FileHandler.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
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//    may be used to endorse or promote products derived from this software
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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