// ############################## START FUNC ############################################
// Here is the main function that loopes through all molecules and gathers the information.
// Missing information pieces are calculated in routines and put in. So if there is no 
// bit string in frame1, frame2 is checked. If feature information is availible in frame2
// it is converted to a bit string by calling the function over_all2. If there is no information
// in frame2 either, frame3 is checked for information about cartesian coordinates of the atoms.
// This information is (by calling the function over_all1) converted to input information for
// the function over_all2 and so on. The objective is to get a final bitstring for each molecule
// placed in bitstrings[n] where n is the row for the molecule in the file list.

function mega2(bitstrings,f_ligands,f_ex,angle_intervals,dist_intervals,groups,files, g_commands, saved)
{

// Please note that f_ex is the table for features vs feature numbers according to
// the feature_list in the main map.

var bit_string="";
var save=document.form1.save.checked;
var convert=document.form1.cb.checked;
var texx=document.form1.tex.checked;
var tupp=new Array(0);
var temp="";

// First, the frame 1 is checked for content. If there is content it will be a bitstring
// which can then just be read into the memory.

if(verify_frame_content(1)){
transfer(2);
bit_string=read(1,1000000,1,1);
}

// If frame 1 has no content, it means that no bitstring information are availible. It
// must then be calculated, either from a feature file, or from the base file for the
// cartesian coordinates for the atoms whithin the molecule.

else{


//---------------------

// If frame 2 has content there are a feature file stored for the molecule

   if(verify_frame_content(2)){
   transfer_and_mod(2, f_ex);
   over_all2(f_ex,angle_intervals,dist_intervals,groups, g_commands);
   bit_string=read(1,1000000,1,1);
   }
   else{

// If not, there are no direct bitstring information and no direct information availible.
// All this information must be calculated from scratch, first by calculating features,
// then by calculating a bitstring.

   //*******************

     if(verify_frame_content(3)){
     transfer(3);
     over_all1();                                                        // calculating features
     transfer_and_mod(100, f_ex);
if(save) saved=saved+"\n\n"+files[g_commands[3]]+"\n"+document.form1.text1.value;
     over_all2(f_ex,angle_intervals,dist_intervals,groups, g_commands);  // calculating bitstring
     bit_string=read(1,1000000,1,1);
     }
     else{
     alert("No files on: "+files[g_commands[3]]);      // In this case no file is availible at all.
     }
   //*******************
   }
//---------------------

}

// The bitstring is now hopefully stored in the singular variable bit_string. For comparation
// of different bitstrings, it must be transferred to a 1 dim vector as bitstrings[N] where
// -1 < N < number of molecules.

bitstrings[g_commands[3]]=bit_string;

g_commands[3]++;     // This is the molecule counter. Prepare for next loop and next molecule.

// ^^^^^^^^^^^^^^^^^marker^^^^^^^^^^^^^^^^^^
      if(g_commands[3]<files.length){
// ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

      frame_1="bitstrings/"+files[g_commands[3]]+".txt";         // files[N].txt is one of the files
      frame_2="featurecollection/"+files[g_commands[3]]+".txt";  // -1 < N < number of molecules.
      frame_3="basic_molecules/"+files[g_commands[3]]+".txt";
      load_frames(frame_1,frame_2,frame_3);

// Now all frames will load. Frame 1 & 2 can be empty, but then frame 3 has hopefully content.
// To accomplish the loading process, the program waits 100 ms before next "loop."
      window.setTimeout(function(){mega2(bitstrings,f_ligands,f_ex,angle_intervals,dist_intervals,groups,files,g_commands, saved);},300);

      }
// ^^^^^^^^^^^^^^^^^marker^^^^^^^^^^^^^^^^^^
      else{
// ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^

if(save){

  if(convert){
    for(n=0;n<f_ex.length;n++){
    tupp=saved.split(" "+f_ex[n][1]+"  ");
    saved=tupp.join(" "+f_ex[n][0]+"  ");
    }
  }

// The procedure if(texx) converts the output to a table in a TeX-document. 

  if(texx) saved=mega2tex(saved);

  saved="<html><pre>"+saved+"\n\n\n</pre></html>";
  parent.right.document.write(saved);
  saved="";


}

      mega3(bitstrings,files, f_ex);  // in this case the counter = the number of mulecules.
                                // Then it is time to compare all bitstrings.
      }

}

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