UniPEFFEntries.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 "UniProtXMLFile.h"
 
#include <cstdint>
#include <limits>
#include <map>
#include <string>
#include <unordered_map>
#include <vector>
 
namespace OpenMS::UniPEFFEntries
{
  // ──────────────────────────────────────────────────────────────────
  // ptmlist.txt — UniProt PTM controlled vocabulary
  // ──────────────────────────────────────────────────────────────────
 
  enum class ChainPosition
  {
    Anywhere,   
    NTerminal,  
    CTerminal   
  };
 
  struct PtmEntry
  {
    std::string id;               
    std::string accession;        
    std::string psi_mod;          
    std::string unimod;           
    std::vector<ChainPosition> chain_positions{};
  };
 
  using PtmMap = std::unordered_map<std::string, PtmEntry>;
 
  std::vector<ChainPosition> parseChainPositions(const std::string& pp);
 
  using SkippedIsoformCounts = std::map<std::string, size_t>;
 
  // ──────────────────────────────────────────────────────────────────
  // Intermediate annotation structures (built per UniProtEntry)
  // ──────────────────────────────────────────────────────────────────
 
  constexpr uint32_t kNoId = std::numeric_limits<uint32_t>::max();
 
  struct ModResItem
  {
    int  position{0};        
    bool is_halfcys{false};  
    const PtmEntry* ptm{nullptr};  
    std::string name;        
    uint32_t annotation_id{kNoId};  
  };
 
  struct VariantSimpleItem
  {
    int  position{0};
    char new_aa{'?'};
    uint32_t annotation_id{kNoId};  
  };
 
  struct VariantComplexItem
  {
    int begin{0};
    int end{0};
    std::string new_seq;
    uint32_t annotation_id{kNoId};  
  };
 
  struct ProcessedItem
  {
    int begin{0};
    int end{0};
    std::string cv;          
    std::string type_name;   
    uint32_t annotation_id{kNoId};  
  };
 
  struct DisulfidePairItem
  {
    size_t idx_a{0};
    size_t idx_b{0};
    bool valid{false};       
    uint32_t annotation_id{kNoId};  
  };
 
  struct EntryAnnotations
  {
    std::vector<ModResItem> regular_mods;
    std::vector<ModResItem> halfcys;
    std::vector<DisulfidePairItem> disulfides;   
    std::vector<VariantSimpleItem> simple_variants;
    std::vector<VariantComplexItem> complex_variants;
    std::vector<ProcessedItem> processed;
 
    std::vector<ModResItem> mods;
  };
 
  struct IsoformEntry
  {
    std::string accession;  
    std::string name;       
    std::string sequence;   
    EntryAnnotations annotations;
  };
 
  struct PreparedEntry
  {
    UniProtEntry source;
    EntryAnnotations annotations;
    size_t isoform_scoped_applied{0};  
    size_t isoform_scoped_skipped{0};  
    size_t canonical_mapped{0};
    size_t canonical_unmapped{0};
    std::string prefix;       
    std::vector<IsoformEntry> isoforms;  
  };
 
  struct IsoformScopedTracker
  {
    size_t applied{0};
    size_t applied_entries{0};
    size_t skipped{0};
    size_t skipped_entries{0};
 
    void add(size_t applied_in_entry, size_t skipped_in_entry)
    {
      applied += applied_in_entry;
      if (applied_in_entry > 0) ++applied_entries;
      skipped += skipped_in_entry;
      if (skipped_in_entry > 0) ++skipped_entries;
    }
  };
 
  bool isResidueCode(char c);
 
  std::string positionOrUnknown(int p);
 
  PreparedEntry prepareEntry(UniProtEntry&& e, const PtmMap& ptms, const std::string& prefix_override,
                             bool option_b, bool record_processing, bool record_aa_mods,
                             bool record_variants, bool record_isoforms, bool map_canonical_features,
                             SkippedIsoformCounts& skipped_isoforms);
} // namespace OpenMS::UniPEFFEntries