TransitionPQPFile.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: George Rosenberger $
// $Authors: George Rosenberger, Hannes Roest $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathLibraryIDNormalizer.h>
#include <OpenMS/ANALYSIS/OPENSWATH/TransitionTSVFile.h>
 
#include <optional>
#include <string>
 
namespace OpenMS
{
  class SqliteConnector;
 
  class OPENMS_DLLAPI TransitionPQPFile :
    public TransitionTSVFile
  {
 
private:
 
    struct PQPSqlQueryInfo
    {
      std::string select_sql;      
      bool drift_time_exists;      
      bool gene_exists;            
      bool compound_exists;        
      bool peptidoforms_exists;    
    };
 
    PQPSqlQueryInfo buildPQPSelectQuery_(SqliteConnector& conn, bool legacy_traml_id, bool stable_order) const;
 
    void readPQPInput_(const char* filename, std::vector<TSVTransition>& transition_list, bool legacy_traml_id = false);
 
    void streamPQPToLightTargetedExperiment_(const char* filename, OpenSwath::LightTargetedExperiment& exp, bool legacy_traml_id = false);
 
    void writePQPOutput_(const char* filename, OpenMS::TargetedExperiment& targeted_exp);
 
public:
 
 
    TransitionPQPFile();
 
    ~TransitionPQPFile() override;
 
    void convertTargetedExperimentToPQP(const char* filename, OpenMS::TargetedExperiment& targeted_exp);
 
    void convertLightTargetedExperimentToPQP(
      const char* filename,
      const OpenSwath::LightTargetedExperiment& targeted_exp);
 
    void convertLightTargetedExperimentToPQP(
      const char* filename,
      const OpenSwath::LightTargetedExperiment& targeted_exp,
      const OpenSwathLibraryIDNormalizer::SourceIDMapping* source_ids);
 
    void appendLightTargetedExperimentToPQP(
      const std::string& filename,
      const OpenSwath::LightTargetedExperiment& targeted_exp,
      const std::optional<OpenSwathLibraryIDNormalizer::SourceIDMapping>& source_ids = std::nullopt);
 
    void convertPQPToTargetedExperiment(const char* filename, OpenMS::TargetedExperiment& targeted_exp, bool legacy_traml_id = false);
 
    void convertPQPToTargetedExperiment(const char* filename, OpenSwath::LightTargetedExperiment& targeted_exp, bool legacy_traml_id = false);
 
    std::unordered_map<std::string, std::string> getPQPIDToTraMLIDMap(const char* filename, std::string tableName);
 
    std::unordered_map<std::string, std::string> getPQPCurrentIDToTraMLIDMap(
      const char* filename,
      const std::string& tableName);
 
  };
}