Method main_

src/topp/OpenSwathFileSplitter.cpp:88–126

  }

  ExitCodes main_(int, const char**) override
  {
    ///////////////////////////////////
    // Prepare Parameters
    ///////////////////////////////////
    String file_in = getStringOption_("in");

    // make sure tmp is a directory with proper separator at the end (downstream methods simply do path + filename)
    // (do not use QDir::separator(), since its platform specific (/ or \) while absolutePath() will always use '/')
    String tmp_dir = String(QDir(getStringOption_("outputDirectory").c_str()).absolutePath()).ensureLastChar('/');

    QFileInfo fi(file_in.toQString());
    String tmp = tmp_dir + String(fi.baseName());

    String out_qc = getStringOption_("out_qc");

    ///////////////////////////////////
    // Load the SWATH files
    ///////////////////////////////////
    boost::shared_ptr<ExperimentalSettings> exp_meta(new ExperimentalSettings);
    std::vector<OpenSwath::SwathMap> swath_maps;

    // collect some QC data
    if (out_qc.empty())
    {
      loadSwathFiles(file_in, tmp, "split", exp_meta, swath_maps);
    }
    else
    {
      OpenSwath::SwathQC qc(30, 0.04);
      MSDataTransformingConsumer qc_consumer; // apply some transformation
      qc_consumer.setSpectraProcessingFunc(qc.getSpectraProcessingFunc());
      qc_consumer.setExperimentalSettingsFunc(qc.getExpSettingsFunc());
      loadSwathFiles(file_in, tmp, "split", exp_meta, swath_maps, &qc_consumer);
      qc.storeJSON(out_qc);
    }

    return EXECUTION_OK;
  }
};

int main(int argc, const char** argv)