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);
    }
}
Exemplo n.º 2
0
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))
Exemplo n.º 3
0
  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;
  }