void QuantitativeExperimentalDesign::mergeConsensusMaps_(ConsensusMap & out, const String & experiment, StringList & file_paths)
{
ConsensusMap map;
LOG_INFO << "Merge consensus maps: " << endl;
UInt counter = 1;
for (StringList::Iterator file_it = file_paths.begin(); file_it != file_paths.end(); ++file_it, ++counter)
{
//load should clear the map
ConsensusXMLFile().load(*file_it, map);
for (ConsensusMap::iterator it = map.begin(); it != map.end(); ++it)
{
it->setMetaValue("experiment", DataValue(experiment));
}
out += map;
}
LOG_INFO << endl;
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
//file list
StringList file_list = getStringList_("in");
//file type
FileHandler fh;
FileTypes::Type force_type;
if (getStringOption_("in_type").size() > 0)
{
force_type = FileTypes::nameToType(getStringOption_("in_type"));
}
else
{
force_type = fh.getType(file_list[0]);
}
//output file names and types
String out_file = getStringOption_("out");
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
bool annotate_file_origin = getFlag_("annotate_file_origin");
if (force_type == FileTypes::FEATUREXML)
{
FeatureMap<> out;
for (Size i = 0; i < file_list.size(); ++i)
{
FeatureMap<> map;
FeatureXMLFile fh;
fh.load(file_list[i], map);
if (annotate_file_origin)
{
for (FeatureMap<>::iterator it = map.begin(); it != map.end(); ++it)
{
it->setMetaValue("file_origin", DataValue(file_list[i]));
}
}
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
FeatureXMLFile f;
f.store(out_file, out);
}
else if (force_type == FileTypes::CONSENSUSXML)
{
ConsensusMap out;
ConsensusXMLFile fh;
fh.load(file_list[0], out);
//skip first file
for (Size i = 1; i < file_list.size(); ++i)
{
ConsensusMap map;
ConsensusXMLFile fh;
fh.load(file_list[i], map);
if (annotate_file_origin)
{
for (ConsensusMap::iterator it = map.begin(); it != map.end(); ++it)
{
it->setMetaValue("file_origin", DataValue(file_list[i]));
}
}
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
ConsensusXMLFile f;
f.store(out_file, out);
}
else if (force_type == FileTypes::TRAML)
{
TargetedExperiment out;
for (Size i = 0; i < file_list.size(); ++i)
{
TargetedExperiment map;
TraMLFile fh;
fh.load(file_list[i], map);
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
Software software;
software.setName("FileMerger");
software.setVersion(VersionInfo::getVersion());
out.addSoftware(software);
TraMLFile f;
f.store(out_file, out);
}
else
{
// we might want to combine different types, thus we only
// query in_type (which applies to all files)
// and not the suffix or content of a single file
force_type = FileTypes::nameToType(getStringOption_("in_type"));
//rt
bool rt_auto_number = getFlag_("raw:rt_auto");
bool rt_filename = getFlag_("raw:rt_filename");
bool rt_custom = false;
DoubleList custom_rts = getDoubleList_("raw:rt_custom");
if (custom_rts.size() != 0)
{
rt_custom = true;
if (custom_rts.size() != file_list.size())
{
writeLog_("Custom retention time list must have as many elements as there are input files!");
printUsage_();
return ILLEGAL_PARAMETERS;
}
}
//ms level
bool user_ms_level = getFlag_("raw:user_ms_level");
MSExperiment<> out;
out.reserve(file_list.size());
UInt rt_auto = 0;
UInt native_id = 0;
std::vector<MSChromatogram<ChromatogramPeak> > all_chromatograms;
for (Size i = 0; i < file_list.size(); ++i)
{
String filename = file_list[i];
//load file
MSExperiment<> in;
fh.loadExperiment(filename, in, force_type, log_type_);
if (in.empty() && in.getChromatograms().empty())
{
writeLog_(String("Warning: Empty file '") + filename + "'!");
continue;
}
out.reserve(out.size() + in.size());
//warn if custom RT and more than one scan in input file
if (rt_custom && in.size() > 1)
{
writeLog_(String("Warning: More than one scan in file '") + filename + "'! All scans will have the same retention time!");
}
for (MSExperiment<>::const_iterator it2 = in.begin(); it2 != in.end(); ++it2)
{
//handle rt
Real rt_final = it2->getRT();
if (rt_auto_number)
{
rt_final = ++rt_auto;
}
else if (rt_custom)
{
rt_final = custom_rts[i];
}
else if (rt_filename)
{
if (!filename.hasSubstring("rt"))
{
writeLog_(String("Warning: cannot guess retention time from filename as it does not contain 'rt'"));
}
for (Size i = 0; i < filename.size(); ++i)
{
if (filename[i] == 'r' && ++i != filename.size() && filename[i] == 't' && ++i != filename.size() && isdigit(filename[i]))
{
String rt;
while (i != filename.size() && (filename[i] == '.' || isdigit(filename[i])))
{
rt += filename[i++];
}
if (rt.size() > 0)
{
// remove dot from rt3892.98.dta
// ^
if (rt[rt.size() - 1] == '.')
{
// remove last character
rt.erase(rt.end() - 1);
}
}
try
{
float tmp = rt.toFloat();
rt_final = tmp;
}
catch (Exception::ConversionError)
{
writeLog_(String("Warning: cannot convert the found retention time in a value '" + rt + "'."));
}
}
}
}
// none of the rt methods were successful
if (rt_final == -1)
{
writeLog_(String("Warning: No valid retention time for output scan '") + rt_auto + "' from file '" + filename + "'");
}
out.addSpectrum(*it2);
out.getSpectra().back().setRT(rt_final);
out.getSpectra().back().setNativeID(native_id);
if (user_ms_level)
{
out.getSpectra().back().setMSLevel((int)getIntOption_("raw:ms_level"));
}
++native_id;
}
// if we had only one spectrum, we can annotate it directly, for more spectra, we just name the source file leaving the spectra unannotated (to avoid a long and redundant list of sourceFiles)
if (in.size() == 1)
{
out.getSpectra().back().setSourceFile(in.getSourceFiles()[0]);
in.getSourceFiles().clear(); // delete source file annotated from source file (its in the spectrum anyways)
}
// copy experimental settings from first file
if (i == 0)
{
out.ExperimentalSettings::operator=(in);
}
else // otherwise append
{
out.getSourceFiles().insert(out.getSourceFiles().end(), in.getSourceFiles().begin(), in.getSourceFiles().end()); // could be emtpty if spectrum was annotated above, but that's ok then
}
// also add the chromatograms
for (std::vector<MSChromatogram<ChromatogramPeak> >::const_iterator it2 = in.getChromatograms().begin(); it2 != in.getChromatograms().end(); ++it2)
{
all_chromatograms.push_back(*it2);
}
}
// set the chromatograms
out.setChromatograms(all_chromatograms);
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
MzMLFile f;
f.setLogType(log_type_);
f.store(out_file, out);
}
return EXECUTION_OK;
}
ExitCodes main_(int, const char **)
{
// data to be passed through the algorithm
vector<vector<SILACPattern> > data;
MSQuantifications msq;
vector<Clustering *> cluster_data;
//
// Parameter handling
//
map<String, DoubleReal> label_identifiers; // list defining the mass shifts of each label (e.g. "Arg6" => 6.0201290268)
handleParameters_sample();
handleParameters_algorithm();
handleParameters_labels(label_identifiers);
handleParameters();
if (selected_labels.empty() && !out.empty()) // incompatible parameters
{
writeLog_("Error: The 'out' parameter cannot be used without a label (parameter 'sample:labels'). Use 'out_features' instead.");
return ILLEGAL_PARAMETERS;
}
//
// Initializing the SILACAnalzer with our parameters
//
SILACAnalyzer analyzer;
analyzer.setLogType(log_type_);
analyzer.initialize(
// section "sample"
selected_labels,
charge_min,
charge_max,
missed_cleavages,
isotopes_per_peptide_min,
isotopes_per_peptide_max,
// section "algorithm"
rt_threshold,
rt_min,
intensity_cutoff,
intensity_correlation,
model_deviation,
allow_missing_peaks,
// labels
label_identifiers);
//--------------------------------------------------
// loading input from .mzML
//--------------------------------------------------
MzMLFile file;
MSExperiment<Peak1D> exp;
// only read MS1 spectra ...
/*
std::vector<int> levels;
levels.push_back(1);
file.getOptions().setMSLevels(levels);
*/
LOG_DEBUG << "Loading input..." << endl;
file.setLogType(log_type_);
file.load(in, exp);
// set size of input map
exp.updateRanges();
// extract level 1 spectra
exp.getSpectra().erase(remove_if(exp.begin(), exp.end(), InMSLevelRange<MSExperiment<Peak1D>::SpectrumType>(IntList::create("1"), true)), exp.end());
// sort according to RT and MZ
exp.sortSpectra();
if (out_mzq != "")
{
vector<vector<String> > SILAClabels = analyzer.getSILAClabels(); // list of SILAC labels, e.g. selected_labels="[Lys4,Arg6][Lys8,Arg10]" => SILAClabels[0][1]="Arg6"
std::vector<std::vector<std::pair<String, DoubleReal> > > labels;
//add none label
labels.push_back(std::vector<std::pair<String, DoubleReal> >(1, std::make_pair<String, DoubleReal>(String("none"), DoubleReal(0))));
for (Size i = 0; i < SILAClabels.size(); ++i) //SILACLabels MUST be in weight order!!!
{
std::vector<std::pair<String, DoubleReal> > one_label;
for (UInt j = 0; j < SILAClabels[i].size(); ++j)
{
one_label.push_back(*(label_identifiers.find(SILAClabels[i][j]))); // this dereferencing would break if all SILAClabels would not have been checked before!
}
labels.push_back(one_label);
}
msq.registerExperiment(exp, labels); //add assays
msq.assignUIDs();
}
MSQuantifications::QUANT_TYPES quant_type = MSQuantifications::MS1LABEL;
msq.setAnalysisSummaryQuantType(quant_type); //add analysis_summary_
//--------------------------------------------------
// estimate peak width
//--------------------------------------------------
LOG_DEBUG << "Estimating peak width..." << endl;
PeakWidthEstimator::Result peak_width;
try
{
peak_width = analyzer.estimatePeakWidth(exp);
}
catch (Exception::InvalidSize &)
{
writeLog_("Error: Unable to estimate peak width of input data.");
return INCOMPATIBLE_INPUT_DATA;
}
if (in_filters == "")
{
//--------------------------------------------------
// filter input data
//--------------------------------------------------
LOG_DEBUG << "Filtering input data..." << endl;
analyzer.filterData(exp, peak_width, data);
//--------------------------------------------------
// store filter results
//--------------------------------------------------
if (out_filters != "")
{
LOG_DEBUG << "Storing filtering results..." << endl;
ConsensusMap map;
for (std::vector<std::vector<SILACPattern> >::const_iterator it = data.begin(); it != data.end(); ++it)
{
analyzer.generateFilterConsensusByPattern(map, *it);
}
analyzer.writeConsensus(out_filters, map);
}
}
else
{
//--------------------------------------------------
// load filter results
//--------------------------------------------------
LOG_DEBUG << "Loading filtering results..." << endl;
ConsensusMap map;
analyzer.readConsensus(in_filters, map);
analyzer.readFilterConsensusByPattern(map, data);
}
//--------------------------------------------------
// clustering
//--------------------------------------------------
LOG_DEBUG << "Clustering data..." << endl;
analyzer.clusterData(exp, peak_width, cluster_data, data);
//--------------------------------------------------------------
// write output
//--------------------------------------------------------------
if (out_debug != "")
{
LOG_DEBUG << "Writing debug output file..." << endl;
std::ofstream out((out_debug + ".clusters.csv").c_str());
vector<vector<DoubleReal> > massShifts = analyzer.getMassShifts(); // list of mass shifts
// generate header
out
<< std::fixed << std::setprecision(8)
<< "ID,RT,MZ_PEAK,CHARGE";
for (UInt i = 1; i <= massShifts[0].size(); ++i)
{
out << ",DELTA_MASS_" << i + 1;
}
for (UInt i = 0; i <= massShifts[0].size(); ++i)
{
for (UInt j = 1; j <= isotopes_per_peptide_max; ++j)
{
out << ",INT_PEAK_" << i + 1 << '_' << j;
}
}
out << ",MZ_RAW";
for (UInt i = 0; i <= massShifts[0].size(); ++i)
{
for (UInt j = 1; j <= isotopes_per_peptide_max; ++j)
{
out << ",INT_RAW_" << i + 1 << '_' << j;
}
}
for (UInt i = 0; i <= massShifts[0].size(); ++i)
{
for (UInt j = 1; j <= isotopes_per_peptide_max; ++j)
{
out << ",MZ_RAW_" << i + 1 << '_' << j;
}
}
out << '\n';
// write data
UInt cluster_id = 0;
for (vector<Clustering *>::const_iterator it = cluster_data.begin(); it != cluster_data.end(); ++it)
{
analyzer.generateClusterDebug(out, **it, cluster_id);
}
}
if (out != "")
{
LOG_DEBUG << "Generating output consensus map..." << endl;
ConsensusMap map;
for (vector<Clustering *>::const_iterator it = cluster_data.begin(); it != cluster_data.end(); ++it)
{
analyzer.generateClusterConsensusByCluster(map, **it);
}
LOG_DEBUG << "Adding meta data..." << endl;
// XXX: Need a map per mass shift
ConsensusMap::FileDescriptions& desc = map.getFileDescriptions();
Size id = 0;
for (ConsensusMap::FileDescriptions::iterator it = desc.begin(); it != desc.end(); ++it)
{
if (test_mode_) it->second.filename = in; // skip path, since its not cross platform and complicates verification
else it->second.filename = File::basename(in);
// Write correct label
// (this would crash if used without a label!)
if (id > 0) it->second.label = StringList(analyzer.getSILAClabels()[id - 1]).concatenate(""); // skip first round (empty label is not listed)
++id;
}
std::set<DataProcessing::ProcessingAction> actions;
actions.insert(DataProcessing::DATA_PROCESSING);
actions.insert(DataProcessing::PEAK_PICKING);
actions.insert(DataProcessing::FILTERING);
actions.insert(DataProcessing::QUANTITATION);
addDataProcessing_(map, getProcessingInfo_(actions));
analyzer.writeConsensus(out, map);
if (out_mzq != "")
{
LOG_DEBUG << "Generating output mzQuantML file..." << endl;
ConsensusMap numap(map);
//calc. ratios
for (ConsensusMap::iterator cit = numap.begin(); cit != numap.end(); ++cit)
{
//~ make ratio templates
std::vector<ConsensusFeature::Ratio> rts;
for (std::vector<MSQuantifications::Assay>::const_iterator ait = msq.getAssays().begin() + 1; ait != msq.getAssays().end(); ++ait)
{
ConsensusFeature::Ratio r;
r.numerator_ref_ = String(msq.getAssays().begin()->uid_);
r.denominator_ref_ = String(ait->uid_);
r.description_.push_back("Simple ratio calc");
r.description_.push_back("light to medium/.../heavy");
//~ "<cvParam cvRef=\"PSI-MS\" accession=\"MS:1001132\" name=\"peptide ratio\"/>"
rts.push_back(r);
}
const ConsensusFeature::HandleSetType& feature_handles = cit->getFeatures();
if (feature_handles.size() > 1)
{
std::set<FeatureHandle, FeatureHandle::IndexLess>::const_iterator fit = feature_handles.begin(); // this is unlabeled
fit++;
for (; fit != feature_handles.end(); ++fit)
{
Size ri = std::distance(feature_handles.begin(), fit);
rts[ri - 1].ratio_value_ = feature_handles.begin()->getIntensity() / fit->getIntensity(); // a proper silacalanyzer algo should never have 0-intensities so no 0devison ...
}
}
cit->setRatios(rts);
}
msq.addConsensusMap(numap); //add SILACAnalyzer result
//~ msq.addFeatureMap();//add SILACAnalyzer evidencetrail as soon as clear what is realy contained in the featuremap
//~ add AuditCollection - no such concept in TOPPTools yet
analyzer.writeMzQuantML(out_mzq, msq);
}
}
if (out_clusters != "")
{
LOG_DEBUG << "Generating cluster output file..." << endl;
ConsensusMap map;
for (vector<Clustering *>::const_iterator it = cluster_data.begin(); it != cluster_data.end(); ++it)
{
UInt cluster_id = 0;
analyzer.generateClusterConsensusByPattern(map, **it, cluster_id);
}
ConsensusMap::FileDescription & desc = map.getFileDescriptions()[0];
desc.filename = in;
desc.label = "Cluster";
analyzer.writeConsensus(out_clusters, map);
}
if (out_features != "")
{
LOG_DEBUG << "Generating output feature map..." << endl;
FeatureMap<> map;
for (vector<Clustering *>::const_iterator it = cluster_data.begin(); it != cluster_data.end(); ++it)
{
analyzer.generateClusterFeatureByCluster(map, **it);
}
analyzer.writeFeatures(out_features, map);
}
return EXECUTION_OK;
}
ExitCodes main_(int, const char**)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
// file list
StringList file_list = getStringList_("in");
// file type
FileHandler file_handler;
FileTypes::Type force_type;
if (getStringOption_("in_type").size() > 0)
{
force_type = FileTypes::nameToType(getStringOption_("in_type"));
}
else
{
force_type = file_handler.getType(file_list[0]);
}
// output file names and types
String out_file = getStringOption_("out");
bool annotate_file_origin = getFlag_("annotate_file_origin");
rt_gap_ = getDoubleOption_("rt_concat:gap");
vector<String> trafo_out = getStringList_("rt_concat:trafo_out");
if (trafo_out.empty())
{
// resize now so we don't have to worry about indexing out of bounds:
trafo_out.resize(file_list.size());
}
else if (trafo_out.size() != file_list.size())
{
writeLog_("Error: Number of transformation output files must equal the number of input files (parameters 'rt_concat:trafo_out'/'in')!");
return ILLEGAL_PARAMETERS;
}
//-------------------------------------------------------------
// calculations
//-------------------------------------------------------------
if (force_type == FileTypes::FEATUREXML)
{
FeatureMap out;
FeatureXMLFile fh;
for (Size i = 0; i < file_list.size(); ++i)
{
FeatureMap map;
fh.load(file_list[i], map);
if (annotate_file_origin)
{
for (FeatureMap::iterator it = map.begin(); it != map.end(); ++it)
{
it->setMetaValue("file_origin", DataValue(file_list[i]));
}
}
if (rt_gap_ > 0.0) // concatenate in RT
{
adjustRetentionTimes_(map, trafo_out[i], i == 0);
}
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
// annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
fh.store(out_file, out);
}
else if (force_type == FileTypes::CONSENSUSXML)
{
ConsensusMap out;
ConsensusXMLFile fh;
fh.load(file_list[0], out);
// skip first file
for (Size i = 1; i < file_list.size(); ++i)
{
ConsensusMap map;
fh.load(file_list[i], map);
if (annotate_file_origin)
{
for (ConsensusMap::iterator it = map.begin(); it != map.end(); ++it)
{
it->setMetaValue("file_origin", DataValue(file_list[i]));
}
}
if (rt_gap_ > 0.0) // concatenate in RT
{
adjustRetentionTimes_(map, trafo_out[i], i == 0);
}
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
// annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
fh.store(out_file, out);
}
else if (force_type == FileTypes::TRAML)
{
TargetedExperiment out;
TraMLFile fh;
for (Size i = 0; i < file_list.size(); ++i)
{
TargetedExperiment map;
fh.load(file_list[i], map);
out += map;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
// annotate output with data processing info
Software software;
software.setName("FileMerger");
software.setVersion(VersionInfo::getVersion());
out.addSoftware(software);
fh.store(out_file, out);
}
else // raw data input (e.g. mzML)
{
// RT
bool rt_auto_number = getFlag_("raw:rt_auto");
bool rt_filename = getFlag_("raw:rt_filename");
bool rt_custom = false;
DoubleList custom_rts = getDoubleList_("raw:rt_custom");
if (!custom_rts.empty())
{
rt_custom = true;
if (custom_rts.size() != file_list.size())
{
writeLog_("Custom retention time list (parameter 'raw:rt_custom') must have as many elements as there are input files (parameter 'in')!");
return ILLEGAL_PARAMETERS;
}
}
// MS level
Int ms_level = getIntOption_("raw:ms_level");
MSExperiment<> out;
UInt rt_auto = 0;
UInt native_id = 0;
for (Size i = 0; i < file_list.size(); ++i)
{
String filename = file_list[i];
// load file
force_type = file_handler.getType(file_list[i]);
MSExperiment<> in;
file_handler.loadExperiment(filename, in, force_type, log_type_);
if (in.empty() && in.getChromatograms().empty())
{
writeLog_(String("Warning: Empty file '") + filename + "'!");
continue;
}
out.reserve(out.size() + in.size());
// warn if custom RT and more than one scan in input file
if (rt_custom && in.size() > 1)
{
writeLog_(String("Warning: More than one scan in file '") + filename + "'! All scans will have the same retention time!");
}
// handle special raw data options:
for (MSExperiment<>::iterator spec_it = in.begin();
spec_it != in.end(); ++spec_it)
{
float rt_final = spec_it->getRT();
if (rt_auto_number)
{
rt_final = ++rt_auto;
}
else if (rt_custom)
{
rt_final = custom_rts[i];
}
else if (rt_filename)
{
static const boost::regex re("rt(\\d+(\\.\\d+)?)");
boost::smatch match;
bool found = boost::regex_search(filename, match, re);
if (found)
{
rt_final = String(match[1]).toFloat();
}
else
{
writeLog_("Warning: could not extract retention time from filename '" + filename + "'");
}
}
// none of the rt methods were successful
if (rt_final < 0)
{
writeLog_(String("Warning: No valid retention time for output scan '") + rt_auto + "' from file '" + filename + "'");
}
spec_it->setRT(rt_final);
spec_it->setNativeID("spectrum=" + String(native_id));
if (ms_level > 0)
{
spec_it->setMSLevel(ms_level);
}
++native_id;
}
// if we have only one spectrum, we can annotate it directly, for more spectra, we just name the source file leaving the spectra unannotated (to avoid a long and redundant list of sourceFiles)
if (in.size() == 1)
{
in[0].setSourceFile(in.getSourceFiles()[0]);
in.getSourceFiles().clear(); // delete source file annotated from source file (it's in the spectrum anyways)
}
if (rt_gap_ > 0.0) // concatenate in RT
{
adjustRetentionTimes_(in, trafo_out[i], i == 0);
}
// add spectra to output
for (MSExperiment<>::const_iterator spec_it = in.begin();
spec_it != in.end(); ++spec_it)
{
out.addSpectrum(*spec_it);
}
// also add the chromatograms
for (vector<MSChromatogram<ChromatogramPeak> >::const_iterator
chrom_it = in.getChromatograms().begin(); chrom_it !=
in.getChromatograms().end(); ++chrom_it)
{
out.addChromatogram(*chrom_it);
}
// copy experimental settings from first file
if (i == 0)
{
out.ExperimentalSettings::operator=(in);
}
else // otherwise append
{
out.getSourceFiles().insert(out.getSourceFiles().end(), in.getSourceFiles().begin(), in.getSourceFiles().end()); // could be emtpty if spectrum was annotated above, but that's ok then
}
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
// annotate output with data processing info
addDataProcessing_(out, getProcessingInfo_(DataProcessing::FORMAT_CONVERSION));
MzMLFile f;
f.setLogType(log_type_);
f.store(out_file, out);
}
return EXECUTION_OK;
}