C++ PeakMap::getSpectra方法代码示例

  ExitCodes main_(int, const char**)
  {
    // instance specific location of settings in INI file (e.g. 'TOPP_Skeleton:1:')
    String ini_location;
    // path to the log file
    String logfile(getStringOption_("log"));
    String xtandem_executable(getStringOption_("xtandem_executable"));
    String inputfile_name;
    String outputfile_name;

    //-------------------------------------------------------------
    // parsing parameters
    //-------------------------------------------------------------

    inputfile_name = getStringOption_("in");
    writeDebug_(String("Input file: ") + inputfile_name, 1);
    if (inputfile_name == "")
    {
      writeLog_("No input file specified. Aborting!");
      printUsage_();
      return ILLEGAL_PARAMETERS;
    }

    outputfile_name = getStringOption_("out");
    writeDebug_(String("Output file: ") + outputfile_name, 1);
    if (outputfile_name == "")
    {
      writeLog_("No output file specified. Aborting!");
      printUsage_();
      return ILLEGAL_PARAMETERS;
    }

    // write input xml file
    String temp_directory = QDir::toNativeSeparators((File::getTempDirectory() + "/" + File::getUniqueName() + "/").toQString()); // body for the tmp files
    {
      QDir d;
      d.mkpath(temp_directory.toQString());
    }

    String input_filename(temp_directory + "_tandem_input_file.xml");
    String tandem_input_filename(temp_directory + "_tandem_input_file.mzData");
    String tandem_output_filename(temp_directory + "_tandem_output_file.xml");
    String tandem_taxonomy_filename(temp_directory + "_tandem_taxonomy_file.xml");

    //-------------------------------------------------------------
    // Validate user parameters
    //-------------------------------------------------------------
    if (getIntOption_("min_precursor_charge") > getIntOption_("max_precursor_charge"))
    {
      LOG_ERROR << "Given charge range is invalid: max_precursor_charge needs to be >= min_precursor_charge." << std::endl;
      return ILLEGAL_PARAMETERS;
    }

    //-------------------------------------------------------------
    // reading input
    //-------------------------------------------------------------

    String db_name(getStringOption_("database"));
    if (!File::readable(db_name))
    {
      String full_db_name;
      try
      {
        full_db_name = File::findDatabase(db_name);
      }
      catch (...)
      {
        printUsage_();
        return ILLEGAL_PARAMETERS;
      }
      db_name = full_db_name;
    }


    PeakMap exp;
    MzMLFile mzml_file;
    mzml_file.getOptions().addMSLevel(2); // only load msLevel 2
    mzml_file.setLogType(log_type_);
    mzml_file.load(inputfile_name, exp);

    if (exp.getSpectra().empty())
    {
      throw OpenMS::Exception::FileEmpty(__FILE__, __LINE__, __FUNCTION__, "Error: No MS2 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 MS2 spectra expected. To enforce processing of the data set the -force flag.");
      }
    }

    // we need to replace the native id with a simple numbering schema, to be able to
    // map the IDs back to the spectra (RT, and MZ information)
    Size native_id(0);
    for (PeakMap::Iterator it = exp.begin(); it != exp.end(); ++it)
//.........这里部分代码省略.........

  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**) override
  {
    //-------------------------------------------------------------
    // parsing parameters
    //-------------------------------------------------------------
    
    // do this early, to see if comet is installed
    String comet_executable = getStringOption_("comet_executable");
    String tmp_param = File::getTemporaryFile();
    writeLog_("Comet is writing the default parameter file...");
    runExternalProcess_(comet_executable.toQString(), QStringList() << "-p" << tmp_param.c_str());

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


    //-------------------------------------------------------------
    // reading input
    //-------------------------------------------------------------

    String db_name(getStringOption_("database"));
    if (!File::readable(db_name))
    {
      String full_db_name;
      try
      {
        full_db_name = File::findDatabase(db_name);
      }
      catch (...)
      {
        printUsage_();
        return ILLEGAL_PARAMETERS;
      }
      db_name = full_db_name;
    }

    //tmp_dir
    String tmp_dir = makeAutoRemoveTempDirectory_();
    String tmp_pepxml = tmp_dir + "result.pep.xml";
    String tmp_pin = tmp_dir + "result.pin";
    String default_params = getStringOption_("default_params_file");
    String tmp_file;

    //default params given or to be written
    if (default_params.empty())
    {
        tmp_file = tmp_dir + "param.txt";
        ofstream os(tmp_file.c_str());
        createParamFile_(os);
        os.close();
    }
    else
    {
        tmp_file = default_params;
    }

    PeakMap exp;
    MzMLFile mzml_file;
    mzml_file.getOptions().setMSLevels({2}); // only load msLevel 2 
    mzml_file.setLogType(log_type_);
    mzml_file.load(inputfile_name, exp);

    if (exp.getSpectra().empty())
    {
      throw OpenMS::Exception::FileEmpty(__FILE__, __LINE__, __FUNCTION__, "Error: No MS2 spectra in input file.");
    }

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

    if (spectrum_type == SpectrumSettings::PROFILE)
    {
      if (!getFlag_("force"))
      {
        throw OpenMS::Exception::IllegalArgument(__FILE__, __LINE__, __FUNCTION__, "Error: Profile data provided but centroided MS2 spectra expected. To enforce processing of the data set the -force flag.");
      }
    }

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------
    String paramP = "-P" + tmp_file;
    String paramN = "-N" + File::removeExtension(File::removeExtension(tmp_pepxml));
    QStringList arguments;
    arguments << paramP.toQString() << paramN.toQString() << inputfile_name.toQString();

    //-------------------------------------------------------------
    // run comet
    //-------------------------------------------------------------
    // Comet execution with the executable and the arguments StringList
    TOPPBase::ExitCodes exit_code = runExternalProcess_(comet_executable.toQString(), arguments);
    if (exit_code != EXECUTION_OK)
    {
      return exit_code;
    }
    //-------------------------------------------------------------
    // writing IdXML output
    //-------------------------------------------------------------

    // read the pep.xml put of Comet and write it to idXML
//.........这里部分代码省略.........

//.........这里部分代码省略.........
    parameters << "-cfg" << cfg_file;

    // path to input file must be the last parameter
    parameters << inputfile_name;

    //-------------------------------------------------------------
    // calculations
    //-------------------------------------------------------------
    QStringList qparam;
    writeDebug_("MyriMatch arguments:", 1);
    writeDebug_(String("\"") + ListUtils::concatenate(parameters, "\" \"") + "\"", 1);
    for (Size i = 0; i < parameters.size(); ++i)
    {
      qparam << parameters[i].toQString();
    }
    QProcess process;

    // Bad style, because it breaks relative paths?
    process.setWorkingDirectory(tmp_dir.toQString());

    process.start(myrimatch_executable.toQString(), qparam, QIODevice::ReadOnly);
    bool success = process.waitForFinished(-1);
    String myri_msg(QString(process.readAllStandardOutput()));
    String myri_err(QString(process.readAllStandardError()));
    writeDebug_(myri_msg, 1);
    writeDebug_(myri_err, 0);
    if (!success || process.exitStatus() != 0 || process.exitCode() != 0)
    {
      writeLog_("Error: MyriMatch problem! (Details can be seen in the logfile: \"" + logfile + "\")");
      writeLog_("Note: This message can also be triggered if you run out of space in your tmp directory");
      return EXTERNAL_PROGRAM_ERROR;
    }

    //-------------------------------------------------------------
    // reading MyriMatch output
    //-------------------------------------------------------------

    writeDebug_("Reading output of MyriMatch", 5);
    String exp_name = File::basename(inputfile_name);
    String pep_file = tmp_dir + File::removeExtension(exp_name) + ".pepXML";

    vector<ProteinIdentification> protein_identifications;
    vector<PeptideIdentification> peptide_identifications;

    PeakMap exp;
    if (File::exists(pep_file))
    {
      MzMLFile fh;
      fh.load(inputfile_name, exp);

      SpectrumMetaDataLookup lookup;
      lookup.readSpectra(exp.getSpectra());
      PepXMLFile().load(pep_file, protein_identifications,
                        peptide_identifications, exp_name, lookup);
    }
    else
    {
      writeLog_("Error: MyriMatch problem! No pepXML output file (expected as '" + pep_file + "') was generated by MyriMatch.");
      writeLog_("Note: This message can be triggered if no MS2 spectra were found or no identifications were made.");
      writeLog_("      Myrimatch expects MS2 spectra in mzML files to contain the MSn tag. MSSpectrum with MS level 2 is not sufficient. You can use FileConverter to create such an mzML file by converting from mzML --> mzXML --> mzML.");
      return EXTERNAL_PROGRAM_ERROR;
    }

    if (debug_level_ == 0)
    {
      QFile(pep_file.toQString()).remove();
      QFile(cfg_file.toQString()).remove();
    }
    else
    {
      writeDebug_(String("Not removing '") + pep_file + "' for debugging purposes. Please delete manually!", 1);
      writeDebug_(String("Not removing '") + cfg_file + "' for debugging purposes. Please delete manually!", 1);
    }
    //-------------------------------------------------------------
    // writing results
    //-------------------------------------------------------------
    ProteinIdentification::SearchParameters search_parameters;
    search_parameters.db = getStringOption_("database");
    ProteinIdentification::PeakMassType mass_type = getFlag_("precursor_mass_tolerance_avg") == true ? ProteinIdentification::AVERAGE : ProteinIdentification::MONOISOTOPIC;
    search_parameters.mass_type = mass_type;
    search_parameters.fixed_modifications = getStringList_("fixed_modifications");
    search_parameters.variable_modifications = getStringList_("variable_modifications");
    search_parameters.missed_cleavages = getIntOption_("MaxMissedCleavages");
    search_parameters.fragment_mass_tolerance = getDoubleOption_("fragment_mass_tolerance");
    search_parameters.precursor_mass_tolerance = getDoubleOption_("precursor_mass_tolerance");
    search_parameters.precursor_mass_tolerance_ppm = getStringOption_("precursor_mass_tolerance_unit") == "ppm" ? true : false;
    search_parameters.fragment_mass_tolerance_ppm = getStringOption_("fragment_mass_tolerance_unit") == "ppm" ? true : false;
    protein_identifications[0].setSearchParameters(search_parameters);
    protein_identifications[0].setSearchEngineVersion(myrimatch_version);
    protein_identifications[0].setSearchEngine("MyriMatch");

    if (!protein_identifications.empty())
    {
      StringList ms_runs;
      exp.getPrimaryMSRunPath(ms_runs);
      protein_identifications[0].setPrimaryMSRunPath(ms_runs);
    }
    IdXMLFile().store(outputfile_name, protein_identifications, peptide_identifications);
    return EXECUTION_OK;
  }

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

    //input/output files
    String in(getStringOption_("in")), out(getStringOption_("out"));
    FileHandler fh;
    FileTypes::Type in_type = fh.getType(in);

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

    PeakMap exp;
    // keep only MS2 spectra
    fh.getOptions().addMSLevel(2);
    fh.loadExperiment(in, exp, in_type, log_type_);
    writeDebug_(String("Spectra loaded: ") + exp.size(), 2);

    if (exp.getSpectra().empty())
    {
      throw OpenMS::Exception::FileEmpty(__FILE__, __LINE__, __FUNCTION__, "Error: No MS2 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 MS2 spectra expected. To enforce processing of the data set the -force flag.");
      }
    }

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

    Param mascot_param = getParam_().copy("Mascot_parameters:", true);
    MascotGenericFile mgf_file;
    Param p;
    // TODO: switch this to mzML (much smaller)
    p.setValue("internal:format", "Mascot generic", "Sets the format type of the peak list, this should not be changed unless you write the header only.", ListUtils::create<String>("advanced"));
    p.setValue("internal:HTTP_format", "true", "Write header with MIME boundaries instead of simple key-value pairs. For HTTP submission only.", ListUtils::create<String>("advanced"));
    p.setValue("internal:content", "all", "Use parameter header + the peak lists with BEGIN IONS... or only one of them.", ListUtils::create<String>("advanced"));
    mgf_file.setParameters(mascot_param);

    // get the spectra into string stream
    writeDebug_("Writing MGF file to stream", 1);
    stringstream ss;
    mgf_file.store(ss, in, exp, true); // write in compact format

    // Usage of a QCoreApplication is overkill here (and ugly too), but we just use the
    // QEventLoop to process the signals and slots and grab the results afterwards from
    // the MascotRemotQuery instance
    char** argv2 = const_cast<char**>(argv);
    QCoreApplication event_loop(argc, argv2);
    MascotRemoteQuery* mascot_query = new MascotRemoteQuery(&event_loop);
    Param mascot_query_param = getParam_().copy("Mascot_server:", true);
    writeDebug_("Setting parameters for Mascot query", 1);
    mascot_query->setParameters(mascot_query_param);
    writeDebug_("Setting spectra for Mascot query", 1);
    mascot_query->setQuerySpectra(ss.str());

    // remove unnecessary spectra
    ss.clear();

    QObject::connect(mascot_query, SIGNAL(done()), &event_loop, SLOT(quit()));
    QTimer::singleShot(1000, mascot_query, SLOT(run()));
    writeDebug_("Fire off Mascot query", 1);
    event_loop.exec();
    writeDebug_("Mascot query finished", 1);

    if (mascot_query->hasError())
    {
      writeLog_("An error occurred during the query: " + mascot_query->getErrorMessage());
      delete mascot_query;
      return EXTERNAL_PROGRAM_ERROR;
    }

    // write Mascot response to file
    String mascot_tmp_file_name(File::getTempDirectory() + "/" + File::getUniqueName() + "_Mascot_response");
    QFile mascot_tmp_file(mascot_tmp_file_name.c_str());
    mascot_tmp_file.open(QIODevice::WriteOnly);
    mascot_tmp_file.write(mascot_query->getMascotXMLResponse());
    mascot_tmp_file.close();

    // clean up
    delete mascot_query;

    vector<PeptideIdentification> pep_ids;
    ProteinIdentification prot_id;

    // set up mapping between scan numbers and retention times:
    MascotXMLFile::RTMapping rt_mapping;
    MascotXMLFile::generateRTMapping(exp.begin(), exp.end(), rt_mapping);

//.........这里部分代码省略.........