PeptideIndexing.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: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/FASTAContainer.h>
#include <OpenMS/DATASTRUCTURES/ListUtils.h>
#include <OpenMS/DATASTRUCTURES/StringUtilsSimple.h>
#include <OpenMS/FORMAT/FASTAFile.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
 
namespace OpenMS
{
 
 class OPENMS_DLLAPI PeptideIndexing :
    public DefaultParamHandler, public ProgressLogger
  {
public:
    static char const* const AUTO_MODE; /* = 'auto' */ 
 
    enum ExitCodes
    {
      EXECUTION_OK,
      DATABASE_EMPTY,
      PEPTIDE_IDS_EMPTY,
      ILLEGAL_PARAMETERS,
      UNEXPECTED_RESULT
    };
 
    enum class Unmatched
    {
      IS_ERROR,  
      WARN,      
      REMOVE,    
      SIZE_OF_UNMATCHED
    };
    static const std::array<std::string, (Size)Unmatched::SIZE_OF_UNMATCHED> names_of_unmatched;
    
    enum class MissingDecoy
    {
      IS_ERROR,
      WARN,
      SILENT,
      SIZE_OF_MISSING_DECOY
    };
    static const std::array<std::string, (Size)MissingDecoy::SIZE_OF_MISSING_DECOY> names_of_missing_decoy;
 
    PeptideIndexing();
 
    ~PeptideIndexing() override;
 
    ExitCodes run(std::vector<FASTAFile::FASTAEntry>& proteins, std::vector<ProteinIdentification>& prot_ids, PeptideIdentificationList& pep_ids);
 
    ExitCodes run(FASTAContainer<TFI_File>& proteins, std::vector<ProteinIdentification>& prot_ids, PeptideIdentificationList& pep_ids);
 
    ExitCodes run(FASTAContainer<TFI_Vector>& proteins, std::vector<ProteinIdentification>& prot_ids, PeptideIdentificationList& pep_ids);
 
    const String& getDecoyString() const;
 
    bool isPrefix() const;
 
 protected:
    void updateMembers_() override;
 
    template<typename T> ExitCodes run_(FASTAContainer<T>& proteins, std::vector<ProteinIdentification>& prot_ids, PeptideIdentificationList& pep_ids);
 
    String decoy_string_{};
    bool prefix_{ false };
    MissingDecoy missing_decoy_action_ = MissingDecoy::IS_ERROR;
    String enzyme_name_{};
    String enzyme_specificity_{};
 
    bool write_protein_sequence_{ false };
    bool write_protein_description_{ false };
    bool keep_unreferenced_proteins_{ false };
    Unmatched unmatched_action_ = Unmatched::IS_ERROR;
    bool IL_equivalent_{ false };
    bool allow_nterm_protein_cleavage_{ true };
 
    Int aaa_max_{0};
    Int mm_max_{0};
 };
}