Sorry, but I don't get what you are doing with getPauseTime(), because
the result is also relative to startTime.

To get it clear, an Alpha's startTime is the wall clock time all other
times in the alpha object are relative to (e.g. triggerTime). By default
it is the (absolute) start time of the application.

You can get the current (absolute) time with the static
    System.currrentTimeMillis()
method. So you use
    alpha.setStartTime(System.currrentTimeMillis());
to start an alpha object immediately, i.e. as soon as this line of code
is executed. To start it in 2 seconds you can do either
    alpha.setStartTime(System.currrentTimeMillis()+2000);
or
    alpha.setStartTime(System.currrentTimeMillis());
    alpha.setTriggerTime(2000);
If you still need the milliseconds since the start of the app
    long t=System.currentTimeMillis()-alpha.getStartTime();
does the job.

Hope this answers your question.
JK.