To understand the Java Class you need to think of it as a modular design composed not only of three sections (Command, Engineering, Aft), but also "pallets" (rectangular, flat sections connected to Deck Six of the Command & Engineering sections/Deck D of the Aft) and Containers which are latched onto the pallets.
The Command Section goes in front, followed by 1, 2 or 3 Pallets, followed by the Engineering Section, followed by an equal number of pallets as found behind the Command section, followed by the Aft section. The number of Pallets can be changed at a shipyard facility. The containers are loaded onto the top (these are odd-numbered) and bottom (these are even-numbered) of the pallets, port and starboard of the central line of the ship (sometimes referred to by Quartermasters as a "two by two" arrangement). While changing pallet configurations is a lengthy affair, containers can be switched out at any starbase facility with minimal problem within an hour each (unless you have multiple teams working on the connections in different sections).
While made by Federation for use in Starfleet applications (military, exploration and colonization), these vessels are attached to the Merchant Marine in service and can even be purchased by colonies and private concerns/corporations. They are therefore found spread out over a large area of space and can be customized.
The Command section is the easiest section to detach from the rest of the ship, and the only one which can be detached with relatively simple automated commands from the bridge or Cargo Monitoring room on Deck Four. (Note that the Containers can be detached easily as well, although not with a simple command from the Bridge/Cargo Monitoring unless it is set up to do so in advance – i.e. some 'switches/hoses/cables/whatever must be dinked with at the site of the containers at some point – either in advance or at the time they are to be jettisoned)
Crew quarters are found here as well as Passenger Staterooms. A 'Stateroom' is the term used for passengers accommodations on Cargo Vessels of this nature, while 'quarters' are generally used for the Crew. Staterooms and Quarters tend to be functionally identical, although they have different amenities, including the expanded entertainment systems of staterooms and the direct communications and monitoring trunks in the Crew Quarters. In the TNG era, both have Food Replicator consoles in addition to those found in the Mess/Dining facilities; in the original 2320 design Food Dispensers are located only in the Mess/Dining Room areas. There are no true 'luxury' accommodations on the Ships, although 4 rooms do not have to share restroom facilities and have slightly larger common areas because they are not 'common' to anyone but the occupant. Some private concerns have modified staterooms to accommodate luxury suites but these are not shown here.
The 'Standard' Crew of JAVA-class Cargo ships varies from a low of 30 (when there are few if any passengers) to 56 (using all of the staterooms/Quarters on Deck 5 for Crewmembers assuming you want them in the Command section rather than using the Engineering and Aft Quarters instead) or more (using the 34 berths in the Engineering Section and 20 Berths in the Aft Section). Passenger capacity in the Command Section also has a range, normally 200 (when slightly more than half of the "quad" staterooms in the Passenger Decks are are used to maximum 8-person capacity) ranging up to as much as 224 without straining the capacity of the ship (i.e. without doubling up on beds outside of the Quads).
Deck One really doesn't exist. Okay, it does, but it is small, and consists primarily of the top of the Impulse Engine Exhaust. I started numbering here however because otherwise the Engineering Deck would be one off of the Command Section Deck. Think of it as having the reaction mass reservoir for the Impulse engines. The Vertical Fusion Reactor/Impulse system was considered somewhat experimental when the ships were first laid down and their results were mixed enough that the design was never widely incorporated elsewhere.
Contains: Bridge, Head, Armory, emergency equipment storage, Captain's Office, Impulse Control Room, Impulse Exhaust, Captain's Quarters, Executive Officer's Quarters.
The Bridge is 'thinner' than most Starfleet vessels, and although there are 6 duty stations (Conn, Ops, Communications/Ship Linkage, Engineering, Sensors station/Cargo Monitoring/Science, Tactical) in addition to the Captain's chair it is relatively rare that they are all used at the same time. There are two staterooms behind the bridge, one for the Captain and another for the XO. [I did this primarily because there were a lot of windows along the sides, for what I don't know, but rather than making them into yet another rec or mess or observation room I used them for the Captain's Office and C.O./X.O. Quarters, figuring that these crewmembers would want to remain close to the bridge at all times]. The Impulse Control room is a vital part of the impulse system, but it not used most of the time simply because the Command Section, when docked to a load, cannot fire her Command Impulse Engines without frying something. Nevertheless, these are moderately powerful engines, since there are many times between hauls that the Command section must move on it's own.
Contains: Crew Mess/Observation Lounge, Crew Conference Room, Multi-use room (Captain's formal Dining, gym, etc.), Security office w/ small Brig, 2 Emergency Transporters (18-person pads), Restrooms, Escape Pods, Shield Generators.
Deck Three is a "Crew Deck" although it is not restricted, it is generally only used by Crewmembers (unless there is an emergency and passengers are diverted to the Deck 3 escape pods). The Crew Mess is moderately large for her crew compliment [In the TNG era it has Food replicator consoles built in, in the 2320 version each bank of two constitutes a single Food Dispenser, complete with microtransporter linked to the Organic Fabrication machinery on Deck 7 or the Main Kitchens in the Aft Section; the options are much more limited and the taste is not as flavorful]. The Crew Conference room is attached, but can be sealed for privacy easily with a heavy screen (slightly thicker than a normal door). The Configurable room on the other side of the Mess Hall is used for a wide variety of purposes, and is often peculiar to each ship. On some it is a gymnasium (often converted to a small Holodeck in the TNG era, sometimes along with the conference room), others a Private Dining area for the Captain and any VIP's. In others, it is a simple rec area, in at least one it has been made into the Ship's Library. The Emergency Transporters have 18 pads [By the TNG era and later, we see very little of the Emergency Transporters in actual use, and by Voyager there is some indication that the Emergency Transporters see no use at all as the standard transports are used even for larger beam-in/out ("expanding the buffers" I think Ensign Kim said) these can be converted in those eras to 18-man transporters with slightly limited range/power compared to the "normal" transporters]. Security is a small area here, but really sees very little use most of the time. There are two brigs in the security area, "drunk tank" style (minimal facilities, generally a temporary holding area, longer term facilities can be set up in the Engineering Section or Aft Section in 'Open' Areas). The Shield Generators provide protection for the entire command section, and are designed to link with the Engineering and Aft Section's Shield generators when the vessel is linked up). There are also 2 Crew Stowage areas here, [although if one prefers to have an armed vessel, these can be easily converted to a Port and Starboard Phaser chamber].
Contains: Sickbay, Medical Lab, M.O's Office, Isolation, Medical Quarters, Crew Quarters, Quartermaster's Office & Cargo Monitoring Station, Ship's Purser/Counselor's Office, Science Station, Support Section.
Deck Four contains ship's services and vessel Support. Still primarily a 'Crew Deck', it sees much more passenger traffic (especially to the Sickbay) than the above decks. The Sickbay has six standard exam beds, one surgical bed and one isolation bed (although all set up for isolation to one extent or another esp. by the TNG era where medical forcefields are employed) and the Office of the Ship's Doctor/Medical Officer. There is also a separate office for the Ship's Purser/Counselor to help with the needs of passengers and crew [In the pre-TNG era this position is more or less a liaison between Crew and Passenger, in the TNG era, this position is expanded considerably to become a true Counselor's Position plus accommodating any needs of passengers].
The Science section is also located on Deck four. While Cargo Carriers are hardly hotbeds of pure research, the Science Section is included (along with Science Officers) because experience has shown that Carriers can sometimes encounter strange phenomenon (or worse yet, take on cargo which threatens her crew) that must be explored without access to 'real' labs. It is sometimes considered punishment duty by Science officers, primarily because it consists of long periods of extreme boredom when the Science station is considered superfluous punctuated by brief intense activity when facilities are considered inadequate.
The Quartermaster's office is located here as well [Note: in most Merchant Marine vessels the Quartermaster is also the X.O., often serving double duty because of the small crew]. There is a second area attached to the QM's office for Cargo Systems Monitoring, which usually is configured to keep a constant monitor on the linkage between the sections and sensor scans of any sensitive cargo (although this can also be done by the bridge stations, but this provides much more detailed information). Security will sometimes use this area to monitor visuals from around the ship because it is a nexus for the network of internal sensors.
The Support section includes life support equipment, the bottom of the Vertical Fusion Reactor system used by the Impulse Engines and the horizontal Computer Cores. It is accessed primarily through Jefferies tubes.
Contains: Crew Quarter's, Gymnasium [TNG: can be converted to a Holodeck], Command Stowage/Cargo (see below for specific components). Z+ Vestibule.
The forward section of this deck consists primarily of Quarters/Staterooms (although when the Crew must be maximized, these are all Quarters). The deck also contains a Gymnasium [In some, but by no means all TNG era ship's, this area is converted to a Holodeck]. In the aft portion, the deck contains the Command Stowage area. including the Command Section Cargo Transporters (p/s), Airlock Docking Collars (p/s) and Cargo Elevators.
There is also access here to the Cargo Container systems, this area, known as the 'Z+ vestibule' allows those in the Command section to gain access to the containers directly behind them.
Contains: Staterooms, Recreation Area, Stairwell to Main Dining, Observation Rooms, Shuttle Bay, Pallet Access/Connectors.
The Recreation area is large, and generally appointed to suit the primary function of the ship for a given mission (including being stripped down considerably and used as an open gymnasium area if there are fewer than normal passengers). The staterooms here are all "Quad" style, consisting of a configurable upper/lower bunk area for each bed shown. Approximately half of these "Quad" staterooms have both bunks, some have only one or the other bunk (depending on availability), leaving the open area for passenger stowage. Observation rooms on the side of the forward section provide excellent viewing and are often used as informal meeting areas for small parties on the ship.
The Shuttlebay is also located here, but there are no direct means of entry from the main deck (without using Jefferies tubes of course). cargo and personnel brought in via Shuttle use the elevators to go up to Deck five to access the rest of the command section or proceed through the Pallet Access doors to the Pallet sections.
Contains: Passenger Staterooms, Main Dining Room
(aka "Passenger Mess" by some crewmembers), Transporter Rooms, Stairs
(up to Recreation Area and in a separate area down to Deck Eight). Large
Restrooms, Food Replicator Heads [Food Fabrication Equipment in pre-TNG era],
RCS Thrusters, Z- vestibule (High Bay).
A large deck, Deck Seven consists primarily of Passenger Staterooms, with a few other important sections. The most impressive is the Main Dining Room, which some crewmembers refer to as the Passenger Mess (rarely around the Captain or Chief Purser however). [As with the Crew mess, the plan shows replicator banks here, but in the pre-TNG era, these are replaced by a single Food Dispenser for each bank of 2, see notes above.] Food Replicators are also located here, although they area rarely used exclusively to meet the needs of the Dining area at high traffic [In the Pre-TNG era this area consists of the Organic (Food) Fabrication machinery, which provided service to the dining room only and there were no replicator consoles in the rooms as there are in the TNG era, note the larger open space here, which would be completely filled by the Fabricators]. The Command Section Personnel Transporters area also located here [Even if the Emergency Transporters are converted over for use as less-range large capacity transporters these remain because they are 'standard' full-range (and more 'powerful' in terms of signal strength) transporters].
Contains: Passenger Staterooms, Main Airlock w/
waiting room, Transporter Rooms & Emergency Transporter rooms*, Stairs (to
Deck Seven & Nine). Large Restrooms, Small Conference Rooms [Although this
area is used for the raw material storage for Food the Fabrication Equipment
above it in the pre-TNG era], RCS Thrusters, Z- vestibule (High Bay).
Other than the Airlock area and Emergency Transporters, this deck is nearly identical to the one above; as a result, the color scheme is almost always completely different [A note on Color scheme, while the top few 'Crew Decks' tend to be Starfleet off-white the passenger areas, minimally Decks 6-9 tend to have different colored walls and carpet: blue, green, purple and amber schemes are most common but this does vary from ship to ship].
NOTE: The Emergency Transporters on this deck can be removed for those of you who think that the Ship should be armed (which I would agree with although the exterior views do not seem to show any visible phaser banks or strips). These areas would be used for the Phasers, either if they were forward firing banks or as command/maintenance/emitters for the Strip in the TNG era.
Contains: Passenger Staterooms, Main Deflector,
Deflector/ Sensor Maintenance, main and lateral Sensors. Stairwell to Deck Eight
& Ten.
A Small Deck, it is dominated by the Main deflector dish. The Deflector/Sensor Maintenance room controls the Deflector and serves as the primary monitoring station for the Ships sensor systems. There are some Staterooms here as well.
Contains: Escape Pods, Stairwell.
Used exclusively for the Escape Pods [of which the ship has way too few overall but as there is no 'bottom view' I decided to make these all-Escape Pod areas].
Note that the Escape Pods (see detail on Deck Ten of the Command Section and Deck Eleven of the Engineering Section, both shown at double normal size) hold 15 people each. Using roughly 1 meter circles to represent passengers I was able to fill the pods with 15 "people", but there can be more "jammed in" under duress, probably no more than 2 or 3 however because I already used a major shoehorn. The 15-person standard however provides an escape pod capacity from Deck Ten for 210 people. Note this is only 10 more than a 'standard' passenger allotment of 200; when combined however with the 6 'Crew' pods on Deck Three, there is a total capacity for 300 for the Command Section, which is a much more comfortable (although still insufficient) margin.
Can anyone say 'Titanic'?