Yessir. You have a couple of choices. You could use the 'session' object, documented in the javadocs installed with TDI under the docs/api sub-folder of the installation directory. The index.html is in my browser favorites bar :) Stephen Swann's copy looks like this:
Here you can see handy functions like getAssemblyLines() and and getConfigInstance(). The config instance (CI) is the object representing the project running on the server. So a single configuration xml can be loaded multiple times to create multiple instances.
With the CI you can do stuff like getAssemblyLineNames() and getAssemblyLines, this latter returning a collection of running ALs, from which you can check state, get the current Work Entry and more.
Apart from starting and stopping ALs using the CI, you can also do things like reload configs and change properties settings.
You also have the 'main' object, which is the TDI Server itself:
This is the guy you typically use to launch ALs: main.startAL().
Hope this helps!