This cannot be done using some cleaver regular expression (regular expressions can not "count parenthesis"). Your best option is to use some parser generator and parse the string into an abstract syntax tree (AST for short).
Have a look at JFlex/JavaCUP for instance.
As it turns out, the CUP manual actually has an example covering your situation:
// CUP specification for a simple expression evaluator (w/ actions)
import java_cup.runtime.*;
/* Preliminaries to set up and use the scanner. */
init with {: scanner.init(); :};
scan with {: return scanner.next_token(); :};
/* Terminals (tokens returned by the scanner). */
terminal SEMI, PLUS, MINUS, TIMES, DIVIDE, MOD;
terminal UMINUS, LPAREN, RPAREN;
terminal Integer NUMBER;
/* Non-terminals */
non terminal expr_list, expr_part;
non terminal Integer expr;
/* Precedences */
precedence left PLUS, MINUS;
precedence left TIMES, DIVIDE, MOD;
precedence left UMINUS;
/* The grammar */
expr_list ::= expr_list expr_part
|
expr_part;
expr_part ::= expr:e
{: System.out.println("= " + e); :}
SEMI
;
expr ::= expr:e1 PLUS expr:e2
{: RESULT = new Integer(e1.intValue() + e2.intValue()); :}
|
expr:e1 MINUS expr:e2
{: RESULT = new Integer(e1.intValue() - e2.intValue()); :}
|
expr:e1 TIMES expr:e2
{: RESULT = new Integer(e1.intValue() * e2.intValue()); :}
|
expr:e1 DIVIDE expr:e2
{: RESULT = new Integer(e1.intValue() / e2.intValue()); :}
|
expr:e1 MOD expr:e2
{: RESULT = new Integer(e1.intValue() % e2.intValue()); :}
|
NUMBER:n
{: RESULT = n; :}
|
MINUS expr:e
{: RESULT = new Integer(0 - e.intValue()); :}
%prec UMINUS
|
LPAREN expr:e RPAREN
{: RESULT = e; :}
;