Well what do you mean "ruled" for the Tokugawa Shogunate? "Ruled" as in "administrated directly", or "ruled" as in "exercised political control over"?

The relationship between the Shogun and the Daimyo of Tokugawa Japan is complicated.

Here's a map for you for Tokugawa Japan 1664

http://earlgreyimperial.bufsiz.jp/edo_q/daimyou_haitizu.gif

Orange: Lands the Tokugawa directly controlled Green: Lands controlled by daimyo that were related to the Tokugawa family or were vassals of the Tokugawa family before 1600 controlled Blue: Lands controlled by daimyo who swore loyalty after 1600 (called Tozama Daimyo)

Roughly in terms of productive capacity: Tokugawa family controlled 1/4 of Japan

Tokugawa relatives and vassals controlled another 1/4 of Japan

Tozama Daimyo collectively controlled 1/2 of Japan

The ratio fluctuated over time. In general, the lands of the Tozama Daimyo went down while the land under the control of the vassal daimyo went up as time passed.