How can I wrap a method so that I can kill its execution if it exceeds a specified timeout?

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You should take a look at these classes :
FutureTask, Callable, Executors

Here is an example :

public class TimeoutExample {
    public static Object myMethod() {
        // does your thing and taking a long time to execute
        return someResult;
    }

    public static void main(final String[] args) {
        Callable<Object> callable = new Callable<Object>() {
            public Object call() throws Exception {
                return myMethod();
            }
        };
        ExecutorService executorService = Executors.newCachedThreadPool();

        Future<Object> task = executorService.submit(callable);
        try {
            // ok, wait for 30 seconds max
            Object result = task.get(30, TimeUnit.SECONDS);
            System.out.println("Finished with result: " + result);
        } catch (ExecutionException e) {
            throw new RuntimeException(e);
        } catch (TimeoutException e) {
            System.out.println("timeout...");
        } catch (InterruptedException e) {
            System.out.println("interrupted");
        }
    }
}

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