ExitCodes main_(int, const char **)
{
FeatureGroupingAlgorithmUnlabeled * algorithm = new FeatureGroupingAlgorithmUnlabeled();
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
StringList ins;
ins = getStringList_("in");
String out = getStringOption_("out");
//-------------------------------------------------------------
// check for valid input
//-------------------------------------------------------------
// check if all input files have the correct type
FileTypes::Type file_type = FileHandler::getType(ins[0]);
for (Size i = 0; i < ins.size(); ++i)
{
if (FileHandler::getType(ins[i]) != file_type)
{
writeLog_("Error: All input files must be of the same type!");
return ILLEGAL_PARAMETERS;
}
}
//-------------------------------------------------------------
// set up algorithm
//-------------------------------------------------------------
Param algorithm_param = getParam_().copy("algorithm:", true);
writeDebug_("Used algorithm parameters", algorithm_param, 3);
algorithm->setParameters(algorithm_param);
Size reference_index(0);
//-------------------------------------------------------------
// perform grouping
//-------------------------------------------------------------
// load input
ConsensusMap out_map;
StringList ms_run_locations;
if (file_type == FileTypes::FEATUREXML)
{
// use map with highest number of features as reference:
Size max_count(0);
FeatureXMLFile f;
for (Size i = 0; i < ins.size(); ++i)
{
Size s = f.loadSize(ins[i]);
if (s > max_count)
{
max_count = s;
reference_index = i;
}
}
// Load reference map and input it to the algorithm
UInt64 ref_id;
Size ref_size;
std::vector<PeptideIdentification> ref_pepids;
std::vector<ProteinIdentification> ref_protids;
{
FeatureMap map_ref;
FeatureXMLFile f_fxml_tmp;
f_fxml_tmp.getOptions().setLoadConvexHull(false);
f_fxml_tmp.getOptions().setLoadSubordinates(false);
f_fxml_tmp.load(ins[reference_index], map_ref);
algorithm->setReference(reference_index, map_ref);
ref_id = map_ref.getUniqueId();
ref_size = map_ref.size();
ref_pepids = map_ref.getUnassignedPeptideIdentifications();
ref_protids = map_ref.getProteinIdentifications();
}
ConsensusMap dummy;
// go through all input files and add them to the result one by one
for (Size i = 0; i < ins.size(); ++i)
{
FeatureXMLFile f_fxml_tmp;
FeatureMap tmp_map;
f_fxml_tmp.getOptions().setLoadConvexHull(false);
f_fxml_tmp.getOptions().setLoadSubordinates(false);
f_fxml_tmp.load(ins[i], tmp_map);
// copy over information on the primary MS run
StringList ms_runs;
tmp_map.getPrimaryMSRunPath(ms_runs);
ms_run_locations.insert(ms_run_locations.end(), ms_runs.begin(), ms_runs.end());
if (i != reference_index)
{
algorithm->addToGroup(i, tmp_map);
// store some meta-data about the maps in the "dummy" object -> try to
// keep the same order as they were given in the input independent of
// which map is the reference.
dummy.getFileDescriptions()[i].filename = ins[i];
dummy.getFileDescriptions()[i].size = tmp_map.size();
dummy.getFileDescriptions()[i].unique_id = tmp_map.getUniqueId();
// add protein identifications to result map
dummy.getProteinIdentifications().insert(
dummy.getProteinIdentifications().end(),
tmp_map.getProteinIdentifications().begin(),
tmp_map.getProteinIdentifications().end());
// add unassigned peptide identifications to result map
dummy.getUnassignedPeptideIdentifications().insert(
dummy.getUnassignedPeptideIdentifications().end(),
tmp_map.getUnassignedPeptideIdentifications().begin(),
tmp_map.getUnassignedPeptideIdentifications().end());
}
else
{
// copy the meta-data from the refernce map
dummy.getFileDescriptions()[i].filename = ins[i];
dummy.getFileDescriptions()[i].size = ref_size;
dummy.getFileDescriptions()[i].unique_id = ref_id;
// add protein identifications to result map
dummy.getProteinIdentifications().insert(
dummy.getProteinIdentifications().end(),
ref_protids.begin(),
ref_protids.end());
// add unassigned peptide identifications to result map
dummy.getUnassignedPeptideIdentifications().insert(
dummy.getUnassignedPeptideIdentifications().end(),
ref_pepids.begin(),
ref_pepids.end());
}
}
// get the resulting map
out_map = algorithm->getResultMap();
//
// Copy back meta-data (Protein / Peptide ids / File descriptions)
//
// add protein identifications to result map
out_map.getProteinIdentifications().insert(
out_map.getProteinIdentifications().end(),
dummy.getProteinIdentifications().begin(),
dummy.getProteinIdentifications().end());
// add unassigned peptide identifications to result map
out_map.getUnassignedPeptideIdentifications().insert(
out_map.getUnassignedPeptideIdentifications().end(),
dummy.getUnassignedPeptideIdentifications().begin(),
dummy.getUnassignedPeptideIdentifications().end());
out_map.setFileDescriptions(dummy.getFileDescriptions());
// canonical ordering for checking the results, and the ids have no real meaning anyway
// the way this was done in DelaunayPairFinder and StablePairFinder
// -> the same ordering as FeatureGroupingAlgorithmUnlabeled::group applies!
out_map.sortByMZ();
out_map.updateRanges();
}
else
{
vector<ConsensusMap> maps(ins.size());
ConsensusXMLFile f;
for (Size i = 0; i < ins.size(); ++i)
{
f.load(ins[i], maps[i]);
StringList ms_runs;
maps[i].getPrimaryMSRunPath(ms_runs);
ms_run_locations.insert(ms_run_locations.end(), ms_runs.begin(), ms_runs.end());
}
// group
algorithm->FeatureGroupingAlgorithm::group(maps, out_map);
// set file descriptions:
bool keep_subelements = getFlag_("keep_subelements");
if (!keep_subelements)
{
for (Size i = 0; i < ins.size(); ++i)
{
out_map.getFileDescriptions()[i].filename = ins[i];
out_map.getFileDescriptions()[i].size = maps[i].size();
out_map.getFileDescriptions()[i].unique_id = maps[i].getUniqueId();
}
}
else
{
// components of the output map are not the input maps themselves, but
// the components of the input maps:
algorithm->transferSubelements(maps, out_map);
}
}
// assign unique ids
out_map.applyMemberFunction(&UniqueIdInterface::setUniqueId);
// annotate output with data processing info
addDataProcessing_(out_map, getProcessingInfo_(DataProcessing::FEATURE_GROUPING));
out_map.setPrimaryMSRunPath(ms_run_locations);
// write output
ConsensusXMLFile().store(out, out_map);
// some statistics
map<Size, UInt> num_consfeat_of_size;
for (ConsensusMap::const_iterator cmit = out_map.begin(); cmit != out_map.end(); ++cmit)
{
++num_consfeat_of_size[cmit->size()];
}
LOG_INFO << "Number of consensus features:" << endl;
for (map<Size, UInt>::reverse_iterator i = num_consfeat_of_size.rbegin(); i != num_consfeat_of_size.rend(); ++i)
{
LOG_INFO << " of size " << setw(2) << i->first << ": " << setw(6) << i->second << endl;
}
LOG_INFO << " total: " << setw(6) << out_map.size() << endl;
delete algorithm;
return EXECUTION_OK;
}
ExitCodes common_main_(FeatureGroupingAlgorithm * algorithm,
bool labeled = false)
{
//-------------------------------------------------------------
// parameter handling
//-------------------------------------------------------------
StringList ins;
if (labeled) ins.push_back(getStringOption_("in"));
else ins = getStringList_("in");
String out = getStringOption_("out");
//-------------------------------------------------------------
// check for valid input
//-------------------------------------------------------------
// check if all input files have the correct type
FileTypes::Type file_type = FileHandler::getType(ins[0]);
for (Size i = 0; i < ins.size(); ++i)
{
if (FileHandler::getType(ins[i]) != file_type)
{
writeLog_("Error: All input files must be of the same type!");
return ILLEGAL_PARAMETERS;
}
}
//-------------------------------------------------------------
// set up algorithm
//-------------------------------------------------------------
Param algorithm_param = getParam_().copy("algorithm:", true);
writeDebug_("Used algorithm parameters", algorithm_param, 3);
algorithm->setParameters(algorithm_param);
//-------------------------------------------------------------
// perform grouping
//-------------------------------------------------------------
// load input
ConsensusMap out_map;
StringList ms_run_locations;
if (file_type == FileTypes::FEATUREXML)
{
vector<ConsensusMap > maps(ins.size());
FeatureXMLFile f;
FeatureFileOptions param = f.getOptions();
// to save memory don't load convex hulls and subordinates
param.setLoadSubordinates(false);
param.setLoadConvexHull(false);
f.setOptions(param);
Size progress = 0;
setLogType(ProgressLogger::CMD);
startProgress(0, ins.size(), "reading input");
for (Size i = 0; i < ins.size(); ++i)
{
FeatureMap tmp;
f.load(ins[i], tmp);
out_map.getFileDescriptions()[i].filename = ins[i];
out_map.getFileDescriptions()[i].size = tmp.size();
out_map.getFileDescriptions()[i].unique_id = tmp.getUniqueId();
// copy over information on the primary MS run
const StringList& ms_runs = tmp.getPrimaryMSRunPath();
ms_run_locations.insert(ms_run_locations.end(), ms_runs.begin(), ms_runs.end());
// to save memory, remove convex hulls, subordinates:
for (FeatureMap::Iterator it = tmp.begin(); it != tmp.end();
++it)
{
it->getSubordinates().clear();
it->getConvexHulls().clear();
it->clearMetaInfo();
}
MapConversion::convert(i, tmp, maps[i]);
maps[i].updateRanges();
setProgress(progress++);
}
endProgress();
// exception for "labeled" algorithms: copy file descriptions
if (labeled)
{
out_map.getFileDescriptions()[1] = out_map.getFileDescriptions()[0];
out_map.getFileDescriptions()[0].label = "light";
out_map.getFileDescriptions()[1].label = "heavy";
}
// group
algorithm->group(maps, out_map);
}
else
{
vector<ConsensusMap> maps(ins.size());
ConsensusXMLFile f;
for (Size i = 0; i < ins.size(); ++i)
{
f.load(ins[i], maps[i]);
maps[i].updateRanges();
// copy over information on the primary MS run
const StringList& ms_runs = maps[i].getPrimaryMSRunPath();
ms_run_locations.insert(ms_run_locations.end(), ms_runs.begin(), ms_runs.end());
}
// group
algorithm->group(maps, out_map);
// set file descriptions:
bool keep_subelements = getFlag_("keep_subelements");
if (!keep_subelements)
{
for (Size i = 0; i < ins.size(); ++i)
{
out_map.getFileDescriptions()[i].filename = ins[i];
out_map.getFileDescriptions()[i].size = maps[i].size();
out_map.getFileDescriptions()[i].unique_id = maps[i].getUniqueId();
}
}
else
{
// components of the output map are not the input maps themselves, but
// the components of the input maps:
algorithm->transferSubelements(maps, out_map);
}
}
// assign unique ids
out_map.applyMemberFunction(&UniqueIdInterface::setUniqueId);
// annotate output with data processing info
addDataProcessing_(out_map,
getProcessingInfo_(DataProcessing::FEATURE_GROUPING));
// set primary MS runs
out_map.setPrimaryMSRunPath(ms_run_locations);
// write output
ConsensusXMLFile().store(out, out_map);
// some statistics
map<Size, UInt> num_consfeat_of_size;
for (ConsensusMap::const_iterator cmit = out_map.begin();
cmit != out_map.end(); ++cmit)
{
++num_consfeat_of_size[cmit->size()];
}
LOG_INFO << "Number of consensus features:" << endl;
for (map<Size, UInt>::reverse_iterator i = num_consfeat_of_size.rbegin();
i != num_consfeat_of_size.rend(); ++i)
{
LOG_INFO << " of size " << setw(2) << i->first << ": " << setw(6)
<< i->second << endl;
}
LOG_INFO << " total: " << setw(6) << out_map.size() << endl;
return EXECUTION_OK;
}
ExitCodes outputTo(ostream& os)
{
//-------------------------------------------------------------
// Parameter handling
//-------------------------------------------------------------
// File names
String in = getStringOption_("in");
// File type
FileHandler fh;
FileTypes::Type in_type = FileTypes::nameToType(getStringOption_("in_type"));
if (in_type == FileTypes::UNKNOWN)
{
in_type = fh.getType(in);
writeDebug_(String("Input file type: ") + FileTypes::typeToName(in_type), 2);
}
if (in_type == FileTypes::UNKNOWN)
{
writeLog_("Error: Could not determine input file type!");
return PARSE_ERROR;
}
MSExperiment<Peak1D> exp;
FeatureMap feat;
ConsensusMap cons;
if (in_type == FileTypes::FEATUREXML) //features
{
FeatureXMLFile().load(in, feat);
feat.updateRanges();
}
else if (in_type == FileTypes::CONSENSUSXML) //consensus features
{
ConsensusXMLFile().load(in, cons);
cons.updateRanges();
}
//-------------------------------------------------------------
// meta information
//-------------------------------------------------------------
if (getFlag_("m"))
{
os << endl
<< "-- General information --" << endl
<< endl
<< "file name: " << in << endl
<< "file type: " << FileTypes::typeToName(in_type) << endl;
//basic info
os << endl
<< "-- Meta information --" << endl
<< endl;
if (in_type == FileTypes::FEATUREXML) //features
{
os << "Document id : " << feat.getIdentifier() << endl << endl;
}
else if (in_type == FileTypes::CONSENSUSXML) //consensus features
{
os << "Document id : " << cons.getIdentifier() << endl << endl;
}
}
//-------------------------------------------------------------
// data processing
//-------------------------------------------------------------
if (getFlag_("p"))
{
//basic info
os << endl
<< "-- Data processing information --" << endl
<< endl;
//get data processing info
vector<DataProcessing> dp;
if (in_type == FileTypes::FEATUREXML) //features
{
dp = feat.getDataProcessing();
}
else if (in_type == FileTypes::CONSENSUSXML) //consensus features
{
dp = cons.getDataProcessing();
}
int i = 0;
for (vector<DataProcessing>::iterator it = dp.begin(); it != dp.end(); ++it)
{
os << "Data processing " << i << endl;
os << "\tcompletion_time: " << (*it).getCompletionTime().getDate() << 'T' << (*it).getCompletionTime().getTime() << endl;
os << "\tsoftware name: " << (*it).getSoftware().getName() << " version " << (*it).getSoftware().getVersion() << endl;
for (set<DataProcessing::ProcessingAction>::const_iterator paIt = (*it).getProcessingActions().begin(); paIt != (*it).getProcessingActions().end(); ++paIt)
{
os << "\t\tprocessing action: " << DataProcessing::NamesOfProcessingAction[*paIt] << endl;
}
}
++i;
}
//-------------------------------------------------------------
// statistics
//-------------------------------------------------------------
if (getFlag_("s"))
{
//-------------------------------------------------------------
// Content statistics
//-------------------------------------------------------------
Map<String, int> meta_names;
if (in_type == FileTypes::FEATUREXML) //features
{
os << "Number of features: " << feat.size() << endl
<< endl
<< "Ranges:" << endl
<< " retention time: " << String::number(feat.getMin()[Peak2D::RT], 2) << " : " << String::number(feat.getMax()[Peak2D::RT], 2) << endl
<< " mass-to-charge: " << String::number(feat.getMin()[Peak2D::MZ], 2) << " : " << String::number(feat.getMax()[Peak2D::MZ], 2) << endl
<< " intensity: " << String::number(feat.getMinInt(), 2) << " : " << String::number(feat.getMaxInt(), 2) << endl
<< endl;
// Charge distribution
Map<UInt, UInt> charges;
for (Size i = 0; i < feat.size(); ++i)
{
charges[feat[i].getCharge()]++;
}
os << "Charge distribution" << endl;
for (Map<UInt, UInt>::const_iterator it = charges.begin();
it != charges.end(); ++it)
{
os << "charge " << it->first << ": " << it->second << endl;
}
}
else if (in_type == FileTypes::CONSENSUSXML) //consensus features
{
map<Size, UInt> num_consfeat_of_size;
for (ConsensusMap::const_iterator cmit = cons.begin();
cmit != cons.end(); ++cmit)
{
++num_consfeat_of_size[cmit->size()];
}
os << endl << "Number of consensus features:" << endl;
for (map<Size, UInt>::reverse_iterator i = num_consfeat_of_size.rbegin(); i != num_consfeat_of_size.rend(); ++i)
{
os << " of size " << setw(2) << i->first << ": " << setw(6) << i->second << endl;
}
os << " total: " << setw(6) << cons.size() << endl << endl;
os << "Ranges:" << endl
<< " retention time: " << String::number(cons.getMin()[Peak2D::RT], 2) << " : " << String::number(cons.getMax()[Peak2D::RT], 2) << endl
<< " mass-to-charge: " << String::number(cons.getMin()[Peak2D::MZ], 2) << " : " << String::number(cons.getMax()[Peak2D::MZ], 2) << endl
<< " intensity: " << String::number(cons.getMinInt(), 2) << " : " << String::number(cons.getMaxInt(), 2) << endl;
// file descriptions
const ConsensusMap::FileDescriptions& descs = cons.getFileDescriptions();
if (!descs.empty())
{
os << endl <<
"File descriptions:" << endl;
for (ConsensusMap::FileDescriptions::const_iterator it = descs.begin(); it != descs.end(); ++it)
{
os << " - " << it->second.filename << endl
<< " identifier: " << it->first << endl
<< " label : " << it->second.label << endl
<< " size : " << it->second.size << endl;
}
}
}
os << endl
<< "-- Summary Statistics --" << endl
<< endl;
}
if (in_type == FileTypes::FEATUREXML) //features
{
feat.sortByRT();
vector<double> slice_stats;
Size n = getIntOption_("n");
Size begin = 0;
Size end = 0;
os << "#slice\tRT_begin\tRT_end\tnumber_of_features\ttic\t"
<< "int_mean\tint_stddev\tint_min\tint_max\tint_median\tint_lowerq\tint_upperq\t"
<< "mz_mean\tmz_stddev\tmz_min\tmz_max\tmz_median\tmz_lowerq\tmz_upperq\t"
<< "width_mean\twidth_stddev\twidth_min\twidth_max\twidth_median\twidth_lowerq\twidth_upperq\t"
<< "qual_mean\tqual_stddev\tqual_min\tqual_max\tqual_median\tqual_lowerq\tqual_upperq\t"
<< "rt_qual_mean\trt_qual_stddev\trt_qual_min\trt_qual_max\trt_qual_median\trt_qual_lowerq\trt_qual_upperq\t"
<< "mz_qual_mean\tmz_qual_stddev\tmz_qual_min\tmz_qual_max\tmz_qual_median\tmz_qual_lowerq\tmz_qual_upperq"
<< endl;
double rt_begin = 0.0;
for (Size slice = 0; slice < n; ++slice)
{
// Determine slice boundaries.
double rt_end = feat.back().getRT() / (double)n * (slice + 1);
for (end = begin; end < feat.size() && feat[end].getRT() < rt_end; ++end) {}
// Compute statistics on all features in this slice.
slice_stats = sliceStatistics(feat, begin, end);
// Write the beginning and end of the slices to the output as well as the slice index.
os << slice << "\t" << rt_begin << "\t" << rt_end << "\t" << end - begin << "\t";
// Write the statistics as a line of an csv file
copy(slice_stats.begin(), slice_stats.end(), ostream_iterator<double>(os, "\t"));
os << endl;
begin = end;
rt_begin = rt_end;
}
}
else if (in_type == FileTypes::CONSENSUSXML) //consensus features
{
Size size = cons.size();
vector<double> intensities;
intensities.reserve(size);
vector<double> qualities(size);
qualities.reserve(size);
vector<double> widths(size);
widths.reserve(size);
vector<double> rt_delta_by_elems;
vector<double> rt_aad_by_elems;
vector<double> rt_aad_by_cfs;
rt_aad_by_cfs.reserve(size);
vector<double> mz_delta_by_elems;
vector<double> mz_aad_by_elems;
vector<double> mz_aad_by_cfs;
mz_aad_by_cfs.reserve(size);
vector<double> it_delta_by_elems;
vector<double> it_aad_by_elems;
vector<double> it_aad_by_cfs;
it_aad_by_cfs.reserve(size);
for (ConsensusMap::const_iterator cm_iter = cons.begin();
cm_iter != cons.end(); ++cm_iter)
{
double rt_aad = 0;
double mz_aad = 0;
double it_aad = 0;
intensities.push_back(cm_iter->getIntensity());
qualities.push_back(cm_iter->getQuality());
widths.push_back(cm_iter->getWidth());
for (ConsensusFeature::HandleSetType::const_iterator hs_iter = cm_iter->begin();
hs_iter != cm_iter->end(); ++hs_iter)
{
double rt_diff = hs_iter->getRT() - cm_iter->getRT();
rt_delta_by_elems.push_back(rt_diff);
if (rt_diff < 0)
{
rt_diff = -rt_diff;
}
rt_aad_by_elems.push_back(rt_diff);
rt_aad += rt_diff;
double mz_diff = hs_iter->getMZ() - cm_iter->getMZ();
mz_delta_by_elems.push_back(mz_diff);
if (mz_diff < 0)
{
mz_diff = -mz_diff;
}
mz_aad_by_elems.push_back(mz_diff);
mz_aad += mz_diff;
double it_ratio = hs_iter->getIntensity() / (cm_iter->getIntensity() ? cm_iter->getIntensity() : 1.);
it_delta_by_elems.push_back(it_ratio);
if (it_ratio < 1.)
{
it_ratio = 1. / it_ratio;
}
it_aad_by_elems.push_back(it_ratio);
it_aad += it_ratio;
}
if (!cm_iter->empty())
{
rt_aad /= cm_iter->size();
mz_aad /= cm_iter->size();
it_aad /= cm_iter->size();
} // otherwise rt_aad etc. are 0 anyway
rt_aad_by_cfs.push_back(rt_aad);
mz_aad_by_cfs.push_back(mz_aad);
it_aad_by_cfs.push_back(it_aad);
}
OpenMS::SomeStatistics some_statistics;
os.precision(writtenDigits(ConsensusFeature::IntensityType()));
os << "Intensities of consensus features:" << endl << some_statistics(intensities) << endl;
os.precision(writtenDigits(ConsensusFeature::QualityType()));
os << "Qualities of consensus features:" << endl << some_statistics(qualities) << endl;
os.precision(writtenDigits(ConsensusFeature::CoordinateType()));
os << "Retention time differences ( element-center, weight 1 per element):" << endl << some_statistics(rt_delta_by_elems) << endl;
os << "Absolute retention time differences ( |element-center|, weight 1 per element):" << endl << some_statistics(rt_aad_by_elems) << endl;
os << "Average absolute differences of retention time within consensus features ( |element-center|, weight 1 per consensus features):" << endl << some_statistics(rt_aad_by_cfs) << endl;
os.precision(writtenDigits(ConsensusFeature::CoordinateType()));
os << "Mass-to-charge differences ( element-center, weight 1 per element):" << endl << some_statistics(mz_delta_by_elems) << endl;
os << "Absolute differences of mass-to-charge ( |element-center|, weight 1 per element):" << endl << some_statistics(mz_aad_by_elems) << endl;
os << "Average absolute differences of mass-to-charge within consensus features ( |element-center|, weight 1 per consensus features):" << endl << some_statistics(mz_aad_by_cfs) << endl;
os.precision(writtenDigits(ConsensusFeature::IntensityType()));
os << "Intensity ratios ( element/center, weight 1 per element):" << endl << some_statistics(it_delta_by_elems) << endl;
os << "Relative intensity error ( max{(element/center),(center/element)}, weight 1 per element):" << endl << some_statistics(it_aad_by_elems) << endl;
os << "Average relative intensity error within consensus features ( max{(element/center),(center/element)}, weight 1 per consensus features):" << endl << some_statistics(it_aad_by_cfs) << endl;
}
return EXECUTION_OK;
}