Java Documentation – How to Document High-Level Structure

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Background:
My collaborators and I are writing an article for an academic journal.
In the course of our research,
we wrote a simulation program in Java.
We want to make the simulation program freely available for others to use.
We have decided on hosting the code on a GitHub repository.
In order to make it easy for others to use,
we want to write good documentation for our program, including:

  • Javadocs for each class and method
  • How to use the code
  • Describing the high-level structure of the code

My high-level question is:
Could you provide a good example of the words and diagrams
that can be used to describe the high-level structure of a program?
This includes as sub-questions:

  1. How do we show what classes are contained in which packages?
  2. How do we show what packages depend on other packages?
  3. How do we show how the objects/classes in the program work together?
  4. We have tried to use domain-driven design principles
    in the design of my code.
    How do we show the correspondence between the objects in the domain
    and the particular source code files encoding these objects?
    (See my "ubiquitous language" description of the project below.)

What I have done so far

Ubiquitous language

We put a "ubiquitous language" description of the code
in a file ubiquitous-language.md,
contents below.

The purpose of this project is to study how well a replenishment policy
performs in a simple supply chain with a single facility,
under different lead time models, report delays and demand models.

In each period, the following events occur:

  1. If a shipment is scheduled to arrive at the facility at the
    current period, then the inventory level of the facility is
    incremented by X units.
  2. If the schedule indicates that the current period is a reporting
    period, then the facility submits a report to the
    supplier. The supplier may receive the report
    instantaneously, or with a delay of several weeks, as specified by
    the schedule.
  3. If the supplier has received a report, then based on the
    replenishment policy, it will calculate a replenishment
    quantity of X units. A shipment of X units of the product will
    be scheduled to arrive after a lead time of l periods.
  4. Customers arrive at the facility and demand X units of the
    product. Any unmet demand is lost.

Source Code Structure

We put an incomplete "high-level" description of the code
in a file structure.md,
contents below.

Package Level Structure

At the highest level, the source code is organized into three packages

  • com.gly.sfs
    The main class with the main method resides in this package.
  • com.gly.sfs.model
    The domain model classes reside in this package.
  • com.gly.sfs.util
    Helper classes reside in this package.

Best Answer

Normally, you'd use UML for the purpose you describe. UML basically breaks down into two types of diagrams: structural and behavioral.

Structural diagrams include: composition, deployment, package, class, object, and component. Behavioral diagrams include: sequence, state machine, communication, use case, activity, and interaction overview.

Depending on what you're trying to convey, you pick a few of these diagrams which best represent whatever you're trying to convey, and by so doing you allow the conversation to "move up a level". Instead of talking about methods, parameters, and code, you're talking about sequence of interactions, or static class dependencies, or whatever diagrams you choose to create.

I've attached an example of a sequence diagram (one of the behavior diagrams). I personally like the sequence diagram because it's right in the middle of the design artifact process -- roughly an equal number of diagrams depend on it as it expects as input. I find that the input diagrams are typically "understood" anyway, or the sequence diagram already implies their existence. However, sometimes I do both static class diagrams and sequence diagrams (one structural and one behavioral diagram).

http://omarfrancisco.com/wp-content/uploads/2011/07/sequencediagram.png

I have never seen this diagram before in my life, but I can tell a number of things about this system. There are four major components (the nouns in your system -- typically the classes): View, Controller, Data Proxy, and Data Provider. The arrows are "behaviors" or method invocations. A sequence diagram is basically good for showing a single important interaction between a bunch of components. You have one sequence diagram for each important flow through your system. I can tell from this particular diagram that "Controller" exposes a method called "phoneIsComplete()", which in turn depends on DataProviderProxy's "lookupPhone()" method, which in turn depends on DataProvider's "lookupPhone()" method.

Now, you might groan and think "uggg... this doesn't give me a big picture of the system -- it's just individual interactions through the system". Depending on the sophistication of the system, that might be a valid concern (simple systems can definitely get by with just a collection of sequence diagrams). So, we move over to the structural diagrams and we look at something like a static class diagram:

http://www.f5systems.in/apnashoppe/education//img/chapters/uml_class_diagram.jpg

Class diagrams help us figure out two important things: cardinality, and class relationship types. Classes can be related to one another in different ways: association, aggregation, and composition. Technically speaking, there's a difference between "static class relationships" and "instance relationships". However, in practice you see these lines blurred. The main difference is that static class relationships don't usually include cardinality. Let's look at the example above and see what we can see. First, we can see that "Special Order" and "Normal Order" are subtypes of "Orders" (inheritance). We can also see that one Customer has N Orders (which may be "Normal Orders", "Orders", or "Special Orders") -- the Customer object doesn't really know. We can also see a number of methods (in the bottom half of each class box) and properties (top half of each class box).

I could keep talking about UML diagrams for a long time, but this is the basics. Hopefully that helps.

TLDR; Pick one behavioral and one structural UML diagram, learn how to create it, and you'll accomplish what you're trying to accomplish.

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