Executing an operator in an RPN evaluator
As @DavidHarkness points out, you didn't provide enough context for this question to make sense.  However, I see that this code comes from a doTypeCheck() method, which is at the heart of your RPN calculator implementation.  I'll reproduce that method here, along with its call site:

private void doTypeCheck(Fraction op1, Fraction op2)
{
    Fraction answer = null;
    String readIn = "";
    boolean valid = true;
    readIn = stdin.next();

    while(!readIn.equals("#") &amp;&amp; valid == true)
    {
       if(!isOperator(readIn) &amp;&amp; isOperand(readIn))
       {
          processOperand(readIn);
          readIn = stdin.next();
       }
       else if(isOperator(readIn))
       {
          System.out.print(readIn);
          if(myStack.isEmpty())
             valid = false;
          else
             op2 = (Fraction)myStack.pop();

          if(myStack.isEmpty())
          {
             valid = false;
             throwLine(readIn);
          }
          else
          {
             runTheOperator(op2, op1, readIn);
             readIn = stdin.next();
          }
       }
       else
       {  
          System.out.print(readIn);
          valid = false;
          throwLine(readIn);
       }
    }
    System.out.println();
    if(myStack.isEmpty())
       valid = false;
    else
       answer = (Fraction)myStack.pop(); 
    if(!myStack.isEmpty())
       valid = false;
    checkMessageValid(valid, answer);
}

private void runOnce(int count)
{
    Fraction op1 = null;
    Fraction op2 = null;
    clear(myStack, myQueue);

    System.out.print("Expression " + count++ + " is: ");
    doTypeCheck(op1, op2); 
 }




The root problem is that your method has no clear purpose, and tries to do many things:


Read tokens from the input stream, and decide whether they are operands or operators
If it sees invalid input, discard the rest of the input and display an error
Pop an operand from the stack, with error handling
Feed two operands to the calculating function
Check that the stack is empty afterwards
Display the answer


As I mentioned in my other answer, that's not a good way to write an RPN calculator.

The main loop of an RPN evaluator should probably look something like this:

try {
    while (in.hasNext()) {
        String token = in.next();
        RpnOperator op = RpnOperator.forSymbol(token);
        if (op != null) {
            op.operate(calcStack);
        } else {
            calcStack.push(new Fraction(token));
        }
    }
    System.out.println(calcStack.peek());
} catch (EmptyStackException emptyStack) {
    System.out.println("Error: empty stack");
}


That's all!  To summarize:


Let the operators manipulate the stack.  The main loop just needs to dispatch to the appropriate operators.
Use exceptions for error handling.