#
# = lib/evo/tool/multi_domain_seq_extractor - MultiDomainSeqExtractor class
#
# Copyright::    Copyright (C) 2017 Christian M. Zmasek
# License::      GNU Lesser General Public License (LGPL)

require 'lib/evo/util/constants'
require 'lib/evo/util/util'
require 'lib/evo/util/command_line_arguments'
require 'lib/evo/io/parser/hmmscan_multi_domain_extractor'

module Evoruby
  class MultiDomainSeqExtractor

    PRG_NAME       = "mdsx"
    PRG_VERSION    = "1.000"
    PRG_DESC       = "Extraction of multi domain sequences from hmmscan output"
    PRG_DATE       = "20170307"
    WWW            = "https://sites.google.com/site/cmzmasek/home/software/forester"

    HELP_OPTION_1                      = 'help'
    HELP_OPTION_2                      = 'h'
    def run()

      Util.print_program_information( PRG_NAME,
      PRG_VERSION,
      PRG_DESC ,
      PRG_DATE,
      WWW,
      STDOUT )

      if ( ARGV == nil || ( ARGV.length < 1 )  )
        print_help
        exit( -1 )
      end

      begin
        cla = CommandLineArguments.new( ARGV )
      rescue ArgumentError
        Util.fatal_error( PRG_NAME, "error: " + $!, STDOUT )
      end

      if ( cla.is_option_set?( HELP_OPTION_1 ) ||
      cla.is_option_set?( HELP_OPTION_2 ) )
        print_help
        exit( 0 )
      end

      unless ( cla.get_number_of_files == 2 || cla.get_number_of_files == 3 )
        print_help
        exit( -1 )
      end

      allowed_opts = Array.new

      disallowed = cla.validate_allowed_options_as_str( allowed_opts )
      if ( disallowed.length > 0 )
        Util.fatal_error( PRG_NAME,
        "unknown option(s): " + disallowed,
        STDOUT )
      end

      domain_id           = cla.get_file_name( 0 )
      hmmscan_output      = cla.get_file_name( 1 )
      fasta_sequence_file = ""
      outfile_base        = ""

      if cla.get_number_of_files == 3
        fasta_sequence_file = cla.get_file_name( 2 )
      else
        hmmscan_index = hmmscan_output.index(Constants::HMMSCAN)
        if ( hmmscan_index != nil )
          prefix = hmmscan_output[0 .. hmmscan_index-1 ]
          suffix = Constants::ID_NORMALIZED_FASTA_FILE_SUFFIX
          files = Dir.entries( "." )
          matching_files = Util.get_matching_files( files, prefix, suffix)
          if matching_files.length < 1
            Util.fatal_error( PRG_NAME, 'no file matching [' + prefix +
            '...' + suffix + '] present in current directory: need to indicate <file containing complete sequences in fasta format> as second argument' )
          end
          if matching_files.length > 1
            Util.fatal_error( PRG_NAME, 'more than one file matching [' +
            prefix  + '...' + suffix + '] present in current directory: need to indicate <file containing complete sequences in fasta format> as second argument' )
          end
          fasta_sequence_file = matching_files[ 0 ]
        else
          Util.fatal_error( PRG_NAME, 'input files do not seem in format for standard analysis pipeline, need to explicitly indicate all' )
        end
      end
      hmmscan_index = hmmscan_output.index(Constants::HMMSCAN)
      if hmmscan_index != nil
        outfile_base = hmmscan_output.sub(Constants::HMMSCAN, '_')
      else
        Util.fatal_error( PRG_NAME, 'input files do not seem in format for standard analysis pipeline, need to explicitly indicate all' )
      end

      log_str = ''

      log_str << PRG_NAME << Constants::LINE_DELIMITER
      log_str <<  PRG_VERSION << Constants::LINE_DELIMITER
      log_str << PRG_DESC << Constants::LINE_DELIMITER
      log_str << PRG_DATE << Constants::LINE_DELIMITER
      log_str << Constants::LINE_DELIMITER

      begin
        parser = HmmscanMultiDomainExtractor.new()
        parser.parse( domain_id,
        hmmscan_output,
        fasta_sequence_file,
        outfile_base,
        log_str)
      rescue ArgumentError, IOError => e
        Util.fatal_error( PRG_NAME, "error: " + e.to_s, STDOUT )

      rescue Exception => e
        puts e.backtrace
        Util.fatal_error( PRG_NAME, "unexpected exception: " + e.to_s, STDOUT )
      end

      puts
      Util.print_message( PRG_NAME, "OK" )
      puts

    end

    def print_help()
      puts
      puts "Usage:"
      puts
      puts "  " + PRG_NAME + ".rb <da> <hmmscan outputfile> [file containing complete sequences in fasta format]"
      puts
      puts "  options: -"
      puts
      puts "Examples:"
      puts
      puts "  " + PRG_NAME + ".rb "
      puts
      puts
    end

  end # class MultiDomainSeqExtractor

end # module Evoruby