Method writeTo

src/openms/source/FORMAT/HANDLERS/MzQuantMLHandler.cpp:690–1223

    }

    void MzQuantMLHandler::writeTo(std::ostream& os)
    {
      //~ TODO logger_.startProgress(0,exp.size(),"storing mzQuantML file");
      String line; //everyone walk the line!!!

      //---header---
      os << "<?xml version=\"1.0\" encoding=\"ISO-8859-1\"?>\n";
      os << R"(<MzQuantML xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://psidev.info/psi/pi/mzQuantML/1.0.0-rc3 ../../schema/mzQuantML_1_0_0-rc3.xsd" xmlns="http://psidev.info/psi/pi/mzQuantML/1.0.0-rc3" id="OpenMS_)" << String(UniqueIdGenerator::getUniqueId()) << R"(" version="1.0.0")" << " creationDate=\"" << DateTime::now().get() << "\">\n";

      //---CVList---
      os << "<CvList>\n";
      os << " \t<Cv id=\"PSI-MS\" fullName=\"Proteomics Standards Initiative Mass Spectrometry Vocabularies\"  uri=\"http://psidev.cvs.sourceforge.net/viewvc/*checkout*/psidev/psi/psi-ms/mzML/controlledVocabulary/psi-ms.obo\" version=\"3.41.0\"/>\n";
      os << "\t<Cv id=\"PSI-MOD\" fullName=\"Proteomics Standards Initiative Protein Modifications Vocabularies\" uri=\"http://psidev.cvs.sourceforge.net/psidev/psi/mod/data/PSI-MOD.obo\" version=\"1.2\"/>\n";
      os << "\t<Cv id=\"UO\" fullName=\"Unit Ontology\" uri=\"http://obo.cvs.sourceforge.net/*checkout*/obo/obo/ontology/phenotype/unit.obo\"/>\n";
      os << "</CvList>\n";

      //---AnalysisSummary---
      os << "\t<AnalysisSummary>\n";
      // cmsq_->getAnalysisSummary().quant_type_;
      //~ os << "\t\t<userParam name=\"QuantType\" value=\"";
      //~ os << String(MSQuantifications::NamesOfQuantTypes[cmsq_->getAnalysisSummary().quant_type_]);
      switch (cmsq_->getAnalysisSummary().quant_type_)
      {
      case 0:
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1002018\" name=\"MS1 label-based analysis\"/>\n";
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1001837\" name=\"SILAC quantitation analysis\"/>\n";
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1002001\" name=\"MS1 label-based raw feature quantitation\" value=\"true\"/>\n";
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1002002\" name=\"MS1 label-based peptide level quantitation\" value=\"true\"/>\n";
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1002003\" name=\"MS1 label-based protein level quantitation\" value=\"false\"/>\n";
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1002004\" name=\"MS1 label-based proteingroup level quantitation\" value=\"false\"/>\n";
        break;

      case 1:
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1002023\" name=\"MS2 tag-based analysis\"/>\n";
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1002024\" name=\"MS2 tag-based analysis feature level quantitation\" value=\"true\"/>\n";
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1002025\" name=\"MS2 tag-based peptide level quantitation\" value=\"true\"/>\n";
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1002026\" name=\"MS2 tag-based analysis protein level quantitation\" value=\"false\"/>\n";
        os << "\t\t<cvParam cvRef=\"PSI-MS\" accession=\"MS:1002027\" name=\"MS2 tag-based analysis protein group level quantitation\" value=\"false\"/>\n";
        break;

      case 2:
        os << "\t\t<cvParam accession=\"MS:1001834\" cvRef=\"PSI-MS\" name=\"LC-MS label-free quantitation analysis\"/>\n";
        os << "\t\t<cvParam accession=\"MS:1002019\" cvRef=\"PSI-MS\" value=\"false\" name=\"label-free raw feature quantitation\"/>\n";
        os << "\t\t<cvParam accession=\"MS:1002020\" cvRef=\"PSI-MS\" value=\"true\" name=\"label-free peptide level quantitation\"/>\n";
        //~ TODO
        //~ os << "\t\t<cvParam accession=\"MS:1002021\" cvRef=\"PSI-MS\" value=\"true\" name=\"label-free protein level quantitation\"/>\n";
        //~ os << "\t\t<cvParam accession=\"MS:1002022\" cvRef=\"PSI-MS\" value=\"false\" name=\"label-free proteingroup level quantitation\"/>\n";
        break;

      case 3:
        break; //why SIZE_OF_QUANT_TYPES anyway?
      }
      //~ writeUserParam_(dataprocessinglist_tag, cmsq_->getAnalysisSummary().getUserParams(), UInt(2));
      //~ writeCVParams_(dataprocessinglist_tag, (cmsq_->getAnalysisSummary().getCVTerms(), UInt(2));
      os << "\n\t</AnalysisSummary>\n";
      //---AnalysisSummary---

      //---Software & DataProcessing---