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( [id://3333]=superdoc: print w/replies, xml ) Need Help??
Any help optimizing this slow code would be great.

Thanks in advance

-Mark 


# circularGenome.pm
#

package RG::circularGenome;

# If this WERE a module, the boilerplate would look something like thi
+s:
#
# require Block;
#
# our @ISA    = qw(Exporter);
# our @EXPORT = qw(
#     ...
# );

1;


package main;

use strict;                                                           
+  # DEBUG
use warnings;                                                         
+  # DEBUG

use Data::Dumper;                                                     
+  # DEBUG



sub create_circularGenome
{
   #
   # Create a circular genome canvas.
   #
   # Open window, set org.
   #
   # Input:        $c      source canvas
   # Output:       -
   # Global:       %global
   main::trace_me();

   my ($c) = @_;
   our (%global,$canvas);
  # our $scale = $global{$c}->{SCALE};


   $canvas = create_canvas(-type    => 'circular',
                           -org     => $global{$c}->{org_name},
                           -buttons => \&scatterplot_buttonbar);


   ############# Create window elements #######################
   our $label_status = 0;
   our $cvh = 500;   # canvas height
   our $cvw = 700;   # canvas width
   our $org = $global{$c}->{org_name};

 #  my $label_toggle = $canvas->Checkbutton(-text=>'Turn on gene names
+',
 #                                          -onvalue=>1,
 #                                          -offvalue=>0,
 #                                          -variable=> \$label_status
+,
 #                                          -command=> [\&drawGenome, 
+$canvas, $cvh, $cvw, $label_status, $scale ]
 #                                          )->pack(-side=>'bottom');


   &drawGenome($canvas,$cvh,$cvw,$label_status,$org);

   # Graph Label
}






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

######################################################################
+##
sub drawGenome
{
   my ($canvas,$cvh,$cvw,$label_status,$org) = @_;
   print"label status=$label_status\n";
  # print"scale=$scale\n";
   my ($circumference,$pi,$genome_length,$radius,$message,$deg2rad,$dr
+awn_angle);
   my @colors = qw/grey purple pink blue turquoise green chartreuse ye
+llow gold orange/;
   our($dbh,$sth,@myorfs,@orfids,$gene_name);
   ########################### Database section ################


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

   # grab protein positions
   $sth = $dbh->prepare("select id from org where full_name='$org'") o
+r die "Can't prepare SQL statement ", $dbh->errstr(),"\n";
   $sth->execute() or die "Can't execute SQL statement: ", $sth->errst
+r(), "\n";
   my($orgid) = $sth->fetchrow_array();


    print"org=$org\torgid=$orgid\n";


   $sth = $dbh->prepare ("select text_id,gene_name,protein5, protein3 
+from protein where org_id=$orgid order by protein5 desc") or die "Can
+'t prepare SQL statement ", $dbh->errstr(),"\n";
   $sth->execute() or die "Can't execute SQL statement: ", $sth->errst
+r(), "\n";

   my $count=0;
   while (my($text_id,$gene_name,$protein5,$protein3) = $sth->fetchrow
+_array())
   {
      $myorfs[$count]= [$text_id,$gene_name,$protein5,$protein3];
      $count++;
   }

   my $orfcount = $#myorfs+1;
   print" There are $orfcount orfs in $org\n";

   # 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 fu
+ll 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 s
+o that the next one will be placed
   # correctly.

   $pi = 3.1416;
   $deg2rad = $pi/180;
   $radius = 230;                        # define radius
   $circumference = 2 * $pi * $radius;   # define circumference
   $drawn_angle=0;
   $genome_length=0;

   for (my $i=0;$i<$orfcount;$i++)
   {
      my $distance = $myorfs[$i][3] - $myorfs[$i][2];  # calc orf leng
+th
      $genome_length = $genome_length + $distance;     # calc total ge
+nome length
   }
   $canvas->createText(350, 250, -fill => 'black', -text => "$org Geno
+me");
   $canvas->createText(350, 265, -fill => 'black', -text => "$genome_l
+ength bp");

   $drawn_angle=0;
   for (my $i=0;$i<$orfcount;$i++)
   {
      my $color = int($i % 10);
      my $orig_dist = $myorfs[$i][3] - $myorfs[$i][2];  # calc origina
+l 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 equival
+ent arc length corresponding to same pct of circum.
      my $central_angle = 360 * ($graph_arc_length / $circumference); 
+# calc central angle for that arc

#      $message = "label status = $label_status";
      if ($i == 0)
      {
         $canvas->createArc($cvw / 2 - $radius,         # draw first a
+rc all the way around circle
                            $cvh / 2 - $radius,         # set drawn_an
+gle = angle you want this orf to be
                            $cvw / 2 + $radius,         # It will be u
+sed to set the extent for the next arc
                            $cvh / 2 + $radius,         # drawn, leavi
+ng the right arc length exposed for this orf.
                            -width=> 10,
                            -fill=> $colors[$color],
                            -outline=> $colors[$color],
                            -style=> 'arc',
                            -start=>90,
                            -extent=> -359.99999999,
                            -tags=>$myorfs[$i][1]);

         $drawn_angle = 360 - $central_angle;
         $gene_name = $myorfs[$i][1];
      }
      else
      {
         $canvas->createArc($cvw / 2 - $radius,         # draw all of 
+the other arcs on top of the first arc
                            $cvh / 2 - $radius,
                            $cvw / 2 + $radius,
                            $cvh / 2 + $radius,
                            -width=> 10,
                            -fill=> $colors[$color],
                            -outline=> $colors[$color],
                            -style=> 'arc',
                            -start=>90,
                            -extent=> -$drawn_angle,
                            -tags=>$myorfs[$i][1]);

         $drawn_angle = $drawn_angle - $central_angle;
         $gene_name = $myorfs[$i][1];

      }
#      if ($scale < 1)
#      {
#         &drawLabels($drawn_angle,$gene_name);
         my $tick_length = 15;
         my $real_angle = 360-$drawn_angle+90;
         my $xstart = $cvw/2.0 + $radius      * cos($real_angle*$deg2r
+ad);
         my $ystart = $cvh/2.0 - $radius      * sin($real_angle*$deg2r
+ad);
         my $xstop  = $xstart  + $tick_length * cos($real_angle*$deg2r
+ad);
         my $ystop  = $ystart  - $tick_length * sin($real_angle*$deg2r
+ad);

         $canvas->createLine($xstart,$ystart,$xstop,$ystop);
         if (89< $real_angle && $real_angle <= 112.5)
         {
            $canvas->createText($xstop,$ystop, -anchor=>'s', -text=>"$
+gene_name");
                     }
         elsif ((112.5 < $real_angle) && ($real_angle <= 157.5))
         {
            $canvas->createText($xstop,$ystop, -anchor=>'se', -text=>"
+$gene_name");

         }

         elsif ((157.5 < $real_angle) && ($real_angle <= 202.5))
         {
            $canvas->createText($xstop,$ystop, -anchor=>'e', -text=>"$
+gene_name");
                     }

         elsif ((202.5 < $real_angle) && ($real_angle <= 247.5))
         {
            $canvas->createText($xstop,$ystop, -anchor=>'ne', -text=>"
+$gene_name");

         }

         elsif ((247.5 < $real_angle) && ($real_angle <= 292.5))
         {
            $canvas->createText($xstop,$ystop, -anchor=>'n', -text=>"$
+gene_name");
         }

         elsif ((292.5 < $real_angle) && ($real_angle <= 337.5))
         {
            $canvas->createText($xstop,$ystop, -anchor=>'nw', -text=>"
+$gene_name");
         }

         elsif ((337.5 < $real_angle) && ($real_angle <= 382.5))
         {
            $canvas->createText($xstop,$ystop, -anchor=>'w', -text=>"$
+gene_name");
         }

         elsif ((382.5 < $real_angle) && ($real_angle < 427.5))
         {
            $canvas->createText($xstop,$ystop, -anchor=>'sw', -text=>"
+$gene_name");
         }

         elsif ((427.5 < $real_angle) && ($real_angle < 475))
         {
            $canvas->createText($xstop,$ystop, -anchor=>'s', -text=>"$
+gene_name");
         }
 #     }
   }
}
#####################################################



# 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]

update (broquaint): added formatting + <readmore> tag

In reply to sloooowwwwww code! by Anonymous Monk

Title:
Use:  <p> text here (a paragraph) </p>
and:  <code> code here </code>
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