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 2002-2017.
//
// This software is released under a three-clause BSD license:
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Chris Bielow $
// $Authors: Andreas Bertsch, Chris Bielow, Knut Reinert $
// --------------------------------------------------------------------------

#ifndef OPENMS_ANALYSIS_ID_PEPTIDEINDEXING_H
#define OPENMS_ANALYSIS_ID_PEPTIDEINDEXING_H

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/FORMAT/FASTAFile.h>

#include <fstream>

namespace OpenMS
{

 class OPENMS_DLLAPI PeptideIndexing :
    public DefaultParamHandler
  {
public:

    enum ExitCodes
    {
      EXECUTION_OK,
      DATABASE_EMPTY,
      PEPTIDE_IDS_EMPTY,
      DATABASE_CONTAINS_MULTIPLES,
      ILLEGAL_PARAMETERS,
      UNEXPECTED_RESULT
    };

    PeptideIndexing();

    virtual ~PeptideIndexing();

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

protected:
    virtual void updateMembers_();

    void writeLog_(const String& text) const;

    void writeDebug_(const String& text, const Size min_level) const;

    String log_file_;
    mutable std::ofstream log_;
    bool debug_;

    String decoy_string_;
    bool prefix_;
    String missing_decoy_action_;
    String enzyme_name_;
    String enzyme_specificity_;

    bool write_protein_sequence_;
    bool write_protein_description_;
    bool keep_unreferenced_proteins_;
    bool allow_unmatched_;
    bool full_tolerant_search_;
    bool IL_equivalent_;

    Size aaa_max_;
    UInt mismatches_max_;
    bool filter_aaa_proteins_;

  };
}

#endif // OPENMS_ANALYSIS_ID_PEPTIDEINDEXING_H