#!/usr/bin/perl -w

use strict;

my $dinu_r;  # um... nothing is ever assigned to this variable

my @energyGrid; # this will be the AoA

my $i;
for my $x ( 1 .. 5 )
{
    open( AA, "shuffle$x" ) or die "Can't open shuffle$x ($!)\n"; # LINE A

    my $Sequence;
    $i=length($Sequence);  # um... this is always zero

    while (<AA>) {
        $Sequence=$_;  # um... $Sequence will only be the last line of "shuffle$x"
    }
    close(AA);

    my %Winenergy = Energy( $Sequence, $dinu_r );
    open (OUT, ">shuffle$x.stb"); # LINE B

    foreach my $el1 (sort{$a <=> $b} keys %Winenergy) {
        push( @{$energyGrid[$x]} , $Winenergy{$el1} ); #LINE C
    }
    close (OUT);
}

open(FILE,">total_shuffle.stb");
my $m=8;

for my $j ( 0 .. $i )  # um... $i is still zero here
{
    my $avg = 0;
    for my $x ( 1 .. 5 ) {
        $avg += $energyGrid[$x][$j];
    }
    $avg /= 5;
    print FILE "$m\t$avg\n";
    $m++;
}
close (FILE);

sub Energy
{
    my ($sequence,$dinu_r) = @_;
    my %dinu = %$dinu_r;   # um... $dinu_r was never a hash ref
       # (and is undef), so this line will cause a run-time error

    my $win=15;
    my $limit1 = length( $sequence ) - $win + 1;
    my $wincenpos = 1 + ($win-1)/2;
    my %winenergy = ();
    for my $j ( 0 .. $limit1-1 ) {
        my $winseq = substr($sequence,$j,$win);
        my $energy = 0;
        for my $k  ( 0 .. $win-2 ) {
            my $dinucle_temp = substr($winseq,$k,2);
            my $dinucle = uc($dinucle_temp);
            $energy = $energy + $dinu{$dinucle};
        }
        my $wincentre = $j+$wincenpos;
        $winenergy{$wincentre} = $energy;
    }
    return %winenergy;
}