OpenSwathOSWWriter.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 $
// --------------------------------------------------------------------------
 
#pragma once
 
// Interfaces
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
#include <OpenMS/CONCEPT/UniqueIdGenerator.h>
 
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/FORMAT/SqliteConnector.h>
 
#include <array>
#include <cstddef>
#include <fstream>
#include <string>
#include <vector>
#include <memory>
#include <mutex>
 
namespace OpenMS
{
 
  class OPENMS_DLLAPI OpenSwathOSWWriter
  {
    std::string output_filename_;
    OpenMS::UInt64 run_id_ = 0;
    bool doWrite_;
    bool enable_uis_scoring_;
    // persistent sqlite connector to avoid reopening DB on each write
    mutable std::unique_ptr<SqliteConnector> conn_;
    mutable std::mutex conn_mutex_;
 
  public:
    struct OPENMS_DLLAPI OSWValue
    {
      enum class Type : unsigned char
      {
        Null,
        Int64,
        Double,
        Text
      };
 
      union Storage
      {
        Int64 int_value;
        double double_value;
        std::string* text_value; 
 
        Storage();
        ~Storage();
      };
 
      Type type;
      Storage storage;
 
      OSWValue();
      ~OSWValue();
      OSWValue(std::nullptr_t);
      OSWValue(const char* value);
      OSWValue(const std::string& value);
      OSWValue(Int64 value);
      OSWValue(UInt64 value);
      OSWValue(int value);
      OSWValue(double value);
      OSWValue(const OSWValue& rhs);
      OSWValue(OSWValue&& rhs) noexcept;
      OSWValue& operator=(const OSWValue& rhs);
      OSWValue& operator=(OSWValue&& rhs) noexcept;
 
      static OSWValue null();
 
      static OSWValue text(const std::string& value);
 
      bool isNull() const;
 
      Int64 asInt() const;
 
      double asDouble() const;
 
      const std::string& asText() const;
 
    private:
      void destroyText_();
      void copyFrom_(const OSWValue& rhs);
      void moveFrom_(OSWValue&& rhs);
    };
 
    static constexpr Size FEATURE_COLUMN_COUNT = 11;
    static constexpr Size FEATURE_MS1_COLUMN_COUNT = 18;
    static constexpr Size FEATURE_MS2_COLUMN_COUNT = 38;
    static constexpr Size FEATURE_PRECURSOR_COLUMN_COUNT = 4;
    static constexpr Size FEATURE_TRANSITION_COLUMN_COUNT = 43;
 
    using FeatureRow = std::array<OSWValue, FEATURE_COLUMN_COUNT>;
    using FeatureMS1Row = std::array<OSWValue, FEATURE_MS1_COLUMN_COUNT>;
    using FeatureMS2Row = std::array<OSWValue, FEATURE_MS2_COLUMN_COUNT>;
    using FeaturePrecursorRow = std::array<OSWValue, FEATURE_PRECURSOR_COLUMN_COUNT>;
    using FeatureTransitionRow = std::array<OSWValue, FEATURE_TRANSITION_COLUMN_COUNT>;
 
    struct OPENMS_DLLAPI OSWData
    {
      std::vector<FeatureRow> feature_rows;
      std::vector<FeatureMS1Row> feature_ms1_rows;
      std::vector<FeatureMS2Row> feature_ms2_rows;
      std::vector<FeaturePrecursorRow> feature_precursor_rows;
      std::vector<FeatureTransitionRow> feature_transition_rows;
 
      void reserve(Size row_count);
 
      void reserve(Size feature_row_count, Size transition_row_count);
 
      void append(OSWData&& rhs);
 
      bool empty() const;
 
      Size rowCount() const;
 
      UInt64 estimateMemoryUsage() const;
    };
 
    OpenSwathOSWWriter(const std::string& output_filename,
              bool uis_scores = false);
 
    bool isActive() const;
 
    void writeHeader();
 
    void addRun(const UInt64 run_id, const std::string& input_filename);
 
    void setRunId(const UInt64 run_id);
 
    UInt64 countFeaturesForRun(const UInt64 run_id) const;
 
    void clearRunData(const UInt64 run_id);
 
    std::string getScore(const Feature& feature, const std::string& score_name) const;
 
    std::vector<std::string> getSeparateScore(const Feature& feature, const std::string& score_name) const;
 
    OSWData prepareRows(const OpenSwath::LightCompound& pep,
        const OpenSwath::LightTransition* transition,
        const FeatureMap& output, const std::string& id) const;
 
    void prepareRowsInto(OSWData& rows,
        const OpenSwath::LightCompound& pep,
        const OpenSwath::LightTransition* transition,
        const FeatureMap& output, const std::string& id) const;
 
    std::string prepareLine(const OpenSwath::LightCompound& pep,
        const OpenSwath::LightTransition* transition,
        const FeatureMap& output, const std::string& id) const;
 
    void writeRows(const OSWData& osw_output);
 
    void writeLines(const std::vector<std::string>& to_osw_output);
 
  };
 
 
}