C++ MzMLFile::getOptions方法代码示例

  ExitCodes main_(int, const char **)
  {
    //input and output file names ..
    String in = getStringOption_("in");
    String out = getStringOption_("out");

    //prevent loading of fragment spectra
    PeakFileOptions options;
    options.setMSLevels(vector<Int>(1, 1));

    //reading input data
    MzMLFile f;
    f.getOptions() = options;
    f.setLogType(log_type_);

    PeakMap exp;
    f.load(in, exp);
    exp.updateRanges();

    //no seeds supported
    FeatureMap<> seeds;

    //setup of FeatureFinder
    FeatureFinder ff;
    ff.setLogType(log_type_);

    // A map for the resulting features
    FeatureMap<> features;

    // get parameters specific for the feature finder
    Param feafi_param = getParam_().copy("algorithm:", true);
    writeDebug_("Parameters passed to FeatureFinder", feafi_param, 3);

    // Apply the feature finder
    ff.run(FeatureFinderAlgorithmIsotopeWavelet<Peak1D, Feature>::getProductName(), exp, features, feafi_param, seeds);
    features.applyMemberFunction(&UniqueIdInterface::setUniqueId);

    // DEBUG
    if (debug_level_ > 10)
    {
      FeatureMap<>::Iterator it;
      for (it = features.begin(); it != features.end(); ++it)
      {
        if (!it->isMetaEmpty())
        {
          vector<String> keys;
          it->getKeys(keys);
          LOG_INFO << "Feature " << it->getUniqueId() << endl;
          for (Size i = 0; i < keys.size(); i++)
          {
            LOG_INFO << "  " << keys[i] << " = " << it->getMetaValue(keys[i]) << endl;
          }
        }
      }
    }

    //-------------------------------------------------------------
    // writing files
    //-------------------------------------------------------------

    //annotate output with data processing info
    addDataProcessing_(features, getProcessingInfo_(DataProcessing::QUANTITATION));

    // write features to user specified output file
    FeatureXMLFile map_file;
    map_file.store(out, features);

    return EXECUTION_OK;
  }

  ExitCodes main_(int, const char **) override
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    //input/output files
    String in(getStringOption_("in"));
    String out(getStringOption_("out"));

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------

    PeakMap exp;
    MzMLFile f;
    f.setLogType(log_type_);

    PeakFileOptions options;
    options.clearMSLevels();
    options.addMSLevel(2);
    f.getOptions() = options;
    f.load(in, exp);

    writeDebug_("Data set contains " + String(exp.size()) + " spectra", 1);

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------

    vector<PeptideIdentification> pep_ids;
    CompNovoIdentificationCID comp_novo_id;

    // set the options
    Param algorithm_param = getParam_().copy("algorithm:", true);
    comp_novo_id.setParameters(algorithm_param);
    comp_novo_id.getIdentifications(pep_ids, exp);
    algorithm_param = comp_novo_id.getParameters();

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------

    DateTime now = DateTime::now();
    String date_string = now.get();
    String identifier("CompNovoCID_" + date_string);

    for (vector<PeptideIdentification>::iterator it = pep_ids.begin(); it != pep_ids.end(); ++it)
    {
      it->assignRanks();
      it->setIdentifier(identifier);
    }

    vector<ProteinIdentification> prot_ids;
    ProteinIdentification prot_id;
    prot_id.setIdentifier(identifier);
    prot_id.setDateTime(now);
    StringList ms_runs;
    exp.getPrimaryMSRunPath(ms_runs);
    prot_id.setPrimaryMSRunPath(ms_runs);

    ProteinIdentification::SearchParameters search_parameters;
    search_parameters.charges = "+2-+3";
    if (algorithm_param.getValue("tryptic_only").toBool())
    {
      search_parameters.digestion_enzyme = *(ProteaseDB::getInstance()->getEnzyme("Trypsin"));
    }
    else
    {
      search_parameters.digestion_enzyme = *(ProteaseDB::getInstance()->getEnzyme("no cleavage"));
    }
    search_parameters.mass_type = ProteinIdentification::MONOISOTOPIC;
    search_parameters.fixed_modifications = algorithm_param.getValue("fixed_modifications");
    search_parameters.variable_modifications = algorithm_param.getValue("variable_modifications");

    search_parameters.missed_cleavages = (UInt)algorithm_param.getValue("missed_cleavages");
    search_parameters.fragment_mass_tolerance = (double)algorithm_param.getValue("fragment_mass_tolerance");
    search_parameters.precursor_mass_tolerance = (double)algorithm_param.getValue("precursor_mass_tolerance");
    search_parameters.fragment_mass_tolerance_ppm = false;
    search_parameters.precursor_mass_tolerance_ppm = false;
    prot_id.setSearchParameters(search_parameters);
    prot_id.setSearchEngineVersion("0.9beta");
    prot_id.setSearchEngine("CompNovo");
    prot_ids.push_back(prot_id);

    IdXMLFile().store(out, prot_ids, pep_ids);

    return EXECUTION_OK;
  }

  ExitCodes main_(int, const char**)
  {
    //input file names
    String in = getStringOption_("in");
    String out = getStringOption_("out");
    String out_mzq = getStringOption_("out_mzq");

    //prevent loading of fragment spectra
    PeakFileOptions options;
    options.setMSLevels(vector<Int>(1, 1));

    //reading input data
    MzMLFile f;
    f.getOptions() = options;
    f.setLogType(log_type_);

    PeakMap exp;
    f.load(in, exp);
    exp.updateRanges();

    if (exp.getSpectra().empty())
    {
      throw OpenMS::Exception::FileEmpty(__FILE__, __LINE__, __FUNCTION__, "Error: No MS1 spectra in input file.");
    }

    // determine type of spectral data (profile or centroided)
    SpectrumSettings::SpectrumType  spectrum_type = exp[0].getType();

    if (spectrum_type == SpectrumSettings::RAWDATA)
    {
      if (!getFlag_("force"))
      {
        throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, __FUNCTION__, "Error: Profile data provided but centroided spectra expected. To enforce processing of the data set the -force flag.");
      }
    }

    //load seeds
    FeatureMap seeds;
    if (getStringOption_("seeds") != "")
    {
      FeatureXMLFile().load(getStringOption_("seeds"), seeds);
    }

    //setup of FeatureFinder
    FeatureFinder ff;
    ff.setLogType(log_type_);

    // A map for the resulting features
    FeatureMap features;

    // get parameters specific for the feature finder
    Param feafi_param = getParam_().copy("algorithm:", true);
    writeDebug_("Parameters passed to FeatureFinder", feafi_param, 3);

    // Apply the feature finder
    ff.run(FeatureFinderAlgorithmPicked::getProductName(), exp, features, feafi_param, seeds);
    features.applyMemberFunction(&UniqueIdInterface::setUniqueId);

    // DEBUG
    if (debug_level_ > 10)
    {
      FeatureMap::Iterator it;
      for (it = features.begin(); it != features.end(); ++it)
      {
        if (!it->isMetaEmpty())
        {
          vector<String> keys;
          it->getKeys(keys);
          LOG_INFO << "Feature " << it->getUniqueId() << endl;
          for (Size i = 0; i < keys.size(); i++)
          {
            LOG_INFO << "  " << keys[i] << " = " << it->getMetaValue(keys[i]) << endl;
          }
        }
      }
    }

    //-------------------------------------------------------------
    // writing files
    //-------------------------------------------------------------

    //annotate output with data processing info
    addDataProcessing_(features, getProcessingInfo_(DataProcessing::QUANTITATION));

    // write features to user specified output file
    FeatureXMLFile map_file;

    // Remove detailed convex hull information and subordinate features
    // (unless requested otherwise) to reduce file size of feature files
    // unless debugging is turned on.
    if (debug_level_ < 5)
    {
      FeatureMap::Iterator it;
      for (it = features.begin(); it != features.end(); ++it)
      {
        it->getConvexHull().expandToBoundingBox();
        for (Size i = 0; i < it->getConvexHulls().size(); ++i)
        {
          it->getConvexHulls()[i].expandToBoundingBox();
        }
//.........这里部分代码省略.........

  ExitCodes main_(int, const char**)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    String in(getStringOption_("in"));
    String id(getStringOption_("id"));
    String out(getStringOption_("out"));
    double fragment_mass_tolerance(getDoubleOption_("fragment_mass_tolerance"));
    bool fragment_mass_unit_ppm = getStringOption_("fragment_mass_unit") == "Da" ? false : true;
    Size max_peptide_len = getIntOption_("max_peptide_length");
    Size max_num_perm = getIntOption_("max_num_perm");
    
    AScore ascore;

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------
    
    vector<PeptideIdentification> pep_ids;
    vector<ProteinIdentification> prot_ids;
    vector<PeptideIdentification> pep_out;
    IdXMLFile().load(id, prot_ids, pep_ids);

    MSExperiment<> exp;
    MzMLFile f;
    f.setLogType(log_type_);

    PeakFileOptions options;
    options.clearMSLevels();
    options.addMSLevel(2);
    f.getOptions() = options;
    f.load(in, exp);
    exp.sortSpectra(true);
    
    SpectrumLookup lookup;
    lookup.readSpectra(exp.getSpectra());

    for (vector<PeptideIdentification>::iterator pep_id = pep_ids.begin(); pep_id != pep_ids.end(); ++pep_id)
    {
      Size scan_id = lookup.findByRT(pep_id->getRT());
      PeakSpectrum& temp = exp.getSpectrum(scan_id);
      
      vector<PeptideHit> scored_peptides;
      for (vector<PeptideHit>::const_iterator hit = pep_id->getHits().begin(); hit < pep_id->getHits().end(); ++hit)
      {
        PeptideHit scored_hit = *hit;
        addScoreToMetaValues_(scored_hit, pep_id->getScoreType()); // backup score value
        
        LOG_DEBUG << "starting to compute AScore RT=" << pep_id->getRT() << " SEQUENCE: " << scored_hit.getSequence().toString() << std::endl;
        
        PeptideHit phospho_sites = ascore.compute(scored_hit, temp, fragment_mass_tolerance, fragment_mass_unit_ppm, max_peptide_len, max_num_perm);
        scored_peptides.push_back(phospho_sites);
      }

      PeptideIdentification new_pep_id(*pep_id);
      new_pep_id.setScoreType("PhosphoScore");
      new_pep_id.setHigherScoreBetter(true);
      new_pep_id.setHits(scored_peptides);
      pep_out.push_back(new_pep_id);
    }
    
    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------

    IdXMLFile().store(out, prot_ids, pep_out);
    return EXECUTION_OK;
  }

  ExitCodes main_(int, const char **)
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    String in = getStringOption_("in");
    String out = getStringOption_("out");

    //-------------------------------------------------------------
    // loading input
    //-------------------------------------------------------------
    MzMLFile mzMLFile;
    mzMLFile.setLogType(log_type_);
    MSExperiment<Peak1D> input;
    mzMLFile.getOptions().addMSLevel(1);
    mzMLFile.load(in, input);

    if (input.empty())
    {
      LOG_WARN << "The given file does not contain any conventional peak data, but might"
                  " contain chromatograms. This tool currently cannot handle them, sorry.";
      return INCOMPATIBLE_INPUT_DATA;
    }

    //check if spectra are sorted
    for (Size i = 0; i < input.size(); ++i)
    {
      if (!input[i].isSorted())
      {
        writeLog_("Error: Not all spectra are sorted according to peak m/z positions. Use FileFilter to sort the input!");
        return INCOMPATIBLE_INPUT_DATA;
      }
    }

    //-------------------------------------------------------------
    // pick
    //-------------------------------------------------------------
    FeatureMap<> output;

    FeatureFinder ff;
    Param param = getParam_().copy("algorithm:", true);

    FFSH ffsh;
    ffsh.setParameters(param);
    ffsh.setData(input, output, ff);
    ffsh.run();

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------
    //annotate output with data processing info
    addDataProcessing_(output, getProcessingInfo_(DataProcessing::PEAK_PICKING));
    addDataProcessing_(output, getProcessingInfo_(DataProcessing::QUANTITATION));
    output.ensureUniqueId();
    for (Size i = 0; i < output.size(); i++)
    {
      output[i].ensureUniqueId();
    }
    FeatureXMLFile().store(out, output);

    return EXECUTION_OK;
  }

//.........这里部分代码省略.........
      cm.sortByPosition();
      if ((out_type != FileTypes::FEATUREXML) &&
          (out_type != FileTypes::CONSENSUSXML))
      {
        // You you will lose information and waste memory. Enough reasons to issue a warning!
        writeLog_("Warning: Converting consensus features to peaks. You will lose information!");
        exp.set2DData(cm);
      }
    }
    else if (in_type == FileTypes::FEATUREXML ||
             in_type == FileTypes::TSV ||
             in_type == FileTypes::PEPLIST ||
             in_type == FileTypes::KROENIK)
    {
      fh.loadFeatures(in, fm, in_type);
      fm.sortByPosition();
      if ((out_type != FileTypes::FEATUREXML) &&
          (out_type != FileTypes::CONSENSUSXML))
      {
        // You will lose information and waste memory. Enough reasons to issue a warning!
        writeLog_("Warning: Converting features to peaks. You will lose information! Mass traces are added, if present as 'num_of_masstraces' and 'masstrace_intensity_<X>' (X>=0) meta values.");
        exp.set2DData<true>(fm);
      }
    }
    else if (process_lowmemory)
    {
      // Special switch for the low memory options:
      // We can transform the complete experiment directly without first
      // loading the complete data into memory. PlainMSDataWritingConsumer will
      // write out mzML to disk as they are read from the input.
      if (in_type == FileTypes::MZML && out_type == FileTypes::MZML)
      {
        PlainMSDataWritingConsumer consumer(out);
        consumer.getOptions().setWriteIndex(write_mzML_index);
        consumer.addDataProcessing(getProcessingInfo_(DataProcessing::CONVERSION_MZML));
        MzMLFile mzmlfile; 
        mzmlfile.setLogType(log_type_);
        mzmlfile.transform(in, &consumer);
        return EXECUTION_OK;
      }
      else if (in_type == FileTypes::MZXML && out_type == FileTypes::MZML)
      {
        PlainMSDataWritingConsumer consumer(out);
        consumer.getOptions().setWriteIndex(write_mzML_index);
        consumer.addDataProcessing(getProcessingInfo_(DataProcessing::CONVERSION_MZML));
        MzXMLFile mzxmlfile; 
        mzxmlfile.setLogType(log_type_);
        mzxmlfile.transform(in, &consumer);
        return EXECUTION_OK;
      }
      else
      {
        throw Exception::IllegalArgument(__FILE__, __LINE__, __PRETTY_FUNCTION__,
          "Process_lowmemory option can only be used with mzML / mzXML input and mzML output data types.");
      }
    }
    else
    {
      fh.loadExperiment(in, exp, in_type, log_type_);
    }

    //-------------------------------------------------------------
    // writing output
    //-------------------------------------------------------------

    writeDebug_(String("Writing output file"), 1);

  ExitCodes main_(int, const char**) override
  {
    //-------------------------------------------------------------
    // parameter handling
    //-------------------------------------------------------------

    //input file names
    String in = getStringOption_("in");
    String read_method = getStringOption_("read_method");
    bool load_data = getStringOption_("loadData") == "true";

    if (read_method == "streaming")
    {
      std::cout << "Read method: streaming" << std::endl;

      // Create the consumer, set output file name, transform
      TICConsumer consumer;
      MzMLFile mzml;
      mzml.setLogType(log_type_);

      PeakFileOptions opt = mzml.getOptions();
      opt.setFillData(load_data); // whether to actually load any data
      opt.setSkipXMLChecks(true); // save time by not checking base64 strings for whitespaces 
      opt.setMaxDataPoolSize(100);
      opt.setAlwaysAppendData(false);
      mzml.setOptions(opt);
      mzml.transform(in, &consumer, true, true);

      std::cout << "There are " << consumer.nr_spectra << " spectra and " << consumer.nr_peaks << " peaks in the input file." << std::endl;
      std::cout << "The total ion current is " << consumer.TIC << std::endl;
      size_t after;
      SysInfo::getProcessMemoryConsumption(after);
      std::cout << " Memory consumption after " << after << std::endl;
    }
    else if (read_method == "regular")
    {
      std::cout << "Read method: regular" << std::endl;

      MzMLFile mzml;
      mzml.setLogType(log_type_);
      PeakFileOptions opt = mzml.getOptions();
      opt.setFillData(load_data); // whether to actually load any data
      opt.setSkipXMLChecks(true); // save time by not checking base64 strings for whitespaces 
      mzml.setOptions(opt);
      PeakMap map;
      mzml.load(in, map);
      double TIC = 0.0;
      long int nr_peaks = 0;
      for (Size i =0; i < map.size(); i++)
      {
        nr_peaks += map[i].size();
        for (Size j = 0; j < map[i].size(); j++)
        {
          TIC += map[i][j].getIntensity();
        }
      }

      std::cout << "There are " << map.size() << " spectra and " << nr_peaks << " peaks in the input file." << std::endl;
      std::cout << "The total ion current is " << TIC << std::endl;
      size_t after;
      SysInfo::getProcessMemoryConsumption(after);
      std::cout << " Memory consumption after " << after << std::endl;
    }
    else if (read_method == "indexed")
    {
      std::cout << "Read method: indexed" << std::endl;
      
      IndexedMzMLFileLoader imzml;
      // load data from an indexed MzML file
      OnDiscPeakMap map;
      imzml.load(in, map);
      double TIC = 0.0;
      long int nr_peaks = 0;
      if (load_data)
      {
        for (Size i =0; i < map.getNrSpectra(); i++)
        {
          OpenMS::Interfaces::SpectrumPtr sptr = map.getSpectrumById(i);

          nr_peaks += sptr->getIntensityArray()->data.size();
          TIC += std::accumulate(sptr->getIntensityArray()->data.begin(), sptr->getIntensityArray()->data.end(), 0.0);
        }
      }

      std::cout << "There are " << map.getNrSpectra() << " spectra and " << nr_peaks << " peaks in the input file." << std::endl;
      std::cout << "The total ion current is " << TIC << std::endl;
      size_t after;
      SysInfo::getProcessMemoryConsumption(after);
      std::cout << " Memory consumption after " << after << std::endl;
    }
    else if (read_method == "indexed_parallel")
    {
      std::cout << "Read method: indexed (parallel)" << std::endl;
      
      IndexedMzMLFileLoader imzml;
      PeakFileOptions opt = imzml.getOptions();
      opt.setFillData(load_data); // whether to actually load any data
      imzml.setOptions(opt);

      // load data from an indexed MzML file
//.........这里部分代码省略.........