Q:
Is it possible to initialize more than one object with the parse method?

I have 2 objects I'd like to initialize at startup. This is a Turing
machine, I would
like to give the program object its state information and I'd also like to
initialize the
Tape... Can I do that with 1 or more .input files?

A:
Yes.
Questions like this are best answered by trying to find an example on the net.
Demeter/Java reads multiple files so we can reuse some of that code.
This brings us to:

http://www.ccs.neu.edu/research/demeter/DemeterJava/use/latest-demjava

In which file are the input files read: probably main.beh

Indeed, we find:

while (behfileEnum.hasMoreElements()) {
File behfile = (File) behfileEnum.nextElement();
try {
InputStream in = makeInputStream(behfile);
log.print(" " + behfile); log.flush();
ProgramBehavior beh = ProgramBehavior.parse(in);
beh.collectBehavior(behfile.toString());
got_beh = true;
} catch (IOException exc) {}
}

The above is the code which reads in multiple behavior files.

Demeter/Java also reads in a cd:

if (curarg.endsWith(".cd")) {cdfile = new File(curarg);}
InputStream in = makeInputStream(cdfile);
prog = Program.parse(in);

-- Karl L.