C++ ParameterList::getValueInt方法代码示例

// -------------------------------------------------------------------------
bool performPairSpectra(ParameterList & ip,
                        PeptideSpectrumMatchSet &peptideResults,
                        SpecSet &specSet,
                        bool gridExecutionFlag)
{
  DEBUG_TRACE;
  DEBUG_VAR(peptideResults.size());
  DEBUG_VAR(specSet.size());
  ExecPairSpectra modulePairSpectra(ip,
      &peptideResults,
      &specSet);
  DEBUG_TRACE;

  string errorString;
  bool isValid = modulePairSpectra.validateParams(errorString);
  DEBUG_VAR(isValid);
  if (!isValid)
  {
    ERROR_MSG(errorString);
    return false;
  }

  bool returnStatus;

  if (!modulePairSpectra.loadInputData())
  {
    return false;
  }

  if (!ip.exists("GRID_NUMNODES") || ip.getValueInt("GRID_NUMNODES") <= 0)
  {
    returnStatus = modulePairSpectra.invoke();
  }
  else
  {
    DEBUG_MSG("Grid execution not supported for ExecPairSpectra");
    returnStatus = modulePairSpectra.invoke();
  }
// Test for return status
  DEBUG_VAR( returnStatus);
  if (!returnStatus)
  {
    ERROR_MSG("invoking modulePairSpectra exited in error.");
    return false;
  }

  DEBUG_TRACE;

  modulePairSpectra.saveOutputData();
  return true;
}

// -------------------------------------------------------------------------
int main(int argc, char ** argv)
{
  Logger::setDefaultLogger(Logger::getLogger(0));

  if (argc < 3)
  {
    cerr << "Usage: main_execmodule moduleName parametersFileName [options]" << endl;
    return -1;
  }

  // Parse the command line parameters
  vector<CommandLineParser::Option> listOptions;
  listOptions.push_back(CommandLineParser::Option("t", "NUM_THREADS", true));
  listOptions.push_back(CommandLineParser::Option("lf", "LOG_FILE_NAME", true));
  listOptions.push_back(CommandLineParser::Option("ll", "LOG_LEVEL", true));

  // Command line parameters for ExecSpectraExtraction for CCMS Workflows
  listOptions.push_back(CommandLineParser::Option("ccms_output_library", "OUTPUT_MGF", true));
  listOptions.push_back(CommandLineParser::Option("ccms_input_library", "EXISTING_LIBRARY_MGF", true));
  listOptions.push_back(CommandLineParser::Option("ccms_input_spectradir", "SPECTRA_DIR", true));
  listOptions.push_back(CommandLineParser::Option("ccms_results_dir", "RESULTS_DIR", true));
  listOptions.push_back(CommandLineParser::Option("ccms_newresults_dir", "NEWLIBRARYRESULTS_DIR", true));
  listOptions.push_back(CommandLineParser::Option("ccms_input_spectradatafile", "INPUTSPECTRA_DATAFILE", true));
  listOptions.push_back(CommandLineParser::Option("ccms", "CCMS", true));

  CommandLineParser clp(argc, argv, 2, listOptions);
  string parser_error;
  if (!clp.validate(parser_error))
  {
    ERROR_MSG(parser_error);
    return -2;
  }

  ParameterList commandLineParams;
  clp.getOptionsAsParameterList(commandLineParams);

  // Load the parameter file
  ParameterList ip;
  std::string paramsFileName = argv[2];
  std::string::size_type idx = paramsFileName.rfind(".");
  if( idx != std::string::npos &&
      paramsFileName.substr(idx + 1) == "xml"){
    if (!ip.readFromProteosafeXMLFile(argv[2]))
    {
        ERROR_MSG("Can not read parameter file [" << argv[2] << "].");
        return -3;
    }
  }
  else{
    if (!ip.readFromFile(argv[2]))
    {
        ERROR_MSG("Can not read parameter file [" << argv[2] << "].");
        return -3;
    }
  }

  // Combine the command line parameters to the file ones
  //   Command line parameters take precedence (hence the overwrite flag set)
  ip.addList(commandLineParams, true);

  int logLevel = ip.getValueInt("LOG_LEVEL", 0);
  if (ip.exists("LOG_FILE_NAME"))
  {
    string logFileName = ip.getValue("LOG_FILE_NAME");
    Logger::setDefaultLogger(Logger::getLogger(logFileName, logLevel));
  }
  else
  {
    Logger::setDefaultLogger(Logger::getLogger(logLevel));
  }

  DEBUG_TRACE;
  // Fill the factory with all known module types
  ExecModuleFactoryLP::RegisterAllModules();

  DEBUG_TRACE;
  // Get the exemplar from the factory
  ExecBase * moduleExemplar = ExecModuleFactoryLP::getModule(argv[1]);

  if (moduleExemplar == 0)
  {
    ERROR_MSG("Module name [" << argv[1] << "] not found in factory.");
    ExecModuleFactoryLP::cleanup();
    return -4;
  }

  DEBUG_TRACE;
  // Clone the exemplar and create a real module with the desired parameters
  ExecBase * moduleReal = moduleExemplar->clone(ip);

  string jobDoneFile(moduleReal->getName());
  jobDoneFile += "_";
  string numNode = moduleReal->m_params.getValue("NUM_SPLIT");
  jobDoneFile += numNode;
  jobDoneFile += "_results.param";

  DEBUG_VAR(jobDoneFile);

  // Validate all the parameters before invoking
//.........这里部分代码省略.........

// -------------------------------------------------------------------------
int main(int argc, char ** argv)
{
  int logLevel = 5;
  Logger::setDefaultLogger(Logger::getLogger(logLevel));

  string initialStageString("");
  string finalStageString("");
  string statusFileName("status.txt");

  bool resumeFlag = false;
  bool gridExecutionFlag = false;
  bool runGenoMSFlag = false;
  bool runMergedFlag = false;

  bool showHelp = false;
  for (size_t i = 0; i < argc; i++)
  {
    string arg(argv[i]);
    if (arg.compare("--help") == 0)
    {
      showHelp = true;
    }
  }

  if (argc < 2 || showHelp)
  {
    if (showHelp)
    {
      cout << "Usage: main_flr [PARAM FILE] [OPTION]..." << endl << endl;
      cout << "Optional arguments are listed below " << endl;
      cout << "  -i  <intialstage>   begin processing at specified stage:"
          << endl;
      cout << "                         begin,pairspectra,lpsolver,flr" << endl;
      cout
          << "  -f  <finalstage>   end processing after completing specified stage:"
          << endl;
      cout << "                        lpsolver,flr" << endl;

      cout << "  -g                  execution is on a grid" << endl;
      cout << "  -lf <filename>      name of log file for output" << endl;
      cout << "  -ll <loglevel>      log level for debug/warn/error output:"
          << endl;
      cout << "                         9 for errors only" << endl;
      cout << "                         5 for warnings and errors" << endl;
      cout << "                         0 for all debug output" << endl;
      cout << "  -s                   execute a single step then exit" << endl;
    }
    else
    {
      cerr << "main_specnets: insufficient arguments" << endl;
      cerr << "Try \'main_specnets --help\' for more information." << endl
          << endl;
    }

    cout << PROGRAM_NAME << endl;
    cout << "main_specnets 3.0." << XSTR(SPS_VERSION) << endl;
    cout << endl;

    cout << COPYRIGHT1 << endl;
    cout << COPYRIGHT2 << endl;
    cout << endl;

    return -1;
  }
  // Parse the command line parameters
  vector<CommandLineParser::Option> listOptions;
  listOptions.push_back(CommandLineParser::Option("i", "INITIAL_STAGE", 1));
  listOptions.push_back(CommandLineParser::Option("f", "FINAL_STAGE", 1));
  listOptions.push_back(CommandLineParser::Option("g", "GRID_EXECUTION", 0));
  listOptions.push_back(CommandLineParser::Option("lf", "LOG_FILE_NAME", 1));
  listOptions.push_back(CommandLineParser::Option("ll", "LOG_LEVEL", 1));
  listOptions.push_back(CommandLineParser::Option("s", "SINGLE_STEP", 0));

  CommandLineParser clp(argc, argv, 1, listOptions);
  string parser_error;
  if (!clp.validate(parser_error))
  {
    ERROR_MSG(parser_error);
    return -2;
  }

  ParameterList commandLineParams;
  clp.getOptionsAsParameterList(commandLineParams);

  ParameterList ip;
  ip.readFromFile(argv[1]);
  ip.writeToFile("debug_sps.params");

  // Combine the command line parameters to the file ones
  //   Command line parameters take precedence (hence the overwrite flag set)
  ip.addList(commandLineParams, true);
  ip.writeToFile("debug_wcommand.params");

  logLevel = ip.getValueInt("LOG_LEVEL", 5);
  if (ip.exists("LOG_FILE_NAME"))
  {
    string logFileName = ip.getValue("LOG_FILE_NAME");
    Logger::setDefaultLogger(Logger::getLogger(logFileName, logLevel));
  }
//.........这里部分代码省略.........

// -------------------------------------------------------------------------
bool performFlr(ParameterList & ip, bool gridExecutionFlag)
{
  DEBUG_TRACE;
  ExecFlr moduleFlr(ip);
  DEBUG_TRACE;

  string errorString;
  bool isValid = moduleFlr.validateParams(errorString);
  DEBUG_VAR(isValid);
  if (!isValid)
  {
    ERROR_MSG(errorString);
    return false;
  }

  isValid = moduleFlr.loadInputData();
  DEBUG_VAR(isValid);
  if (!isValid)
  {
    ERROR_MSG(errorString);
    return false;
  }

  bool returnStatus;

  if (!ip.exists("GRID_NUMNODES") || ip.getValueInt("GRID_NUMNODES") <= 0)
  {
    returnStatus = moduleFlr.invoke();
  }
  else
  {
    DEBUG_TRACE;
    int numNodes = ip.getValueInt("GRID_NUMNODES");

    string gridType = ip.getValue("GRID_TYPE");
    if (gridType == "pbs")
    {
      ParallelPbsExecution exec(&moduleFlr,
          gridExecutionFlag,
          !gridExecutionFlag,
          false);
      returnStatus = exec.invoke(numNodes);
    }
    else if (gridType == "sge")
    {
      ParallelSgeExecution exec(&moduleFlr,
          gridExecutionFlag,
          !gridExecutionFlag,
          false);
      returnStatus = exec.invoke(numNodes);
    }
  }
  // Test for return status
  DEBUG_VAR( returnStatus);
  if (!returnStatus)
  {
    ERROR_MSG("invoking moduleFlr exited in error.");
    return false;
  }

  DEBUG_TRACE;

  moduleFlr.saveOutputData();
  return true;
}