Seats of trains in Japan are different depending on the type of the trains. Local trains running in Tokyo metropolitan area have 3 doors or more on the each side of the trains and the seats are bench(long) seats which you sit along the window/wall and facing the opposite window/wall. Then, modern trains usually have handrails attached between the bottom of the seat and the ceiling. These handrails are not only for the safety for the standing passengers but also have a function to let the maximum number of passengers to have a seat.
Majority of trains in Tokyo metropolitan area have 4 doors on the each side of the trains and the seats are calculated to sit 7 passengers next to each other on the seats. However, usually passengers want to make spaces between each other, then sometimes only 6 passengers can sit on the seat. Therefore if there are the handrails mounted at the seats, passengers must sit properly.
Limited express trains or local trains with Green cars(1st class) are usually equipped with seats similar to aircraft. Which means there is a window seat and an aisle seat. Then, all trains are equipped with luggage rack above the seats, even on subway trains. Although you can not put you large suitcase on the rack but the racks are sufficient for putting carry on luggage.