Need Help to Convert Pascal to C, C++ or Java

[Munna2002]

I'm currently doing a research project dealing with genetic genome matching across multiple DNA bases. I'm most familiar with Java, C, and C++. I was able to write some code to match DNA base strings against DNA base substrings across multiple genetic genomes. It works but it is very slow for large sets.

As a result, to improve on the running time, I decided to research on some substring matching algorithms and I found many, but none that incorporate wildcards in C++, C, or Java. However, I was able to find a similar problem dealing with a delete that creates wildcards in a ACM programming contest in 1996. http://www.educa.fmf.uni-lj.si/ACM/priprave99/2krog/DEL.htm

However, its solution is in Pascal and I am not familiar with Pascal. Can anyone translate this code from Pascal into C, C++, or Java? C# is also welcome as I know how to program in that too. I normally don't ask for help and can figure things out on my own but this is a special case.

Here is the Pascal code. If you've any questions, please post back to ask. Thanks.

{ACM NEERC, St.Petersburg, December 3, 1996}
{??襭?? ?????? "???? DEL"}

{$A-,B-,D+,E-,F+,G+,I+,L+,N+,O-,P-,Q-,R+,S+,T-,V+,X+,Y+}
{$M 16384,0,655360}

program DEL;
const maxN = 1000;
	  Blanks = [' ', #13, #10];
type TNameList = array [1..MaxN] of string [8];
	 TFileList = record names, exts: TNameList;
				 end;

var F: array [0..1] of TFileList;
	N: array [0..1] of integer;
	inf, ouf: TEXT;

function CreateMask (L: TNameList; N: integer): string;
var s: string;
	i, j: integer;
	same_char, one_end, all_end: boolean;
begin
   s := '';
   for i := 1 to 8 do
   begin
	  same_char := true; all_end := true; one_end := false;
	  for j := 1 to N do
		if length (L[j]) < i then one_end := true
		else if length (L [j]) >= i then
		begin
		   all_end := false;
		   if j > 1 then same_char := same_char and (copy (L[j-1],i,1) = L[j][i]);
		end;

	  if all_end {??? ??????, ????? N = 0} or one_end then
	  begin
		 if not all_end then s := s + '*';
		 CreateMask := s;
		 exit
	  end;

	  if same_char then s := s + L [j] [i] else s := s + '?';
   end;
   CreateMask := s;
end;

function Fit (s, mask: string): boolean;
var i: integer;
begin
   Fit := True;
   for i := 1 to length (mask) do
	 if mask [i] = '*' then exit
	 else if (i > length (s)) or ((mask [i] <> '?') and (mask [i] <> s [i]))
	 then begin
		Fit := false;
		exit
	 end;
   Fit := length (s) = length (mask);
end;

VAR Flag, FName, FExt, help: string;
	point, x, i: integer;
	Mask_Ext, Mask_Name: string;
	NoAnswer: boolean;

BEGIN
   assign (inf, 'INPUT.TXT');  reset (inf);
   assign (ouf, 'OUTPUT.TXT'); rewrite (ouf);

   while not eof (inf) do
   begin
	  readln (inf, help);
	  if help [1] = '+' then x := 1 else x := 0;
	  point := pos ('.', help);
	  if point = 0 then point := length (help)+1;
	  inc (N [x]);
	  F [x]. names [N[x]] := copy (help, 2, point-2);
	  F [x]. exts  [N[x]] := copy (help, point+1, 255);
   end;

   Mask_Name := CreateMask (F [0].names, N [0]);
   Mask_Ext   := CreateMask (F [0].exts, N [0]);

   NoAnswer := false;
   for i := 1 to N [1] do
	 NoAnswer := NoAnswer or (Fit (F [1] . names [i], Mask_name) and Fit (F [1] . exts [i], Mask_Ext));

   if NoAnswer then writeln (ouf, 'IMPOSSIBLE')
			   else writeln (ouf, 'DEL ' + Mask_Name + '.' + Mask_Ext);

   close (ouf);
   close (inf);
END.

Edited October 14, 2006 by Munna2002

[_kane81]

so java regular expressions is too slow?

[Munna2002]

No, it's not a question of java regular expressions being too slow. It's the problem of efficiently generating a proper regular expression pattern programmatically. I believe the Pascal code above does that: given list of filenames to be deleted and not deleted, it creates a regular expression pattern for deleted filenames and NOT non-deleted filenames that can be used by a delete command only once. If you see the link, it'll make more sense.

In my case, I am doing repeated calls on large strings that are computationally expensive because I don't have that regular expression pattern that are common across base strings that require those calls.

If I can somehow adapt this code to generate (which I why I am asking your help to translate Pascal into a language I'm more familiar with like C, C++, Java or C#), then it would result in less computationally command calls by requiring me to make only one or significantly less command calls with a given pattern matching string.

So can someone help translate please? I understand I can read a Pascal book but I am hoping that I can ask some fellow peers who are more knowledgeable than me to help out with the translation to save time.

[Munna2002]

Bump....can anyone help?