QPXIdentity.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: Timo Sachsenberg $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/config.h>
 
#include <OpenMS/CONCEPT/Types.h>
 
#include <cstdint>
#include <optional>
#include <string>
#include <unordered_map>
#include <variant>
#include <vector>
 
namespace OpenMS
{
 
namespace QPXIdentity
{
  using FeatureLinks = std::unordered_map<Int64, Int64>;
 
  struct Null {};
 
  struct Float32
  {
    float value;
  };
 
  using Value = std::variant<Null,                      
                             std::string,               
                             Int64,                     
                             Float32,                   
                             std::vector<Int32>,        
                             std::vector<std::string>>; 
 
  OPENMS_DLLAPI std::string formatFloat(float value);
 
  OPENMS_DLLAPI std::string canonical(const std::vector<Value>& values,
                                      const std::vector<size_t>& unordered_list_indices = {});
 
  OPENMS_DLLAPI Int64 deriveId(const std::vector<Value>& values,
                               const std::vector<size_t>& unordered_list_indices = {});
 
  // -------------------------------------------------------------------------------------
  // Per-view identities
  //
  // The composite and its ORDER are declared once, here, and every exporter goes through
  // these functions. The order is part of the hash, so a call site assembling its own vector
  // would be one argument swap away from ids that no other reader can reproduce.
  //
  // These are the composites qpxc hard-codes for OpenMS `-out_qpx` input
  // (qpx/converters/openms/converter.py), so a conversion re-derives the same values.
  // -------------------------------------------------------------------------------------
 
  OPENMS_DLLAPI extern const char* const FEATURE_COMPOSITE;
  OPENMS_DLLAPI extern const char* const PSM_COMPOSITE;
  OPENMS_DLLAPI extern const char* const PG_COMPOSITE;
 
  OPENMS_DLLAPI Int64 featureId(const std::string& run_file_name,
                                const std::string& peptidoform,
                                Int64 charge,
                                std::optional<float> rt,
                                const std::vector<Int32>& scan,
                                float observed_mz);
 
  OPENMS_DLLAPI Int64 psmId(const std::string& run_file_name,
                            const std::vector<Int32>& scan,
                            const std::string& peptidoform,
                            Int64 charge);
 
  OPENMS_DLLAPI Int64 pgId(const std::vector<std::string>& pg_accessions,
                           const std::vector<std::string>& grouped_runs,
                           const std::optional<std::string>& label);
 
} // namespace QPXIdentity
 
} // namespace OpenMS