use Tk;

  $idea = 0;
  
  $rawSequence="atggcgacgaaggccgtgtgcgtgctgaagggcgacggcccagtgcagggcatcatcaatttcgagcagaaggaaagtaatggaccagtgaaggtgtggggaagcattaaaggactgactgaaggcctgcatggattccatgttcatgagtttggagataatacagcaggctgtaccagtgcaggtcctcactttaatcctctatccagaaaacacggtgggccaaaggatgaagagaggcatgttggagacttgggcaatgtgactgctgacaaagatggtgtggccgatgtgtctattgaagattctgtgatctcactctcaggagaccattgcatcattggccgcacactggtggtccatgaaaaagcagatgacttgggcaaaggtggaaatgaagaaagtacaaagacaggaaacgctggaagtcgtttggcttgtggtgtaattgggatcgcccaataaacattcccttggatgtagtctgaggcccct";
  my $mainWindow = MainWindow->new();

  if( $idea)
  {
    # Main Window
    $mainWindow->title("Regex Problem Example 1");    
    $mainWindow->minsize(qw(500 500));  #Sets Minimum Size - note lack of comma
    $mainWindow->geometry('+500+200');  #Sets Position - note lack of comma
    $mainWindow->optionAdd('*font'=>'Courier 10');
  
    $ROText = $mainWindow->Scrolled('ROText',
                                -scrollbars=>'osoe');
  
    $formattedSequence = formatSequence($rawSequence);
    $ROText->Insert($formattedSequence);
    $ROText->pack;
    
    highlightText($ROText, "gca");
  }
  else
  {
    # Main Window
    $mainWindow->title("Regex Problem Example 2");    #Sets Title
    $mainWindow->minsize(qw(500 500));  #Sets Minimum Size - note lack of comma
    $mainWindow->geometry('+500+200');  #Sets Position - note lack of comma
    $mainWindow->optionAdd('*font'=>'Courier 10');
  
    $ROText = $mainWindow->Scrolled('ROText',
                                -scrollbars=>'osoe');
  
    $formattedSequence = searchAndFormatSequence($rawSequence);
    $ROText->Insert($formattedSequence);
    $ROText->pack;
    
    #This works, but I can't make Uppercase->Lowercase
    #without removing the tags.
    highlightText2($ROText, "[A-Z]+");
    
  }
MainLoop();


sub highlightText {
    my ($widget, $searchString) = @_;
 
    #alter search string - HOW?    
    
    # Create a tag to configure the text
    $widget->tagConfigure('foundtag',
                            -foreground => "white",
                            -background => "red");
    $widget->FindAll(-regex, -nocase, $searchString);
    if ($widget->tagRanges('sel'))
    {
        my %startfinish  = $widget->tagRanges('sel');
        foreach(sort keys %startfinish)
        {
            $widget->tagAdd("foundtag", $_, $startfinish{$_});
        }
        $widget->tagRemove('sel', '1.0', 'end');
    }
}

sub highlightText2 {
    my ($widget, $searchString) = @_;
 
    #alter search string - HOW?    
    
    # Create a tag to configure the text
    $widget->tagConfigure('foundtag',
                            -foreground => "white",
                            -background => "red");
    $widget->FindAll(-regex, -case, $searchString);
    if ($widget->tagRanges('sel'))
    {
        my %startfinish  = $widget->tagRanges('sel');
        foreach(sort keys %startfinish)
        {
            $widget->tagAdd("foundtag", $_, $startfinish{$_});
        }
        $widget->tagRemove('sel', '1.0', 'end');
    }
    #UNCOMMENT TO BREAK! Doesn't like a regex in the replace string
    #$widget->FindAndReplaceAll(-regex, -case, "G", "g");
    #$widget->FindAndReplaceAll(-regex, -case, "C", "c");
    #$widget->FindAndReplaceAll(-regex, -case, "A", "a");

}


sub searchAndFormatSequence
{
    #I search the sequence and change any gca in the sequence to GCA then
    #format the sequence, the end result of which is

    return "        1 atggcgacga aggccgtgtg cgtgctgaag ggcgacggcc cagtGCAggG CAtcatcaat
       61 ttcgaGCAga aggaaagtaa tggaccagtg aaggtgtggg gaaGCAttaa aggactgact
      121 gaaggcctGC Atggattcca tgttcatgag tttggagata atacaGCAgg ctgtaccagt
      181 GCAggtcctc actttaatcc tctatccaga aaacacggtg ggccaaagga tgaagagagG
      241 CAtgttggag acttggGCAa tgtgactgct gacaaagatg gtgtggccga tgtgtctatt
      301 gaagattctg tgatctcact ctcaggagac cattGCAtca ttggccGCAc actggtggtc
      361 catgaaaaaG CAgatgactt ggGCAaaggt ggaaatgaag aaagtacaaa gacaggaaac
      421 gctggaagtc gtttggcttg tggtgtaatt gggatcgccc aataaacatt cccttggatg
      481 tagtctgagg cccct";
    
}


sub formatSequence
{
    #I do some really neat formatting here the end result of which is...
    
    return "        1 atggcgacga aggccgtgtg cgtgctgaag ggcgacggcc cagtgcaggg catcatcaat
       61 ttcgagcaga aggaaagtaa tggaccagtg aaggtgtggg gaagcattaa aggactgact
      121 gaaggcctgc atggattcca tgttcatgag tttggagata atacagcagg ctgtaccagt
      181 gcaggtcctc actttaatcc tctatccaga aaacacggtg ggccaaagga tgaagagagg
      241 catgttggag acttgggcaa tgtgactgct gacaaagatg gtgtggccga tgtgtctatt
      301 gaagattctg tgatctcact ctcaggagac cattgcatca ttggccgcac actggtggtc
      361 catgaaaaag cagatgactt gggcaaaggt ggaaatgaag aaagtacaaa gacaggaaac
      421 gctggaagtc gtttggcttg tggtgtaatt gggatcgccc aataaacatt cccttggatg
      481 tagtctgagg cccct";

}