#!/usr/bin/perl -w

#    winlock.pl
#    Copyright 2002-2004 Charlie Kim
#
#    This program is free software; you can redistribute it and/or modify
#    it under the terms of the GNU General Public License as published by
#    the Free Software Foundation; either version 2 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU General Public License for more details.
#
#    For a copy of the GNU General Public License, write to the Free Software
#    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA

# This program uses the following modules

# Perl/Tk 800.023  Copyright (c) 1995-1996 Nick Ing-Simmons. 
# http://starbase.neosoft.com/%7Eclaird/comp.lang.perl.tk/ptkFAQ.html

# Win32::FileOp 0.11.3
# Module built by :
#  Jan Krynicky <Jenda@Krynicky.cz>
#  Bill Luebkert <dbe@wgn.net>
#  Mike Blazer <blazer@peterlink.ru>
#  Aldo Calpini <a.calpini@romagiubileo.it>
#  Michael Yamada <myamada@gj.com>

# GD 1.33 Copyright 1995-2000, Lincoln D. Stein
# Perl "Artistic License"

# GDGraph 1.33
# Copyright (c) 1999 Martien Verbruggen. All rights reserved.

# Statistics-Descriptive 2.4
# Copyright (c) 1997,1998 Colin Kuskie.
# Copyright (c) 1998 Andrea Spinelli.
# Copyright (c) 1994,1995 Jason Kastner.

use strict;
use Tk;
use Tk::ErrorDialog;
use Tk::Scale;
use Win32::FileOp;

&lockwin;
1;

sub lockwin {
    my $mw = MainWindow->new;
    $mw->title("LOCK");
    $mw->Label(-text=>'Locater of Oligomers by Charlie Kim')->pack();
    $mw->Label(-text=>"Copyright 2002-2004 Charlie Kim GNU General Public License\n")->pack();
    # MAIN FRAMES #
    my $file_fr = $mw->Frame(-relief=>'groove',
			  -borderwidth=>2,
			  -label=>'File Input/Output',
			  )->pack(#-fill=>'x',
				  );
    my $lvl2fr = $mw->Frame()->pack();
    my $maincol1 = $lvl2fr->Frame()->pack(-side=>'left');
    my $maincol2 = $lvl2fr->Frame()->pack(-side=>'right');

    my $oligo_fr = $maincol1->Frame(-relief=>'groove',
				 -borderwidth=>2,
				 -label=>'Input Oligo Sequences',
				 )->pack(-side=>'top',
					 -fill=>'y',
					 -anchor=>'nw',
					 );
    my $raw_fr = $maincol1->Frame(-relief=>'groove',
			       -borderwidth=>2,
			       )->pack(-side=>'top',
				       -fill=>'both',
				       -anchor=>'nw',
				       );
    my $analtype_fr = $maincol2->Frame(-relief=>'groove',
				    -borderwidth=>2,
				    -label=>'Type of analysis',
				    )->pack(-side=>'top',
					    -anchor=>'nw',
					    );
    
    my $strand_fr = $maincol2->Frame(-relief=>'groove',
				  -borderwidth=>2,
				  -label=>'Strands to Analyze',
				  )->pack(-side=>'left',
					  -fill=>'both',
					  );
    my $bin_fr = $maincol2->Frame(-relief=>'groove',
			       -borderwidth=>2,
			       -label=>'Bins in Histogram',
			       )->pack(-side=>'left',
				       -fill=>'both',
				       );
    my $command_fr = $maincol2->Frame(-relief=>'groove',
				   )->pack(-side=>'right',
					   -fill=>'y',
					   );

    # LOG FRAME #
    my $log_f = $mw->Frame(-relief=>'groove',
			   -borderwidth=>2,
			   )->pack(-fill=>'both',
				   -expand=>1,
				   -side=>'bottom',
				   );
    my $logwin = $log_f->Scrolled("Text")->pack(-fill=>'both',
						-expand=>1,
						);
    $logwin->configure(-height=>15,
		       -width=>50,
		       -wrap=>'none',
		       -state=>'disabled',
		       );


    # FILE FRAME #
    my $filec1_fr = $file_fr->Frame()->pack(-side=>'left');
    my $filec2_fr = $file_fr->Frame()->pack(-side=>'left');
    my $filec3_fr = $file_fr->Frame()->pack(-side=>'left');
    
    my $seqfile = '';
    my $outdir = '';
    $filec1_fr->Label(-text=>'Load Sequence File',
		      )->pack(-anchor=>'nw',
			      );
    $filec1_fr->Label(-text=>'Output Directory',
		      )->pack(-anchor=>'nw',
			      );
    $filec2_fr->Entry(-textvariable=> \$seqfile,
		      )->pack(-anchor=>'nw',
			      -pady=>2,
			      );
    $filec2_fr->Entry(-textvariable=> \$outdir,
		      )->pack(-anchor=>'nw',
			      -pady=>2,
			      );
    $filec3_fr->Button(-text=>'browse',
		       -command=> [\&getfile, \$mw, \$seqfile, \$outdir],
		       -borderwidth=>1,
		       -pady=>0,
		       )->pack();
    $filec3_fr->Button(-text=>'browse',
		       -command=> [\&getdir, \$mw, \$outdir],
		       -borderwidth=>1,
		       -pady=>0,
		       )->pack();

    # OLIGO FRAME #
    my $oligocol1 = $oligo_fr->Frame()->pack(-side=>'left');
    my $oligocol2 = $oligo_fr->Frame()->pack(-side=>'left');
    my $oligocol3 = $oligo_fr->Frame()->pack(-side=>'left');

    my ($oligo1, $oligo2, $oligo3, $oligo4, $oligo5, $oligo6);

    $oligocol2->Entry(-textvariable=> \$oligo1,
		      )->pack(-pady=>4);
    $oligocol2->Entry(-textvariable=> \$oligo2,
		      )->pack(-pady=>4);
    $oligocol2->Entry(-textvariable=> \$oligo3,
		      )->pack(-pady=>4);
    $oligocol2->Entry(-textvariable=> \$oligo4,
		      )->pack(-pady=>4);
    $oligocol2->Entry(-textvariable=> \$oligo5,
		      )->pack(-pady=>4);
    $oligocol2->Entry(-textvariable=> \$oligo6,
		      )->pack(-pady=>4);

    $oligocol3->Label(-text=>'Oligo 1')->pack(-pady=>4);
    $oligocol3->Label(-text=>'Oligo 2')->pack(-pady=>4);
    $oligocol3->Label(-text=>'Oligo 3')->pack(-pady=>4);
    $oligocol3->Label(-text=>'Oligo 4')->pack(-pady=>4);
    $oligocol3->Label(-text=>'Oligo 5')->pack(-pady=>4);
    $oligocol3->Label(-text=>'Oligo 6')->pack(-pady=>4);

    # RAW DATA OUTPUT #
    
    my $raw = 'n';
    $raw_fr->Checkbutton(-text=>'Create raw output',
			 -variable=> \$raw,
			 -onvalue=>'y',
			 -offvalue=>'n',
			 )->pack(-anchor=>'center');

    # ANALYSIS #
    my $analtype = 'single';
    my $outprefix;
    $analtype_fr->Radiobutton(-text=>'Individual analysis (separate results files for each oligo)',
			      -variable=> \$analtype,
			      -value=>'single',
			      -pady=>0,
			      )->pack(-anchor=>'nw');
    $analtype_fr->Radiobutton(-text=>'Combined analysis (single analysis for all selected oligos)',
			      -variable=> \$analtype,
			      -value=>'combo',
			      -pady=>0,
			      )->pack(-anchor=>'nw');
    $analtype_fr->Label(-text=>'          Prefix for output files')->pack(-side=>'left',
							      -anchor=>'nw');
    $analtype_fr->Entry(-textvariable=> \$outprefix,
			)->pack(-side=>'left',
				-anchor=>'nw',
				);

    # STRANDS #
    my $strand = 'both';
    $strand_fr->Radiobutton(-text=>'Positive',
			    -variable=> \$strand,
			    -value=>'pos',
			    -pady=>0,
			    )->pack(-anchor=>'nw');
    $strand_fr->Radiobutton(-text=>'Negative',
			    -variable=> \$strand,
			    -value=>'neg',
			    -pady=>0,
			    )->pack(-anchor=>'nw');
    $strand_fr->Radiobutton(-text=>'Both Strands',
			    -variable=> \$strand,
			    -value=>'both',
			    -pady=>0,
			    )->pack(-anchor=>'nw');
    $strand_fr->Radiobutton(-text=>'All Analyses',
			    -variable=> \$strand,
			    -value=>'all',
			    -pady=>0,
			    )->pack(-anchor=>'nw');

    # BINS #
    my $bins = 20;
    $bin_fr->Scale(-from=>3,
		   -to=>40,
		   -resolution=>1,
		   -variable=> \$bins,
		   )->pack();

    # COMMAND FRAME #
    $command_fr->Button(-text=>'Exit',
			-command=> sub { exit },
			)->pack(-side=>'bottom',
				-pady=> 5,				
				);

    $command_fr->Button(-text=>'Reset Fields')->pack(-side=>'bottom',
						     -pady=> 5,
						     );
    $command_fr->Button(-text=>'Run LOCK',
			-command=> [\&lockmain,\$mw,\$oligo1,\$oligo2,\$oligo3,\$oligo4,\$oligo5,\$oligo6,\$analtype,\$outprefix,\$seqfile,\$outdir,\$bins,\$strand,\$raw,\$logwin],
			)->pack(-side=>'bottom',
				-pady=> 5,
				);

    MainLoop;

}

sub getfile {
    my ($mwref, $seqfileref, $outdirref) = @_;
    my $file = OpenDialog();
    $$seqfileref = $file;
    
    if ($$outdirref eq '') {
	my $newdir = $file;
	$newdir =~ /^(.*)\\/;
	$$outdirref = $1;
    }
    $$mwref->raise;
}

sub getdir {
    my ($mwref, $outdirref) = @_;
    my $dir = BrowseForFolder('Choose a directory for all output files: ');
    $$outdirref = $dir;
    $$mwref->raise;
}

sub printlog {
    my $line = shift;
    my $logwinref = shift;
    my $logwin = $$logwinref;
    $logwin->configure(-state=>'normal');
    $logwin->insert('end',$line);
    $logwin->yview(moveto=>1);
    $logwin->configure(-state=>'disabled');
    $logwin->update();
}

sub lockmain {
    my $mwref = shift;
    my $oligo1ref = shift;
    my $oligo2ref = shift;
    my $oligo3ref = shift;
    my $oligo4ref = shift;
    my $oligo5ref = shift;
    my $oligo6ref = shift;
    my $analtyperef = shift;
    my $outprefixref = shift;
    my $seqfileref = shift;
    my $outdirref = shift;
    my $binsref = shift;
    my $strandref = shift;
    my $rawref = shift;
    my $logwinref = shift;
    
    if ($$analtyperef eq 'combo' && $$outprefixref eq '') {
	$$mwref->messageBox(-title => 'Error',
			    -message => 'Please type in an output prefix',
			    -type => 'OK');
	return;
    }

    if ($$analtyperef eq 'combo') {
	my @oligos = ();
	&printlog("Running combo analysis\n",$logwinref);
	push @oligos, $$oligo1ref if $$oligo1ref;
	push @oligos, $$oligo2ref if $$oligo2ref;
	push @oligos, $$oligo3ref if $$oligo3ref;
	push @oligos, $$oligo4ref if $$oligo4ref;
	push @oligos, $$oligo5ref if $$oligo5ref;
	push @oligos, $$oligo6ref if $$oligo6ref;
	&runlock($mwref,$logwinref,$$analtyperef,$$seqfileref,$$outdirref,$$binsref,$$strandref,$$rawref,$$outprefixref,@oligos);
    }
    elsif ($$analtyperef eq 'single') {
	my @oligos = ();
	&printlog("Running single analyses\n",$logwinref);
	push @oligos, $$oligo1ref if $$oligo1ref;
	push @oligos, $$oligo2ref if $$oligo2ref;
	push @oligos, $$oligo3ref if $$oligo3ref;
	push @oligos, $$oligo4ref if $$oligo4ref;
	push @oligos, $$oligo5ref if $$oligo5ref;
	push @oligos, $$oligo6ref if $$oligo6ref;
	foreach (@oligos) {
	    &runlock($mwref,$logwinref,$$analtyperef,$$seqfileref,$$outdirref,$$binsref,$$strandref,$$rawref,$_,$_);
	}
    }
    $$mwref->messageBox(-title => 'Program Finished',
			-message => 'Processing complete',
			-type => 'OK');
}

sub runlock {
    my $mwref = shift;
    my $logwinref = shift;
    my $analtype = shift;
    my $seqfile = shift;
    my $outdir = shift;
    my $bins = shift;
    my $strand = shift;
    my $raw = shift;
    my $prefix = shift;
    my @mainoligos = @_;

#    print "oligos: @mainoligos\n";
    
    my $longestlength = 0;
    foreach (@mainoligos) {
	my $length = length($_);
	$longestlength = $length if $length > $longestlength;
    }

#    print "seqfile: $seqfile\n";

    open(SEQFILE,$seqfile) or die "Can't open seqfile\n";

    my $seq = '';
    my $count = 0;
    &printlog("Reading sequence ...\n",$logwinref);
    while(<SEQFILE>) {
	if (/>/) {
	    die "More than one sequence present -- only one sequence allowed" if $count == 1;
	    $count++;
	    next;
	}
	chomp($_);
	$seq .= $_;
    }
    
    my $wrapseq = substr($seq,0,length($longestlength));
    $seq .= $wrapseq; # this accounts for the cirularity of the genome

#    print "seq: $seq\n";
    
    my @revoligos = ();
    foreach my $entry (@mainoligos) {
	my $newoligo = &revcom($entry);
	push @revoligos,$newoligo;
    }

#    print "revoligos: @revoligos\n";
    
    if ($strand eq 'pos' || $strand eq 'all') {
	&printlog("Finding matches on positive strand ...\n",$logwinref);
	&findoligos($mwref,$logwinref,\$seq,$outdir,$raw,$bins,'pos',$prefix,@mainoligos); # the last argument is used in the
	# filename prefixes
    }
    if ($strand eq 'neg' || $strand eq 'all') {
	&printlog("Finding matches on negative strand ...\n",$logwinref);
	&findoligos($mwref,$logwinref,\$seq,$outdir,$raw,$bins,'neg',$prefix,@revoligos);
    }
    if ($strand eq 'both' || $strand eq 'all') {
	&printlog("Finding matches on both strands ... \n",$logwinref);
	&findoligos($mwref,$logwinref,\$seq,$outdir,$raw,$bins,'both',$prefix,@mainoligos,@revoligos);
    }
}

sub findoligos {
    my $mwref = shift;
    my $logwinref = shift;
    my $seqref = shift;
    my $seq = $$seqref;
    my $outdir = shift;
    my $raw = shift;
    my $bins = shift;
    my $strand = shift;
    my $prefix = shift;
    my @oligos = @_;

#    print "Entering findoligos sub\n";

    my %oligocheck = ();
    foreach my $entry (@oligos) {
	&printlog("\tMatching oligo $entry\n",$logwinref);
	while ($seq =~ /$entry/gi) {
	    $oligocheck{pos($seq)-2} = 1;
	}
    }

#    print " size of oligos: $#oligos\n";
#    print " oligo: $oligos[0]\n";
#    print "prefix: $prefix\n";

    chdir $outdir;
    while() {
	last if $raw =~ /^n$/i;
	my $oligocoord = $prefix . "_$strand" . '_coord.txt';
	&open_writefile(*OUTFILE,$mwref,$oligocoord);
	if (!%oligocheck) { die "No matches found\n"; }
	&printlog("Generating output ...\n",$logwinref);
	print OUTFILE "$strand strand, $prefix analysis\n";
	print OUTFILE "Raw match coordinates\n";
	print OUTFILE "---------------------\n";
	foreach my $entry (sort {$a<=>$b} keys %oligocheck ) {
	    print OUTFILE "$entry\n";
	}
	last;
    }
    close OUTFILE;
    
    my $length = length($seq);
    
##############
# Statistics #
##############
    
    use Statistics::Descriptive;
    my $oligostat = $prefix . "_$strand" . '_stats.txt';
    &open_writefile(*STATFILE,$mwref,$oligostat);
    my @position = sort {$a<=>$b} keys %oligocheck;
    my @distance = ();
    my %distancecoordstart = ();
    my %distancecoordend = ();
    for (my $k = 0; $k < $#position; $k++) {
	push @distance, $position[$k+1] - $position[$k];
	$distancecoordstart{$position[$k]} = $position[$k+1]-$position[$k];
	$distancecoordend{$position[$k]} = $position[$k+1];
    }
    push @distance, $length - $position[$#position] + $position[0]; # circular
    $distancecoordstart{$position[$#position]} = $length-$position[$#position]+$position[0];
    $distancecoordend{$position[$#position]} = $position[0];
    
    while() {
	last if $raw =~ /^n$/i;
	my $oligodist = $prefix . "_$strand" . '_dist.txt';
	&open_writefile(*DISTANCEFILE,$mwref,$oligodist);
	print DISTANCEFILE "$strand strand for $prefix analysis\n";
	print DISTANCEFILE "The output is generated twice: first organized by\n";
	print DISTANCEFILE "length, then organized by position\n";
	print DISTANCEFILE "-------------------------------------------------\n\n";
	print DISTANCEFILE "Organized by distance length\n";
	print DISTANCEFILE "----------------------------\n";
	foreach my $entry (sort {$distancecoordstart{$b} <=> $distancecoordstart{$a} } keys %distancecoordstart) {
	    print DISTANCEFILE "From match at \t$entry\t to match at \t$distancecoordend{$entry}\t is \t$distancecoordstart{$entry}\t bp\n";
	}
	print DISTANCEFILE "\nOrganized by position\n";
	print DISTANCEFILE "---------------------\n";
	foreach my $entry (sort {$a<=>$b} keys %distancecoordstart) {
	    print DISTANCEFILE "From match at \t$entry\t to match at \t$distancecoordend{$entry}\t is \t$distancecoordstart{$entry}\t bp\n";
	}
	close DISTANCEFILE;
	last;
    }

    
    my $stat = Statistics::Descriptive::Full->new();
    $stat->add_data(@distance);
    my $count = $stat->count();
    my $mean = $stat->mean();
    my $stdev = $stat->standard_deviation();
    my $median = $stat->median();
    my $var = $stat->variance();
    my $min = $stat->min();
    my $max = $stat->max();
    
    my %histo = $stat->frequency_distribution($bins);
    
    print STATFILE "Statistics on distance between matches (bp) for oligos\n";
    foreach my $entry (@oligos) {
	print STATFILE "\t$entry\n";
    }
    print STATFILE "$strand strand of $prefix analysis\n";
    print STATFILE "sequence of length $length\n";
    print STATFILE "------------------------------------------------------\n";
    print STATFILE "Count\t$count\nMean\t$mean\nStdDev\t$stdev\n";
    print STATFILE "Variance\t$var\nMedian\t$median\n";
    print STATFILE "Minimum\t$min\nMaximum\t$max\n\n";
    
    print STATFILE "Frequency Distribution\n";
    print STATFILE "----------------------\n";
    print STATFILE "\tDistance (bp)\t\tNumber of Matches\n";
    my $marker = 0;
    my @xval = ();
    my @yval = ();
    for (sort {$a<=>$b} keys %histo) {
	print STATFILE "\t$marker to $_\t\t$histo{$_}\n";
	push @xval, int($_);
	push @yval, $histo{$_};
	$marker = $_;
    }
    close STATFILE;

##################################
# Distance Distribution Graphics #
##################################
    
    use GD::Graph;
    use GD::Graph::bars;
    use GD::Graph::Data;
    use GD::Graph::colour;
    
    my @data = (\@xval,\@yval);
    my $graph = GD::Graph::bars->new(800,400);
    $graph->set( x_label => 'Distance (bp)',
		 x_label_position => 1/2,
		 y_label => 'Number of Distances',
		 title   => "Distribution of Distances Between Matches: $prefix analysis, $strand strand",
		 fgclr => 'black',
		 );
    $graph->set_text_clr('black');
    
# add values to plot
    my $datavals = GD::Graph::Data->new(\@data);
    my $values = $datavals->copy;
    $graph->set(show_values => $values);
    
    my $plot = $graph->plot(\@data);
    
#    $graph->plot($data);
    
    my $oligodistgraph = $prefix . "_$strand" . '_dist.jpg';
    &open_writefile(*DISTRIBUTION,$mwref,$oligodistgraph,);
    binmode DISTRIBUTION;
    print DISTRIBUTION $plot->jpeg(100);
    close DISTRIBUTION;
    
#####################
# Position Graphics #
#####################
    
    use GD;
    
    my $innerradius = 150;
    my $outerradius = 200;
    
    my $im = new GD::Image($outerradius*2+1, $outerradius*2+1);
    
    my $white = $im->colorAllocate(255,255,255);
    my $black = $im->colorAllocate(0,0,0);
    my $red = $im->colorAllocate(255,0,0);
    
    $im->transparent($white);
    $im->interlaced('true');
    
# Draw Marks #
    foreach my $entry (keys %oligocheck) {
	my $radians = 2*3.14159265358979*($entry/$length);
	my $xin = int($outerradius+1 + (sin($radians) * $innerradius) );
	my $yin = int($outerradius+1 - (cos($radians) * $innerradius) );
	my $xout = int($outerradius+1 + (sin($radians) * ($outerradius-2) ) );
	my $yout = int($outerradius+1 - (cos($radians) * ($outerradius-2) ) );
	$im->line($xin,$yin,$xout,$yout,$red);
    }
    
    $im->arc($outerradius+1, $outerradius+1, $innerradius*2, $innerradius*2, 0, 360, $black);
    $im->arc($outerradius+1, $outerradius+1, $outerradius*2, $outerradius*2, 0, 360, $black);
    
# Draw Minute Marks #
    my $fwidth;
    my $font;
    my $fheight;
    for (my $l = 0; $l <= 99; $l++) {
	if ($l % 10 == 0) {
	    my $radians = 2*3.14159265358979*($l/100);
	    my $x1 = int($outerradius+1 + (sin($radians) * ($innerradius-1) ) );
	    my $y1 = int($outerradius+1 - (cos($radians) * ($innerradius-1) ) );
	    my $x2 = int($outerradius+1 + (sin($radians) * ($innerradius*0.75) ) );
	    my $y2 = int($outerradius+1 - (cos($radians) * ($innerradius*0.75) ) );
	    $im->line($x1,$y1,$x2,$y2,$black);
	    
	    $font = GD::Font->MediumBold;
	    $fwidth = $font->width;
	    $fwidth *= length($l);
	    $fheight = $font->height;
	    my $fontx = int($outerradius+1 + (sin($radians) * ($innerradius*0.65) ) );
	    my $fonty = int($outerradius+1 - (cos($radians) * ($innerradius*0.65) ) );
	    $im->string($font,$fontx-($fwidth/3),$fonty-($fheight/3),$l,$black);
	    next;
	}
	elsif ($l % 5 == 0) {
	    my $radians = 2*3.14159265358979*($l/100);
	    my $x1 = int($outerradius+1 + (sin($radians) * ($innerradius-1) ) );
	    my $y1 = int($outerradius+1 - (cos($radians) * ($innerradius-1) ) );
	    my $x2 = int($outerradius+1 + (sin($radians) * ($innerradius*0.85) ) );
	    my $y2 = int($outerradius+1 - (cos($radians) * ($innerradius*0.85) ) );
	    $im->line($x1,$y1,$x2,$y2,$black);
	    next;
	}
	else {
	    my $radians = 2*3.14159265358979*($l/100);
	    my $x1 = int($outerradius+1 + (sin($radians) * ($innerradius-1) ) );
	    my $y1 = int($outerradius+1 - (cos($radians) * ($innerradius-1) ) );
	    my $x2 = int($outerradius+1 + (sin($radians) * ($innerradius*0.95) ) );
	    my $y2 = int($outerradius+1 - (cos($radians) * ($innerradius*0.95) ) );
	    $im->line($x1,$y1,$x2,$y2,$black);
	    next;
	}
    }
    
    my $centerx1 = $outerradius+1 - ((length($length)+3)*$fwidth)/4;
    my $centerx2 = $outerradius+1 - ((length($prefix)+9)*$fwidth)/4;
    my $centerx3 = $outerradius+1 - ((length($strand)+7)*$fwidth)/4;
    $im->string($font,$centerx1,$outerradius+1-($fheight),"$length bp",$black);
    $im->string($font,$centerx2,$outerradius+1,"$prefix analysis",$black);
    $im->string($font,$centerx3,$outerradius+1+($fheight),"$strand strand",$black);
        
    my $oligocoordgraph = $prefix . "_$strand" . '_coord.jpg';
    &open_writefile(*GRAPHICFILE,$mwref,$oligocoordgraph);
    binmode GRAPHICFILE;
    print GRAPHICFILE $im->jpeg(100);

    close GRAPHICFILE;
    

}


sub revcom {
    my $oligo = $_[0];
    $oligo =~ tr/gatcGATC/ctagCTAG/;
    my $rcoligo = reverse($oligo);
    return $rcoligo;
}

sub open_writefile {
    my $filehandle = shift;
    my $mwref = shift;
    my $filename = shift;

#    print "Filename: $filename\n";

    if (-e $filename) {
#	print "File exists: $filename\n";
	my $response = $$mwref->messageBox(-title => 'File exists',
					   -message => "Overwrite existing file $filename?",
					   -type => 'YesNo',
					   );
	if ($response =~ /no/i) {
	    die "$filename not overwritten.\n";
	}
	else {
	    open($filehandle, ">$filename") or die "Couldn't open $filename\n";
	}
    }
    else { open($filehandle, ">$filename") or die "Couldn't open $filename\n"; }
}