package Gff;

=head1 NAME

Gff -- An object that keeps track of GFF file information.

=head1 SYNOPSIS

my $gff = Gff->new;
$gff->write;


Object hash entries:

  gff_file_written          boolean

=head1 DESCRIPTION

This object keeps track of the project information.

=head1 VERSION

0.001 (last update:  7/16/04)

=head1 AUTHOR

Chet Langin, clangin@siu.edu

SIU Plant Biotechnology and Genomics Core-facility

=head1 BUGS

None known.

=head1 SEE ALSO

extropy ExtropyConstants ExtropyUtils Extropy::MenuMain

=head1 COPYRIGHT

Copyright 2004, Chet Langin, All Rights Reserved.

This program is free software.  You may copy or
redistribute it under the same terms as Perl itself.

=head1 METHODS

The remainder of this document describes the methods available to the
programmer.

=cut

# load the pragmas
use warnings;
use strict;

# load other modules
use ExtropyConstants;
use ExtropyUtils;

# package variables
my $db_manager;
my $project;

# ********************************  new  ******************************

=head2 new

  my $gff = Gff->new;

Creates an instance of the Project object.

=cut

# ---------------------------------------------------------------------

sub new {
  # instantiate the oject
  my $self = {};
  bless $self;
  my $defined = TRUE;
  $self->reset;

  # return values
  if($defined) {
    $self;
  } # if
  else {
    undef;
  } # else
} # new()

# ********************************  reset *****************************

=head2 reset

  reset;

Resets the variables for the project.  For internal use, only.

=cut

# ---------------------------------------------------------------------

sub reset {
  my $self = shift;

  $self->{loci} = FALSE;
  $self->{clones} = FALSE;
  $self->{contigs} = FALSE;
  $self->{qtls} = FALSE;
  $self->{ends} = FALSE;
  $self->{mtps} = FALSE;
  $self->{ests} = FALSE;
  $self->{seq} = FALSE;
  $self->{rel} = FALSE;
  $self->{con} = FALSE;
  $self->{gff_file_written} = FALSE;
} # reset

# ********************************  write *****************************

=head2 write

  write;

Writes the GFF file.

=cut

# ---------------------------------------------------------------------

sub write {
  my $self = shift;
  $db_manager = shift;
  $project = shift;
  my %mlg_lengths = ();

  my $gff_filename = "$db_manager->{database_name}.gff";

  message_start;

  message("Opening $gff_filename for output");
  my $file_opened = TRUE;
  open(GFF_FILE, ">", $gff_filename)
    or $file_opened = FALSE;

  if($file_opened) {
    # Write to the GFF file
    message("$gff_filename opened for output");

    message("Connecting to the database");
    $db_manager->connect;

    ###########################
    ############ MLG's ########
    ###########################

    message("Getting the MLG info");
    my $sth1 = $db_manager->execute("select mlg, length from mlg");
    message("Saving the MLG's in the GFF file.");
    my @row1 = ();
    while(@row1 = $sth1->fetchrow_array()) {
      my $mlg = shift @row1;
      my $length = shift @row1;
      $mlg_lengths{$mlg} = $length;
      print GFF_FILE "mlg$mlg\tchromosome\tComponent\t1\t$length\t.\t.\t.\tSequence \"mlg$mlg\"\n";
    } # while

    ###########################
    ############ Loci #########
    ###########################

    if($self->{loci}) {
      message("Getting the alpha loci info");
      my $sth2 = $db_manager->execute("select locus, mlg, anchor, comment, type from loci where type = 'alpha'");
      message("Saving the alpha loci in the GFF file.");
      my @row2 = ();
      while(@row2 = $sth2->fetchrow_array()) {
        my $locus = shift @row2;
        my $mlg = shift @row2;
        my $anchor = shift @row2;
        my $comment = shift @row2;
        my $type = shift @row2;
        my $track = "aLoci";
        $anchor = 101 if ($anchor < 101);
        my $overflow = ($anchor + 100) - $mlg_lengths{$mlg};
        if($overflow >= 0) {
          $anchor -= $overflow + 200;
        } # if
        my $start = $anchor - 100;
        my $end = $anchor + 100;
        my $name = $locus;
        my $note = "$comment, $type.  ";
        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
      } # while

      message("Getting the beta loci info");
      my $sth3 = $db_manager->execute("select locus, mlg, anchor, comment, type from loci where type = 'beta'");
      message("Saving the beta loci in the GFF file.");
      my @row3 = ();
      while(@row3 = $sth3->fetchrow_array()) {
        my $locus = shift @row3;
        my $mlg = shift @row3;
        my $anchor = shift @row3;
        my $comment = shift @row3;
        my $type = shift @row3;
        my $track = "bLoci";
        $anchor = 101 if ($anchor < 101);
        my $overflow = ($anchor + 100) - $mlg_lengths{$mlg};
        if($overflow >= 0) {
          $anchor -= $overflow + 200;
        } # if
        my $start = $anchor - 100;
        my $end = $anchor + 100;
        my $name = $locus;

        # Get the matching clones
        my $clones = 0;
        my $sth3a = $db_manager->execute("select clone from clone2locus3 where locus = '$locus'");
        my @row3a = ();
        while(@row3a = $sth3a->fetchrow_array()) {
          my $clone = shift @row3a;
          $clones++;
        } # while

        # Get the matching sequences
        my $sequence = "";
        my $sth3b = $db_manager->execute("select sequence from sequence where hit = '$locus'");
        my @row3b = ();
        while(@row3b = $sth3b->fetchrow_array()) {
          my $hit = shift @row3b;
          if($sequence eq "") {
            $sequence = "$hit";
          } # if
          else {
            $sequence .= ", $hit"
          } # else
        } # while

        # Get the matching Related Genes
        my $relateds = 0;
        my $sth3c = $db_manager->execute("select related from related where hit = '$locus'");
        my @row3c = ();
        while(@row3c = $sth3c->fetchrow_array()) {
          my $related = shift @row3c;
          $relateds++;
        } # while

        my $note = "";
        if($sequence eq "") {
          $note = "$comment, $type, $clones clone/s, $relateds related genes.  ";
        } # if
        else {
          $note = "$comment, $type, $clones clone/s, $relateds related genes, $sequence.  ";
        } # else

        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
      } # while

      message("Getting the gamma loci info");
      my $sth4 = $db_manager->execute("select locus, mlg, anchor, comment, type from loci where type = 'gamma'");
      message("Saving the gamma loci in the GFF file.");
      my @row4 = ();
      while(@row4 = $sth4->fetchrow_array()) {
        my $locus = shift @row4;
        my $mlg = shift @row4;
        my $anchor = shift @row4;
        my $comment = shift @row4;
        my $type = shift @row4;
        my $track = "gLoci";
        $anchor = 101 if ($anchor < 101);
        my $overflow = ($anchor + 100) - $mlg_lengths{$mlg};
        if($overflow >= 0) {
          $anchor -= $overflow + 200;
        } # if
        my $start = $anchor - 100;
        my $end = $anchor + 100;
        my $name = $locus;

        # Get the matching clones
        my $clones = 0;
        my $sth4a = $db_manager->execute("select clone from clone2locus3 where locus = '$locus'");
        my @row4a = ();
        while(@row4a = $sth4a->fetchrow_array()) {
          my $clone = shift @row4a;
          $clones++;
        } # while

        # Get the matching contigs
        my $ctgs = 0;
        my $sth4b = $db_manager->execute("select contig2clone.ctg from clone2locus3, contig2clone where clone2locus3.locus = '$locus' and clone2locus3.clone = contig2clone.clone");           # valid
        my @row4b = ();
        while(@row4b = $sth4b->fetchrow_array()) {
          my $ctg = shift @row4b;
          $ctgs++;
        } # while

        # Get the matching sequences
        my $sequence = "";
        my $sth4c = $db_manager->execute("select sequence from sequence where hit = '$locus'");
        my @row4c = ();
        while(@row4c = $sth4c->fetchrow_array()) {
          my $hit = shift @row4c;
          if($sequence eq "") {
            $sequence = "$hit";
          } # if
          else {
            $sequence .= ", $hit"
          } # else
        } # while

        # Get the matching Related Genes
        my $relateds = 0;
        my $sth4d = $db_manager->execute("select related from related where hit = '$locus'");
        my @row4d = ();
        while(@row4d = $sth4d->fetchrow_array()) {
          my $related = shift @row4d;
          $relateds++;
        } # while

        my $note = "";
        if($sequence eq "") {
          if($relateds > 0) {
            $note = "$comment, $type, $clones clone/s, $ctgs contig/s, $relateds related genes.  ";
          } # if
          else {
            $note = "$comment, $type, $clones clone/s, $ctgs contig/s.  ";
          } # else
        } # if
        else {
          if($relateds > 0) {
            $note = "$comment, $type, $clones clone/s, $ctgs contig/s, $relateds related genes, $sequence.  ";
          } # if
          else {
            $note = "$comment, $type, $clones clone/s, $ctgs contig/s, $sequence.  ";
          } # else
        } # else

        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
      } # while
    } # if (loci)
    else {
      message("Not getting the loci info");
    } # else

    ###########################
    ########### Clones ########
    ###########################

    # Note:  the contig locations have already been set and spread in UpdateContigAnchors.pm

    if($self->{clones}) {
      message("Deleting clone_locations table non-alpha info for new input");
      $db_manager->execute("delete from clone_locations where type != 'alpha'");
        #  The alpha locations were input in UpdateContigAnchors.pm

      message("Getting the gamma clone info");
      my $sth5 = $db_manager->execute("select clone_anchors.clone, clone_anchors.mlg, clone_anchors.anchor, clone_anchors.dup_i, clone_anchors.dup_t, contig2clone.length from clones, clone_anchors, contig2clone where clones.type = 'gamma' and clones.clone = clone_anchors.clone and clones.clone = contig2clone.clone");
      message("Saving the gamma clones in the GFF file");
      message("  and the clone_locations table");
      my @row5 = ();
      while(@row5 = $sth5->fetchrow_array()) {
        my $clone = shift @row5;
        my $mlg = shift @row5;
        my $anchor = shift @row5;
        my $dup_i = shift @row5;
        my $dup_t = shift @row5;
        my $clone_length = shift @row5;
        my $track = "gClones";

        # Determine the starting and ending locations of the clone
        $clone_length = int($clone_length * $project->{band_factor});
        my $half_length = int($clone_length / 2);
        $anchor = $half_length + 1 if ($anchor < $half_length + 1);
        my $overflow = ($anchor + $half_length) - $mlg_lengths{$mlg};
        if($overflow >= 0) {
          $anchor -= $overflow + 200;
        } # if
        my $start = $anchor - $half_length;
        my $end = $start + $clone_length;

        my $name = $clone;
        my $type = "gamma";

        # get the matching loci
        my $matches = "";
        my $sth5a = $db_manager->execute("select locus from clone2locus3 where clone = '$clone'");
        my @row5a = ();
        while(@row5a = $sth5a->fetchrow_array()) {
          my $locus = shift @row5a;
          if($matches eq "") {
            $matches = $locus;
          } # if
          else {
            $matches .= ", $locus";
          } # else
        } # while

        # get the matching contigs
        my $sth5b = $db_manager->execute("select ctg from contig2clone where clone = '$clone'");  # valid
        my @row5b = ();
        while(@row5b = $sth5b->fetchrow_array()) {
          my $contig = shift @row5b;
          if($matches eq "") {
            $matches = $contig;
          } # if
          else {
            $matches .= ", $contig";
          } # else
        } # while

        # get the matching MTP
        my $sth5b1 = $db_manager->execute("select mtp from mtp where clone = '$clone'");  # valid
        my @row5b1 = ();
        while(@row5b1 = $sth5b1->fetchrow_array()) {
          my $mtp = shift @row5b1;
          if($matches eq "") {
            $matches = $mtp;
          } # if
          else {
            $matches .= ", $mtp";
          } # else
        } # while

        # get the matching EST
        my $sth5b2 = $db_manager->execute("select est from est where clone = '$clone'");  # valid
        my @row5b2 = ();
        while(@row5b2 = $sth5b2->fetchrow_array()) {
          my $est = shift @row5b2;
          if($matches eq "") {
            $matches = $est;
          } # if
          else {
            $matches .= ", $est";
          } # else
        } # while

        # Get the matching sequences
        my $sth5b3 = $db_manager->execute("select sequence from sequence where hit = '$clone'");
        my @row5b3 = ();
        while(@row5b3 = $sth5b3->fetchrow_array()) {
          my $hit = shift @row5b3;
          if($matches eq "") {
            $matches = "$hit";
          } # if
          else {
            $matches .= ", $hit"
          } # else
        } # while

        # Get the matching Related Genes
        my $relateds = 0;
        my $sth5b4 = $db_manager->execute("select related from related where hit = '$clone'");
        my @row5b4 = ();
        while(@row5b4 = $sth5b4->fetchrow_array()) {
          my $related = shift @row5b4;
          $relateds++;
        } # while

        my $note = "";
        if($dup_t > 1) {
          if($relateds > 0) {
            $note = "$dup_i of $dup_t, $type, $matches, $relateds related genes.  ";
          } # if
          else {
            $note = "$dup_i of $dup_t, $type, $matches.  ";
          } # else
        } # if
        else {
          if($relateds > 0) {
            $note = "$type, $matches, $relateds related genes.  ";
          } # if
          else {
            $note = "$type, $matches.  ";
          } # else
        } # else
        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        $db_manager->execute("insert into clone_locations values('', '$name', '$mlg', '$start', '$end', 'gamma')");
      } # while

      message("Getting the spread gamma clone info");
      my $sth5c = $db_manager->execute("select contig2clone.clone, contig2clone.start, contig2clone.length, contig2clone.ctg, contig_anchors.mlg, contig_anchors.spread_start, clone_anchors.dup_i, clone_anchors.dup_t, contigs.start from contig2clone, clone_anchors, contig_anchors, clones, contigs where contig2clone.clone = clone_anchors.clone and contig2clone.ctg = contig_anchors.ctg and clone_anchors.clone = clones.clone and clones.type = 'gamma' and contig2clone.ctg = contigs.ctg");  # valid
      message("Saving the spread gamma clones in the GFF file.");
      my @row5c = ();
      while(@row5c = $sth5c->fetchrow_array()) {
        my $clone = shift @row5c;
        my $band_start = shift @row5c;
        my $length = shift @row5c;
        my $ctg = shift @row5c;
        my $mlg = shift @row5c;
        my $spread_start = shift @row5c;
        my $dup_i = shift @row5c;
        my $dup_t = shift @row5c;
        my $ctg_band_start = shift @row5c;
        my $track = "gsClones";
        my $displacement = $band_start - $ctg_band_start;
        my $start = $spread_start + ($displacement * $project->{band_factor});
        my $end = $start + int($length * $project->{band_factor});
        my $name = $clone;
        my $type = "gamma";

        # get the matching loci
        my $matches = "";
        my $sth5d = $db_manager->execute("select locus from clone2locus3 where clone = '$clone'");
        my @row5d = ();
        while(@row5d = $sth5d->fetchrow_array()) {
          my $locus = shift @row5d;
          if($matches eq "") {
            $matches = $locus;
          } # if
          else {
            $matches .= ", $locus";
          } # else
        } # while

        # get the matching contigs
        my $sth5e = $db_manager->execute("select ctg from contig2clone where clone = '$clone'");  # valid
        my @row5e = ();
        while(@row5e = $sth5e->fetchrow_array()) {
          my $contig = shift @row5e;
          if($matches eq "") {
            $matches = $contig;
          } # if
          else {
            $matches .= ", $contig";
          } # else
        } # while

        # get the matching MTP
        my $sth5e1 = $db_manager->execute("select mtp from mtp where clone = '$clone'");  # valid
        my @row5e1 = ();
        while(@row5e1 = $sth5e1->fetchrow_array()) {
          my $mtp = shift @row5e1;
          if($matches eq "") {
            $matches = $mtp;
          } # if
          else {
            $matches .= ", $mtp";
          } # else
        } # while

        # get the matching EST
        my $sth5e2 = $db_manager->execute("select est from est where clone = '$clone'");  # valid
        my @row5e2 = ();
        while(@row5e2 = $sth5e2->fetchrow_array()) {
          my $est = shift @row5e2;
          if($matches eq "") {
            $matches = $est;
          } # if
          else {
            $matches .= ", $est";
          } # else
        } # while

        # Get the matching sequences
        my $sth5e3 = $db_manager->execute("select sequence from sequence where hit = '$clone'");
        my @row5e3 = ();
        while(@row5e3 = $sth5e3->fetchrow_array()) {
          my $hit = shift @row5e3;
          if($matches eq "") {
            $matches = "$hit";
          } # if
          else {
            $matches .= ", $hit"
          } # else
        } # while

        # Get the matching Related Genes
        my $relateds = 0;
        my $sth5e4 = $db_manager->execute("select related from related where hit = '$clone'");
        my @row5e4 = ();
        while(@row5e4 = $sth5e4->fetchrow_array()) {
          my $related = shift @row5e4;
          $relateds++;
        } # while

        my $note = "";
        if($dup_t > 1) {
          if($relateds > 0) {
            $note = "$dup_i of $dup_t, $type, $matches, $relateds related genes.  ";
          } # if
          else {
            $note = "$dup_i of $dup_t, $type, $matches.  ";
          } # else
        } # if
        else {
          if($relateds > 0) {
            $note = "$type, $matches, $relateds related genes.  ";
          } # if
          else {
            $note = "$type, $matches.  ";
          } # else
        } # else
        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        $db_manager->execute("insert into clone_locations values('', '$name', '$mlg', '$start', '$end', 'spread')");
      } # while

      message("Getting the beta 2 clone info");
      my $sth5f = $db_manager->execute("select contig2clone.clone, contig2clone.start, contig2clone.length, contig2clone.ctg, contig_anchors.mlg, contig_anchors.start, contigs.start from contig2clone, contig_anchors, clones, contigs where contig2clone.ctg = contig_anchors.ctg and contig2clone.clone = clones.clone and clones.type = 'beta 2' and contig2clone.ctg = contigs.ctg");  # valid
      message("Saving the beta 2 clones in the GFF file");
      message("  and the clone_locations table");
      my @row5f = ();
      while(@row5f = $sth5f->fetchrow_array()) {
        my $clone = shift @row5f;
        my $band_start = shift @row5f;
        my $length = shift @row5f;
        my $ctg = shift @row5f;
        my $mlg = shift @row5f;
        my $ctg_start = shift @row5f;
        my $ctg_band_start = shift @row5f;
        my $track = "b2Clones";
        my $displacement = $band_start - $ctg_band_start;
        my $start = $ctg_start + ($displacement * $project->{band_factor});
        my $end = $start + int($length * $project->{band_factor});
        my $name = $clone;
        my $type = "beta 2";

        # get the matching contigs
        my $matches = "";
        my $sth5h = $db_manager->execute("select ctg from contig2clone where clone = '$clone'");  # valid
        my @row5h = ();
        while(@row5h = $sth5h->fetchrow_array()) {
          my $contig = shift @row5h;
          if($matches eq "") {
            $matches = $contig;
          } # if
          else {
            $matches .= ", $contig";
          } # else
        } # while

        # get the matching MTP
        my $sth5h1 = $db_manager->execute("select mtp from mtp where clone = '$clone'");  # valid
        my @row5h1 = ();
        while(@row5h1 = $sth5h1->fetchrow_array()) {
          my $mtp = shift @row5h1;
          if($matches eq "") {
            $matches = $mtp;
          } # if
          else {
            $matches .= ", $mtp";
          } # else
        } # while

        # get the matching EST
        my $sth5h2a = $db_manager->execute("select est from est where clone = '$clone'");  # valid
        my @row5h2a = ();
        while(@row5h2a = $sth5h2a->fetchrow_array()) {
          my $est = shift @row5h2a;
          if($matches eq "") {
            $matches = $est;
          } # if
          else {
            $matches .= ", $est";
          } # else
        } # while

        # Get the matching sequences
        my $sth5h2b = $db_manager->execute("select sequence from sequence where hit = '$clone'");
        my @row5h2b = ();
        while(@row5h2b = $sth5h2b->fetchrow_array()) {
          my $hit = shift @row5h2b;
          if($matches eq "") {
            $matches = "$hit";
          } # if
          else {
            $matches .= ", $hit"
          } # else
        } # while

        # Get the matching Related Genes
        my $relateds = 0;
        my $sth5h2c = $db_manager->execute("select related from related where hit = '$clone'");
        my @row5h2c = ();
        while(@row5h2c = $sth5h2c->fetchrow_array()) {
          my $related = shift @row5h2c;
          $relateds++;
        } # while

        my $note = "";
        if($relateds > 0) {
          $note = "$type, $matches, $relateds related genes.  ";
        } # if
        else {
          $note = "$type, $matches.  ";
        } # else

        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        $db_manager->execute("insert into clone_locations values('', '$name', '$mlg', '$start', '$end', 'beta 2')");
      } # while

      message("Getting the beta 2 clone info for Queue");
      my $sth5f0 = $db_manager->execute("select contig2clone.clone, contig2clone.start, contig2clone.length, contig2clone.ctg, contigs_onQ.start, contigs.start from contig2clone, contigs_onQ, clones, contigs where contig2clone.ctg = contigs_onQ.ctg and contig2clone.clone = clones.clone and clones.type = 'beta 2' and contig2clone.ctg = contigs.ctg");  # valid
      message("Saving the beta 2 clones for Queue in the GFF file");
      message("  and the clone_locations table");
      my @row5f0 = ();
      while(@row5f0 = $sth5f0->fetchrow_array()) {
        my $clone = shift @row5f0;
        my $band_start = shift @row5f0;
        my $length = shift @row5f0;
        my $ctg = shift @row5f0;
        my $mlg = "Queue";
        my $ctg_start = shift @row5f0;
        my $ctg_band_start = shift @row5f0;
        my $track = "b2Clones";
        my $displacement = $band_start - $ctg_band_start;
        my $start = $ctg_start + ($displacement * $project->{band_factor});
        my $end = $start + int($length * $project->{band_factor});
        my $name = $clone;
        my $type = "beta 2";

        # get the matching contigs
        my $matches = "";
        my $sth5h2 = $db_manager->execute("select ctg from contig2clone where clone = '$clone'");  # valid
        my @row5h2 = ();
        while(@row5h2 = $sth5h2->fetchrow_array()) {
          my $contig = shift @row5h2;
          if($matches eq "") {
            $matches = $contig;
          } # if
          else {
            $matches .= ", $contig";
          } # else
        } # while

        # get the matching MTP
        my $sth5h3 = $db_manager->execute("select mtp from mtp where clone = '$clone'");  # valid
        my @row5h3 = ();
        while(@row5h3 = $sth5h3->fetchrow_array()) {
          my $mtp = shift @row5h3;
          if($matches eq "") {
            $matches = $mtp;
          } # if
          else {
            $matches .= ", $mtp";
          } # else
        } # while

        # get the matching EST
        my $sth5h3a = $db_manager->execute("select est from est where clone = '$clone'");  # valid
        my @row5h3a = ();
        while(@row5h3a = $sth5h3a->fetchrow_array()) {
          my $est = shift @row5h3a;
          if($matches eq "") {
            $matches = $est;
          } # if
          else {
            $matches .= ", $est";
          } # else
        } # while

        # Get the matching sequences
        my $sth5h3b = $db_manager->execute("select sequence from sequence where hit = '$clone'");
        my @row5h3b = ();
        while(@row5h3b = $sth5h3b->fetchrow_array()) {
          my $hit = shift @row5h3b;
          if($matches eq "") {
            $matches = "$hit";
          } # if
          else {
            $matches .= ", $hit"
          } # else
        } # while

        # Get the matching Related Genes
        my $relateds = 0;
        my $sth5h3c = $db_manager->execute("select related from related where hit = '$clone'");
        my @row5h3c = ();
        while(@row5h3c = $sth5h3c->fetchrow_array()) {
          my $related = shift @row5h3c;
          $relateds++;
        } # while

        my $note = "";
        if($relateds > 0) {
          $note = "$type, $matches, $relateds related genes.  ";
        } # if
        else {
          $note = "$type, $matches.  ";
        } # else

# if($name eq "IS009H03") {
#   print "$name $mlg $start $end second one\n";
# } # if

        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        $db_manager->execute("insert into clone_locations values('', '$name', '$mlg', '$start', '$end', 'beta 2')");
      } # while

      message("Getting the reversed clone info");
      my $sth5f1 = $db_manager->execute("select contig2clone.clone, contig2clone.end, contig2clone.length, contig2clone.ctg, contig_anchors.mlg, contig_anchors.rev_start, contigs.end from contig2clone, contig_anchors, clones, contigs where contig2clone.ctg = contig_anchors.ctg and contig2clone.clone = clones.clone and clones.type = 'beta 2' and contig2clone.ctg = contigs.ctg");  # valid
      message("Saving the reverse beta 2 clones in the GFF file");
      message("  and the clone_locations table");
      my @row5f1 = ();
      while(@row5f1 = $sth5f1->fetchrow_array()) {                                 # xxx
        my $clone = shift @row5f1;
        my $band_end = shift @row5f1;
        my $length = shift @row5f1;
        my $ctg = shift @row5f1;
        my $mlg = shift @row5f1;
        my $rev_start = shift @row5f1;
        my $ctg_band_end = shift @row5f1;
        my $track = "RevClones";
        my $displacement = $ctg_band_end - $band_end;
        my $start = $rev_start + ($displacement * $project->{band_factor});
        my $end = $start + int($length * $project->{band_factor});
        my $name = $clone;
        my $type = "reverse";

        # get the matching contigs
        my $matches = "";
        my $sth5f0 = $db_manager->execute("select ctg from contig2clone where clone = '$clone'");  # valid
        my @row5f0 = ();
        while(@row5f0 = $sth5f0->fetchrow_array()) {
          my $contig = shift @row5f0;
          if($matches eq "") {
            $matches = $contig;
          } # if
          else {
            $matches .= ", $contig";
          } # else
        } # while

        # get the matching MTP
        my $sth5f01 = $db_manager->execute("select mtp from mtp where clone = '$clone'");  # valid
        my @row5f01 = ();
        while(@row5f01 = $sth5f01->fetchrow_array()) {
          my $mtp = shift @row5f01;
          if($matches eq "") {
            $matches = $mtp;
          } # if
          else {
            $matches .= ", $mtp";
          } # else
        } # while

        # get the matching EST
        my $sth5f02 = $db_manager->execute("select est from est where clone = '$clone'");  # valid
        my @row5f02 = ();
        while(@row5f02 = $sth5f02->fetchrow_array()) {
          my $est = shift @row5f02;
          if($matches eq "") {
            $matches = $est;
          } # if
          else {
            $matches .= ", $est";
          } # else
        } # while

        # Get the matching sequences
        my $sth5f0b = $db_manager->execute("select sequence from sequence where hit = '$clone'");
        my @row5f0b = ();
        while(@row5f0b = $sth5f0b->fetchrow_array()) {
          my $hit = shift @row5f0b;
          if($matches eq "") {
            $matches = "$hit";
          } # if
          else {
            $matches .= ", $hit"
          } # else
        } # while

        # Get the matching Related Genes
        my $relateds = 0;
        my $sth5f0c = $db_manager->execute("select related from related where hit = '$clone'");
        my @row5f0c = ();
        while(@row5f0c = $sth5f0c->fetchrow_array()) {
          my $related = shift @row5f0c;
          $relateds++;
        } # while

        my $note = "";
        if($relateds > 0) {
          $note = "$type, $matches, $relateds related genes.  ";
        } # if
        else {
          $note = "$type, $matches.  ";
        } # else

        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        $db_manager->execute("insert into clone_locations values('', '$name', '$mlg', '$start', '$end', 'reverse')");
      } # while

      message("Getting the spread beta 2 clone info");
      my $sth5f2 = $db_manager->execute("select contig2clone.clone, contig2clone.start, contig2clone.length, contig2clone.ctg, contig_anchors.mlg, contig_anchors.spread_start, contigs.start from contig2clone, contig_anchors, clones, contigs where contig2clone.ctg = contig_anchors.ctg and contig2clone.clone = clones.clone and clones.type = 'beta 2' and contig2clone.ctg = contigs.ctg");  # valid
      message("Saving the spread beta 2 clones in the GFF file.");
      my @row5f2 = ();
      while(@row5f2 = $sth5f2->fetchrow_array()) {
        my $clone = shift @row5f2;
        my $band_start = shift @row5f2;
        my $length = shift @row5f2;
        my $ctg = shift @row5f2;
        my $mlg = shift @row5f2;
        my $spread_start = shift @row5f2;
        my $ctg_band_start = shift @row5f2;
        my $track = "b2sClones";
        my $displacement = $band_start - $ctg_band_start;
        my $start = $spread_start + ($displacement * $project->{band_factor});
        my $end = $start + int($length * $project->{band_factor});
        my $name = $clone;
        my $type = "beta 2";

        # get the matching contigs
        my $matches = "";
        my $sth5f3 = $db_manager->execute("select ctg from contig2clone where clone = '$clone'");  # valid
        my @row5f3 = ();
        while(@row5f3 = $sth5f3->fetchrow_array()) {
          my $contig = shift @row5f3;
          if($matches eq "") {
            $matches = $contig;
          } # if
          else {
            $matches .= ", $contig";
          } # else
        } # while

        # get the matching MTP
        my $sth5f4 = $db_manager->execute("select mtp from mtp where clone = '$clone'");  # valid
        my @row5f4 = ();
        while(@row5f4 = $sth5f4->fetchrow_array()) {
          my $mtp = shift @row5f4;
          if($matches eq "") {
            $matches = $mtp;
          } # if
          else {
            $matches .= ", $mtp";
          } # else
        } # while

        # get the matching EST
        my $sth5f4a = $db_manager->execute("select est from est where clone = '$clone'");  # valid
        my @row5f4a = ();
        while(@row5f4a = $sth5f4a->fetchrow_array()) {
          my $est = shift @row5f4a;
          if($matches eq "") {
            $matches = $est;
          } # if
          else {
            $matches .= ", $est";
          } # else
        } # while

        # Get the matching sequences
        my $sth5f4b = $db_manager->execute("select sequence from sequence where hit = '$clone'");
        my @row5f4b = ();
        while(@row5f4b = $sth5f4b->fetchrow_array()) {
          my $hit = shift @row5f4b;
          if($matches eq "") {
            $matches = "$hit";
          } # if
          else {
            $matches .= ", $hit"
          } # else
        } # while

        # Get the matching Related Genes
        my $relateds = 0;
        my $sth5f4c = $db_manager->execute("select related from related where hit = '$clone'");
        my @row5f4c = ();
        while(@row5f4c = $sth5f4c->fetchrow_array()) {
          my $related = shift @row5f4c;
          $relateds++;
        } # while

        my $note = "";
        if($relateds > 0) {
          $note = "$type, $matches, $relateds related genes.  ";
        } # if
        else {
          $note = "$type, $matches.  ";
        } # else

        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        $db_manager->execute("insert into clone_locations values('', '$name', '$mlg', '$start', '$end', 'spread')");
      } # while

      message("Getting the beta 1 clone info");
      my $sth6 = $db_manager->execute("select clone_anchors.clone, clone_anchors.mlg, clone_anchors.anchor, clone_anchors.dup_i, clone_anchors.dup_t from clones, clone_anchors where clones.type = 'beta 1' and clones.clone = clone_anchors.clone");
      message("Saving the beta 1 clones in the GFF file");
      message("  and the clone_locations table");
      my @row6 = ();
      while(@row6 = $sth6->fetchrow_array()) {
        my $clone = shift @row6;
        my $mlg = shift @row6;
        my $anchor = shift @row6;
        my $dup_i = shift @row6;
        my $dup_t = shift @row6;
        my $track = "b1Clones";
        my $half_clone_length = int(AVE_CLONE_LENGTH / 2);
        $anchor = $half_clone_length + 1 if ($anchor < $half_clone_length + 1);
        my $overflow = ($anchor + $half_clone_length) - $mlg_lengths{$mlg};
        if($overflow >= 0) {
          $anchor -= $overflow + 200;
        } # if
        my $start = $anchor - $half_clone_length;
        my $end = $start + AVE_CLONE_LENGTH;
        my $name = $clone;
        my $type = "beta 1";

        # get the matching loci
        my $matches = "";
        my $sth6a = $db_manager->execute("select locus from clone2locus3 where clone = '$clone'");
        my @row6a = ();
        while(@row6a = $sth6a->fetchrow_array()) {
          my $locus = shift @row6a;
          if($matches eq "") {
            $matches = $locus;
          } # if
          else {
            $matches .= ", $locus";
          } # else
        } # while

        # get the matching MTP
        my $sth6b = $db_manager->execute("select mtp from mtp where clone = '$clone'");  # valid
        my @row6b = ();
        while(@row6b = $sth6b->fetchrow_array()) {
          my $mtp = shift @row6b;
          if($matches eq "") {
            $matches = $mtp;
          } # if
          else {
            $matches .= ", $mtp";
          } # else
        } # while

        # get the matching EST
        my $sth6b2 = $db_manager->execute("select est from est where clone = '$clone'");  # valid
        my @row6b2 = ();
        while(@row6b2 = $sth6b2->fetchrow_array()) {
          my $est = shift @row6b2;
          if($matches eq "") {
            $matches = $est;
          } # if
          else {
            $matches .= ", $est";
          } # else
        } # while

        # Get the matching sequences
        my $sth6b3 = $db_manager->execute("select sequence from sequence where hit = '$clone'");
        my @row6b3 = ();
        while(@row6b3 = $sth6b3->fetchrow_array()) {
          my $hit = shift @row6b3;
          if($matches eq "") {
            $matches = "$hit";
          } # if
          else {
            $matches .= ", $hit"
          } # else
        } # while

        # Get the matching Related Genes
        my $relateds = 0;
        my $sth6b4 = $db_manager->execute("select related from related where hit = '$clone'");
        my @row6b4 = ();
        while(@row6b4 = $sth6b4->fetchrow_array()) {
          my $related = shift @row6b4;
          $relateds++;
        } # while

        my $note = "";
        if($dup_t > 1) {
          if($relateds > 0) {
            $note = "$dup_i of $dup_t, $type, $matches, $relateds related genes.  ";
          } # if
          else {
            $note = "$dup_i of $dup_t, $type, $matches.  ";
          } #else
        } # if
        else {
          if($relateds > 0) {
            $note = "$type, $matches, $relateds related genes.  ";
          } # if
          else {
            $note = "$type, $matches.  ";
          } # else
        } # else
        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        $db_manager->execute("insert into clone_locations values('', '$name', '$mlg', '$start', '$end', 'beta 1')");
      } # while

      message("Getting the alpha clone info");
      my $sth6c = $db_manager->execute("select clone, start, end from clone_locations where type = 'alpha'");
      message("Saving the alpha clones in the GFF file");
      my @row6c = ();
      while(@row6c = $sth6c->fetchrow_array()) {
        my $clone = shift @row6c;
        my $mlg = "Queue";
        my $start = shift @row6c;
        my $end = shift @row6c;
        my $track = "aClones";
        my $name = $clone;
        my $type = "alpha";

        # get the matching loci
        my $matches = "";
        my $sth6d = $db_manager->execute("select locus from clone2locus3 where clone = '$clone'");
        my @row6d = ();
        while(@row6d = $sth6d->fetchrow_array()) {
          my $locus = shift @row6d;
          if($matches eq "") {
            $matches = $locus;
          } # if
          else {
            $matches .= ", $locus";
          } # else
        } # while

        # get the matching MTP
        my $sth6e = $db_manager->execute("select mtp from mtp where clone = '$clone'");  # valid
        my @row6e = ();
        while(@row6e = $sth6e->fetchrow_array()) {
          my $mtp = shift @row6e;
          if($matches eq "") {
            $matches = $mtp;
          } # if
          else {
            $matches .= ", $mtp";
          } # else
        } # while

        # get the matching EST
        my $sth6f = $db_manager->execute("select est from est where clone = '$clone'");  # valid
        my @row6f = ();
        while(@row6f = $sth6f->fetchrow_array()) {
          my $est = shift @row6f;
          if($matches eq "") {
            $matches = $est;
          } # if
          else {
            $matches .= ", $est";
          } # else
        } # while

        # Get the matching sequences
        my $sth6g = $db_manager->execute("select sequence from sequence where hit = '$clone'");
        my @row6g = ();
        while(@row6g = $sth6g->fetchrow_array()) {
          my $hit = shift @row6g;
          if($matches eq "") {
            $matches = "$hit";
          } # if
          else {
            $matches .= ", $hit"
          } # else
        } # while

        # Get the matching Related Genes
        my $relateds = 0;
        my $sth6h = $db_manager->execute("select related from related where hit = '$clone'");
        my @row6h = ();
        while(@row6h = $sth6h->fetchrow_array()) {
          my $related = shift @row6h;
          $relateds++;
        } # while

        if($matches ne "") {
        $type .= ", $matches";
        } # if

        my $note = "";
        if($relateds > 0) {
          $note = "$type, $relateds related genes.  ";
        } # if
        else {
          $note = "$type.  ";
        } #else

        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
      } # while
    } # if (clones)
    else {
      message("Not getting the clones info");
    } # else

    ###########################
    ########## Contigs ########
    ###########################

    if($self->{contigs}) {
      message("Getting the gamma contigs info");
      my $sth7 = $db_manager->execute("select contig_anchors.ctg, contig_anchors.mlg, contig_anchors.start, contig_anchors.end, contig_anchors.rev_start, contig_anchors.rev_end, contig_anchors.spread_start, contig_anchors.spread_end, contig_anchors.dup_i, contig_anchors.dup_t from contigs, contig_anchors where contigs.type = 'gamma' and contigs.ctg = contig_anchors.ctg");
      message("Saving the gamma contigs in the GFF file.");
      my @row7 = ();
      while(@row7 = $sth7->fetchrow_array()) {
        my $ctg = shift @row7;
        my $mlg = shift @row7;
        my $start = shift @row7;
        my $end = shift @row7;
        my $rev_start = shift @row7;
        my $rev_end = shift @row7;
        my $spread_start = shift @row7;
        my $spread_end = shift @row7;
        my $dup_i = shift @row7;
        my $dup_t = shift @row7;
        my $overflow = $end - $mlg_lengths{$mlg};
        if($overflow >= 0) {
          $start -= $overflow + 200;
          $end -= $overflow + 200;
        } # if
        $overflow = $rev_end - $mlg_lengths{$mlg};
        if($overflow >= 0) {
          $rev_start -= $overflow + 200;
          $rev_end -= $overflow + 200;
        } # if
        my $track = "gContigs";
        my $name = $ctg;
        my $type = "gamma";

        # get the matching clones
        my $matches = 0;
        my $sth7a = $db_manager->execute("select contig2clone.clone from contig2clone, clones where contig2clone.ctg = '$ctg' and contig2clone.clone = clones.clone and contig2clone.valid = 'yes' and clones.type = 'gamma'");
        my @row7a = ();
        while(@row7a = $sth7a->fetchrow_array()) {
          my $clone = shift @row7a;
          $matches++;
        } # while

        my $note = "";
        if($dup_t > 1) {
          $note = "$dup_i of $dup_t, $type, $matches clone/s.  ";
        } # if
        else {
          $note = "$type, $matches clone/s.  ";
        } # else

        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";

        # Do the reverse contigs
        $track = "RevContigs";
        print GFF_FILE "mlg$mlg\tvarious\t$track\t$rev_start\t$rev_end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";

        # Do the spread
        $track = "sContigs";
        print GFF_FILE "mlg$mlg\tvarious\t$track\t$spread_start\t$spread_end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
      } # while

      message("Getting the beta contigs info");
      my $sth7a = $db_manager->execute("select ctg, start, end from contigs_onQ");
      message("Saving the beta contigs in the GFF file.");
      my @row7a = ();
      while(@row7a = $sth7a->fetchrow_array()) {
        my $ctg = shift @row7a;
        my $start = shift @row7a;
        my $end = shift @row7a;
        print GFF_FILE "mlgQueue\tvarious\tbContigs\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$ctg\" ; Note\n";
      } # while
    } # if (contigs)
    else {
      message("Not getting the contigs info");
    } # else

    ###########################
    ############ QTL's ########
    ###########################

    if($self->{qtls}) {
      message("Getting the QTL info");
      my $sth8 = $db_manager->execute("select qtl, mlg, start, end, gene from qtl");
      message("Saving the QTL's in the GFF file.");
      my @row8 = ();
      while(@row8 = $sth8->fetchrow_array()) {
        my $qtl = shift @row8;
        my $mlg = shift @row8;
        my $start = shift @row8;
        my $end = shift @row8;
        my $gene = shift @row8;
        my $track = "QTL";
        my $name = $qtl;
        print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note\n";
        # print the QTL Gene, if appropriate
        if($gene ne "-1") {
          $track = "QTLGene";
          my $note = $name;
          $name = $gene;
          print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                             "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        } # if
      } # while
    } # if (qtls)
    else {
      message("Not getting the QTL info");
    } # else

    ###########################
    ############ MTP's ########
    ###########################

    if($self->{mtps}) {
      message("Getting the MTP info");
      my $sth9 = $db_manager->execute("select clone, mtp from mtp");
      message("Saving the MTP's in the GFF file.");
      my @row9 = ();
      while(@row9 = $sth9->fetchrow_array()) {
        my $clone = shift @row9;
        my $mtp = shift @row9;
        my $sth9a = $db_manager->execute("select mlg, start, end from clone_locations where clone = '$clone'");
        my @row9a = ();
        while(@row9a = $sth9a->fetchrow_array()) {
          my $mlg = shift @row9a;
          my $start = shift @row9a;
          my $end = shift @row9a;
          my $track = "MTP";
          my $name = $mtp;
          my $note = $clone;
          print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                         "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        } # while
      } # while
    } # if (mtps)
    else {
      message("Not getting the MTP info");
    } # else

    ###########################
    ############ EST's ########
    ###########################

    if($self->{ests}) {
      message("Getting the EST info");
      my $sth10 = $db_manager->execute("select clone, est, comment from est");
      message("Saving the EST's in the GFF file.");
      my @row10 = ();
      while(@row10 = $sth10->fetchrow_array()) {
        my $clone = shift @row10;
        my $est = shift @row10;
        my $comment = shift @row10;
        my $sth10a = $db_manager->execute("select mlg, start, end from clone_locations where clone = '$clone'");
        my @row10a = ();
        while(@row10a = $sth10a->fetchrow_array()) {
          my $mlg = shift @row10a;
          my $start = shift @row10a;
          my $end = shift @row10a;
          my $track = "EST";
          my $name = $est;
          my $note = $clone;
          $note .= ", $comment" if($comment ne "");
          print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                         "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        } # while
      } # while
    } # if (mtps)
    else {
      message("Not getting the EST info");
    } # else

    ###########################
    ######### Sequences #######
    ###########################

    if($self->{seq}) {
      message("Getting the sequence info");
      my $sth11 = $db_manager->execute("select sequence, hit from sequence");
      message("Saving the sequences in the GFF file.");
      my @row11 = ();
      while(@row11 = $sth11->fetchrow_array()) {
        my $sequence = shift @row11;
        my $hit = shift @row11;

        my $sth11a = $db_manager->execute("select mlg, start, end from clone_locations where clone = '$hit'");
        my @row11a = ();
        while(@row11a = $sth11a->fetchrow_array()) {
          my $mlg = shift @row11a;
          my $start = shift @row11a;
          my $end = shift @row11a;
          my $track = "Sequence";
          my $name = $sequence;
          my $note = $hit;
          print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                         "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        } # while

        my $sth11b = $db_manager->execute("select mlg, anchor from loci where locus = '$hit'");
        my @row11b = ();
        while(@row11b = $sth11b->fetchrow_array()) {
          my $mlg = shift @row11b;
          my $anchor = shift @row11b;
          $anchor += 101 if($anchor < 101);
          my $overflow = ($anchor + 100) - $mlg_lengths{$mlg};
          if($overflow >= 0) {
            $anchor -= $overflow + 200;
          } # if
          my $start = $anchor - 100;
          my $end = $anchor + 100;
          my $track = "Sequence";
          my $name = $sequence;
          my $note = $hit;
          print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                         "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        } # while

      } # while
    } # if
    else {
      message("Not getting the Sequence info");
    } # else

    ###########################
    ## Related Genes ##########
    ###########################

    if($self->{rel}) {

      message("Creating a hash of the loci name changes");
      my $loci_file_opened = TRUE;
      open(LOCI_FILE, "<", "../working_data/locus_name_changes.txt")
        or $loci_file_opened = FALSE;
      my %name_changes = ();
      if($loci_file_opened) {
        my @input_array = <LOCI_FILE>;
        my $num_lines = scalar(@input_array);
        for(my $lcv = 0; $lcv < $num_lines; $lcv++) {
          my $current_line = $input_array[$lcv];
          chomp $current_line;
          my @field_array = split /\t/, $current_line;
          my $old_name = $field_array[0];
          my $new_name = $field_array[1];
          $name_changes{$old_name} = $new_name;
        } # for
        close LOCI_FILE;
      } # if
      else {
        message("$gff_filename could not be opened:  $!");
      } # else

      message("Opening output file for bad related locations");
      my $bad_relateds_file_opened = TRUE;
      open(BAD_RELATEDS_FILE, ">", "../working_data/bad_relateds.txt")
        or $bad_relateds_file_opened = FALSE;
      if($bad_relateds_file_opened == FALSE) {
        message("$gff_filename could not be opened:  $!");
      } # if

      message("Substituting bad loci names with their clones");
      my $sth12z = $db_manager->execute("select clone, locus from bad_clone2locus");
      my @row12z = ();
      while(@row12z = $sth12z->fetchrow_array()) {
        my $clone = shift @row12z;
        my $locus = shift @row12z;
        $name_changes{$locus} = $clone;
      } # while

      message("Getting the related genes info");
      my $sth12 = $db_manager->execute("select related, hit, mlg, start, end from related");
      message("Saving the related genes in the GFF file.");
      my @row12 = ();
      my $invalid_counter = 0;

      my $hit_code = 0;

      RELATED:  while(@row12 = $sth12->fetchrow_array()) {
        my $related = shift @row12;
        my $hit = shift @row12;
        my $mlg = shift @row12;
        my $start = shift @row12;
        my $end = shift @row12;
        my $valid = FALSE;

        # See if the locus name was changed
        if(exists($name_changes{$hit})) {
          $hit = $name_changes{$hit};
        } # if

        my $sth12a = $db_manager->execute("select mlg, start, end from clone_locations where clone = '$hit'");
        my @row12a = ();
        while(@row12a = $sth12a->fetchrow_array()) {
          $valid = TRUE;
          my $mlg = shift @row12a;
          my $start = shift @row12a;
          my $end = shift @row12a;
          my $track = "RelatedGenes";
          if($related =~ /^Glycine/) {
            $track = "RelatedG";
          } # if
          if($related =~ /^G.max/) {
            $track = "RelatedG";
          } # if
          my $name = $related;
          my $note = $hit;
          print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                         "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        } # while

        # precheck the ambiguous sat's
        if($hit =~ /^Sat\d/) {
          substr($hit, 3, 0) = "t";
          $hit_code = 0;
          my $sth12a1 = $db_manager->execute("select mlg from loci where locus = '$hit'");
          my @row12a1 = ();
          while(@row12a1 = $sth12a1->fetchrow_array()) {
            my $mlg = shift @row12a1;
            $hit_code = 1;
          } # while
          substr($hit, 3, 1) = "_";
          my $sth12a2 = $db_manager->execute("select mlg from loci where locus = '$hit'");
          my @row12a2 = ();
          while(@row12a2 = $sth12a2->fetchrow_array()) {
            my $mlg = shift @row12a2;
            if($hit_code == 1) {
              $hit_code = 3;
            } # if
            else {
              $hit_code = 2;
            } # else
          } # while

          if($hit_code == 0) {
            substr($hit, 3, 1) = "";
          } # if
          elsif($hit_code == 1) {
            substr($hit, 3, 1) = "t";
          } # if
          elsif($hit_code == 3) {
            substr($hit, 3, 1) = "";
          } # elsif
        } # if

        my $sth12b = $db_manager->execute("select mlg, anchor from loci where locus = '$hit'");
        my @row12b = ();
        while(@row12b = $sth12b->fetchrow_array()) {
          $valid = TRUE;
          my $mlg = shift @row12b;
          my $anchor = shift @row12b;
          $anchor += 101 if($anchor < 101);
          my $overflow = ($anchor + 100) - $mlg_lengths{$mlg};
          if($overflow >= 0) {
            $anchor -= $overflow + 200;
          } # if
          my $start = $anchor - 100;
          my $end = $anchor + 100;
          my $track = "RelatedGenes";
          if($related =~ /^Glycine/) {
            $track = "RelatedG";
          } # if
          if($related =~ /^G.max/) {
            $track = "RelatedG";
          } # if
          my $name = $related;
          my $note = $hit;
          print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                         "\t.\t+\t.\tSequence \"$name\" ; Note \"$note\"\n";
        } # while

        if($valid == FALSE) {
          $invalid_counter++;
          if($bad_relateds_file_opened == TRUE) {
            print BAD_RELATEDS_FILE "$hit\t$mlg\t$start\t$end\t$related\n";
          } # if
        } # if

      } # while

    if($bad_relateds_file_opened == TRUE) {
      close BAD_RELATEDS_FILE;
    } # if

    message("Related Genes not located:  $invalid_counter");

    } # if
    else {
      message("Not getting the Related Genes info");
    } # else

    ###########################
    ########## Confirmed ######
    ###########################

    if($self->{con}) {
      message("Getting the Confirmed info");
      my $sth13 = $db_manager->execute("select clone, mlg, cM from confirmed");
      message("Saving the Confirmeds in the GFF file.");
      my @row13 = ();
      while(@row13 = $sth13->fetchrow_array()) {
        my $clone = shift @row13;
        my $mlg = shift @row13;
        my $cM = shift @row13;
        next if($cM == -1);
        next if($mlg =~ /^Y/);
        my $anchor = int($cM * FACTOR);
        my $half_length = int(AVE_CLONE_LENGTH / 2);

        $anchor = $half_length + 1 if ($anchor < $half_length + 1);
        my $overflow = ($anchor + $half_length) - $mlg_lengths{$mlg};
        if($overflow >= 0) {
          $anchor -= $overflow + 200;
        } # if

        my $start = $anchor - $half_length;
        my $end = $start + AVE_CLONE_LENGTH;

        # see if this clone matches any existing clones
        my $matches = FALSE;
        my $sth13a = $db_manager->execute("select clone from clone_locations where clone = '$clone'");
        my @row13a = ();
        while(@row13a = $sth13a->fetchrow_array()) {
          my $temp_clone = shift @row13a;
          $matches = TRUE;
        } # while

        my $track = "Confirmed";
        my $name = $clone;
#        my $note = $clone;
#          $note .= ", $comment" if($comment ne "");
        if($matches == TRUE) {
          print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                         "\t.\t+\t.\tSequence \"$name\" ; Note \"Matches\"\n";
        } # if
        else {
          print GFF_FILE "mlg$mlg\tvarious\t$track\t$start\t$end" .
                         "\t.\t+\t.\tSequence \"$name\" ; Note\n";
        } # else

      } # while
    } # if (mtps)
    else {
      message("Not getting the EST info");
    } # else

    message("Disconnecting from the database");
    $db_manager->disconnect;

    close GFF_FILE;
  } # if($file_opened)
  else {
    # The GFF file could not be opened
    message("$gff_filename could not be opened:  $!");
  } # else

  press_enter;
} # write

1