// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * 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.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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
{
  /**
      @brief Representation of an Inspect outfile

      This class serves to read in an Inspect outfile and write an idXML file

  @todo Handle Modifications (Andreas)

      @ingroup FileIO
  */
  class OPENMS_DLLAPI InspectOutfile
  {
public:
    /// default constructor
    InspectOutfile();

    /// copy constructor
    InspectOutfile(const InspectOutfile & inspect_outfile);

    /// destructor
    virtual ~InspectOutfile();

    /// assignment operator
    InspectOutfile & operator=(const InspectOutfile & inspect_outfile);

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

    /** load the results of an Inspect search

            @param result_filename Input parameter which is the file name of the input file
            @param peptide_identifications Output parameter which holds the peptide identifications from the given file
            @param protein_identification Output parameter which holds the protein identifications from the given file
            @param p_value_threshold
            @param database_filename
            @throw FileNotFound is thrown if the given file could not be found
            @throw ParseError is thrown if the given file could not be parsed
            @throw FileEmpty is thrown if the given file is empty
    */
    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 = "");

    /** loads only results which exceeds a given P-value threshold

            @param result_filename The filename of the results file
            @param p_value_threshold Only identifications exceeding this threshold are read
            @throw FileNotFound is thrown is the file is not found
            @throw FileEmpty is thrown if the given file is empty
    */
    std::vector<Size> getWantedRecords(const String & result_filename, double p_value_threshold);

    /** generates a trie database from another one, using the wanted records only

            @throw Exception::FileNotFound
            @throw Exception::ParseError
            @throw Exception::UnableToCreateFile

    */
    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);

    /** generates a trie database from a given one (the type of database is determined by getLabels)
            @throw Exception::FileNotFound
            @throw Exception::UnableToCreateFile
    */
    void generateTrieDB(const String & source_database_filename, const String & database_filename, const String & index_filename, bool append = false, const String& species = "");


    /// retrieve the accession type and accession number from a protein description line
    /// (e.g. from FASTA line: >gi|5524211|gb|AAD44166.1| cytochrome b [Elephas maximus maximus], get ac:AAD44166.1 ac type: GenBank)
    void getACAndACType(String line, String & accession, String & accession_type);

    /** retrieve the precursor retention time and mz value

            @throw Exception::ParseError
    */
    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);

    /** retrieve the labels of a given database (at the moment FASTA and Swissprot)

            @throw Exception::FileNotFound
            @throw Exception::ParseError
    */
    void getLabels(const String & source_database_filename, String & ac_label, String & sequence_start_label, String & sequence_end_label, String & comment_label, String & species_label);

    /** retrieve sequences from a trie database

            @throw Exception::FileNotFound
    */
    std::vector<Size> getSequences(const String & database_filename, const std::map<Size, Size> & wanted_records, std::vector<String> & sequences);

    /** 
      get the experiment from a file

      @throw Exception::ParseError is thrown if the file could not be parsed or the filetype could not be determined
    */
    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);
    }

    /**
        @brief get the search engine and its version from the output of the InsPecT executable without parameters

            returns true on success, false otherwise
    */
    bool getSearchEngineAndVersion(const String & cmd_output, ProteinIdentification & protein_identification);

    /** @brief read the header of an inspect output file and retrieve various information
            @throw Exception::ParseError
    */
    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:
    /// a record in the index file that belongs to a trie database consists of three parts
    /// 1) the protein's position in the original database
    /// 2) the protein's position in the trie database
    /// 3) the name of the protein (the line with the accession identifier)
    static const Size db_pos_length_;         ///< length of 1)
    static const Size trie_db_pos_length_;         ///< length of 2)
    static const Size protein_name_length_;         ///< length of 3)
    static const Size record_length_;         ///< length of the whole record
    static const char trie_delimiter_;         ///< the sequences in the trie database are delimited by this character
    static const String score_type_;        ///< type of score
  };

} //namespace OpenMS

