#!/usr/bin/perl 
use Tk;
require Tk::DialogBox;
use Tk::ROText;
use Tk::Bitmap;
use SOAP::Lite;
use Bio::SeqIO;
use IO::String;

## global variables
my $return_result="Welcome to SubLoc!";

$wsdl = 'http://www.bioinfo.tsinghua.edu.cn/~tigerchen/SubLoc.wsdl';
$server = SOAP::Lite->service($wsdl);
#main window

my $main = MainWindow->new();
$main->geometry('800x600');
$main->title("SubLocSOAPClient");

#menu bar
my $menu=$main->Frame(-relief=>'groove', 
	-borderwidth=>3, 
	-background=>'gray',)
	->pack(-side=>'top',-fill=>'x');

# File Menu
my $button_file = $menu->Menubutton(-text=>'File',
	-background=>'gray',
	-activebackground=>'blue',
	-foreground=>'black',)
	->pack(-side=>'left');

$button_file -> command(-label=>'Open Fasta File',
	-activebackground=>'blue',
	-foreground=>'black',
	-command=>\&open_file,
	-accelerator=>'Ctrl-o');

$button_file -> command(-label=>'Save Result',
	-activebackground=>'blue',
	-foreground=>'black',
	-command=>\&save_file,
	-accelerator=>'Ctrl-s');

$button_file -> command(-label=>'Exit',
	-activebackground=>'blue',
	-foreground=>'black',
	-command=>sub{$main->destroy},
	-accelerator=>'Ctrl-q');

#Search Menu
my $button_search = $menu->Menubutton(-text=>'Search',
	-background=>'gray',
	-activebackground=>'blue',
	-foreground=>'black',)
	->pack(-side=>'left');

$button_search -> command(-label=>'Search by Id',
	-activebackground=>'blue',
	-foreground=>'black',
	-command=>\&search_by_id,
	-accelerator => 'Ctrl-i');

$button_search -> command(-label=>'Search by Name',
	-activebackground=>'blue',
	-foreground=>'black',
	-command=>\&search_by_name,
	-accelerator =>'Ctrl-n');

$button_search -> command(-label=>'Search by Blast',
	-activebackground=>'blue',
	-foreground=>'black',
	-command=>\&search_by_blast,
	-accelerator => 'Ctrl-b');

#Prediction Menu

my $button_predict = $menu->Menubutton(-text=>'Predict',
	-background=>'gray',
	-activebackground=>'blue',
	-foreground=>'black',)
	->pack(-side=>'left');

$button_predict -> command(-label=>'SVM prediction',
	-activebackground=>'blue',
	-foreground=>'black',
	-command=>\&predict_by_svm,
	-accelerator => 'Alt-s');

$button_predict -> command(-label=>'PSORT prediction',
	-activebackground=>'blue',
	-foreground=>'black',
	-command=>\&predict_by_psort,
	-accelerator => 'Alt-p');
#Feed menu

my $button_feed =  $menu->Menubutton(-text=>'Feed',
	-background=>'gray',
	-activebackground=>'blue',
	-foreground=>'black',)
	->pack(-side=>'left');

$button_feed -> command(-label=>'Feed',
	-activebackground=>'blue',
        -foreground=>'black',
        -command=>\&feed_entry,
	-accelerator=>'Ctrl-f');
#Help Menu

my $button_help = $menu->Menubutton(-text=>'Help',
	-background=>'gray',
	-activebackground=>'blue',
	-foreground=>'black',)
	->pack(-side=>'left');

$button_help -> command(-label=>'Help',
	-activebackground=>'blue',
	-foreground=>'black',
	-command=>\&help_text);

$button_help -> command(-label=>'About',
	-activebackground=>'blue',
	-foreground=>'black',
	-command=>\&about_text);

# main frame
my $mainframe = $main-> Frame(-relief=>'groove',
	-borderwidth=>3,
	-background=>'gray')
	->pack(-expand=>1,-side=>'top',-fill=>'both');

my $seq_label= $mainframe -> Label(
	-text=>'The Result Output Area: you could use "save to file" in menu to save.                                                ', -background=>'gray')
	->pack(-side=>'top');

my $res_area= $mainframe -> 
	Scrolled('ROText')->
	pack(-expand=>1,-fill=>'both');

my $seq_label= $mainframe -> Label(
	-text=>'Sequence Area: your Sequences (fasta format) here, Open a fasta file or mannually input sequences    Log Area: Your operations',
	-background=>"gray")
	->pack(-side=>'top',-anchor=>'nw');

my $seq_area= $mainframe -> 
	Scrolled('Text')
	->pack(-side=>'left',-expand=>1,-fill=>'both');

my $log_area= $mainframe -> 
	Scrolled('ROText')
	->pack(-side=>'right',-expand=>1,-fill=>'both');

## key binding
$main -> bind('<Control-o>' => \&open_file);
$main -> bind('<Control-s>' => \&save_file);
$main -> bind('<Control-q>' => sub{$main->destroy});
$main -> bind('<Control-i>' => \&search_by_id);
$main -> bind('<Control-n>' => \&search_by_name);
$main -> bind('<Control-b>' => \&search_by_blast);
$main -> bind('<Alt-s>' => \&predict_by_svm);
$main -> bind('<Alt-p>' => \&predict_by_psort);
$main -> bind('<Control-f>' => \&feed_entry);

MainLoop(); 
## subs
sub about_text {
	my $popup=$main->DialogBox(-title=>"ABOUT",-buttons=>["OK"],);

	$popup->add("Label", -text=>"SubLocSOAPClient--A Client for SubLoc SOAP Server:\n http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html\nversion 1.0\nby Tiger Chen")->pack;

	$popup->Show;
}

sub help_text {
	my $popup=$main->DialogBox(-title=>"HELP", -buttons=>["OK"],);

	$popup->add("Label", -text=>"lol, you need help?!\nPlease read the Readme file\nor\nsee http://www.bioinfo.tsinghua.edu.cn/dbsubloc.html",)->pack;

	$popup->Show;
} 

sub open_file {
	#my $types = [['All Files',        '*.*',             ]];
	my $openfile = $main-> getOpenFile();
	my $file_content="";
	open f,$openfile;
	while (<f>) {
		$file_content.=$_;
	}
	close(f);
	$seq_area -> delete('1.0','end');
	$seq_area -> insert('end',$file_content);
	return 1;
}

sub save_file {
	#my $types = [['All Files',        '*.*',             ]];
	my $savefile = $main -> getSaveFile();
	my $file_content = $res_area-> get('1.0','end');
	open f, ">$savefile";
	print f $file_content;
	close(f);
	return 1;
}

sub search_by_id {
	my $dbname="SWISSPROT";
	my ($id,$de,$lc,$cx,$os,$sq)=(1,0,1,0,0,0);
	my @pl = qw/-side top -pady 2 -anchor w/;
	my $popup=$main->DialogBox(-title=>"search by id",-buttons => ['OK','Cancel']);	
	$popup -> geometry("250x410");
	$popup -> add('Label',-text=>'select id type')->pack(@pl);
	$popup -> add('Radiobutton',-text => 'SWISSPROT',-variable => \$dbname,-relief =>'flat',-anchor=>'w',-value=>'SWISSPROT')->pack(@pl);
	$popup -> add('Radiobutton',-text => 'GO', -variable => \$dbname, -relief => 'flat',-anchor=>'w',-value=>'GO')->pack(@pl);
	$popup -> add('Radiobutton',-text => 'DBSUBLOC', -variable => \$dbname, -relief=>'flat',-anchor=>'w',-value=>'DBSUBLOC') ->pack(@pl);
	$popup -> add('Label',-text=>'Input the id')->pack(@pl);
	my $id_entry = $popup -> add('Entry')->pack(@pl);
	#$popup -> add('Button',-text=>'Search')->pack();
	#$popup -> add('Button',-text=>'Cancel ',-command=>sub{$popup->destroy})->pack();
	$popup -> add('Label',-text=>'Select what fields you want to display')->pack(@pl);
	$popup -> add('Checkbutton',-text=>'DBSubLoc ID',-variable=>\$id,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);
	$popup -> add('Checkbutton',-text=>'SubCellular Location',-variable=>\$lc,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);
	$popup -> add('Checkbutton',-text=>'Cross Database Reference',-variable=>\$cx,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);
	$popup -> add('Checkbutton',-text=>'Description',-variable=>\$de,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);
	$popup -> add('Checkbutton',-text=>'Organism',-variable=>\$os,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);
	$popup -> add('Checkbutton',-text=>'Sequence',-variable=>\$sq,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);

	$popup -> add('Label',-text=>"Note that the Search maybe quite slow\nPlease be patient")->pack(@pl);

	my $button = $popup->Show;
	if($button eq "OK") {
		my $id = $id_entry ->get;
		$log_area->insert('end',"Your Search by id: type=$dbname, id=$id\n");
		#my $search_result="DBSubLoc ID\tDescription\tSubCellular Location\tOrganism\tCross Database Reference\tSequence\n";
		my $search_result="";
		my $returnValue = $server -> id_search($dbname,$id);
		for(my $index=0;$index<=$#$returnValue;$index++){
		    $returnValue->[$index]->{ID} =~ s/\n/ /g;
		    $returnValue->[$index]->{DE} =~ s/\n/ /g;
		    $returnValue->[$index]->{OS} =~ s/\n/ /g;
		    $returnValue->[$index]->{SQ} =~ s/\n/ /g;
		    $returnValue->[$index]->{LC} =~ s/\n/ /g;
		    $returnValue->[$index]->{CX} =~ s/\n/ /g;
		    if($id){
		    $search_result.= "ID\t".$returnValue->[$index]->{ID}."\n";
		    }
		    if($de){
		    $search_result.= "DE\t".$returnValue->[$index]->{DE}."\n";
		    }
		    if($lc){
		    $search_result.= "LC\t".$returnValue->[$index]->{LC}."\n";
		    }
		    if($os){
		    $search_result.= "OS\t".$returnValue->[$index]->{OS}."\n";
		    }
		    if($cx){
		    $search_result.= "CX\t".$returnValue->[$index]->{CX}."\n";
		    }
		    if($sq){
		    $search_result.= "SQ\t".$returnValue->[$index]->{SQ}."\n";
		    }
		    $search_result.="//\n";
		}
		$res_area->delete('1.0','end');
		$res_area->insert('end',$search_result);
	}
	if($button eq 'Cancel'){
		$log_area->insert('end',"Job canceled\n");
	}
}

sub search_by_name {
	my $name="";
	my @pl = qw/-side top -pady 2 -anchor w/;
	my ($id,$de,$lc,$os,$cx,$sq)=(1,0,1,0,0,0);
	my $popup=$main->DialogBox(-title=>"search by name",-buttons => ['OK','Cancel']);	
	$popup -> geometry("250x350");
	$popup -> add('Label',-text=>'Input the name')->pack(@pl);
	my $name_entry = $popup -> add('Entry')->pack(@pl);
	#$popup -> add('Button',-text=>'Search')->pack();
	#$popup -> add('Button',-text=>'Cancel ',-command=>sub{$popup->destroy})->pack();
	$popup -> add('Label',-text=>'Select what fields you want to display')->pack(@pl);
	$popup -> add('Checkbutton',-text=>'DBSubLoc ID',-variable=>\$id,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);
	$popup -> add('Checkbutton',-text=>'SubCellular Location',-variable=>\$lc,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);
	$popup -> add('Checkbutton',-text=>'Cross Database Reference',-variable=>\$cx,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);
	$popup -> add('Checkbutton',-text=>'Description',-variable=>\$de,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);
	$popup -> add('Checkbutton',-text=>'Organism',-variable=>\$os,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);
	$popup -> add('Checkbutton',-text=>'Sequence',-variable=>\$sq,-relief=>'flat',-anchor=>'w',-onvalue=>1,-offvalue=>0)->pack(@pl);

	$popup -> add('Label',-text=>"Note that the Search maybe quite slow\nPlease be patient")->pack(@pl);
	my $button = $popup->Show;
	if($button eq "OK") {
		my $name = $name_entry ->get;
		$log_area->insert('end',"Your Search by name: name=$name\n");
		my $search_result="DBSubLoc ID\tDescription\tSubCellular Location\tOrganism\tCross Database Reference\tSequence\n";
		my $returnValue = $server -> name_search($name);
		for(my $index=0;$index<=$#$returnValue;$index++){
		    $returnValue->[$index]->{ID} =~ s/\n/ /g;
		    $returnValue->[$index]->{DE} =~ s/\n/ /g;
		    $returnValue->[$index]->{OS} =~ s/\n/ /g;
		    $returnValue->[$index]->{SQ} =~ s/\n/ /g;
		    $returnValue->[$index]->{LC} =~ s/\n/ /g;
		    $returnValue->[$index]->{CX} =~ s/\n/ /g;
		    if($id){
		    $search_result.= "ID\t".$returnValue->[$index]->{ID}."\n";
		    }
		    if($de){
		    $search_result.= "DE\t".$returnValue->[$index]->{DE}."\n";
		    }
		    if($lc){
		    $search_result.= "LC\t".$returnValue->[$index]->{LC}."\n";
		    }
		    if($os){
		    $search_result.= "OS\t".$returnValue->[$index]->{OS}."\n";
		    }
		    if($cx){
		    $search_result.= "CX\t".$returnValue->[$index]->{CX}."\n";
		    }
		    if($sq){
		    $search_result.= "SQ\t".$returnValue->[$index]->{SQ}."\n";
		    }
		    $search_result.="//\n";
		}
		$res_area->delete('1.0','end');
		$res_area->insert('end',$search_result);
	}
	if($button eq 'Cancel'){
		$log_area->insert('end',"Job canceled\n");
	}
}

sub search_by_blast {
	#my $name="";
	my @pl = qw/-side top -pady 2 -anchor w/;
	my $isplain= 1;
	my $popup=$main->DialogBox(-title=>"search by blast",-buttons => ['Ready','Wait']);	
	$popup -> geometry("320x300");
	$popup -> add('Label',-text=>"Please input the sequences in fasta format\ninto the Sequence Area,\nyou can mannually input them or\nyour can load a fasta file using \nOpen File command of the top menubar")->pack(@pl);
	$popup -> add('Label',-text=>"Note that the Search maybe quite slow\nPlease be patient")->pack(@pl);
	$popup -> add('Label',-text=>'Select what kind of output you want to display:')->pack(@pl);
	$popup -> add('Radiobutton',-text => 'BLAST ORIGINAL OUTPUT',-variable => \$isplain,-relief =>'flat',-anchor=>'w',-value=>1)->pack(@pl);
	$popup -> add('Radiobutton',-text => 'PARSED OUTPUT',-variable => \$isplain,-relief =>'flat',-anchor=>'w',-value=>0)->pack(@pl);
	$popup -> add('Label',-text=>"Input the e-value threshold")->pack(@pl);
	my $evalue_entry = $popup -> add('Entry')->pack(@pl);
	my $button = $popup->Show;
	if($button eq "Ready") {
		my $evalue=$evalue_entry->get;
		my $seqio = IO::String -> new($seq_area ->get('1.0','end'));
		my $fasta = Bio::SeqIO -> new('-fh'=>$seqio,'-format'=>'fasta');
		$res_area->delete('1.0','end');
		while (my $seq = $fasta->next_seq){
			$log_area->insert('end',"Your Search by blast\n");
			$log_area->insert('end',($seq->id()).($seq->desc())."evalue:".$evalue.("\n"));
			$res_area->insert('end',"Your Blast Result for ".($seq->id())."  ".($seq->desc())." evalue: ".$evalue.("\n"));
			if($isplain){
			$res_area->insert('end',$server-> blast_search('all','full',$seq->seq(),$evalue)->{plain});
			}
			else{
			$res_area->insert('end',$server-> blast_search('all','full',$seq->seq(),$evalue)->{parsed});
			}
		}
	}
	if($button eq 'Wait'){
		$log_area->insert('end',"Waiting for your sequences...,please fill the sequence area above with a fasta file\n");
	}
}

sub predict_by_svm {
	my $organism="prokaryote";
	my @pl = qw/-side top -pady 2 -anchor w/;
	my $popup=$main->DialogBox(-title=>"predict by svm",-buttons => ['Ready','Wait']);	
	$popup -> geometry("350x250");
	$popup -> add('Label',-text=>"Please input the sequences in fasta format\ninto the Sequence Area,\nyou can mannually input them or\nyour can load a fasta file using \nOpen File command of the top menubar")->pack(@pl);
	$popup -> add('Label',-text=>"Note that the Search maybe quite slow\nPlease be patient")->pack(@pl);
	$popup -> add('Label',-text=>'select organism type')->pack(@pl);
	$popup -> add('Radiobutton',-text => 'prokaryote',-variable => \$organism,-relief =>'flat',-anchor=>'w',-value=>'prokaryote')->pack(@pl);
	$popup -> add('Radiobutton',-text => 'eukaryote', -variable => \$organism, -relief => 'flat',-anchor=>'w',-value=>'eukaryote')->pack(@pl);

	my $button = $popup->Show;
	if($button eq "Ready") {
		my $seqio = IO::String -> new($seq_area ->get('1.0','end'));
		my $fasta = Bio::SeqIO -> new('-fh'=>$seqio,'-format'=>'fasta');
		$res_area->delete('1.0','end');
		while (my $seq = $fasta->next_seq){
			$log_area->insert('end',"Your predict by svm\n");
			$log_area->insert('end',($seq->id()).($seq->desc()).("\n"));
			$res_area->insert('end',"Prediction Result for ". ($seq->id()).($seq->desc()).("\n"));
			if ($organism eq "prokaryote"){
				$res_area->insert('end',"Prediction\t".$server-> pro_predict($seq->seq())->{Prediction}."\n");
				$res_area->insert('end',"Expected Accuracy\t".$server-> pro_predict($seq->seq())->{ExpectAcc}."\n");
				$res_area->insert('end',"Reliability Index\t".$server-> pro_predict($seq->seq())->{RI}."\n");
			}
			if ($organism eq "eukaryote"){
				$res_area->insert('end',"Prediction\t".$server-> eu_predict($seq->seq())->{Prediction}."\n");
				$res_area->insert('end',"Expected Accuracy\t".$server-> eu_predict($seq->seq())->{ExpectAcc}."\n");
				$res_area->insert('end',"Reliability Index\t".$server-> eu_predict($seq->seq())->{RI}."\n");

			}
		}
	}
	if($button eq 'Wait'){
		$log_area->insert('end',"Waiting for your sequences...,please fill the sequence area above with a fasta file\n");
	}
}

sub predict_by_psort {
	#my $organism="prokaryotic";
	my @pl = qw/-side top -pady 2 -anchor w/;
	my $popup=$main->DialogBox(-title=>"predict by psort",-buttons => ['Ready','Wait']);	
	$popup -> geometry("350x250");
	$popup -> add('Label',-text=>"Please input the sequences in fasta format\ninto the Sequence Area,\nyou can mannually input them or\nyour can load a fasta file using \nOpen File command of the top menubar")->pack(@pl);
	$popup -> add('Label',-text=>"Note that the Search maybe quite slow\nPlease be patient")->pack(@pl);
	#$popup -> add('Label',-text=>'select organism type')->pack(@pl);
	#$popup -> add('Radiobutton',-text => 'prokaryotic',-variable => \$organism,-relief =>'flat',-anchor=>'w',-value=>'prokaryotic')->pack(@pl);
	#$popup -> add('Radiobutton',-text => 'eukaryotic', -variable => \$organism, -relief => 'flat',-anchor=>'w',-value=>'eukaryotic')->pack(@pl);

	my $button = $popup->Show;
	if($button eq "Ready") {
		my $seqio = IO::String -> new($seq_area ->get('1.0','end'));
		my $fasta = Bio::SeqIO -> new('-fh'=>$seqio,'-format'=>'fasta');
		$res_area->delete('1.0','end');
		while (my $seq = $fasta->next_seq){
			$log_area->insert('end',"Your predict by psort\n");
			$log_area->insert('end',($seq->id()).($seq->desc()).("\n"));
			$res_area->insert('end',"Prediction Result for ". ($seq->id()).($seq->desc()).("\n"));
			$res_area->insert('end',"Predicted Location: ".$server-> psort_predict($seq->seq())->{Prediction}."\n");
			$res_area->insert('end',"Details: ".$server-> psort_predict($seq->seq())->{Detail}."\n");

		}
	}
	if($button eq 'Wait'){
		$log_area->insert('end',"Waiting for your sequences...,please fill the sequence area above with a fasta file\n");
	}
}

sub feed_entry {
	my @pl = qw/-side top -pady 2 -anchor w/;
        my $popup=$main->DialogBox(-title=>"Submit your own sequences to DBSubLoc",-buttons => ['Ready','Wait']);
        $popup -> geometry("350x250");
        $popup -> add('Label',-text=>"Please input the sequences and information\ninto the Sequence Area,\nyou can mannually input them or\nyour can load from a file using \nOpen File command of the top menubar")->pack(@pl);
	my $button = $popup->Show;
	if($button eq "Ready"){
	    my $feeddata=$seq_area -> get('1.0','end');
	    $res_area->insert('end',$server->feed_entry($feeddata,"","","","",""));
	}
	if($button eq "Wait"){
	    $log_area->insert('end',"Waiting for your own sequences and information...\n");
	}
}