#!/usr/bin/perl
############################################################
# file: index.cgi, in tools/MeltMap
# desc: cgi-script for PubGene MeltMap viewer
# auth: Tor-Kristian Jenssen, PubGene AS
# comm:
#===========================================================
#
# Copyright 2003 PubGene AS, all rights reserved
#
#===========================================================
# who | dd/mm/yyyy | what
#-----------------------------------------------------------
# tkj | 03/03/2003 | created
############################################################

use lib '../../lib';

use strict;
use Carp;
use Benchmark;

require PubGene;
require MeltMap::Configuration;
require MeltMap::Database;
require MeltMap::Plot;
require NucleosomePostion::Database;
require GeneralMap::Database;

# file globals
my $DEBUG=0;

# start program
my $pg = PubGene::Web::Page->new("Chromosome Viewer", 'melting_map');

unless (defined $pg){
  exit(PubGene::Web::Page::FATAL_ERROR("cannot create Page Object"));
}
#$DEBUG && $pg->list_params();
my $q = $pg->{'cgi'};
if ($q->param('gethelp') eq 'yes') {
  exit(PubGene::Web::Page::Help::layout($pg));
}

$pg->add(chrmenu($pg));

if ($q->param('GetMeltMap')) {
  $pg->add(results($pg));
}
$pg->layout($DEBUG);
exit;

######
# results
######
sub results {
  my $pg = shift;
  my $q = $pg->{'cgi'};
    
  my $error = 0;		# error code
  my $msg;
  my $t0 = Benchmark->new();
  my $results = "";		# result buffer (string)

  my $organism = 'hs';
  #my $freeze = $q->param('freeze');
  #$results .= $freeze;
  my $freeze = 'hg17';
  #$results .= $freeze;
  my $chr = $q->param('chr');
  my $start = $q->param('startpos');
  my $end = $q->param('endpos');
  my $avg_check = $q->param('avg_check') || 'off';
  my $avg_method = $q->param('avg_method');
  my $avg_wsize = $q->param('avg_wsize');
  my @gen_files = $q->param('gen_files');
  my $sel_all = $q->param('select_all');
  my $singel_plot = $q->param('singel_plot');
  my $multi_plot = $q->param('multi_plot');
  my $chk_human = $q->param('chk_human');
  my $chk_nuc = $q->param('chk_nuc');
  my $chk_bendy = $q->param('chk_bendy');
  my $chk_curve = $q->param('chk_curve');

  my $fname = MeltMap::Configuration::get_full_chr_fname($chr, 'bin', 'maps', 'hs', 'golden', $freeze);

  open(DEBUG, ">/usit/titan/u1/geirij/public_html/svg_browser/browser/tools/MeltMap/debug.txt") or die ;
  print DEBUG join ("\n" , @gen_files);
  closedir(DEBUG);

  my $num_bps = $end - $start + 1;
  $results .= "Melting map for bases $start to $end ($num_bps)";
  $results .= "&nbsp;from chromosome $chr<br>";


  $results .= $sel_all;
  if ($sel_all eq 'on') {
    # include all files for calulation
    my $gen_dir = qq (../../data/meltmap/maps/alt/);
    opendir(DIR, $gen_dir);
    @gen_files = grep(/[^\.*]/,readdir(DIR));
    closedir(DIR);
  }

  my @plot_points;

  my %multi_shot = ();
  my %single = ();

  if ($singel_plot eq 'on' || $multi_plot eq 'on') {
    #Human
    if ($chk_human eq 'on') {
      my @tmp = ();
      MeltMap::Database::get_melt_map_chr_segment($fname, 'bin', $start, $end, \@tmp);
      $multi_shot{'Human_melt'} = \@tmp;
    }
    # Nucleosome pos
    if ($chk_nuc eq 'on') {
      my @tmp;
      NucleosomePostion::Database::get_nuc_pos_chr_segment($start, $end, \@tmp );
      $multi_shot{'Nuc_pos'} = \@tmp;
    }

    if ($chk_bendy eq 'on') {
      my @tmp;
      GeneralMap::Database::get_plot_data($chr, $start, $end, \@tmp, "bendability");
      $multi_shot{'Bendability'} = \@tmp;
    }

    if ($chk_curve eq 'on') {
      my @tmp;
      GeneralMap::Database::get_plot_data($chr, $start, $end, \@tmp, "curvature");
      $multi_shot{'Curvature'} = \@tmp;
    }

    foreach my $genome (@gen_files) {
      my @values = ();
      # Retrieve data
      get_chr_segment($genome, $start, $end, \@values);
      $multi_shot{$genome} = \@values;
    }
  }


  if ($singel_plot eq 'on') {
    foreach my $plot (keys %multi_shot) {
      my $ref_values = $multi_shot{$plot};
      my @values = @$ref_values;
      # Retrieve data
      $single{"single"} = \@values;

      # Create SVG
      $results .= qq(<br> $plot <br>);
      $results .= create_svg(\%single, $start, $end);
    }
  }

  # Creating a multiplot if two or more files has been selected
  if ($multi_plot eq 'on') {
    $results .= qq(<br> Multiplot <br>);
    foreach my $key (keys %multi_shot) {
      # Normalizing the plots
      $results .= qq(<br> $key <br>);
      my $tmp_ref = $multi_shot{$key};
      my @tmp_arr = @$tmp_ref;
      my @tmp_norm = normalize(@tmp_arr);
      $multi_shot{$key} = \@tmp_norm;
    }

    $results .= create_svg(\%multi_shot, $start, $end);
  }
  return $results;

}

sub get_chr_segment {
  my $genome = shift;
  my $start_bp = shift;
  my $end_bp = shift;
  my $ra_temperatures = shift;

  my @chr_array = ();
  tie @chr_array, 'Tie::File', "/usit/titan/u1/geirij/public_html/svg_browser/browser/data/meltmap/maps/alt/$genome" or die "$!";
  # Slice'n dice..:
  my @temp = @chr_array[$start_bp-1..$end_bp-1];
  untie @chr_array;
  
  open(DEBUG, ">/usit/titan/u1/geirij/public_html/svg_browser/browser/tools/MeltMap/debug.txt") or die ;
  print DEBUG "($start_bp - $end_bp)\n";
  print DEBUG join ("\n" , @temp);
  closedir(DEBUG);

  @$ra_temperatures = @temp;
}

sub create_svg{
  my ($genome,$start,$end) = @_;
  my $results = "";

  my $tmp_fname = $pg->create_image_fname('svg');
  my $tmp_fname .= rand();
  my $image_fname = $PubGene::TMP_DIR . $tmp_fname;
  my $image_url = $PubGene::Web::TMP_DIR . $tmp_fname;

  my ($error, $msg) = MeltMap::Plot::svg($genome, $start, $end, 1 , 800,400,$image_fname, );
  if ($error) {
    $results .= $pg->error("failed to create svg file",  $msg);
    return $results;
  }
  return $pg->svgimage($image_url,800,400);
}

sub normalize{
  my @lines = @_;
  my @norm_array = ();
  my ($max, $min) = (-10000, 10000);
  foreach my $line (@lines) {
    # finding max min
    if ($line > $max) {
      $max = $line;
    }
    if ($line < $min) { 
      $min = $line
    }
  }
  
  # Normalizing
  foreach my $line (@lines) {
    my $val_norm = 0;
    #    $val_norm = ( ($max-$line) / ($max-$min));
    $val_norm = 100-( (($max-$line)*100) / ($max-$min) );
    push(@norm_array, $val_norm);
  }
  return @norm_array;
}



######
# chrmenu
######
sub chrmenu {
  my $pg = shift;

  my $q = $pg->{'cgi'};
    
  my $organism = 'hs';
  my $nmenu = $q->startform('POST');
  my %freezes = %MeltMap::Configuration::FREEZES;
  my @freezes = keys %freezes;
  #$nmenu .= "Select golden path freeze:&nbsp;";
  #$nmenu .= $q->popup_menu('-name' => 'freeze',
  #												 '-values' => \@freezes,
  #												 '-labels' => \%freezes,
  #												 '-default' => '1');
  #$nmenu .= "<br>";
  my @chrs = MeltMap::Configuration::get_chromosomes($organism);
  my %chrs;
  @chrs{@chrs} = @chrs;

  $nmenu .= qq(<span class="style4"> Navigator:</span><br>);
  $nmenu .= "Select subsequence: ";
  $nmenu .= "start base ";
  $nmenu .= $q->textfield('-name' => 'startpos',							'-default' => 1,
			  #'-align' => 'right',
			  '-size' => 12);
  $nmenu .= "end base ";
  $nmenu .= $q->textfield('-name' => 'endpos',
			  '-default' => 1000,
			  #'-align' => 'right',
			  '-size' => 12);
  $nmenu .= "<br><hr/>";
  $nmenu .= qq(
Select data source..:<br />
  <label><INPUT TYPE=checkbox NAME=chk_human checked="checked">Human melting map </label>
<br />);

  $nmenu .= qq(
  <label><INPUT TYPE=checkbox NAME=chk_bendy >Bendability </label>
<br />);

  $nmenu .= qq(
  <label><INPUT TYPE=checkbox NAME=chk_curve >Curveability </label>
<br />);

  $nmenu .= "Select chromosome:&nbsp;";
  $nmenu .= $q->popup_menu('-name' => 'chr',
			   '-values' => \@chrs,
			   '-labels' => \%chrs,
			   '-default' => '1');
  $nmenu .= "Check this to compute average";
  $nmenu .= $q->checkbox('-name' => 'avg_check',
			 '-checked' => 'on',
			 '-value' => 'on',
			 '-label' => '');
  my @avg = ('mean','median','max','min');
  my %avg;
  @avg{@avg} = @avg;
  $nmenu .= "Select averaging method";
  $nmenu .= $q->popup_menu('-name' => 'avg_method',
			   '-values' => \@avg,
			   '-labels' => \%avg,
			   '-default' => '1');
  my @wsizes = ('auto', 10, 50, 100, 500, 1000, 5000, 10000, 50000, 100000);
  my %wsizes;
  @wsizes{@wsizes} = @wsizes;
  $nmenu .= "Window size:";
  $nmenu .= $q->popup_menu('-name' => 'avg_wsize',
			   '-values' => \@wsizes,
			   '-labels' => \%wsizes,
			   '-default' => 'auto');
  $nmenu .= "<br> <br> <hr />";	

  #G Legger til listen over tilgjengelige genomer..:
  my $gen_dir = qq (../../data/meltmap/maps/alt/);
  opendir(DIR, $gen_dir);
  my @gen_files = grep(/[^\.*]/,readdir(DIR));
  closedir(DIR);
	
  my @sel_gen_files = ();
  for (my $i=0; $i < @gen_files; $i++) {
    my $tmp_gen = qq (<OPTION VALUE="$gen_files[$i]">$gen_files[$i]\n);
    push (@sel_gen_files,  $tmp_gen);
  }

  my $select_genomes = qq(
<label><INPUT TYPE=checkbox NAME=chk_nuc>Nucleosome positioning</label>
<br/>
<TABLE BORDER=0 CELLPADDING=1 CELLSPACING=2><TR><TD><B>Available genomes:</B><BR>
<label><INPUT TYPE=checkbox NAME=select_all>Select all</label>
<BR>
<SELECT NAME="gen_files" STYLE="width: auto;" MULTIPLE  SIZE=15>
@sel_gen_files
</SELECT></TD>

</TR></TR>

</TABLE>  );

  $nmenu .= $select_genomes;
  $nmenu .= qq (
<hr/>
Plot settings..:<br />
<label><INPUT TYPE=checkbox NAME=singel_plot checked="checked">Create seperate plots</label>
<BR>
<label><INPUT TYPE=checkbox NAME=multi_plot>Create multiplot (Normalized data)</label>
<BR>);

  $nmenu .= $q->submit('-name' => 'GetMeltMap',
		       '-value' => 'Submit');

  $nmenu .= $q->endform();
	
  return $nmenu;
}