use G::IO::Annotation;
 G::IO::Annotation::annotate_with_glimmer();
 G::IO::Annotation::annotate_with_LORF();

 Annotates the genome sequence. 
 Only serves immature functions only.
 Intended for internal use only.

    my $self = shift;

    undef %{$self};

    my $this = shift;
    my $gb = shift;
    my $seq = $gb->{SEQ};
    my ($start,$end,$i);
    my $count = 0;

    $this->{"LOCUS"} = $gb->{"LOCUS"};
    $this->{"HEADER"} = $gb->{"HEADER"};
    $this->{"COMMENT"} = $gb->{"COMMENT"};
    $this->{"CDS0"}->{dummy} = 1;
    $this->{"FEATURE0"} = $gb->{"FEATURE0"};
    $this->{"SEQ"} = $seq;

    for ($i = 0; $i <= 1; $i ++){
	$seq = complement($gb->{SEQ}) if ($i);
	$start = 0;
	$end = 0;
	
	while(0 <= ($start = index($seq, 'atg', $start + 1))){
	    next if ($start < $end && ($start - $end + 1) % 3 == 0);
	    my $tmp = $start;
	    my $stopcodon = '';
	    while(0 <= ($tmp = index($seq, 'tag', $tmp +1))){
		if (($tmp - $start + 1) % 3 == 0 && $tmp - $start > 49){
		    $count ++;
		    $end = $tmp;
		    $stopcodon = 'tag';
		    last;
		}
	    }
	    $tmp = $start;
	    while(0 <= ($tmp = index($seq, 'taa', $tmp +1))){
		if (($tmp - $start + 1) % 3 == 0 && $tmp - $start > 49){
		    if ($tmp < $end){
			$count ++;
			$end = $tmp;
			$stopcodon = 'taa';
			last;
		    }else{
			last;
		    }
		}
	    }
	    $tmp = $start;
	    while(0 <= ($tmp = index($seq, 'tga', $tmp +1))){
		if (($tmp - $start + 1) % 3 == 0 && $tmp - $start > 49){
		    if ($tmp < $end){
			$count ++;
			$end = $tmp;
			$stopcodon = 'tga';
			last;
		    }else{
			last;
		    }
		}
	    }
	    if ($i){
		if ($end > 0 && ($end - $start + 1) / 3 > opt::val("length")){
		    $this->{"CDS$count"}->{start} = length($gb->{SEQ}) - $end + 1;
		    $this->{"CDS$count"}->{end} = length($gb->{SEQ}) - $start + 1;
		    $this->{"CDS$count"}->{feature} = $count;
		    $this->{"CDS$count"}->{direction} = "complement";

		    $this->{"FEATURE$count"}->{type} = "CDS";
		    $this->{"FEATURE$count"}->{start} = length($gb->{SEQ}) - $end + 1;
		    $this->{"FEATURE$count"}->{end} = length($gb->{SEQ}) - $start + 1;
		    $this->{"FEATURE$count"}->{feature} = $count;
		    $this->{"FEATURE$count"}->{direction} = "complement";
		}
	    }else{
		if ($end > 0 && ($end - $start + 1) / 3 > opt::val("length")){
		    $this->{"CDS$count"}->{start} = $start + 1;
		    $this->{"CDS$count"}->{end} = $end + 1;
		    $this->{"CDS$count"}->{feature} = $count;
		    $this->{"CDS$count"}->{direction} = "direct";

		    $this->{"FEATURE$count"}->{type} = "CDS";
		    $this->{"FEATURE$count"}->{start} = $start + 1;
		    $this->{"FEATURE$count"}->{end} = $end + 1;
		    $this->{"FEATURE$count"}->{feature} = $count;
		    $this->{"FEATURE$count"}->{direction} = "direct";
		}
	    }

    my $this = shift;
    my $file = shift;
    
    open (FASTA, $file);
    while(<FASTA>){
	if (/^\>/){
	    s/\>//;
	    my @hoge = split;
	    $this->{LOCUS}->{id} = $hoge[0];
	    next;
	}else{
	    s/[^a-zA-Z]//g;
	    $this->{SEQ} .= lc($_);
	}
    }
    close(FASTA);

    $this->{COMMENT} = "COMMENT     Annotated with G-language GAE. Arakawa et al. (2003) Bioinformatics\n";
    $this->{"CDS0"}->{dummy} = 1;
    $this->{"FEATURE0"}->{dummy} = 1;

    my $count = 0;
    my $cdscount = 0;
    open (GLIMMER, 'g2.coord') || die();
    while(<GLIMMER>){
	$count ++;
	$cdscount ++;
	my $nextcount = $count + 1;
	my @line = split;

	$this->{"FEATURE$count"}->{type} = 'gene';
	$this->{"FEATURE$count"}->{gene} = sprintf "g%04d", $cdscount;
	$this->{"FEATURE$count"}->{note} = sprintf "locus_tag: g%04d", $cdscount;
	$this->{"FEATURE$count"}->{on} = 1;

	$this->{"CDS$cdscount"}->{feature} = $count;
	$this->{"CDS$cdscount"}->{on} = 1;

	$this->{"FEATURE$nextcount"}->{cds} = $cdscount;
	$this->{"FEATURE$nextcount"}->{type} = 'CDS';
	$this->{"FEATURE$nextcount"}->{gene} = sprintf "g%04d", $cdscount;
	$this->{"FEATURE$nextcount"}->{function} = "orf; Unknown";
	$this->{"FEATURE$nextcount"}->{note} = "predicted by Glimmer 2.2";
	$this->{"FEATURE$nextcount"}->{codon_start} = 1;
	$this->{"FEATURE$nextcount"}->{transl_table} = 11;
	$this->{"FEATURE$nextcount"}->{product} = "orf, hypothetical protein";
	$this->{"FEATURE$nextcount"}->{protein_id} = "N/A";
	$this->{"FEATURE$nextcount"}->{db_xref} = "N/A";
	$this->{"FEATURE$nextcount"}->{on} = 1;

	if ($line[1] > $line[2]){
	    $this->{"CDS$cdscount"}->{start} = $line[2];
	    $this->{"CDS$cdscount"}->{end} = $line[1];
	    $this->{"CDS$cdscount"}->{direction} = "complement";
	    $this->{"FEATURE$count"}->{start} = $line[2];
	    $this->{"FEATURE$count"}->{end} = $line[1];
	    $this->{"FEATURE$count"}->{direction} = "complement";
	    $this->{"FEATURE$nextcount"}->{start} = $line[2];
	    $this->{"FEATURE$nextcount"}->{end} = $line[1];
	    $this->{"FEATURE$nextcount"}->{direction} = "complement";
	}else{
	    $this->{"CDS$cdscount"}->{start} = $line[1];
	    $this->{"CDS$cdscount"}->{end} = $line[2];
	    $this->{"CDS$cdscount"}->{direction} = "direct";
	    $this->{"FEATURE$count"}->{start} = $line[1];
	    $this->{"FEATURE$count"}->{end} = $line[2];
	    $this->{"FEATURE$count"}->{direction} = "direct";
	    $this->{"FEATURE$nextcount"}->{start} = $line[1];
	    $this->{"FEATURE$nextcount"}->{end} = $line[2];
	    $this->{"FEATURE$nextcount"}->{direction} = "direct";
	}

	$this->{"FEATURE$nextcount"}->{translation} = 
	    translate($this->get_geneseq("FEATURE$nextcount"));
	    $count ++;
    }
    close(GLIMMER);

    my $this = shift;
    my $file = shift;

    system("./run-glimmer2 $file");