PeptideIndexing.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
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//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// --------------------------------------------------------------------------
// $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/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, std::vector<PeptideIdentification>& pep_ids);

    ExitCodes run(FASTAContainer<TFI_File>& proteins, std::vector<ProteinIdentification>& prot_ids, std::vector<PeptideIdentification>& pep_ids);

    ExitCodes run(FASTAContainer<TFI_Vector>& proteins, std::vector<ProteinIdentification>& prot_ids, std::vector<PeptideIdentification>& 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, std::vector<PeptideIdentification>& 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};
 };
}