// ############################## START FUNC ############################################
// Here, all "bit files" (i.e. simulation of bit files with setting data attached) are
// compared pair by pair. Of course the loop for(m=0;m<n;m++){ stops before n to not make
// each comparision twice.

function mega3(bitstrings,file_list, conversions)
{
     var convert=document.form1.cb.checked;
     var number_of_files=file_list.length;
     var n=0;
     var m=0;
     var n_count=0;
     var m_count=0;
     var n_value=0;
     var m_value=0;
     var hitfreq=0;
     var hh=0;
     var n_string="";
     var m_string="";
     var n_mark=0;
     var m_mark=0;
     var hitlist="";   // Used for simplification and check.
     var hit_matrix=def_matrix(number_of_files,number_of_files, 0, "undefined");
     var temp="";
     var tupp=new Array(0);
     var saved="";
     var start="";     // Variable that stores the TeX table header later
     var end="";       // Variable that stores the TeX table end later

for(n=0;n<number_of_files;n++){
for(m=0;m<n;m++){
n_count=0;
m_count=0;
hitlist="";
hitfreq=0;

// The fallowing loop is executed for each molecule pair. n_count counts given LISTED bit positions in
// the "bit string" for one molecule, m_count for the other. All listed positions for a molecule marks
// an occurence, which means that the bit in that position is set 1. If there is a 1 in the same
// position in both molecules (m_count = n_count), a "hit" is counted (hitfreq++). As long as m_count
// is just lower then a given n_count, next occurence, i.e. the next m_count is searched for in that
// molecule and vice versa.

  while(n_count<bitstrings[n].length && m_count<bitstrings[m].length){
  n_string=bitstrings[n][n_count]+"  ";  // Some bug in JavaScript makes "  " necessary to allow substring later.
  m_string=bitstrings[m][m_count]+"  ";
  n_mark=n_string.indexOf("_");
  m_mark=m_string.indexOf("_");
  n_value=parseInt(n_string.substring(0,n_mark));
  m_value=parseInt(m_string.substring(0,m_mark));
   if(n_value<m_value) n_count++;                   // Search for next occurence in molecule n
   if(m_value<n_value) m_count++;                   // Search for next occurence in molecule m
   if(m_value==n_value){                            // A "hit"
   hitlist=hitlist+n_value+"  "+n_string.substring(n_mark,n_string.length)+" "+m_string.substring(m_mark,m_string.length)+"\n";
   n_count++;
   m_count++;
   hitfreq++;
   }
  }

if(hitfreq!=0){
hh=hitfreq/100000-(-0.000001);
hit_matrix[n][m]=" /"+hh+"/%%  "+file_list[n]+"%#%"+file_list[m]+" /"+hitfreq+"/\n"+hitlist+"\n\n\n";  // Looks clearer then instantly, in the while-loop hit_matrix[n][m]=hit_matrix[n][m]+...
hit_matrix[n][m]=hit_matrix[n][m].replace(/,/g, "&");  // To not split in these points
}

}
}

// Why use a two dimensional matrix first and then convert it to a one dimensional
// matrix? This procedure is to allow easier adaptments later.

     temp = hit_matrix.join(",");
     temp=temp.replace(/,+/g, ",");
     hit_matrix=temp.split(",");

// The reason for replacement of "," in the molecule names earlier is that "," is the
// predefined separator when two dimensions are converted to one. Therefore, no other
// marker can be used.

     temp="";
     hit_matrix=hit_matrix.sort();
     hit_matrix=hit_matrix.reverse();
     temp=hit_matrix.join("");

     temp=temp.replace(/\s\S+%%\s/g, "");
     temp=temp.replace(/&/g, ",");                // To get back ","- in complex molecule names

// The fallowing procedure uses the table from document feature_list in the main map
// to eventually convert feature numbers back to feature names. This greatly reduces the
// hazzle when checking the results with a human eye.

     convert=document.form1.cb.checked;

     if(convert){
       for(n=0;n<conversions.length;n++){
       hit_matrix=temp.split("%"+conversions[n][1]+"%");
       saved=hit_matrix.join(conversions[n][0]);
       }
     }

// The fallowing 2 rows releases memory space. The third row mainly
// prevents four \n in the end to be converted to "\\\cr&&&&" as TeX later.

     temp=false;
     hit_matrix=false;
     saved=saved.substring(0,saved.length-4);

// The result is sent to a function for eventual modification (TeX) and output.

mega3tex(saved);
}

// ############################### end func ############################################