#!C:\Perl\bin

# Test Widget to try and draw circular genome
# by Mark
#
# Created 08.19.03
# Revised 08.20.03
#
# ver. 0.02


use Cwd;
use DBI;
use Digest::MD5 qw(md5_hex);
use LWP::Simple;
use Text::Wrap;
use lib 'lib';
use lib 'vg/lib';
use lib '../lib';
use Tk;
use Tk::LabEntry;
use Tk::Dialog;
use Tk::DialogBox;
use Tk::TableMatrix;
use Tk::ProgressBar;
use Tk::ROText;
use Tk::Optionmenu;
use Win32;
use Win32::Process;
use Import::Genbank qw(gbk_org_info gbk_write_orfs);
use Functions qw( mysystem );
use Globals;
use strict;
use warnings;   # DEBUG! #
use RG::Fasta;
use RG::DB::Protein;
use RG::DB::Org;
use RG::DB::Contig;
use RG::GUI::Orfscan;
use RG::GUI::ProteinInspector;
use RG::DNA;
use RG::Block;
use RG::ButtonBar;
use RG::Canvas;
use RG::ContigAsm;
use RG::ContigAsmP;
use RG::ContigAsmS;
use RG::ContigAsmY;
use RG::Ephemera;
use RG::FileIO;
use RG::Menubar;
use RG::Organism;
use RG::PropTable;
use RG::ScatterPlot;
use Tk::MyBalloon;
#use Math;

our($dbh,$sth,%myorfs,@orfids);

# Define database connection
$dbh = DBI->connect('dbi:mysql:genomatik','genomatik','3369',{ RaiseEr
+ror => 1,AutoCommit => 1 });

# grab protein positions for halodurans, org_id 106
$sth = $dbh->prepare ("select text_id,gene_name,protein5, protein3 fro
+m protein where org_id=64 order by protein5 desc") or die "Can't prep
+are SQL statement ", $dbh->errstr(),"\n";
$sth->execute() or die "Can't execute SQL statement: ", $sth->errstr()
+, "\n";

my $count=0;
while (my($text_id,$gene_name,$protein5,$protein3) = $sth->fetchrow_ar
+ray())
{
    $myorfs{$count}= [$text_id,$gene_name,$protein5,$protein3];
    $count++;
}
@orfids = keys(%myorfs);
my $orfcount = $#orfids+1;
print" There are $orfcount orfs in halodurans\n";


my $mw = MainWindow->new();
$mw ->title("Circular Genome View");

my $canvas = $mw->Canvas(-height=>600, -width=> 600, -background=> 'wh
+ite')->pack();

# Create area to display ORF ID's
my $message;
my $orf_label = $mw->Label(-textvariable=> \$message, -borderwidth=> 2
+, -relief=> 'groove')->pack(-fill => 'x',-side=>'bottom');

my ($x1,$y1,$x2,$y2,$x_offset,$y_offset,$circumference,$pi,$genome_len
+gth,$radius);
my @colors = qw/grey purple pink blue turquoise green chartreuse yello
+w gold orange/;

# Mathmatical Basis
#
# For a circle with central angle A, arc length S and circumference C,
# S/C = A/360 degrees. Therefore A = 360(S/2*pi*radius)
#
# Since we draw the longest arc (last orf) first, we just draw a full 
+circle.  After that,
# the calculated central_angle is added to drawn_angle. As we draw the
+ other orfs, the arc that is drawn
# is 360 - drawn_angle. The central_angle is added to drawn_angle so t
+hat the next one will be placed
# correctly.

$pi = 3.1417;
$x_offset = 25;
$y_offset = 25;
$x1 = $x_offset;
$y1 = $y_offset;
$x2 = $x_offset + 650;
$y2 = $y_offset + 650;

$circumference = 2 * ($x2 - $x1) * $pi;                         # defi
+ne circumference
$radius = $circumference/2;                                 # define r
+adius
my @orf_keys = keys %myorfs;
my $drawn_angle=0;
my ($remaining_angle,$actual_angle);
$genome_length=0;

foreach my $key(@orf_keys)
{
   my $distance = $myorfs{$key}[3] - $myorfs{$key}[2];  # calc orf len
+gth
   $genome_length = $genome_length + $distance;         # calc total g
+enome length
}

print "circum = $circumference\ngenome length= $genome_length\n";
foreach my $key(@orf_keys)
{
   my $color = int($key % 10);
   my $orig_dist = $myorfs{$key}[3] - $myorfs{$key}[2];  # calc origin
+al orf length
   my $orf_pct = $orig_dist/$genome_length;              # convert orf
+ length to pct of genome length
   my $graph_arc_length = $circumference * $orf_pct;     # calc equiva
+lent arc length corresponding to same pct of circumference
   my $central_angle = 360 * ($graph_arc_length / $circumference); #(2
+ * $pi * $radius)); # calc central angle for that arc

   if ($drawn_angle == 0)
   {
      $canvas->createArc($x1,$y1,$x2,$y2, -width=> 10, -fill=> $colors
+[$color],-outline=> $colors[$color],-style=> 'arc', -start=>90, -exte
+nt=> -359.99);
      &bind_message($canvas,"Edg-1");     # Display gene name when mou
+se is over it.

      $drawn_angle = $central_angle;
   }
   elsif($drawn_angle < 359)
   {
      $actual_angle = 360 - $drawn_angle;
      $canvas->createArc($x1,$y1,$x2,$y2, -width=> 10, -fill=> $colors
+[$color],-outline=> $colors[$color],-style=> 'arc', -start=>90, -exte
+nt=> -$actual_angle);
      $drawn_angle = $drawn_angle + $central_angle;
   }
}

# Graph Label
$canvas->createText($x_offset+375, $y_offset+375, -fill => 'black', -t
+ext => 'Halodurans Genome');
$canvas->createText($x_offset+375, $y_offset+390, -fill => 'black', -t
+ext => "$genome_length bp");
#$canvas->configure(-scrollregion=> [$canvas->bbox("all")]);

$mw->deiconify();
$mw->raise();
MainLoop;

# Displays value of $message in lower box when mouse is over item, goe
+s back to null when mouse leaves.
sub bind_message
{
  my($widget, $msg) = @_;
  $widget->Tk::bind('<Enter>', [ sub { $message = $_[1]; }, $msg ]);
  $widget->Tk::bind('<Leave>',  sub { $message = ""; });
}
[download]