You should use library AutoItX4Java, it allows to execute AutoIt commands in Java.
You need to install AutoIt and use the library Java COM Bridge, then you can program directly in Java. I made a post on my site a while ago, but here is a simple example:
File file = new File("lib", "jacob-1.15-M4-x64.dll"); //path to the jacob dll
System.setProperty(LibraryLoader.JACOB_DLL_PATH, file.getAbsolutePath());
AutoItX x = new AutoItX();
String notepad = "Untitled - Notepad";
String testString = "this is a test.";
x.run("notepad.exe");
x.winActivate(notepad);
x.winWaitActive(notepad);
x.send(testString);
Assert.assertTrue(x.winExists(notepad, testString));
x.winClose(notepad, testString);
x.winWaitActive("Notepad");
x.send("{ALT}n");
Assert.assertFalse(x.winExists(notepad, testString));