FileHandler.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2017.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    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.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------

#ifndef OPENMS_FORMAT_FILEHANDLER_H
#define OPENMS_FORMAT_FILEHANDLER_H

#include <OpenMS/config.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>

namespace OpenMS
{
  class PeakFileOptions;
  class MSSpectrum;
  class MSExperiment;
  class FeatureMap;

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


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

    static bool hasValidExtension(const String& filename, const FileTypes::Type type);

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

    static bool isSupported(FileTypes::Type type);

    PeakFileOptions& getOptions();

    const PeakFileOptions& getOptions() const;

    void setOptions(const PeakFileOptions&);

    bool loadExperiment(const String& filename, MSExperiment& exp, FileTypes::Type force_type = FileTypes::UNKNOWN, ProgressLogger::LogType log = ProgressLogger::NONE, const bool rewrite_source_file = true, const bool compute_hash = true);

    void storeExperiment(const String& filename, const MSExperiment& exp, ProgressLogger::LogType log = ProgressLogger::NONE);

    bool loadFeatures(const String& filename, FeatureMap& map, FileTypes::Type force_type = FileTypes::UNKNOWN);

    static String computeFileHash(const String& filename);

private:
    PeakFileOptions options_;

  };

} //namespace

#endif //OPENMS_FORMAT_FILEHANDLER_H