FileHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2012.
//
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Andreas Bertsch $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_FILEHANDLER_H
#define OPENMS_FORMAT_FILEHANDLER_H

#include <OpenMS/config.h>
#include <OpenMS/FORMAT/FileTypes.h>

#include <OpenMS/FORMAT/DTAFile.h>
#include <OpenMS/FORMAT/DTA2DFile.h>
#include <OpenMS/FORMAT/MzXMLFile.h>
#include <OpenMS/FORMAT/MzMLFile.h>
#include <OpenMS/FORMAT/FeatureXMLFile.h>
#include <OpenMS/FORMAT/MzDataFile.h>
#include <OpenMS/FORMAT/MascotGenericFile.h>
#include <OpenMS/FORMAT/MS2File.h>
#include <OpenMS/FORMAT/XMassFile.h>

#include <OpenMS/FORMAT/MsInspectFile.h>
#include <OpenMS/FORMAT/SpecArrayFile.h>
#include <OpenMS/FORMAT/KroenikFile.h>

#include <OpenMS/KERNEL/ChromatogramTools.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>

namespace OpenMS
{
  class OPENMS_DLLAPI FileHandler
  {
public:
    static FileTypes::Type getType(const String & filename);


    static FileTypes::Type getTypeByFileName(const String & filename);

    static FileTypes::Type getTypeByContent(const String & filename);

    static bool isSupported(FileTypes::Type type);

    PeakFileOptions & getOptions();

    const PeakFileOptions & getOptions() const;

    template <class PeakType>
    bool loadExperiment(const String & filename, MSExperiment<PeakType> & exp, FileTypes::Type force_type = FileTypes::UNKNOWN, ProgressLogger::LogType log = ProgressLogger::NONE)
    {
      //determine file type
      FileTypes::Type type;
      if (force_type != FileTypes::UNKNOWN)
      {
        type = force_type;
      }
      else
      {
        try
        {
          type = getType(filename);
        }
        catch (Exception::FileNotFound)
        {
          return false;
        }
      }

      //load right file
      switch (type)
      {
      case FileTypes::DTA:
        exp.reset();
        exp.resize(1);
        DTAFile().load(filename, exp[0]);
        return true;

        break;

      case FileTypes::DTA2D:
      {
        DTA2DFile f;
        f.getOptions() = options_;
        f.setLogType(log);
        f.load(filename, exp);
        return true;
      }
      break;

      case FileTypes::MZXML:
      {
        MzXMLFile f;
        f.getOptions() = options_;
        f.setLogType(log);
        f.load(filename, exp);
        return true;
      }
      break;

      case FileTypes::MZDATA:
      {
        MzDataFile f;
        f.getOptions() = options_;
        f.setLogType(log);
        f.load(filename, exp);
        return true;
      }
      break;

      case FileTypes::MZML:
      {
        MzMLFile f;
        f.getOptions() = options_;
        f.setLogType(log);
        f.load(filename, exp);
        ChromatogramTools().convertSpectraToChromatograms<MSExperiment<PeakType> >(exp, true);
        return true;
      }
      break;

      case FileTypes::MGF:
      {
        MascotGenericFile f;
        f.setLogType(log);
        f.load(filename, exp);
        return true;
      }

      case FileTypes::MS2:
      {
        MS2File f;
        f.setLogType(log);
        f.load(filename, exp);
        return true;
      }

      case FileTypes::XMASS:
      {
        exp.reset();
        exp.resize(1);
        XMassFile().load(filename, exp[0]);
        XMassFile().importExperimentalSettings(filename, exp);
        return true;
      }

      default:
        break;
      }

      return false;
    }

    template <class PeakType>
    void storeExperiment(const String & filename, const MSExperiment<PeakType> & exp, ProgressLogger::LogType log = ProgressLogger::NONE)
    {
      //load right file
      switch (getTypeByFileName(filename))
      {
      case FileTypes::DTA2D:
      {
        DTA2DFile f;
        f.getOptions() = options_;
        f.setLogType(log);
        f.store(filename, exp);
      }
      break;

      case FileTypes::MZXML:
      {
        MzXMLFile f;
        f.getOptions() = options_;
        f.setLogType(log);
        if (!exp.getChromatograms().empty())
        {
          MSExperiment<PeakType> exp2 = exp;
          ChromatogramTools().convertChromatogramsToSpectra<MSExperiment<PeakType> >(exp2);
          f.store(filename, exp2);
        }
        else
        {
          f.store(filename, exp);
        }
      }
      break;

      case FileTypes::MZDATA:
      {
        MzDataFile f;
        f.getOptions() = options_;
        f.setLogType(log);
        if (!exp.getChromatograms().empty())
        {
          MSExperiment<PeakType> exp2 = exp;
          ChromatogramTools().convertChromatogramsToSpectra<MSExperiment<PeakType> >(exp2);
          f.store(filename, exp2);
        }
        else
        {
          f.store(filename, exp);
        }
      }
      break;

      default:
      {
        MzMLFile f;
        f.getOptions() = options_;
        f.setLogType(log);
        f.store(filename, exp);
      }
      break;
      }
    }

    template <class FeatureType>
    bool loadFeatures(const String & filename, FeatureMap<FeatureType> & map, FileTypes::Type force_type = FileTypes::UNKNOWN)
    {
      //determine file type
      FileTypes::Type type;
      if (force_type != FileTypes::UNKNOWN)
      {
        type = force_type;
      }
      else
      {
        try
        {
          type = getType(filename);
        }
        catch (Exception::FileNotFound)
        {
          return false;
        }
      }

      //load right file
      if (type == FileTypes::FEATUREXML)
      {
        FeatureXMLFile().load(filename, map);
      }
      else if (type == FileTypes::TSV)
      {
        MsInspectFile().load(filename, map);
      }
      else if (type == FileTypes::PEPLIST)
      {
        SpecArrayFile().load(filename, map);
      }
      else if (type == FileTypes::KROENIK)
      {
        KroenikFile().load(filename, map);
      }
      else
      {
        return false;
      }

      return true;
    }

private:
    PeakFileOptions options_;
  };

} //namespace

#endif //OPENMS_FORMAT_FILEHANDLER_H