#
# = bio/db/gff/digest/gffparser.rb - Fully digesting parsing logic for GFF3 file
#
# Copyright::  Copyright (C) 2010
#              Pjotr Prins <pjotr.prins@thebird.nl>
# License::    The Ruby License
#

module Bio
  module GFFbrowser

    # The fully Digesting parser consumes all records and
    # links them together in (in-memory) lists
    module Digest

      # Both in-memory and no-cache fully digest parsers
      # share this Parser module.
      module Parser

        include Bio::GFFbrowser::Helpers
        include Bio::GFFbrowser::Helpers::Validate
        include Bio::GFFbrowser::Helpers::Logger
        include Gff3Component
        include Gff3Features

        # Takes a parsed record +rec+ and stores items in 
        # the relevant lists/tables
        def store_record rec
          return if rec.comment # skip GFF comments
          id = Helpers::Record::formatID(rec)
          @count_ids.add(id)
          @count_seqnames.add(rec.seqname)

          is_component = COMPONENT_TYPES.include?(rec.feature_type.upcase)
          if is_component
            # check for container ID
            warn("Container <#{rec.feature_type}> has no ID, so using sequence name instead",id) if rec.id == nil
            @componentlist[id] = rec
            info "Added feature <#{rec.feature_type}> with component ID",id
            # $stderr.print rec
          end 
          case rec.feature_type
            when 'gene' || 'SO:0000704'
              @orflist.add(id,rec)
            when 'mRNA' || 'SO:0000234'
              @mrnalist.add(id,rec)
            when 'CDS'  || 'SO:0000316'
              @cdslist.add(id,rec)
            when 'exon' || 'SO:0000147'
              @exonlist.add(id,rec)
            else
              if !is_component and !IGNORE_FEATURES.include?(rec.feature_type)
                @unrecognized_features[rec.feature_type] = true
              end
          end
        end

        def show_unrecognized_features 
          @unrecognized_features.keys.each do | k |
            warn "Unknown feature is ignored",k if k
          end
        end

        def read_fasta
          if @options[:fasta_filename]
            File.open(@options[:fasta_filename]) do | f |
              fasta = Bio::GFF::FastaReader.new(f)
              fasta.each do | id, fastarec |
                # p fastarec
                @sequencelist[id] = fastarec
              end
            end
          end
          # p :inmemory, @sequencelist
        end

        # Yield the id, recs, containing component and sequence of genes
        def each_gene
          parse if !@orflist
          each_item(@orflist) { |id, recs, component | yield id, recs, component }
        end

        # Yield the id, recs, containing component and sequence of mRNAs
        def each_mRNA
          parse if !@mrnalist
          each_item(@mrnalist) { |id, recs, component | yield id, recs, component }
        end

        # Yield the id, recs, and containing component
        def each_CDS
          parse if !@cdslist
          each_item(@cdslist) { |id, recs, component | yield id, recs, component }
        end

        # Yield the id, recs, and containing component
        def each_exon
          parse if !@exonlist
          each_item(@exonlist) { |id, recs, component | yield id, recs, component }
        end

        # Yield a unique description and the sequence
        def each_gene_seq
          each_gene do | id, reclist, component |
            if component
              sequence = @sequencelist[component.seqname]
              # p sequence
              if sequence
                yield description(id,component,reclist), assemble(sequence,component.start,reclist)
              else 
                warn "No sequence information for",id
              end
            end
          end
        end

        # Yield a unique description and the sequence
        def each_mRNA_seq
          each_mRNA do | id, reclist, component |
            if component
              sequence = @sequencelist[component.seqname]
              # p sequence
              if sequence
                yield description(id,component,reclist), assemble(sequence,component.start,reclist)
              else 
                warn "No sequence information for",id
              end
            end
          end
        end

        # Yield a unique description and the sequence
        def each_CDS_seq
          each_CDS do | id, reclist, component |
            if component
              # p id,reclist,component
              sequence = @sequencelist[component.seqname]
              # p sequence
              if sequence
                seq = assemble(sequence,component.start,reclist,@options.merge(:codonize=>true))
                if seq.size % 3 != 0
                  p reclist # leave this in
                  # raise "CDS size #{seq.size} is not a multiple of 3! <#{seq}>"
                  warn "CDS size is not a multiple of 3",id
                end
                yield description(id,component,reclist), seq
              else 
                warn "No sequence information for",id
              end
            end
          end
        end

        # Yield a unique description and the sequence
        def each_exon_seq
          each_exon do | id, reclist, component |
            if component
              sequence = @sequencelist[component.seqname]
              if sequence
                seq = assemble(sequence,component.start,reclist)
                yield description(id,component,reclist), seq
              else 
                warn "No sequence information for",id
              end
            end
          end
        end
      end
    end
  end
end