require 'json'
require 'scbi_fasta'
require 'sequence'

require 'fln_stats'
include FlnStats

class MyWorkerManager < ScbiMapreduce::WorkManager

	# open files and prepare global data
	def self.init_work_manager(options,chunk_size=100)

		input_file=options[:fasta]
		
		if !File.exists?('fln_results')
			Dir.mkdir('fln_results')
		end
		
		file_head = "Query_id\tfasta_length\tSubject_id\tdb_name\tStatus\tt_code\te_value\tp_ident\tprotein_length\ts_length\tWarning_msgs\tframe\tORF_start\tORF_end\ts_start\ts_end\tDescription\tProtein_sequence"
		
		@@fasta_file = FastaQualFile.new(input_file,'')
		@@chunk_size=chunk_size
		@@options = options

		@@annotation_file = File.open("fln_results/dbannotated.txt", 'w')
		@@annotation_file.puts file_head

		@@alignment_file = File.open("fln_results/alignments.txt", 'w')
		@@prot_file = File.open("fln_results/proteins.fasta", 'w')
		@@nts_file = File.open("fln_results/nt_seq.txt", 'w')
		@@tcode_file=File.open("fln_results/new_coding.txt", 'w')
		@@tcode_file.puts file_head

		@@nc_rna_file = File.open("fln_results/nc_rnas.txt", 'w')
		@@nc_rna_file.puts file_head

		# @@error_fasta_file = File.open("fln_results/error_seqs.fasta", 'w')
		# @@error_file = File.open("fln_results/errors_info.txt", 'w')

	end
		
	# close files
	def self.end_work_manager
		# @@fasta_file.close
		
		@@annotation_file.close
		@@alignment_file.close
		@@prot_file.close
		@@nts_file.close
		@@tcode_file.close
		@@nc_rna_file.close
		
		# @@error_fasta_file.close
		# @@error_file.close
		
		summary_stats
	end
		
	def error_received(worker_error, obj)
		puts "Error while processing object #{obj.inspect}\n" + worker_error.original_exception.message + ":\n" +worker_error.original_exception.backtrace.join("\n")
  end

  def too_many_errors_received
		$LOG.error "Too many errors: #{@@error_count} errors on #{@@count} executed sequences, exiting before finishing"
  end

	# send initial config
	def worker_initial_config
		return @@options
	end
		 
	# this method is called every time a worker needs a new work
	# Return the work data or nil if no more data is available
	def next_work
		
    # seqs=[]
		# if (@@count % 2==0)
		# 	$LOG.info("Processed #{@@count}")
		# end
					
		# prepare work
    # @@chunk_size.times do
		n,f,q = @@fasta_file.next_seq
		
		if !n.nil?
				return Sequence.new(n,f,q)
			else
				return nil
		end
    
    # end
		
		# return work
		# if !seqs.empty?
		#       return seqs
		#     else
		#       return nil
		#     end
		
	end
  	
		# this method is ejecuted each time an obj is finished
	def work_received(obj)
	
			obj.each do |seq|
				# puts seq.seq_name
				
				write_seq(seq)
				
			end
	end 


	def write_seq(seq)
		begin
# --------------------------------------------------------     Complete Seqs
			if (e=seq.get_annotations(:complete).first)

				@@annotation_file.puts e[:message]
				
				if (a=seq.get_annotations(:alignment).first)
					@@alignment_file.puts a[:message]
				end
				
				if (p=seq.get_annotations(:protein).first)
					@@prot_file.puts p[:message]
				end
				
				if (n=seq.get_annotations(:nucleotide).first)
					@@nts_file.puts n[:message]
				end
# --------------------------------------------------------     Non Complete Seqs
			elsif (e=seq.get_annotations(:tmp_annotation).first)

				@@annotation_file.puts e[:message][0]
				
				if (a=seq.get_annotations(:alignment).first)
					if !a[:message].empty?
						@@alignment_file.puts a[:message]
					end
				end
				
				if (p=seq.get_annotations(:protein).first)
					if !p[:message].empty?
						@@prot_file.puts p[:message]
					end
				end
				
				if (n=seq.get_annotations(:nucleotide).first)
					@@nts_file.puts n[:message]
				end
# --------------------------------------------------------     nc RNA
			elsif (nc=seq.get_annotations(:ncrna).first)
				@@nc_rna_file.puts nc[:message]
# --------------------------------------------------------     Test Code
			elsif (t=seq.get_annotations(:tcode).first) 
  				@@tcode_file.puts t[:message]
			end
# --------------------------------------------------------     errors
			# if e=seq.get_annotations(:error).first
			# 	if !e[:message].empty?
			# 		@@error_fasta_file.puts ">#{seq.seq_name}\n#{seq.seq_fasta}"
			# 		@@error_file.puts e[:message]
			# 	end
			# end

		rescue
			puts "Error printing #{seq.seq_name}"
		end
		
	end
	
	
  	
end