InspectOutfile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
//
// This software is released under a three-clause BSD license:
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//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
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//    documentation and/or other materials provided with the distribution.
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//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// $Maintainer: Timo Sachsenberg $
// $Authors: Martin Langwisch $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/CONCEPT/Exception.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/MSExperiment.h>
#include <OpenMS/KERNEL/StandardTypes.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/FORMAT/FileHandler.h>
#include <OpenMS/FORMAT/FileTypes.h>


namespace OpenMS
{
  class OPENMS_DLLAPI InspectOutfile
  {
public:
    InspectOutfile();

    InspectOutfile(const InspectOutfile & inspect_outfile);

    virtual ~InspectOutfile();

    InspectOutfile & operator=(const InspectOutfile & inspect_outfile);

    bool operator==(const InspectOutfile & inspect_outfile) const;

    std::vector<Size> load(const String & result_filename, std::vector<PeptideIdentification> & peptide_identifications, ProteinIdentification & protein_identification, const double p_value_threshold, const String & database_filename = "");

    std::vector<Size> getWantedRecords(const String & result_filename, double p_value_threshold);

    void compressTrieDB(const String & database_filename, const String & index_filename, std::vector<Size> & wanted_records, const String & snd_database_filename, const String & snd_index_filename, bool append = false);

    void generateTrieDB(const String & source_database_filename, const String & database_filename, const String & index_filename, bool append = false, const String species = "");


    void getACAndACType(String line, String & accession, String & accession_type);

    void getPrecursorRTandMZ(const std::vector<std::pair<String, std::vector<std::pair<Size, Size> > > > & files_and_peptide_identification_with_scan_number, std::vector<PeptideIdentification> & ids);

    void getLabels(const String & source_database_filename, String & ac_label, String & sequence_start_label, String & sequence_end_label, String & comment_label, String & species_label);

    std::vector<Size> getSequences(const String & database_filename, const std::map<Size, Size> & wanted_records, std::vector<String> & sequences);

    void getExperiment(PeakMap & exp, String & type, const String & in_filename)
    {
      type.clear();
      exp.reset();
      //input file type
      FileHandler fh;
      FileTypes::Type in_type = fh.getTypeByContent(in_filename);
      if (in_type == FileTypes::UNKNOWN)
      {
        throw Exception::ParseError(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION, "Could not determine type of the file. Aborting!", in_filename);
      }
      type = FileTypes::typeToName(in_type);
      fh.loadExperiment(in_filename, exp, in_type, ProgressLogger::NONE, false, false);
    }

    bool getSearchEngineAndVersion(const String & cmd_output, ProteinIdentification & protein_identification);

    void readOutHeader(const String & filename, const String & header_line, Int & spectrum_file_column, Int & scan_column, Int & peptide_column, Int & protein_column, Int & charge_column, Int & MQ_score_column, Int & p_value_column, Int & record_number_column, Int & DB_file_pos_column, Int & spec_file_pos_column, Size & number_of_columns);

protected:
    static const Size db_pos_length_;         
    static const Size trie_db_pos_length_;         
    static const Size protein_name_length_;         
    static const Size record_length_;         
    static const char trie_delimiter_;         
    static const String score_type_;        
  };

} //namespace OpenMS