program dotmat(xbook,ybook,mlist,dotmatp,output);
(* dotmat: dot matricies of two books
      by Thomas Schneider

from module libraries: delman, delmods, prgmods
(modules correspond to program matrix)

*)

label 1; (* end of program *)

const
(* begin module version *)
version = 3.08; (* of dotmat 1994 sep 5 *)
(* end module version *)

(* begin module describe.dotmat *)
(*
name
      dotmat: dot matrices of two books

synopsis
      dotmat(xbook: in, ybook: in, mlist: out, dotmatp: in, output: out)

files
      xbook: a book from the delila system

      ybook: a book from the delila system

      mlist: a dot matrix for each sequence pair between the two books.
         the "dots" are printed as numbers:
            1 means gt base pair
            2 means at base pair
            3 means gc base pair
         xbook sequences are written down the page and those of
         ybook go across the page.
         if mlist is wider than your printer, use the split program.

      dotmatp: parameters to control the mlist.
         if dotmatp is empty, default values are used.  otherwise
         if the first line begins with a "g" then g-u pairs are printed.

      output: messages to the user

description
      dotmat produces a dot matrix for all complementary base pairs
      between all pairs of sequences in the two books.  because a list of
      helices is not made, the program is much more efficient for short
      minimum helices than is the pair of programs helix and matrix.

documentation
      delman.use.comparison
      J. V. Maizel, Jr. and R. P. Lenk PNAS 78: 7665-7609 (1981)

see also
      helix.p, matrix.p, split.p

author
      thomas d. schneider

bugs
      none known

*)
(* end module describe.dotmat *)

(* more constants: *)
      nodot = ':'; (* the character to print for background,
                      note: it must not blank, so that the user can
                      align the helices by the numbers. *)
      prime = ''''; (* single quote *)
      pagelength = 48; (* lines printed of dotmat on one page in mlist *)

(* begin module book.const *)
(* constants needed for book manipulations *)

      dnamax = 3000;  (* length of dna arrays *)
      namelength = 20; (* maximum key name length *)
      linelength = 80; (* maximum line readable in book *)

(* end module book.const version = 'delmod 6.54 86 nov 12 tds/gds' *)

type
(* begin module book.type *)
(* types needed for book manipulations *)

      chset = set of 'a'..'z';

      (* types defined in book definition *)

      alpha = packed array[1..namelength] of char; (* this is not alfa *)

      (* name is a left justified string with blanks following the
         characters *)
      name = record
         letters: alpha;
         length: 0..namelength (* zero means an unspecified structure *)
      end;

      lineptr = ^line;
      line = record (* a line of characters *)
         letters: packed array [1..linelength] of char;
         length: 0..linelength;
         next: lineptr
      end;

      direction = (plus, minus, dircomplement, dirhomologous);
      configuration = (linear, circular);
      state = (on, off);


      header = record (* header of key *)
         keynam: name; (* key name of structure *)
         fulnam: lineptr; (* full name of structure *)
         note:   lineptr (* note key *)
      end;


      (* base types *)
      base = (a,c,g,t);
      dnaptr = ^dnastring;
      dnarange = 0..dnamax;
      seq = packed array[1..dnamax] of base;
      dnastring = record
         part: seq;
         length: dnarange;
         next: dnaptr
      end;


      orgkey = record (* organism key *)
         hea: header;
         mapunit: lineptr (* genetic map units *)
      end;

      chrkey = record (* chromosome key *)
         hea: header;
         mapbeg: real; (* number of genetic map beginning *)
         mapend: real (* number of genetic map ending *)
      end;

      pieceptr = ^piece;
      piekey = record (* piece key *)
         hea: header;
         mapbeg: real; (* genetic map beginning *)
         coocon: configuration; (* configruation (circular/linear) *)
         coodir: direction; (* direction (+/-) relative to genetic map *)
         coobeg: integer; (* beginning nucleotide *)
         cooend: integer; (* ending nucleotide *)
         piecon: configuration; (* configruation (circular/linear) *)
         piedir: direction; (* direction (+/-) relative to coordinates *)
         piebeg: integer; (* beginning nucleotide *)
         pieend: integer; (* ending nucleotide *)
      end;


      piece = record
         key: piekey;
         dna: dnaptr
      end;

      reference = record
         pienam : name;  (* name of piece referred to *)
         mapbeg : real;  (* genetic map beginning *)
         refdir : direction;  (* direction relative to coordinates *)
         refbeg : integer;  (* beginning nucleotide *)
         refend : integer;  (* ending nucleotide *)
      end;

      genkey = record  (* gene key *)
         hea : header;
         ref : reference;
      end;

      trakey = record  (* transcript key *)
         hea : header;
         ref : reference;
      end;

      markerptr = ^marker;
      markey = record (* marker key *)
         hea : header;
         ref : reference;
         sta : state;
         phenotype : lineptr;
         next : markerptr;
      end;

      marker = record
         key : markey;
         dna : dnaptr;
      end;

(* end module book.type version = 'delmod 6.54 86 nov 12 tds/gds' *)

var
      xbook, (* one book *)
      ybook, (* the other book *)
      mlist, (* the dot matricies *)
      dotmatp: (* parameters *)
         text;

      xseq, yseq: pieceptr; (* the sequences from the books *)
      xnumber, ynumber: integer; (* the numbers of the sequences *)
      guallowed: boolean; (* true means gu pairs are allowed *)

      xlength, ylength: integer; (* of the sequences *)


(* begin module book.var *)
(* ************************************************************************ *)
(* global variables needed for book manipulations *)

      (* free storage: *)
      freeline: lineptr; (* unused lines *)
      freedna: dnaptr; (* unused dnas *)

      readnumber: boolean; (* whether to read a number from the notes, or
                              to read in the notes *)
      number: integer; (* the number of the item just read *)
      numbered: boolean; (* true when the item just read is numbered *)
      skipunnum: boolean; (* a control variable to allow skipping of
                             un-numbered items in the book *)

(* ************************************************************************ *)
(* end module book.var version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module halt *)
procedure halt;
(* stop the program.  the procedure performs a goto to the end of the
   program.  you must have a label:
      label 1;
   declared, and also the end of the program must have this label:
      1: end.
   examples are in the module libraries.
   this is the only goto in the delila system. *)
begin
      writeln(output,' program halt.');
      goto 1
end;
(* end module halt version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module package.getpiece *)
(* ************************************************************************ *)
(* begin module package.brpiece *)
(* ************************************************************************ *)
(* begin module book.basis *)
(* procedures needed for book manipulations *)

(* get procedures should be used for all linked lists of records *)

procedure getline(var l: lineptr);
(* obtain a line from the free line list or by making a new one *)
begin
      if freeline<>nil
         then begin
            l:=freeline;
            freeline:=freeline^.next
         end
         else new(l);
      l^.length:=0;
      l^.next:=nil
end;

procedure getdna(var l: dnaptr);
begin
      if freedna<>nil
         then begin
            l:=freedna;
            freedna:=freedna^.next
         end
         else new(l);
      l^.length:=0;
      l^.next:=nil
end;

(* clear procedures should be called each time the records are no longer needed
         failure to do this may result in a stack overflow. *)

procedure clearline(var l: lineptr);
(* return a line to the free line list *)
var   lptr: lineptr;
begin
      if l<>nil then begin
         lptr:=l;
         l:=l^.next;
         lptr^.next:=freeline;
         freeline:=lptr
      end
end;

procedure cleardna(var l: dnaptr);
var   lptr: dnaptr;
begin
      if l<>nil then begin
         lptr:=l;
         l:=l^.next;
         lptr^.next:=freedna;
         freedna:=lptr
      end
end;

procedure clearheader(var h: header);
(* clear the header h (remove lines to free storage) *)
begin
      with h do begin
         clearline(fulnam);
         while note<>nil do clearline(note)
      end
end;

procedure clearpiece(var p: pieceptr);
(* clear the dna of the piece *)
begin
      while p^.dna<>nil do cleardna(p^.dna);
      clearheader(p^.key.hea)
end;

function chartobase(ch:char):base;
(* convert a character into a base *)
begin
      case ch of
         'a': chartobase:=a;
         'c': chartobase:=c;
         'g': chartobase:=g;
         't': chartobase:=t
      end
end;

function basetochar(ba:base):char;
(* convert a base into a character *)
begin
      case ba of
         a: basetochar:='a';
         c: basetochar:='c';
         g: basetochar:='g';
         t: basetochar:='t';
      end
end;

function complement(ba:base):base;
(* take the complement of ba *)
begin
      case ba of
         a: complement:=t;
         c: complement:=g;
         g: complement:=c;
         t: complement:=a;
      end
end;

function pietoint(p: integer; pie: pieceptr): integer;
(* p is a coordinate on the piece.
   we want to transform p into a number
   from 1 to n: an internal coordinate system for
   easy manipulation of piece coordinates *)
var   i: integer; (* an intermediate value *)
begin
      with pie^.key do begin
         case piedir of
            plus:  if p>=piebeg
                   then i:=p-piebeg+1
                   else i:=(p-coobeg)+(cooend-piebeg)+2;
            minus: if p<=piebeg
                   then i:=piebeg-p+1
                   else i:=(cooend-p)+(piebeg-coobeg)+2
         end;
         pietoint:=i
      end
end;

function inttopie(i: integer; pie: pieceptr):integer;
(* i is in the range 1 to some maximum.  it is an internal coordinate
   system for the program.  we want to do a
   coordinate transformation to obtain
   a value in the range of the piece called pie:
   i=1 corresponds to piebeg and
   i=its maximum corresponds to pieend *)
var   p: integer; (* an intermediate value *)
begin
      with pie^.key do begin
         case piedir of
            plus: begin
               p:=piebeg+(i-1);
               if p>cooend
                  then if coocon=circular
                     then p:=p-(cooend-coobeg+1)
            end;
            minus: begin
               p:=piebeg-(i-1);
               if p<coobeg
                  then if coocon=circular
                     then p:=p+(cooend-coobeg+1)
            end
         end;
         inttopie:=p
      end
end;

function piecelength(pie: pieceptr): integer;
(* return the length of the dna in pie *)
begin
      piecelength:=pietoint(pie^.key.pieend,pie)
end;

(* end module book.basis version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.getto *)
function getto(var thefile: text; ch: chset): char;
(* search the file for a character in the first line which is a
   member of the set ch. *)
var achar: char;
begin
      achar:=' ';
      while (not(achar in ch)) and (not eof(thefile))
         do readln(thefile,achar);
      if (achar in ch) then getto:=achar
                       else getto:=' '
end;
(* end module book.getto version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.skipstar *)
procedure skipstar(var thefile:text);
(* skip start of line (or star = '*'). *)
begin (* skipstar *)
      if thefile^ <> '*' then begin
         writeln(output,' procedure skipstar: bad book');
         writeln(output,' "*" expected as first character on the line, but "',
                        thefile^,'" was found');
         halt
      end;
      get(thefile); (* skip the star *)

      if thefile^ <> ' ' then begin
         writeln(output,' procedure skipstar: bad book');
         writeln(output,' "* " expected on a line but "*',
                        thefile^,'" was found');
         halt
      end;
      get(thefile) (* skip the blank *)
end; (* skipstar *)
(* end module book.skipstar version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brreanum *)
procedure brreanum(var thefile: text; var reanum: real);
(* read a real number from the file *)
begin
      skipstar(thefile);
      readln(thefile,reanum);
end;
(* end module book.brreanum version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brnumber *)
procedure brnumber(var thefile: text; var num: integer);
(* read a number from the file *)
begin
      skipstar(thefile);
      readln(thefile,num)
end;
(* end module book.brnumber version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brname *)
procedure brname(var thefile: text; var nam: name);
(* read a name from the file *)
var   i: integer; (* an index to the name *)
      c: char; (* a character read *)
begin (* brname *)
      skipstar(thefile);
      with nam do begin
         length:=0;
         repeat
            length:=succ(length);
            read(thefile,c);
            letters[length] := c
         until (eoln(thefile)) or
               (length>=namelength) or
               (letters[length]=' ');
         if letters[length]=' ' then length:=length-1;
         if length<namelength
            then for i:=length+1 to namelength do letters[i]:=' '
      end;
      readln(thefile)
end; (* brname *)
(* end module book.brname version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brline *)
procedure brline(var thefile: text; var l: lineptr);
(* read a line from the file *)
var
      i,j: integer;
      acharacter: char;
begin
      skipstar(thefile);
      i:=0;
      while (not eoln(thefile)) do begin
         i:=succ(i);
         read(thefile,acharacter);
         l^.letters[i]:=acharacter
      end;
      if i<l^.length then for j:=i+1 to l^.length do l^.letters[j]:=' ';
      l^.length:=i;
      l^.next:=nil;
      readln(thefile)
end;
(* end module book.brline version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brdirect *)
procedure brdirect(var thefile: text; var direct: direction);
(* read a direction *)
var   ch: char;
begin
      skipstar(thefile);
      readln(thefile,ch);
      if ch='+' then direct:=plus
                else direct:=minus
end;
(* end module book.brdirect version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brconfig *)
procedure brconfig(var thefile: text; var config: configuration);
(* read a configuration *)
var   ch: char;
begin
      skipstar(thefile);
      readln(thefile,ch);
      if ch='l' then config:=linear
                else config:=circular
end;
(* end module book.brconfig version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brnotenumber *)
procedure brnotenumber(var thefile: text; var note: lineptr);
(* book note reading to obtain the number of the object.
the procedure returns the value of the number as a global.
(this is not such a good practice, but we are stuck with it for now.) *)
begin (* brnotenumber *)
      note:=nil;
      numbered := false;
      number := 0; (* force number to zero if there
         is no number at all *)
      (* the next character is n or * depending on whether there are notes *)
      if thefile^ = 'n' then begin
         readln(thefile);
         if thefile^ <> 'n' then begin
            skipstar(thefile);
            if not eoln(thefile) then begin
               if thefile^ = '#' then begin
                  numbered := true;
                  get(thefile); (* move past the number symbol *)
                  read(thefile,number);
               end
            end;
            repeat
               readln(thefile)
            until thefile^ = 'n';
            readln(thefile)
         end
         else readln(thefile)
      end
end; (* brnotenumber *)
(* end module book.brnotenumber version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brnote *)
procedure brnote(var thefile: text; var note: lineptr);
(* read note key *)
var
      newnote: lineptr; (* the new note *)
      previousnote: lineptr; (* the last line of the notes *)
begin (* brnote *)
      note:=nil;
      if thefile^ = 'n' then begin (* enter note *)
         readln(thefile);
         if thefile^ <> 'n' then begin (* abort null note (n/n) *)
            getline(note);
            newnote:=note;
            while thefile^ <> 'n' do begin (* wait until end of note *)
               brline(thefile,newnote);
               previousnote:=newnote;
               (* get next note *)
               getline(newnote^.next);
               newnote:=newnote^.next;
            end;
            (* last note was not used, so: *)
            clearline(newnote);
            previousnote^.next:=nil;
            readln(thefile)
         end
         else readln(thefile)
      end
end; (* brnote *)
(* end module book.brnote version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brheader *)
procedure brheader(var thefile: text; var hea: header);
(* read the header of a key. *)
begin
      with hea do begin
         (* read key name *)
         brname(thefile,keynam);

         (* read full name *)
         getline(fulnam);
         brline(thefile,fulnam);

         (* read note key *)
         if readnumber then brnotenumber(thefile,note)
                       else brnote(thefile,note)
      end
end;
(* end module book.brheader version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brpiekey *)
procedure brpiekey(var thefile: text; var pie: piekey);
(* read piece key *)
begin
      with pie do begin
         brheader(thefile,hea);
         brreanum(thefile,mapbeg);
         brconfig(thefile,coocon);
         brdirect(thefile,coodir);
         brnumber(thefile,coobeg);
         brnumber(thefile,cooend);
         brconfig(thefile,piecon);
         brdirect(thefile,piedir);
         brnumber(thefile,piebeg);
         brnumber(thefile,pieend);
      end
end;
(* end module book.brpiekey version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brdna *)
procedure brdna(var thefile: text; var dna: dnaptr);
(* read in dna from thefile *)
(* note: if the dna were circularized, by linking the last dnastring
to the first, then the cleardna routine could not clear properly,
and would loop forever... there is no reason to do that, since a simple
mod function will allow one to access the circle. *)
var
      ch: char;
      workdna: dnaptr;
begin
      getdna(dna);
      workdna:=dna;
      ch:=getto(thefile,['d']);
      read(thefile,ch); (* skipstar *)
      while (ch = '*') do
      begin
         read(thefile,ch); (* skip blank *)
         repeat
            read(thefile,ch);
            if ch in ['a','c','g','t'] then begin
               if workdna^.length=dnamax then begin
                  getdna(workdna^.next);
                  workdna:=workdna^.next
               end;
               workdna^.length:=succ(workdna^.length);
               workdna^.part[workdna^.length]:=chartobase(ch)
            end
         until eoln(thefile);
         readln(thefile); (* go to next line *)
         read(thefile,ch); (* ch is either '*' or 'd' *)
      end;
      readln(thefile)
end;
(* end module book.brdna version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brpiece *)
procedure brpiece(var thefile: text; var pie: pieceptr);
(* read in a piece *)
begin
      brpiekey(thefile,pie^.key);
      if numbered or (not skipunnum)
         then brdna(thefile,pie^.dna)
end;
(* end module book.brpiece version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.brinit *)
procedure brinit(var book: text);
(* check that the book is ok to read, and
   set up the global variables for br routines *)
begin (* brinit *)
      (* halt if the book is bad (first word is 'halt') or the first
         character is not * *)
      reset(book);
      if not eof(book) then begin
         (* check for the date line *)
         if book^ <> '*' then begin
            if book^ <> 'h'
            then writeln(output, ' this is not the first line of a book:')
            else writeln(output, ' bad book:');
            write(output, ' ');

            while not (eoln(book) or eof(book)) do begin
               write(output, book^);
               get(book)
            end;
            writeln(output);
            halt
         end
      end
      else begin
         writeln(output, ' book is empty');
         halt
      end;

      (* initialize free storage *)
      freeline:=nil;
      freedna:=nil;

      readnumber:=true; (* usually we read in numbers for items *)
      number:=0; (* arbitrary value *)
      numbered:=false; (* the piece has no number (none yet read in) *)
      skipunnum:=false;
end; (* brinit *)
(* end module book.brinit version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* ************************************************************************ *)
(* end module package.brpiece version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.getpiece *)
procedure getpiece(var thefile: text; var pie: pieceptr);
(* move to and read in the next piece in the book *)
var   ch: char;
begin
      ch:=getto(thefile,['p']); (* get to the next p(iece) in the book *)
      if ch<>' ' then begin
         brpiece(thefile,pie);
         ch:=getto(thefile,['p']); (* read past closing p *)
      end
end;
(* end module book.getpiece version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* ************************************************************************ *)
(* end module package.getpiece version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module book.getbase *)
function getbase(position: integer; pie: pieceptr):base;
(* get a base from the nth position (internal coordinates) of the
   piece.  no protection is made against positions outside the piece *)
var
      workdna: dnaptr;
      p: integer; (* the last base of the dna part *)
begin
      workdna:=pie^.dna;
      p:=dnamax;
      while position>p do begin
         p:=p+dnamax;
         workdna:=workdna^.next
      end;
      getbase:=workdna^.part[position-(p-dnamax)]
end;
(* end module book.getbase version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module basepair *)
function basepair(xseq,yseq: pieceptr; x,y: integer; guallowed: boolean)
                 :boolean;
(* does xseq basepair to yseq at x to y?
allow gu pair if guallowed is true.
a series of if-then statements are used for speed. *)
var
      bx,by: base; (* bases in the sequences *)
begin
      bx := getbase(x,xseq);
      by := getbase(y,yseq);

      if bx = complement(by)
      then basepair := true
      else if guallowed
         then if (bx=g) and (by=t)
            then basepair := true
            else if (bx=t) and (by=g)
               then basepair := true
               else basepair := false
         else basepair := false
end;
(* end module basepair version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module copyaline *)
procedure copyaline(var fin, fout: text);
(* copy a line from file fin to file fout *)
begin (* copyaline *)
      while not eoln(fin) do begin
         fout^ := fin^;
         put(fout);
         get(fin)
      end;
      readln(fin);
      writeln(fout);
end; (* copyaline *)
(* end module copyaline version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module unlimitln *)
procedure unlimitln(var afile: text);
(* this procedure removes a stupid system dependent limit on the number of
lines that one can write to a file.  you may remove it from the code if
your system does not want or need this.  suggested method: place comments
around the contents of the procedure. *)
begin
(*      linelimit(afile, maxint); (@ set 'infinite' lines allowed for afile *)
end;
(* end module unlimitln version = 'delmod 6.54 86 nov 12 tds/gds' *)

(* begin module package.numbar *)
(* ************************************************************************ *)
(* begin module numberdigit *)
function numberdigit(number, logplace:integer): char;
(* return the digit at the place value ('logplace') position of number.
example:
      numberdigit(13625, 3) = 3
      numberdigit(13625, 4) = 1
*)
var
      place: integer; (* the exponent of logplace *)
      count: integer; (* used to make place *)
      absolute: integer; (* the absolute value of number *)
      acharacter: char; (* the character to be returned *)
procedure digit;
(* extract a digit at the place position *)
var
      tenplace: integer; (* ten times place *)
      z: integer; (* an intermediate value *)
      d: integer; (* the digit extracted *)
begin (* digit *)
      tenplace:=10*place;
      z:=absolute-((absolute div tenplace)*tenplace);
      if place = 1
         then d:=z
         else d:= z div place;
      case d of
         0: acharacter:='0';
         1: acharacter:='1';
         2: acharacter:='2';
         3: acharacter:='3';
         4: acharacter:='4';
         5: acharacter:='5';
         6: acharacter:='6';
         7: acharacter:='7';
         8: acharacter:='8';
         9: acharacter:='9';
      end
end; (* digit *)
procedure sign;
(* put a negative sign out or a positive sign *)
begin (* sign *)
      if number <0 then acharacter:='-'
                   else acharacter:='+'
end; (* sign *)
begin (* numberdigit *)
      place:=1;
      for count:=1 to logplace do place:=10*place;

      if number=0 then begin
         if place=1 then acharacter:='0'
                    else acharacter:=' '
      end
      else begin
         absolute:=abs(number);
         if absolute < (place div 10)
            then acharacter:=' '
            else if absolute >= place
                    then digit
                    else sign
      end;
      numberdigit:=acharacter
end; (* numberdigit *)
(* end module numberdigit version = 'prgmod 3.96  85 mar 18 tds'; *)

(* begin module numbersize *)
function numbersize(n: integer):integer;
(* calculate amount of space to be reserved for the integer n *)
const ln10 = 2.30259; (* natural log of 10 - for conversion to log base 10 *)
      epsilon = 0.00001; (* a small number to correct log base 10 errors *)
begin (* numbersize *)
      if n = 0
         then numbersize:=1
         else numbersize:=trunc(ln(abs(n))/ln10 + epsilon) + 2;
(* the epsilon assures that we do not lose a place due to
   roundoff.  eg, sometimes log base 10 of 10 would be
   0.9999 instead of 1, and we would not do it right...
   note: this will fail for very large numbers on the order of 1/epsilon. *)
(* the 2 is for the sign and last digit *)
end; (* numbersize *)
(* end module numbersize version = 'prgmod 3.96  85 mar 18 tds'; *)

(* begin module numberbar *)
procedure numberbar(var afile: text; spaces, firstnumber, lastnumber: integer;
                    var linesused: integer);
(* write a bar of numbers to a file, with several spaces before.
   the number of lines used is returned *)
var
      logplace: integer; (* the log of the digit being looked at *)
      spacecount: integer; (* count of spaces *)
      number: integer; (* the current number being written *)
begin
      if abs(firstnumber) > abs(lastnumber)
         then linesused:= numbersize(firstnumber)
         else linesused:= numbersize(lastnumber);

      for logplace:=linesused-1 downto 0 do begin
         for spacecount:=1 to spaces do write(afile,' ');
         for number:=firstnumber to lastnumber
            do write(afile,numberdigit(number,logplace));
         writeln(afile)
      end
end;
(* end module numberbar version = 'prgmod 3.96  85 mar 18 tds'; *)
(* ************************************************************************ *)
(* end module package.numbar version = 'prgmod 3.96  85 mar 18 tds'; *)

procedure initialize;
(* set up all the variables *)
begin
      writeln(output,' dotmat ',version:4:2);
      brinit(xbook);
      brinit(ybook);
      rewrite(mlist);
      unlimitln(mlist);

      new(xseq);
      new(yseq);

      (* read parameters *)
      reset(dotmatp);
      if eof(dotmatp)
      then guallowed:=false
      else if dotmatp^='g' then guallowed := true
                           else guallowed := false;

      (* put header in mlist *)
      writeln(mlist,' dotmat ',version:4:2,' from:');
      write(mlist,' ');
      copyaline(xbook,mlist);
      write(mlist,' ');
      copyaline(ybook,mlist);

      writeln(mlist);
      write(mlist,' gu pairs are');
      if not guallowed then write(mlist,' not');
      writeln(mlist,' allowed.');

      writeln(mlist);
      writeln(mlist,' symbols used:');
      writeln(mlist,' ',nodot,' no complementary bases between these points');
      writeln(mlist,' 1 gt base pair');
      writeln(mlist,' 2 at base pair');
      writeln(mlist,' 3 gc base pair');
end;

(****************************************************************************)

(* begin module dotmat.piecebar *)
procedure piecebar(var afile: text;
                       spaces: integer;
                       pie: pieceptr;
                       firstnumber,lastnumber: integer;
                   var linesused: integer);
(* write a bar of numbers of the piece pie to a file,
with several spaces before.  the number of lines used is returned.
based on procedure numbar.  external procedures required:
  inttopie
  numbersize
  numberdigit
*)
var
      logpower: integer; (* the log of the digit being looked at *)
      spacecount: integer; (* count of spaces *)
      number: integer; (* the current number being written *)
      numbers: file of integer; (* a file for storing all the piece numbers *)
      width: integer; (* the lines used by one number *)
      index: integer; (* to pie *)
begin
      (* calculate lines used and fill up the numbers file *)
      linesused:=0;
      rewrite(numbers);
      for index:=firstnumber to lastnumber do begin
         number:=inttopie(index,pie);
         write(numbers,number);
         width:=numbersize(number);
         if width > linesused then linesused:=width
      end;

      for logpower:=linesused-1 downto 0 do begin
         for spacecount:=1 to spaces do write(afile,' ');
         reset(numbers);
         while not eof(numbers) do begin
            read(numbers,number);
            write(afile,numberdigit(number,logpower))
         end;
         writeln(afile)
      end
end;
(* end module dotmat.piecebar *)

(* begin module dotmat.makedna *)
procedure makedna(var afile: text;
                      spaces: integer;
                      pie: pieceptr;
                      firstnumber, lastnumber: integer);
(* write a line of dna to a file, preceeded by several spaces *)
var
      spacecount: integer; (* count spaces *)
      index: integer; (* to pie *)
begin
      for spacecount:=1 to spaces - 3 do write(afile,' ');
      write(afile,'5',prime,' ');
      for index:=firstnumber to lastnumber
         do write(afile,basetochar(getbase(index,pie)));
      writeln(afile,' 3',prime)
end;
(* end module dotmat.makedna *)

(* begin module dotmat.makepageheader *)
procedure makepageheader(var pageheader: text);
var
      lines: integer; (* dummy until lines are counted by matrix *)
begin
      rewrite(pageheader);
      page(pageheader);
      writeln(pageheader,' matrix, ',
         ' x down: '  ,xnumber:1,' ',xseq^.key.hea.keynam.letters,
         ' y across: ',ynumber:1,' ',yseq^.key.hea.keynam.letters);
      writeln(pageheader);
      piecebar(pageheader,10,yseq,1,ylength,lines);
      makedna(pageheader,10,yseq,1,ylength);
      writeln(pageheader,'        5',prime);   (* 8 spaces *)
end;
(* end module dotmat.makepageheader *)

(* begin module dotmat.printpageheader *)
procedure printpageheader(var pageheader: text);
(* print the page header *)
begin
      reset(pageheader);
      while not eof(pageheader) do begin
         while not eoln(pageheader) do begin
            write(mlist,pageheader^);
            get(pageheader)
         end;
         readln(pageheader);
         writeln(mlist)
      end
end;
(* end module dotmat.printpageheader *)


procedure printarray;
(* print out the  array to mlist *)
var
      pageheader: text; (* the header for pages of mlist *)
      x, y: integer; (* a point in the matrix *)
      bx, by: base; (* bases at x and y of xseq and yseq respecitvely *)
begin (* print  array *)
      makepageheader(pageheader);
      for x:=1 to xlength do begin
         if ((x mod pagelength) = 0) or (x = 1)
            then printpageheader(pageheader);
         bx := getbase(x, xseq);
         write(mlist,' ',inttopie(x,xseq):6,' ',basetochar(bx),' ');
         for y:=1 to ylength
            do if basepair(xseq,yseq,x,y,guallowed)
               then begin (* make a number at the place *)
                  by := getbase(y, yseq);
                  if bx = complement(by)
                  then case bx of
                     a: write(mlist,'2');
                     c: write(mlist,'3');
                     g: write(mlist,'3');
                     t: write(mlist,'2');
                  end
                  else write(mlist,'1') (* for gu pairs *)
               end
               else write(mlist,nodot);
         writeln(mlist)
      end;
      writeln(mlist,'        3',prime);   (* 8 spaces *)
end;

procedure printdotmat;
(* print the dotmat for xseq and yseq *)
begin
      printarray
end;

begin
      initialize;
      while not eof(xbook) do begin
         getpiece(xbook,xseq);
         xnumber:=number;
         xlength:=piecelength(xseq);
         if not eof(xbook) then begin
            reset(ybook);
            while not eof(ybook) do begin
               getpiece(ybook,yseq);
               ynumber:=number;
               ylength:=piecelength(yseq);
               if not eof(ybook) then begin
                  printdotmat;
                  clearpiece(yseq)
               end
            end;
            clearpiece(xseq)
         end
      end;
1: end. (* of dotmat *)