UniProtXMLFile.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/FORMAT/XMLFile.h>
 
#include <functional>
#include <string>
#include <vector>
 
namespace OpenMS
{
  struct UniProtFeature
  {
    std::string type;          
    std::string id;            
    std::string description;   
    std::string location_sequence; 
    bool has_position{false};  
    bool has_range{false};     
    int  position{0};          
    int  begin{0};             
    int  end{0};               
    std::string original;      
    std::string variation;     
  };
 
  struct UniProtIsoform
  {
    std::string id;             
    std::string name;           
    std::string sequence_type;  
    std::string sequence_ref;   
  };
 
  struct UniProtEntry
  {
    std::string dataset;                       
    std::string accession;                     
    std::vector<std::string> alt_accessions;   
    std::string name;                          
    std::string full_name;                     
    std::string primary_gene;                  
    std::string ncbi_tax_id;                   
    std::string tax_name;                      
    std::string protein_existence;             
    std::string sequence_version;              
    std::string entry_version;                 
    std::string sequence;                      
    std::vector<UniProtFeature> features;      
    std::vector<UniProtIsoform> isoforms;      
  };
 
  class UniProtXMLFile :
    public Internal::XMLFile
  {
  public:
    UniProtXMLFile();
 
    ~UniProtXMLFile() override;
 
    void load(const std::string& filename, std::vector<UniProtEntry>& entries);
 
    void loadStreaming(const std::string& filename, const std::function<void(UniProtEntry&&)>& callback);
 
  private:
    UniProtXMLFile(const UniProtXMLFile&) = delete;
    UniProtXMLFile& operator=(const UniProtXMLFile&) = delete;
  };
 
} // namespace OpenMS