good luck in your data structures class!
Generics
In Java, these data structures (i.e. Queue, LinkedList, ...) can hold any kind of object. More often than not, though, a given instance of a Queue or LinkedList will hold a collection of the same type (here integers).
The angle-bracket syntax is used to specify which types are allowed in this specific instance of the collection.
So, the way to read:
Queue<Integer> encodingQueue = new LinkedList<Integer>();
is...
"Create a new linked-list that holds only integers, and assign that instance to the reference variable 'encodingQueue' which will be treated like a queue that holds only integers."
This feature that you're using is called "Generics". You can read up more about it here: http://en.wikipedia.org/wiki/Generics_in_Java
Autoboxing
In Java, there are two kinds of types: primitives and object references. "int" is a primitive and "Integer" is a class.
You cannot create a reference to a primitive in Java and collections (like LinkedList) only hold object references. So, you cannot stuff a primitive into a collection (e.g. you cannot put "int"s into a LinkedList). This is why Java provides the object equivalent for primitives: so that you can create collections of things like integers, floats, booleans, etc.
It can be a little confusing when you first start using primitives; Java will attempt to automatically convert primitives to object references when that's what's clearly needed (and vice-versa). This feature is called "autoboxing".
List myList = new LinkedList<Integer>();
myList.add(2);
Here, 2 is a primitive. But the compiler knows that you need an object reference, not a primitive. So, it automatically "boxes-up" this value by (in the background) creating a new instance of the class Integer and setting it's value to 2.
So, that's equivalent to (and this is what actually happens):
List myList = new LinkedList<Integer>();
myList.add(Integer.valueOf(2));
Where Integer.valueOf() first looks in an internal cache to see if an instance already exists for that value. If it does, that's returned, otherwise a new Integer object for that value is created. (Thank you, Boris, for pointing this out)