#----------------------------------------------------------#
#Shailesh Date and Edward Marcotte, 20th Sept, 2001.
#----------------------------------------------------------#

# PSEUDOCODE generated July 25, 2006        ----####
# PSEUDOCODE updated and posted Aug 3, 2006 ----####


####---- PSEUDOCODE ----####

@queryprofileArray; # put contents in an array
%queryprob = ();  

for ($i=0; $i < lengthOfProfile; $i++) {
  
    #take first place after decimal
    $querybin = (int($queryprofilearray[$i]*10))/10; 

    #round off if value is greater than 0.5
    $querybin = $querybin + 0.1 if (($queryprofilearray[$i] - $querybin) >= 0.05); 

    #add value to hash queryprob      
    $queryprob{$querybin}++; 
} 
  
$queryentropy = 0; 
  
foreach $key (keys %queryprob) {

  $queryprob{$key} = ($queryprob{$key} / lengthOfProfile);
  $querybase2log   = log($queryprob{$key}) / log(2);  
  $queryentropy   += $queryprob{$key} * $querybase2log;

}

$queryentropy = -1*$queryentropy;


# ------ similar steps for relative entropy ------------

$bothbins = $querybin." ".$phylobin;
$prob{$bothbins}++;


# ------ calculate mutual information ------------

$mutualinfo = ($queryentropy + $phyloprofileentropy) - $relativeentropy;


exit