printtext := proc(msg);
  width := Set(screenwidth=80);  
  Set(screenwidth=width);
  if msg <> 0  then 
    l := length(msg);
    times:=round(l/width+0.5);
    for i to times-1 do
        if length(msg)>width*(i-1)+1 then
          printf('%a',  msg[width*(i-1)+1 .. min(width*i, length(msg))] );
        fi;
    od;
    if length(msg)>width*(i-1)+1 then
      printf('%a',  msg[width*(i-1)+1 .. min(width*i, length(msg))] );
    fi;
  fi;
end:

printall := proc(msg);
  width := Set(screenwidth=80);  
  Set(screenwidth=width);
  if msg <> 0  then 
    l := length(msg);
    times:=round(l/width+0.5);
    for i to times-1 do
        if length(msg)>width*(i-1)+1 then
          printf('%a',  msg[width*(i-1)+1 .. min(width*i, length(msg))] );
        fi;
    od;
    if length(msg)>width*(i-1)+1 then
      printf('%a',  msg[width*(i-1)+1 .. min(width*i, length(msg))] );
    fi;
  fi;
end:


CreateDB := proc(filename, title);
 OpenWriting (filename);
 printf('<DBDESCR>Database for %a</DBDESCR>\n', title);
 OpenWriting(terminal); 
 CallSystem ('touch  '.filename.'.tree');
end: 
  
WriteDomainDB := proc(dom: Domain, filename);
  OpenAppending (filename);
  printf('<E>');  
  printf('<DE>%a</DE>', dom['info']);
  seq := dom['seq'];
  printf('<SEQ>');
  printall(seq);
  printf('</SEQ>'); 
  msa := dom['msa']:
  if msa <> 0 then
    WriteMsa(msa);
  else print('0');
  fi;  
  printf('<ID>');
  printf('%a', dom['ID']);
  printf('</ID>'); 
  printf('<LEFT>');
  printf('%a', dom['LEFT']);
  printf('</LEFT>'); 
  printf('<RIGHT>');
  printf('%a', dom['RIGHT']);
  printf('</RIGHT>'); 
  printf('<ENT>');
  printf('%a', dom['entries']);
  printf('</ENT>'); 
  printf('<HIST>');
  printf('%a', dom['hist']);
  printf('</HIST>'); 
  printf('</E>');
  OpenWriting(terminal);
end:

CreateSeqDB := proc(msa: MultiAlign, filename: string);
  CreateDB(filename, msa['title']); 
  seq := msa['seq'];
  ref := msa['ref'];
  OpenAppending(filename);
  for i to length(seq) do
     printf('<E>');
     if ref[i] <> 0 then
      printf('<ID>');
     if type(ref[i]) = string then printtext(ref[i]);
     else print(ref[i]); fi;
    else print('0');
    fi; 
    printf('</ID>'); 
    
    if seq[i] <> 0 then
      printf('<SEQ>');
      printtext(seq[i]);
    else print('0');
    fi; 
    printf('</SEQ>'); 
    printf('<DE>No description</DE>'); 
    printf('</E>');
  od;
  OpenWriting(terminal);
end:

WriteMsa := proc(msa: MultiAlign);
  printf('<REF>');
  ref := msa['ref'];
  if ref <> 0 then
    printf('[\n');
    for j to length(ref)-1 do
      printf('''');printtext(ref[j]);printf('''');
      printf(',');
    od;
    printf('''');printtext(ref[j]);printf('''');
    printf(']\n');
  else print('0');
  fi; 
  printf('</REF>'); 
  printf('<MSA>');
  seq := msa['ma'];
  if seq <> 0 then
    printf('[\n');
    for j to length(seq)-1 do
      printf('''');printtext(seq[j]);printf('''');
      printf(',');
    od;
    printf('''');printtext(seq[j]);printf('''');
    printf(']\n');
  else print('0');
  fi;  
  printf('</MSA>');
  printf('<TREE>');
  tree := msa['tree'];
  if tree <> 0 then print(tree);
  else print('0');
  fi;  
  printf('</TREE>');
end:

WriteMSADB := proc(msa: MultiAlign, filename);
  OpenAppending (filename);
  printf('<E>');  
  printf('<DE>%a</DE>', msa['title']);
  WriteMsa(msa);
  printf('</E>');
  OpenWriting(terminal);
end:

RemoveGaps := proc(ma: array(string));
  n := length(ma);
  manew := CreateArray(1..n);
  for i to n do 
    seq := '';
    for j to length(ma[i]) do 
      if SearchString( ma[i,j], 'ACDEFGHIKLMNPQRSTVWYX_' ) >= 0 then
	seq := seq.ma[i,j];
      fi;
    od;
    manew[i] := copy(seq);
  od;
  return(manew);
end:

Parse := proc(what: string)
global tmp;
  nr := trunc(Rand()*10000);
  dir := '/tmp/';
  file := 'parse'.nr.'.tmp';
  OpenWriting(dir.file);
  printtext(what);lprint(';');
  lprint();
  OpenWriting(terminal);
  ReadProgram(dir.file); 
  CallSystem ('rm -f '.dir.file);
end:

ReadDomain := proc(ent: Entry);
  dom := Domain();  
  dom['id'] := atoi(GetEntryInfo(ent, 'ID')[2]);
  dom['left'] := atoi(GetEntryInfo(ent, 'LEFT')[2]);
  dom['right'] := atoi(GetEntryInfo(ent, 'RIGHT')[2]);
  dom['seq'] := GetEntryInfo(ent, 'SEQ')[2];
  dom['info'] := GetEntryInfo(ent, 'DE')[2];
  temp := GetEntryInfo(ent, 'HIST')[2];  
  temp := 'tmp := '.temp.';';
  Parse(temp);
  dom['hist'] := tmp; 
  temp := GetEntryInfo(ent, 'ENT')[2];  
  temp := 'tmp := '.temp.';';
  Parse(temp);
  dom['Entry'] := tmp;
  if [GetEntryInfo(ent, 'MSA')] <> [] then
    dom['msa'] := ReadMSA(ent);
  fi;
  return(dom);
end:

ReadMSA := proc(ent: Entry);
  temp := GetEntryInfo(ent, 'MSA')[2];
  temp := 'tmp := '.temp.';';
  Parse(temp);
 
#  ma := RemoveGaps(tmp);
  ma := tmp;
  
  temp := GetEntryInfo(ent, 'REF')[2];  
  temp := 'tmp := '.temp.';';
  Parse(temp);
  ref := tmp;
  
  seq := CleanSeq(ma);

  msa := MultiAlign(seq, ref, ma);
  
  temp := GetEntryInfo(ent, 'TREE')[2];
  temp := 'tmp := '.temp.';';
  Parse(temp);
  
  msa['tree'] := tmp;
return(msa);
end:

#test := proc();
#  filename := '~/test.db';
#  CreateDB(filename, 'test DB');
#  WriteDomainDB(domains[1], filename);
#  db := ReadDb(filename);
#  ent := Entry(1);
#  d := ReadDomain(ent);
#end: