#!/usr/bin/perl -w
use Cwd;
use GD;
use Tk;
use Tk::Pane;
use Tk::StayOnTop;
use Tk::BrowseEntry;
use Tk::widgets qw/JPEG PNG/;
use warnings;
$number_of_cpus=$ENV{NUMBER_OF_PROCESSORS};
$cwd=getcwd;

### SETTINGS ###
$operation_mode_selected="compare sequence 1 with sequence 2";
$window_size=10;
$max_mismatch=5;
$bold_for_perfect_match="semi-bold (4 pixel)";
$output_picture=1;
$output_text=1;

### internal settings ###
$picture_size=800;
$fixed_picture_size=1;

### GUI ###
$main_window=MainWindow->new;
$main_window->title("Chromatic Dot Plot");
$main_window->geometry("852x852");
$main_window->maxsize(qw(852 1500)); 
$mw=$main_window->Scrolled('Pane',-scrollbars=>'osoe',-background=>White,-sticky=>'nw',-gridded=>'y')->pack(-fill=>'both',-expand=>1);
$mw->Label(-background=>White,-height=>107,-width=>138)->pack;

# labels
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"cornflower blue",-text=>"C")->place(-width=>30,-x=>25,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"dark slate blue",-text=>"h")->place(-width=>30,-x=>55,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"MediumSeaGreen",-text=>"r")->place(-width=>30,-x=>85,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"khaki",-text=>"o")->place(-width=>30,-x=>115,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"IndianRed",-text=>"m")->place(-width=>30,-x=>145,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"SpringGreen4",-text=>"a")->place(-width=>30,-x=>175,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"goldenrod2",-text=>"t")->place(-width=>30,-x=>205,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"MediumOrchid1",-text=>"i")->place(-width=>30,-x=>235,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"SteelBlue2",-text=>"c")->place(-width=>30,-x=>265,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"seashell2",-text=>"D")->place(-width=>30,-x=>333,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"seashell2",-text=>"O")->place(-width=>30,-x=>367,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"seashell2",-text=>"T")->place(-width=>30,-x=>400,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"seashell2",-text=>"P")->place(-width=>30,-x=>467,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"seashell2",-text=>"L")->place(-width=>30,-x=>500,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"seashell2",-text=>"O")->place(-width=>30,-x=>533,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 14",-background=>"seashell2",-text=>"T")->place(-width=>30,-x=>567,-y=>10);
$mw->Label(-background=>White,-font=>"Courier 8",-background=>"PeachPuff4",-foreground=>"AntiqueWhite2",-text=>"by David Rosenkranz\nUniversity Mainz, 2011")->place(-width=>183,-height=>27,-x=>630,-y=>10);
$mw->Label(-background=>White,-font=>"Arial 8",-background=>"floral white",-text=>"CHROMATIC  DOT  PLOT  draws  dot  plots with  colors  encoding  similarity.\nYou  can choose to compare 2  sequences by  pasting or  loading them  into\nthe boxes below or to process an abitrary number of sequence files.  In the\nlatter case, each sequence will be plotted  against itself. Beside a  graphical\noutput CHROMATIC DOT PLOT can output the plot as text matrix. The results\ncan optionally be saved in a folder named /CDP_results[date+time].                ")->place(-width=>414,-height=>150,-x=>400,-y=>60);
$mw->Label(-background=>White,-text=>"mode of operation")->place(-x=>25,-y=>60);
$mw->Label(-background=>White,-text=>"window size [nt]")->place(-x=>25,-y=>85);
$mw->Label(-background=>White,-text=>"maximum mismatch [nt]")->place(-x=>25,-y=>110);
$mw->Label(-background=>White,-text=>"print perfect match")->place(-x=>25,-y=>135);
$mw->Label(-background=>White,-text=>"save dotplot(s) as picture")->place(-x=>25,-y=>160);
$mw->Label(-background=>White,-text=>"save dotplot(s) as text matrix")->place(-x=>25,-y=>185);
$mw->Label(-background=>White,-text=>"Sequence 1")->place(-x=>25,-y=>230);
$mw->Label(-background=>White,-text=>"Sequence 2")->place(-x=>300,-y=>230);
$mw->Label(-background=>White,-text=>"Sequence files to process")->place(-x=>615,-y=>230);
$mw->Label(-background=>"grey50")->place(-width=>1000,-height=>2,-x=>2,-y=>500);

# settings
$be_operation_mode=$mw->BrowseEntry(-variable=>\$operation_mode_selected,-font=>"Arial 8",-width=>32,-listwidth=>214,-listheight=>2,-state=>'readonly')->place(-x=>150,-y=>60);
$be_operation_mode->insert('end',"compare sequence 1 with sequence 2","process sequence files from list");
$mw->Entry(-width=>5,-justify=>'right',-font=>"Arial 8",-textvariable=>\$window_size)->place(-height=>20,-x=>150,-y=>85);
$mw->Entry(-width=>5,-justify=>'right',-font=>"Arial 8",-textvariable=>\$max_mismatch)->place(-height=>20,-x=>150,-y=>110);
$be_bold_for_perfect_match=$mw->BrowseEntry(-variable=>\$bold_for_perfect_match,-font=>"Arial 8",-width=>32,-listwidth=>214,-listheight=>3,-state=>'readonly')->place(-x=>150,-y=>135);
$be_bold_for_perfect_match->insert('end',"regular (1 pixel)","semi-bold (4 pixel)","bold (9 pixel)");
$mw->Checkbutton(-background=>White,-activebackground=>White,-variable=>\$output_picture)->place(-height=>14,-width=>26,-x=>170,-y=>165);
$mw->Checkbutton(-background=>White,-activebackground=>White,-variable=>\$output_text)->place(-height=>14,-width=>26,-x=>170,-y=>190);

# sequence boxes
$sequence_1_box=$mw->Scrolled("Text",-scrollbars=>'oe')->place(-x=>25,-y=>250,-width=>200,-height=>200);
$sequence_2_box=$mw->Scrolled("Text",-scrollbars=>'oe')->place(-x=>300,-y=>250,-width=>200,-height=>200);
$mw->Button(-font=>"Arial 8",-text=>"clear seq.",-command=>sub{$sequence_1_box->delete("1.0",'end');})->place(-width=>70,-x=>40,-y=>460);
$mw->Button(-font=>"Arial 8",-text=>"clear seq.",-command=>sub{$sequence_2_box->delete("1.0",'end');})->place(-width=>70,-x=>315,-y=>460);
$mw->Button(-font=>"Arial 8",-text=>"load file",-command=>sub{sequence_from_file();$sequence_1_box->delete("1.0",'end');$sequence_1_box->insert("1.0",$seq);})->place(-width=>70,-x=>130,-y=>460);
$mw->Button(-font=>"Arial 8",-text=>"load file",-command=>sub{sequence_from_file();$sequence_2_box->delete("1.0",'end');$sequence_2_box->insert("1.0",$seq);})->place(-width=>70,-x=>405,-y=>460);
$mw->Button(-font=>"Arial 8",-text=>"use demo",-command=>sub{$sequence_1_box->delete("1.0",'end');$sequence_2_box->delete("1.0",'end');demo_seq();$sequence_1_box->insert("1.0",$seq1);$sequence_2_box->insert("1.0",$seq2);})->place(-width=>60,-x=>232,-y=>320);	
$mw->Button(-font=>"Arial 8",-text=>"copy seq.",-command=>sub{$sequence_2_box->delete("1.0",'end');$copy_text=$sequence_1_box->get("1.0",'end');$sequence_2_box->insert("1.0",$copy_text);})->place(-width=>60,-x=>232,-y=>350);
$mw->Button(-font=>"Arial 8",-text=>"rotate",-command=>sub{$seq1=$sequence_1_box->get("1.0",'end');$seq2=$sequence_2_box->get("1.0",'end');$sequence_1_box->delete("1.0",'end');$sequence_2_box->delete("1.0",'end');$seq1=~s/\n+$//;$seq2=~s/\n+$//;$sequence_1_box->insert("1.0",$seq2);$sequence_2_box->insert("1.0",$seq1);})->place(-width=>60,-x=>232,-y=>380);

# files box
$files_box=$mw->Scrolled("Listbox",-scrollbars=>'se',-selectmode=>"extended")->place(-x=>615,-y=>250,-width=>200,-height=>200);
$mw->Button(-font=>"Arial 8",-text=>"browse & add",-command=>\&open_files)->place(-width=>85,-x=>625,-y=>460);
$mw->Button(-font=>"Arial 8",-text=>"remove files",-command=>\&remove_files)->place(-width=>85,-x=>720,-y=>460);

# display plot
$display_label=$mw->Label(-background=>"grey10")->place(-width=>802,-height=>802,-x=>18,-y=>570);

# start
$start_button=$mw->Button(-font=>"Arial 8",-text=>"START",-command=>\&check_settings)->place(-width=>50,-x=>400,-y=>520);
$exit_button=$mw->Button(-font=>"Arial 8",-text=>"EXIT",-command=>sub{exit;})->place(-width=>50,-x=>465,-y=>520);
$mw->Label(-relief=>'groove',-font=>"Arial 8",-background=>White,-text=>"color code [ID]")->place(-width=>82,-height=>25,-x=>18,-y=>520);
$mw->Label(-font=>"Arial 8",-background=>RoyalBlue3,-text=>"100%")->place(-width=>40,-height=>24,-x=>100,-y=>520);
$mw->Label(-font=>"Arial 8",-background=>RoyalBlue1,-text=>">90%")->place(-width=>40,-height=>24,-x=>140,-y=>520);
$mw->Label(-font=>"Arial 8",-background=>SteelBlue2,-text=>">80%")->place(-width=>40,-height=>24,-x=>180,-y=>520);
$mw->Label(-font=>"Arial 8",-background=>DarkSeaGreen1 ,-text=>">70%")->place(-width=>40,-height=>24,-x=>220,-y=>520);
$mw->Label(-font=>"Arial 8",-background=>khaki2,-text=>">60%")->place(-width=>40,-height=>24,-x=>260,-y=>520);
$mw->Label(-font=>"Arial 8",-background=>goldenrod2,-text=>">50%")->place(-width=>40,-height=>24,-x=>300,-y=>520);
$mw->Label(-font=>"Arial 8",-background=>brown2,-text=>">40%")->place(-width=>40,-height=>24,-x=>340,-y=>520);

$sequence_1_length="";
$sequence_2_length="";
$seq_info_label=$mw->Label(-font=>"Arial 7",-justify=>'left',-anchor=>'w',-background=>White,-text=>"sequence 1 (horizontal) length: $sequence_1_length\nsequence 2 (vertical) length: $sequence_2_length")->place(-width=>200,-height=>24,-x=>530,-y=>520);

MainLoop;