OSWParquetFile.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: Justin Sing $
// $Authors: Justin Sing, Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathExportConfig.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathExportData.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathInferenceData.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/config.h>
#include <map>
#include <memory>
#include <string>
#include <vector>
 
namespace OpenSwath
{
struct LightTargetedExperiment;
}
 
namespace OpenMS
{
class OPENMS_DLLAPI OSWParquetFile : public ProgressLogger
{
public:
  struct OPENMS_DLLAPI InferenceResults
  {
    InferenceLevel level = InferenceLevel::Peptide;
    InferenceContext context = InferenceContext::Global;
    std::vector<LevelContextResultRow> rows;
  };
 
  OSWParquetFile(const std::string& filename, const OpenSwath::LightTargetedExperiment& library, bool load_transition_metadata = true);
  ~OSWParquetFile() override;
  OSWParquetFile(const OSWParquetFile&) = delete;
  OSWParquetFile& operator=(const OSWParquetFile&) = delete;
  OSWParquetFile(OSWParquetFile&&);
  OSWParquetFile& operator=(OSWParquetFile&&);
 
  std::vector<LevelContextInputRow> readLevelContextData(InferenceLevel level, InferenceContext context) const;
 
  void writeLevelContextResults(std::vector<InferenceResults> results);
 
  std::vector<OpenSwathExportRow> readOpenSwathExportRows(const OpenSwathExportFilterConfig& config) const;
  OpenSwathFeatureScoreTable readOpenSwathFeatureScoreTable(const OpenSwathParquetExportConfig& config) const;
  OpenSwathTransitionScoreTable readOpenSwathTransitionScoreTable(const OpenSwathParquetExportConfig& config) const;
  std::map<Int64, std::string> readRunBasenames() const;
 
  void commit();
 
private:
  class Impl;
  std::unique_ptr<Impl> impl_;
};
} // namespace OpenMS