#!c:\perl\bin\perl

use strict;
use warnings;


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

my $sequence="ACTGACN";
my $distance_index = 2;
my $window = 2;

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

for my $hashRef (@$arr_ref) {
    print join "\n", map {"$_ => $hashRef->{$_}"} keys %$hashRef;
    print "\n";
}


sub alpha_index {
    my $self=shift;
    my $sequence=$self->{sequence};
    my $distance=$self->{distance};
    my $aa_index=$self->{aa_index};
    my @carbon_index;
    my $window_size = int $self->{window_size};

    $window_size = int ($window_size - 1) / 2 if $window_size > 1;

    foreach my $len (0 .. (length($sequence)-1)) {
        my %carbon_aa;
        my ($left, $middle, $right) = splitStr ($sequence, $len);
        $carbon_aa{$middle} = $aa_index->{$middle} if $middle;
        $left = reverse $left;

        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) {
            my $left_aa=substr($left,$increment,1);
            next if not exists $aa_index->{$left_aa};
            
            my $distance_index= $initial_index ** $distance;
            
            $carbon_aa{$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) {
            my $right_aa=substr ($right, $increment, 1);
            next if not exists $aa_index->{$right_aa};
            
            my $distance_index= $initial_index ** $distance;
            
            $carbon_aa{$middle} += $aa_index->{$right_aa} * (1 / $distance_index);
            $initial_index++;
        }
        
        push @carbon_index, \%carbon_aa if %carbon_aa;
    }

    return \@carbon_index;
}


sub splitStr {
    return (
        substr($_[0], 0, $_[1]),
        substr($_[0], $_[1], 1),
        substr($_[0], $_[1] + 1)
        );
}