package Mutual;
use strict;

require Exporter;
our @ISA = qw(Exporter);
our @EXPORT = qw(log_2 get_index get_Hx fisher_yates_shuffle);


 # fisher_yates_shuffle( \@array ) : 
     # generate a random permutation of @array in place
     sub fisher_yates_shuffle {
         my $array = shift;
         my $i;
         for ($i = @$array; --$i; ) {
             my $j = int rand ($i+1);
             next if $i == $j;
             @$array[$i,$j] = @$array[$j,$i];
         }
     }

    # fisher_yates_shuffle( \@array );    # permutes @array in place

sub log_2 {
    my $base = 2;
    my $value = $_[0];
    return log($value)/log($base);
}


sub get_index{
    $_[0] lt $_[1] ? ($_[0].$_[1]) : ($_[1].$_[0])
    }




sub get_Hx{
my $site = $_[0];
my $no_of_sequences =length($site);
my $count_A=0 ;                     
my $count_C=0 ;
my $count_D=0 ;
my $count_E=0 ;
my $count_F=0 ;
my $count_G=0 ;
my $count_H=0 ;
my $count_I=0 ;
my $count_J=0 ;
my $count_K=0 ;
my $count_L=0 ;
my $count_M=0 ;
my $count_N=0 ;
my $count_P=0 ;
my $count_Q=0 ;
my $count_R=0 ;
my $count_S=0 ;
my $count_T=0 ;
my $count_V=0 ;
my $count_W=0 ;
my $count_Y=0 ;
my $count_ =0 ;
my $sum1=0;
my $sum2=0;
my $sum3=0;
my $sum4=0;
my $sum5=0;
my $sum6=0;
my $sum7=0;
my $sum8=0;
my $sum9=0;
my $sum10=0;
my $sum11=0;
my $sum12=0;
my $sum13=0;
my $sum14=0;
my $sum15=0;
my $sum16=0;
my $sum17=0;
my $sum18=0;
my $sum19=0;
my $sum20=0;
my $sum21=0;
 
 while($site =~m/A/g){   
    $count_A++;
    }
 while($site =~m/C/g){   
    $count_C++;
    }
 while($site =~m/D/g){   
    $count_D++;
    }
 while($site =~m/E/g){   
    $count_E++;
    }
 while($site =~m/F/g){   
    $count_F++;
    }
 while($site =~m/G/g){   
    $count_G++;
    }
 while($site =~m/H/g){   
    $count_H++;
    }
 while($site =~m/I/g){   
    $count_I++;
    }
 while($site =~m/K/g){   
    $count_K++;
    }
while($site =~m/L/g){   
    $count_L++;
    }
while($site =~m/M/g){   
    $count_M++;
    }
while($site =~m/N/g){   
    $count_N++;
    }
while($site =~m/P/g){   
    $count_P++;
    }
while($site =~m/Q/g){   
    $count_Q++;
    }
while($site =~m/R/g){   
    $count_R++;
    }
while($site =~m/S/g){   
    $count_S++;
    }
while($site =~m/T/g){   
    $count_T++;
    }
while($site =~m/V/g){   
    $count_V++;
    }
while($site =~m/W/g){   
    $count_W++;
    }
while($site =~m/Y/g){   
    $count_Y++;
    }
while($site =~m/\./g){   
    $count_++;
    }
while($site =~m/\_/g){
    $count_++;
}

#if there is a counter with +ve value in any position of the array, then calculate the mutual information
#value and store it there.
if ($count_A > 0){
     $sum1= -($count_A/$no_of_sequences)*log_2($count_A/$no_of_sequences);
}
if ($count_C > 0){
     $sum2= -($count_C/$no_of_sequences)*log_2($count_C/$no_of_sequences);
}
if ($count_D > 0){
     $sum3= -($count_D/$no_of_sequences)*log_2($count_D/$no_of_sequences);
}
if ($count_E > 0){
     $sum4= -($count_E/$no_of_sequences)*log_2($count_E/$no_of_sequences);
}
if ($count_F > 0){
     $sum5= -($count_F/$no_of_sequences)*log_2($count_F/$no_of_sequences);
}
if ($count_G > 0){
     $sum6= -($count_G/$no_of_sequences)*log_2($count_G/$no_of_sequences);
}
if ($count_H > 0){
     $sum7= -($count_H/$no_of_sequences)*log_2($count_H/$no_of_sequences) ;
}
if ($count_I > 0){
     $sum8= -($count_I/$no_of_sequences)*log_2($count_I/$no_of_sequences) ;
}
if ($count_J > 0){
     $sum9= -($count_J/$no_of_sequences)*log_2($count_J/$no_of_sequences);
}
if ($count_K > 0){
     $sum10= -($count_K/$no_of_sequences)*log_2($count_K/$no_of_sequences);
}
if ($count_L > 0){
     $sum11=-($count_L/$no_of_sequences)*log_2($count_L/$no_of_sequences);
}
if ($count_M > 0){
     $sum12=-($count_M/$no_of_sequences)*log_2($count_M/$no_of_sequences);
}
if ($count_N > 0){
     $sum13= -($count_N/$no_of_sequences)*log_2($count_N/$no_of_sequences);
}
if ($count_P > 0){
     $sum14= -($count_P/$no_of_sequences)*log_2($count_P/$no_of_sequences);
}
if ($count_R > 0){
     $sum15= -($count_R/$no_of_sequences)*log_2($count_R/$no_of_sequences);
}
if ($count_S > 0){
     $sum16= -($count_S/$no_of_sequences)*log_2($count_S/$no_of_sequences);
}
if ($count_T > 0){
     $sum17= -($count_T/$no_of_sequences)*log_2($count_T/$no_of_sequences);
}
if ($count_V > 0){
     $sum18= -($count_V/$no_of_sequences)*log_2($count_V/$no_of_sequences);
}
if ($count_W > 0){
     $sum19= -($count_W/$no_of_sequences)*log_2($count_W/$no_of_sequences);
}
if ($count_Y > 0){
     $sum20= -($count_Y/$no_of_sequences)*log_2($count_Y/$no_of_sequences);
}
if ($count_ > 0){
     $sum21= -($count_/$no_of_sequences)*log_2($count_/$no_of_sequences);
}


 my $Hx = $sum1+$sum2+$sum3+$sum4+$sum5+$sum6+$sum7+$sum8+$sum9+$sum10+$sum11+$sum12+$sum13+$sum14
    +$sum15+$sum16+$sum17+$sum18+$sum19+$sum20+$sum21;
    
    
        return $Hx;
}#end of foreach 

1;