FileHandler.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: Marc Sturm $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/TransformationDescription.h>
#include <OpenMS/FORMAT/FileTypes.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/OPTIONS/PeakFileOptions.h>
#include <OpenMS/FORMAT/OPTIONS/FeatureFileOptions.h>
 
// Forward declarations instead of full includes — all these types appear only
// as references/pointers in method signatures, so full definitions are not needed.
namespace OpenMS
{
  class PeakFileOptions;
  class MSSpectrum;
  class MSExperiment;
  class FeatureMap;
  class ConsensusMap;
  class TargetedExperiment;
  class ProteinIdentification;
  class PeptideIdentificationList;
 
  class OPENMS_DLLAPI FileHandler
  {
public:
    static FileTypes::Type getType(const std::string& filename);
 
 
    static FileTypes::Type getTypeByFileName(const std::string& filename);
 
 
    static bool hasValidExtension(const std::string& filename, const FileTypes::Type type);
 
 
    static std::string stripExtension(const std::string& filename);
 
 
    static std::string swapExtension(const std::string& filename, const FileTypes::Type new_type);
 
    
    static FileTypes::Type getConsistentOutputfileType(const std::string& output_filename, const std::string& requested_type);
 
 
    static FileTypes::Type getTypeByContent(const std::string& filename);
 
    static bool isSupported(FileTypes::Type type);
 
    PeakFileOptions& getOptions();
 
    const PeakFileOptions& getOptions() const;
 
    FeatureFileOptions& getFeatOptions();
 
    const FeatureFileOptions& getFeatOptions() const;
 
    void setOptions(const PeakFileOptions&);
 
    void setFeatOptions(const FeatureFileOptions&);
 
    void loadExperiment(const std::string& filename, PeakMap& exp, const std::vector<FileTypes::Type> allowed_types = std::vector<FileTypes::Type>(),
                        ProgressLogger::LogType log = ProgressLogger::NONE, const bool rewrite_source_file = false,
                        const bool compute_hash = false);
 
    void storeExperiment(const std::string& filename, const PeakMap& exp, const std::vector<FileTypes::Type> allowed_types = {}, ProgressLogger::LogType log = ProgressLogger::NONE);
 
    void loadSpectrum(const std::string& filename, MSSpectrum& spec, const std::vector<FileTypes::Type> allowed_types = {});
 
    void storeSpectrum(const std::string& filename, MSSpectrum& spec, const std::vector<FileTypes::Type> allowed_types = {});
 
    void loadFeatures(const std::string& filename, FeatureMap& map, const std::vector<FileTypes::Type> allowed_types = {}, ProgressLogger::LogType log = ProgressLogger::NONE);
 
    void storeFeatures(const std::string& filename, const FeatureMap& map, const std::vector<FileTypes::Type> allowed_types = {}, ProgressLogger::LogType log = ProgressLogger::NONE);
 
    void loadConsensusFeatures(const std::string& filename, ConsensusMap& map, const std::vector<FileTypes::Type> allowed_types = {}, ProgressLogger::LogType log = ProgressLogger::NONE);
 
    void storeConsensusFeatures(const std::string& filename, const ConsensusMap& map, const std::vector<FileTypes::Type> allowed_types = {}, ProgressLogger::LogType log = ProgressLogger::NONE);
 
    void loadIdentifications(const std::string& filename, std::vector<ProteinIdentification>& additional_proteins, PeptideIdentificationList& additional_peptides, const std::vector<FileTypes::Type> allowed_types = {}, ProgressLogger::LogType log = ProgressLogger::NONE);
 
    void storeIdentifications(const std::string& filename, const std::vector<ProteinIdentification>& additional_proteins, const PeptideIdentificationList& additional_peptides, const std::vector<FileTypes::Type> allowed_types = {}, ProgressLogger::LogType log = ProgressLogger::NONE);
 
    void loadTransitions(const std::string& filename, TargetedExperiment& library, const std::vector<FileTypes::Type> allowed_types = {}, ProgressLogger::LogType log = ProgressLogger::NONE);
 
    void storeTransitions(const std::string& filename, const TargetedExperiment& library, const std::vector<FileTypes::Type> allowed_types = {}, ProgressLogger::LogType log = ProgressLogger::NONE);
 
    void loadTransformations(const std::string& filename, TransformationDescription& map, bool fit_model=true, const std::vector<FileTypes::Type> allowed_types = {});
 
    void storeTransformations(const std::string& filename, const TransformationDescription& map, const std::vector<FileTypes::Type> allowed_types = {});
 
    void storeQC(const std::string& input_file,
               const std::string& filename,
               const MSExperiment& exp,
               const FeatureMap& feature_map,
               std::vector<ProteinIdentification>& prot_ids,
               PeptideIdentificationList& pep_ids,
               const ConsensusMap& consensus_map,
               const std::string& contact_name = "",
               const std::string& contact_address = "",
               const std::string& description = "",
               const std::string& label = "label",
               const bool remove_duplicate_features = false,
               const std::vector<FileTypes::Type> allowed_types = {});
 
    static std::string computeFileHash(const std::string& filename);
 
private:
    void applyPostLoadOptions_(MSExperiment& exp) const;
 
    PeakFileOptions options_;
    FeatureFileOptions f_options_;
  };
 
} //namespace