#
# = lib/evo/io/parser/hmmscan_domain_extractor.rb - HmmscanDomainExtractor class
#
# Copyright::  Copyright (C) 2012 Christian M. Zmasek
# License::    GNU Lesser General Public License (LGPL)
#
# $Id:  $


require 'lib/evo/util/constants'
require 'lib/evo/msa/msa_factory'
require 'lib/evo/io/msa_io'
require 'lib/evo/io/writer/fasta_writer'
require 'lib/evo/io/parser/fasta_parser'


module Evoruby

  class HmmscanDomainExtractor

    def initialize
    end

    # raises ArgumentError, IOError, StandardError
    def parse( domain_id,
        hmmscan_output,
        fasta_sequence_file,
        outfile,
        passed_seqs_outfile,
        failed_seqs_outfile,
        e_value_threshold,
        length_threshold,
        add_position,
        add_domain_number,
        add_species,
        min_linker,
        log )

      Util.check_file_for_readability( hmmscan_output )
      Util.check_file_for_readability( fasta_sequence_file )
      Util.check_file_for_writability( outfile + ".fasta" )
      Util.check_file_for_writability( passed_seqs_outfile )
      Util.check_file_for_writability( failed_seqs_outfile )

      in_msa = nil
      factory = MsaFactory.new()
      in_msa = factory.create_msa_from_file( fasta_sequence_file, FastaParser.new() )

      if ( in_msa == nil || in_msa.get_number_of_seqs() < 1 )
        error_msg = "could not find fasta sequences in " + fasta_sequence_file
        raise IOError, error_msg
      end

      out_msa = Msa.new

      failed_seqs = Msa.new
      passed_seqs = Msa.new
      out_msa_pairs = nil
      out_msa_isolated = nil
      out_msa_singles = nil
      if min_linker
        out_msa_pairs = Msa.new
        out_msa_isolated = Msa.new
        out_msa_singles = Msa.new
      end

      ld = Constants::LINE_DELIMITER

      domain_pass_counter     = 0
      domain_fail_counter     = 0
      proteins_with_failing_domains = 0
      max_domain_copy_number_per_protein = -1
      max_domain_copy_number_sequence    = ""

      hmmscan_datas = Array.new

      File.open( hmmscan_output ) do | file |
        while line = file.gets
          if !is_ignorable?( line ) && line =~ /^\S+\s+/

            #         tn      acc     tlen    query   acc     qlen    Evalue  score   bias    #       of      c-E     i-E     score   bias    hf      ht      af      at      ef      et      acc     desc
            #         1       2       3       4       5       6       7       8       9       10      11      12      13      14      15      16      17      18      19      20      21      22      23
            line =~ /^(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(.*)/

            if domain_id != $1
              next
            end

            sequence = $4
            number   = $10.to_i
            out_of   = $11.to_i
            env_from = $20.to_i
            env_to   = $21.to_i
            i_e_value  = $13.to_f

            if ( ( ( e_value_threshold < 0.0 ) || ( i_e_value <= e_value_threshold ) ) &&
                 ( ( length_threshold <= 0 )   || ( env_to - env_from + 1 ) >= length_threshold.to_f ) )
              hmmscan_datas << HmmsearchData.new( sequence, number, out_of, env_from, env_to, i_e_value )
              if ( number > max_domain_copy_number_per_protein )
                max_domain_copy_number_sequence    = sequence
                max_domain_copy_number_per_protein = number
              end
            else # failed
              print( domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)" )
              log << domain_fail_counter.to_s + ": " + sequence.to_s + " did not meet threshold(s)"
              if ( ( e_value_threshold.to_f >= 0.0 ) && ( i_e_value > e_value_threshold ) )
                print( " iE=" + i_e_value.to_s )
                log << " iE=" + i_e_value.to_s
              end
              if ( ( length_threshold.to_f > 0 ) && ( env_to - env_from + 1 ) < length_threshold.to_f )
                le = env_to - env_from + 1
                print( " l=" + le.to_s )
                log << " l=" + le.to_s
              end
              print( ld )
              log << ld
              domain_fail_counter  += 1
            end

            if number > out_of
              error_msg = "number > out_of ! (this should not have happened)"
              raise StandardError, error_msg
            end

            if number == out_of
              if !hmmscan_datas.empty?
                process_hmmscan_datas( hmmscan_datas,
                  in_msa,
                  add_position,
                  add_domain_number,
                  add_species,
                  out_msa,
                  out_msa_singles,
                  out_msa_pairs,
                  out_msa_isolated,
                  min_linker )
                domain_pass_counter += hmmscan_datas.length
                if passed_seqs.find_by_name_start( sequence, true ).length < 1
                  add_sequence( sequence, in_msa, passed_seqs )
                else
                  error_msg = "this should not have happened"
                  raise StandardError, error_msg
                end
              else
                if failed_seqs.find_by_name_start( sequence, true ).length < 1
                  add_sequence( sequence, in_msa, failed_seqs )
                  proteins_with_failing_domains += 1
                else
                  error_msg = "this should not have happened"
                  raise StandardError, error_msg
                end
              end
              hmmscan_datas.clear
            end

          end
        end #  while line = file.gets
      end # File.open( hmmsearch_output ) do | file |



      if domain_pass_counter < 1
        error_msg = "no domain sequences were extracted"
        raise IOError, error_msg
      end

      log << ld
      puts( "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s )
      log << "Max domain copy number per protein : " + max_domain_copy_number_per_protein.to_s
      log << ld

      if ( max_domain_copy_number_per_protein > 1 )
        puts( "First protein with this copy number: " + max_domain_copy_number_sequence )
        log << "First protein with this copy number: " + max_domain_copy_number_sequence
        log << ld
      end

      write_msa( out_msa, outfile + ".fasta"  )
      write_msa( passed_seqs, passed_seqs_outfile )
      write_msa( failed_seqs, failed_seqs_outfile )

      if out_msa_pairs
        write_msa( out_msa_pairs, outfile +"_" + min_linker.to_s + ".fasta")
      end

      if out_msa_singles
        write_msa( out_msa_singles, outfile +"_singles" + ".fasta")
      end

      if out_msa_isolated
        write_msa( out_msa_isolated, outfile + "_" + min_linker.to_s + "_isolated" + ".fasta");
      end


      log << ld
      log << "passing domains                 : " + domain_pass_counter.to_s + ld
      if ( min_linker )
        log << "single domains                  : " + out_msa_singles.get_number_of_seqs.to_s + ld
        log << "domains in close pairs          : " + out_msa_pairs.get_number_of_seqs.to_s + ld
        log << "isolated domains                : " + out_msa_isolated.get_number_of_seqs.to_s + ld
      end
      log << "failing domains                 : " + domain_fail_counter.to_s + ld
      log << "proteins with passing domains   : " + passed_seqs.get_number_of_seqs.to_s + ld
      log << "proteins with no passing domains: " + proteins_with_failing_domains.to_s + ld
      log << ld

      return domain_pass_counter

    end # parse


    private

    def write_msa( msa, filename )
      io = MsaIO.new()
      w = FastaWriter.new()
      w.set_line_width( 60 )
      w.clean( true )
      begin
        io.write_to_file( msa, filename, w )
      rescue Exception
        error_msg = "could not write to \"" + filename + "\""
        raise IOError, error_msg
      end
    end


    def add_sequence( sequence_name, in_msa, add_to_msa )
      seqs = in_msa.find_by_name_start( sequence_name, true )
      if ( seqs.length < 1 )
        error_msg = "sequence \"" + sequence_name + "\" not found in sequence file"
        raise StandardError, error_msg
      end
      if ( seqs.length > 1 )
        error_msg = "sequence \"" + sequence_name + "\" not unique in sequence file"
        raise StandardError, error_msg
      end
      seq = in_msa.get_sequence( seqs[ 0 ] )
      add_to_msa.add_sequence( seq )
    end

    def process_hmmscan_datas( hmmscan_datas,
        in_msa,
        add_position,
        add_domain_number,
        add_species,
        out_msa,
        out_msa_singles,
        out_msa_pairs,
        out_msa_isolated,
        min_linker )

      actual_out_of = hmmscan_datas.size

      hmmscan_datas.each_with_index do |hmmscan_data, index|
        if hmmscan_data.number < ( index + 1 )
          error_msg = "hmmscan_data.number < ( index + 1 ) (this should not have happened)"
          raise StandardError, error_msg
        end

        extract_domain( hmmscan_data.seq_name,
          index + 1,
          actual_out_of,
          hmmscan_data.env_from,
          hmmscan_data.env_to,
          in_msa,
          out_msa,
          add_position,
          add_domain_number,
          add_species )

        if min_linker
          if actual_out_of == 1
            extract_domain( hmmscan_data.seq_name,
              1,
              1,
              hmmscan_data.env_from,
              hmmscan_data.env_to,
              in_msa,
              out_msa_singles,
              add_position,
              add_domain_number,
              add_species )
          else
            first = index == 0
            last = index == hmmscan_datas.length - 1

            if ( ( first && ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker) )  ||
                 ( last && ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) ||
                 ( !first && !last &&  ( ( hmmscan_datas[ index + 1 ].env_from - hmmscan_data.env_to ) > min_linker ) &&
                   ( ( hmmscan_data.env_from - hmmscan_datas[ index - 1 ].env_to ) > min_linker ) ) )

              extract_domain(  hmmscan_data.seq_name,
                index + 1,
                actual_out_of,
                hmmscan_data.env_from,
                hmmscan_data.env_to,
                in_msa,
                out_msa_isolated,
                add_position,
                add_domain_number,
                add_species )

            elsif !first
              extract_domain(  hmmscan_data.seq_name,
                index.to_s  + "+" + ( index + 1 ).to_s,
                actual_out_of,
                hmmscan_datas[ index - 1 ].env_from,
                hmmscan_data.env_to,
                in_msa,
                out_msa_pairs,
                add_position,
                add_domain_number,
                add_species )
            end
          end
        end
      end # each
    end # def process_hmmscan_data

    def extract_domain( sequence,
        number,
        out_of,
        seq_from,
        seq_to,
        in_msa,
        out_msa,
        add_position,
        add_domain_number,
        add_species )
      if  number.is_a?( Fixnum ) && ( number < 1 || out_of < 1 || number > out_of )
        error_msg = "impossible: number=" + number.to_s + ", out of=" + out_of.to_s
        raise StandardError, error_msg
      end
      if  seq_from < 1 || seq_to < 1 || seq_from >= seq_to
        error_msg = "impossible: seq-f=" + seq_from.to_s + ", seq-t=" + seq_to.to_s
        raise StandardError, error_msg
      end
      seqs = in_msa.find_by_name_start( sequence, true )
      if seqs.length < 1
        error_msg = "sequence \"" + sequence + "\" not found in sequence file"
        raise IOError, error_msg
      end
      if seqs.length > 1
        error_msg = "sequence \"" + sequence + "\" not unique in sequence file"
        raise IOError, error_msg
      end
      # hmmsearch is 1 based, wheres sequences are 0 bases in this package.
      seq = in_msa.get_sequence( seqs[ 0 ] ).get_subsequence( seq_from - 1, seq_to - 1 )

      orig_name = seq.get_name

      seq.set_name( orig_name.split[ 0 ] )

      if add_position
        seq.set_name( seq.get_name + "_" + seq_from.to_s + "-" + seq_to.to_s )
      end

      if out_of != 1 && add_domain_number
        seq.set_name( seq.get_name + "~" + number.to_s + "-" + out_of.to_s )
      end

      if add_species
        a = orig_name.rindex "["
        b = orig_name.rindex "]"
        unless a && b
          error_msg = "species not found in " + orig_name
          raise StandardError, error_msg
        end
        species = orig_name[ a .. b ]
        seq.set_name( seq.get_name + " " + species )
      end
      out_msa.add_sequence( seq )
    end

    def is_ignorable?( line )
      return ( line !~ /[A-Za-z0-9-]/ || line =~/^#/ )
    end

  end # class HmmscanDomainExtractor

  class HmmsearchData
    def initialize( seq_name, number, out_of, env_from, env_to, i_e_value )
      @seq_name = seq_name
      @number = number
      @out_of = out_of
      @env_from = env_from
      @env_to = env_to
      @i_e_value = i_e_value
    end
    attr_reader :seq_name, :number, :out_of, :env_from, :env_to, :i_e_value
  end

end # module Evoruby