Hi,
I have computed one equation based on the given string.
Can anyone please review my code.

 #!c:\perl\bin\perl

use strict;
use warnings;
use Math::BigInt;
use Data::Dumper;


my %index_val = ( A=> 2,
                  C => 3,
                  D => 4, 
                  N => 2,
                  M => 2,
                  T => 1,
                  G => 4);

my $sequence="ACTGACN";

my $distance_index= int(rand(4));

my $window=int(rand(3));

my $arr_ref = &alpha_index({ sequence => $sequence,
                           distance => $distance_index,    
                           aa_index => \%index_val,
                           window_size => $window });

print STDERR Dumper($arr_ref);

sub alpha_index {

    my $self=shift;
    my $sequence=$self->{sequence};
    my $distance=$self->{distance};
      my $aa_index=$self->{aa_index};
    my ($left,$middle,$right,@carbon_index);
    my $window_size= $self->{window_size};

    if($self->{window_size} ==1) { $window_size=1;}
    elsif($self->{window_size} > 1 ) 
        { $window_size = int(($self->{window_size}-1)/2); }
    else { $window_size=0; }

    foreach (0.. (length($sequence)-1)) {
      my %carbon_aa=();
     ($left,$middle,$right) = $sequence =~ m/(\w{$_})?(\w{1})?(\w*)/;
            $carbon_aa{$middle}=$aa_index->{$middle} if($middle);
            $left=reverse($left);
            my ($left_aa,$right_aa,$distance_index,$power)=0;
            my $initial_index=2;
            
    my $length_index= ($window_size) ? $window_size:length($left);
            
            if($self->{window_size} ==1 ) {
                push @carbon_index, \%carbon_aa if(%carbon_aa);
                next;
            } 

            foreach my $increment (0..$length_index-1) {
                    $left_aa=substr($left,$increment,1);
                    next if not exists $aa_index->{$left_aa};
                $power=Math::BigInt->new($initial_index);
                $distance_index=($power->bpow($distance))->numify();
                $carbon_aa{$middle}+=
                      ( $aa_index->{$left_aa} * (1/$distance_index));
                $initial_index++;
            }

            $initial_index=2;
                
    $length_index= ($window_size)?$window_size:length($right);
            
            foreach my $increment (0..$length_index-1) {
                $right_aa=substr($right,$increment,1);
                next if not exists $aa_index->{$right_aa};
                $power=Math::BigInt->new($initial_index);
                $distance_index=($power->bpow($distance))->numify();
                $carbon_aa{$middle}+=
                     ( $aa_index->{$right_aa} * ( 1/$distance_index));
                $initial_index++;
            }

        push @carbon_index, \%carbon_aa if(%carbon_aa);
    }

    return \@carbon_index;
}
[download]

Thanks in advance.
- kulls

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