void QuantitativeExperimentalDesign::applyDesign2Quantifier(PeptideAndProteinQuant & quantifier, TextFile & file, StringList & file_paths)
{
// vector< pair<PeptideAndProteinQuant::PeptideData,PeptideAndProteinQuant::ProteinQuant> >& result)
//create mapping from experimental setting to all respective file names
map<String, StringList> design2FileBaseName;
mapFiles2Design_(design2FileBaseName, file);
//filter out all non-existing files
map<String, StringList> design2FilePath;
findRelevantFilePaths_(design2FileBaseName, design2FilePath, file_paths);
//determine wether we deal with idXML or featureXML
FileTypes::Type in_type = FileHandler::getType(file_paths.front());
if (in_type == FileTypes::FEATUREXML)
{
FeatureMap<> features;
for (map<String, StringList>::iterator iter = design2FilePath.begin(); iter != design2FilePath.end(); ++iter)
{
mergeFeatureMaps_(features, iter->first, iter->second);
}
LOG_INFO << "Number of proteinIdentifications: " << features.getProteinIdentifications().size() << endl;
ProteinIdentification & proteins = features.getProteinIdentifications()[0];
quantifier.quantifyPeptides(features);
quantifier.quantifyProteins(proteins);
}
else
{
ConsensusMap consensus;
for (map<String, StringList>::iterator iter = design2FilePath.begin(); iter != design2FilePath.end(); ++iter)
{
mergeConsensusMaps_(consensus, iter->first, iter->second);
}
LOG_INFO << "Number of proteinIdentifications: " << consensus.getProteinIdentifications().size() << endl;
ProteinIdentification & proteins = consensus.getProteinIdentifications()[0];
quantifier.quantifyPeptides(consensus);
quantifier.quantifyProteins(proteins);
}
}
feature3.setPeptideIdentifications(ids); //feature with convex hulls Feature feature4; feature4.getPosition()[0] = 5.25; feature4.getPosition()[1] = 1.5; feature4.setIntensity(0.5f); std::vector< ConvexHull2D > hulls(1); hulls[0].addPoint(DPosition<2>(-1.0,2.0)); hulls[0].addPoint(DPosition<2>(4.0,1.2)); hulls[0].addPoint(DPosition<2>(5.0,3.123)); feature4.setConvexHulls(hulls); START_SECTION((const std::vector<ProteinIdentification>& getProteinIdentifications() const)) FeatureMap<> tmp; TEST_EQUAL(tmp.getProteinIdentifications().size(),0) END_SECTION START_SECTION((std::vector<ProteinIdentification>& getProteinIdentifications())) FeatureMap<> tmp; tmp.getProteinIdentifications().resize(1); TEST_EQUAL(tmp.getProteinIdentifications().size(),1) END_SECTION START_SECTION((void setProteinIdentifications(const std::vector<ProteinIdentification>& protein_identifications))) FeatureMap<> tmp; tmp.setProteinIdentifications(std::vector<ProteinIdentification>(2)); TEST_EQUAL(tmp.getProteinIdentifications().size(),2) END_SECTION START_SECTION((const std::vector<PeptideIdentification>& getUnassignedPeptideIdentifications() const))
ExitCodes main_(int, const char **)
{
String in = getStringOption_("in"), out = getStringOption_("out"),
id_out = getStringOption_("id_out");
if (out.empty() && id_out.empty())
{
throw Exception::RequiredParameterNotGiven(__FILE__, __LINE__,
__PRETTY_FUNCTION__,
"out/id_out");
}
vector<ProteinIdentification> proteins;
vector<PeptideIdentification> peptides;
FileTypes::Type in_type = FileHandler::getType(in);
if (in_type == FileTypes::MZML)
{
MSExperiment<> experiment;
MzMLFile().load(in, experiment);
// what about unassigned peptide IDs?
for (MSExperiment<>::Iterator exp_it = experiment.begin();
exp_it != experiment.end(); ++exp_it)
{
peptides.insert(peptides.end(),
exp_it->getPeptideIdentifications().begin(),
exp_it->getPeptideIdentifications().end());
exp_it->getPeptideIdentifications().clear();
}
experiment.getProteinIdentifications().swap(proteins);
if (!out.empty())
{
addDataProcessing_(experiment,
getProcessingInfo_(DataProcessing::FILTERING));
MzMLFile().store(out, experiment);
}
}
else if (in_type == FileTypes::FEATUREXML)
{
FeatureMap features;
FeatureXMLFile().load(in, features);
features.getUnassignedPeptideIdentifications().swap(peptides);
for (FeatureMap::Iterator feat_it = features.begin();
feat_it != features.end(); ++feat_it)
{
peptides.insert(peptides.end(),
feat_it->getPeptideIdentifications().begin(),
feat_it->getPeptideIdentifications().end());
feat_it->getPeptideIdentifications().clear();
}
features.getProteinIdentifications().swap(proteins);
if (!out.empty())
{
addDataProcessing_(features,
getProcessingInfo_(DataProcessing::FILTERING));
FeatureXMLFile().store(out, features);
}
}
else // consensusXML
{
ConsensusMap consensus;
ConsensusXMLFile().load(in, consensus);
consensus.getUnassignedPeptideIdentifications().swap(peptides);
for (ConsensusMap::Iterator cons_it = consensus.begin();
cons_it != consensus.end(); ++cons_it)
{
peptides.insert(peptides.end(),
cons_it->getPeptideIdentifications().begin(),
cons_it->getPeptideIdentifications().end());
cons_it->getPeptideIdentifications().clear();
}
consensus.getProteinIdentifications().swap(proteins);
if (!out.empty())
{
addDataProcessing_(consensus,
getProcessingInfo_(DataProcessing::FILTERING));
ConsensusXMLFile().store(out, consensus);
}
}
if (!id_out.empty())
{
// IDMapper can match a peptide ID to several overlapping features,
// resulting in duplicates; this shouldn't be the case for peak data
if (in_type != FileTypes::MZML) removeDuplicates_(peptides);
IdXMLFile().store(id_out, proteins, peptides);
}
return EXECUTION_OK;
}
