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 2002-2023.
//
// This software is released under a three-clause BSD license:
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//  * 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.
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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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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
 
namespace OpenMS
{
  class PeakFileOptions;
  class MSSpectrum;
  class MSExperiment;
  class FeatureMap;
  class ConsensusMap;
  class TargetedExperiment;
 
  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 String stripExtension(const String& filename);
 
    static String swapExtension(const String& filename, const FileTypes::Type new_type);
 
    
    static FileTypes::Type getConsistentOutputfileType(const String& output_filename, const String& requested_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);
 
    bool storeFeatures(const String& filename, const FeatureMap& map);
 
    bool storeConsensusFeatures(const String& filename, const ConsensusMap& map);
 
    bool loadConsensusFeatures(const String& filename, ConsensusMap& map);
 
    bool loadIdentifications(const String& filename, std::vector<ProteinIdentification> additional_proteins, std::vector<PeptideIdentification> additional_peptides);
 
    bool storeTransitions(const String& filename, const TargetedExperiment& library);
 
    static String computeFileHash(const String& filename);
 
private:
    PeakFileOptions options_;
 
  };
 
} //namespace