
return EXECUTION_OK;
}