#!/usr/bin/perl -w

########################
#                      #
# Modules	       #
#                      #
########################

use strict;
use CGI;
use DBI;
use Chart::Gnuplot;

use lib 'lib';
use Crosslinker::HTML;
use Crosslinker::Links;
use Crosslinker::Scoring;
use Crosslinker::Data;
use File::Temp qw/ tempfile tempdir /;
use Crosslinker::Constants;

########################
#                      #
# Import CGI Varibles  #
#                      #
########################

my $query    = new CGI;
my $table    = $query->param('table');
my $scan     = $query->param('scan');
my $d2_scan  = $query->param('d2_scan');
my $fraction = $query->param('fraction');
my $score    = $query->param('score');

########################
#                      #
# Connect to database  #
#                      #
########################
my $results_dbh;
my $settings_dbh;

if ($scan == -1) {
    $results_dbh  = DBI->connect("dbi:SQLite:dbname=db/results_single",  "", "", { RaiseError => 1, AutoCommit => 1 });
    $settings_dbh = DBI->connect("dbi:SQLite:dbname=db/settings_single", "", "", { RaiseError => 1, AutoCommit => 1 });
} else {

    $settings_dbh = connect_settings;


    my $settings_sql = $settings_dbh->prepare("SELECT name FROM settings WHERE name = ?");
    $settings_sql->execute($table);
    my @data = $settings_sql->fetchrow_array();
    if ($data[0] != $table) {
        print "Content-Type: text/plain\n\n";
        print "Cannont find results database";
        exit;
    }
    $results_dbh =     connect_db_results($table);

}


########################
#                      #
# Load Settings        #
#                      #
########################

my $settings = $settings_dbh->prepare("SELECT * FROM settings WHERE name = ?");
$settings->execute($table);
my ($name, $desc, $cut_residues, $protein_sequences, $reactive_site, $mono_mass_diff, $xlinker_mass, $is_finished) =
  $settings->fetchrow_array;
$settings->finish();
$settings_dbh->disconnect();

########################
#                      #
# Constants            #
#                      #
########################

my (
    $mass_of_deuterium, $mass_of_hydrogen, $mass_of_proton,     $mass_of_carbon12,
    $mass_of_carbon13,  $no_of_fractions,  $min_peptide_length, $scan_width
) = constants;

########################
#                      #
# Image	  Gen          #
#                      #
########################

print "Content-Type: image/svg+xml\n\n";

# print "Content-Type: text/plain\n\n";

my $top_hits;

if (defined $d2_scan && $d2_scan ne '') {
    $top_hits = $results_dbh->prepare(
                     "SELECT * FROM results WHERE name=? AND scan = ? AND d2_scan = ? AND fraction = ? AND score = ?  "); 
    $top_hits->execute($table, $scan, $d2_scan, $fraction, $score);
} else {
    $top_hits =
      $results_dbh->prepare("SELECT * FROM results WHERE name=? AND scan = ? AND fraction = ? AND score = ?  ");
    $top_hits->execute($table, $scan, $fraction, $score);
}

my $top_hits_results = $top_hits->fetchrow_hashref();

my $data;
my $top_10;
my @masses;
my $title;

if (!defined $query->param('heavy') || $query->param('heavy') == 0) {
    $data   = $top_hits_results->{'MSn_string'};
    $top_10 = $top_hits_results->{'top_10'};
    @masses = split "\n", $data;
    $title  = $top_hits_results->{'fragment'};
} else {
    $data   = $top_hits_results->{'d2_MSn_string'};
    $top_10 = $top_hits_results->{'d2_top_10'};
    @masses = split "\n", $data;
    $title  = "$top_hits_results->{'fragment'} (Heavy)";
}

# Chart object
my $chart = Chart::Gnuplot->new(
    terminal => 'svg',
    encoding => 'utf8',
    imagesize  => '1024, 768',
    xlabel     => "m/z",
    ylabel     => "relative abundance",
    tmargin    => "5",
    title      => "$title",
    termoption => 'enhanced'
);

$chart->gnuplot('/usr/bin/gnuplot');

my @unmatched = ([ 1, 1 ], [ 2, 2 ]);
my @bions     = ([ 1, 1 ]);
my @yions     = ([ 1, 1 ]);
my @waterions = ([ 1, 1 ]);

foreach my $mass_abundance (@masses) {
    my ($mass, $abundance) = split " ", $mass_abundance;
    $mass =~ s/0*$//;

    if ($top_10 =~ /$mass\<br\/\>/) {

        $top_10 =~ m/(.);(Y|A|B)<sub>(\d*)<\/sub><sup>(\d)\+<\/sup> = $mass/;

        my $chain;
        if (defined $1) {

            if   ($1 eq '5') { $chain = '&#945;' }
            else             { $chain = '&#946;' }
            if ($2 eq 'Y') {
                my $ion_type = 'y';
                push(@yions, [ $mass, $abundance ]);
                $chart->label(
                    text     => "$chain$ion_type$3($4+) = $mass Th",
                    position => "$mass, $abundance",
                    offset   => "-1.5,-6",

                    rotate    => 90,
                    font      => "arial, 10",
                    fontcolor => "dark-green",
                );
            } elsif ($2 eq 'A' || $2 eq 'B') {
                push(@bions, [ $mass, $abundance ]);    #a-ions get stuck with b-ions

                #  		print  "$chain $mass $2$3($4+) Th\n ";
                my $ion_type;
                if ($2 eq 'A') { $ion_type = 'a' }
                if ($2 eq 'B') { $ion_type = 'b' }
                $chart->label(
                              text      => "$chain$ion_type$3($4+) = $mass Th",
                              position  => "$mass, $abundance",
                              offset    => "-1.5,-6",
                              rotate    => 90,
                              font      => "arial, 10",
                              fontcolor => "red",
                );
            }
        } else    #Would rather a Y or B/A drawn before drawing a water loss...
        {
            $top_10 =~ m/(.);(Y\[-H2O\]|A\[-H2O\]|B\[-H2O\])<sub>(\d*)<\/sub><sup>(\d)\+<\/sup> = $mass/;
            if   (defined $1 eq '5') { $chain = '&#945;' }
            else                     { $chain = '&#946;' }
            if (defined $2
                && ($2 eq 'A[-H2O]' || $2 eq 'B[-H2O]' || $2 eq 'Y[-H2O]'))
            {
                my $ion_type;
                if ($2 eq 'A[-H2O]') { $ion_type = 'a' }
                if ($2 eq 'B[-H2O]') { $ion_type = 'b' }
                if ($2 eq 'Y[-H2O]') { $ion_type = 'y' }

                push(@waterions, [ $mass, $abundance ]);
                $chart->label(
                              text      => "$chain$ion_type$3($4+) = $mass Th",
                              position  => "$mass, $abundance",
                              offset    => "-1.5,-6",
                              rotate    => 90,
                              font      => "arial, 10",
                              fontcolor => "blue",
                );
            }
        }

    } else {
        push(@unmatched, [ $mass, $abundance ]);
    }
}


my $impulses =
  Chart::Gnuplot::DataSet->new(
                               title  => 'unmatched ions',
                               points => \@unmatched,
                               color  => 'black',
                               style  => "impulses",
  );

my $impulses2 =
  Chart::Gnuplot::DataSet->new(
                               title  => 'b-ions',
                               points => \@bions,
                               color  => 'red',
                               style  => "impulses",
  );

my $impulses3 =
  Chart::Gnuplot::DataSet->new(
                               title  => 'y-ions',
                               points => \@yions,
                               color  => 'green',
                               style  => "impulses",
  );

my $impulses4 =
  Chart::Gnuplot::DataSet->new(
                               title  => 'neutral-loss ions',
                               points => \@waterions,
                               color  => 'blue',
                               style  => "impulses",
  );

#Plot the graph
binmode STDOUT;
$chart->svg;

$chart->plot2d($impulses, $impulses2, $impulses3, $impulses4);
$top_hits->finish();
$results_dbh->disconnect();

exit;