Did San Francisco ever have a large intercity train station?

Factual Questions
1

Today, there’s no heavy-duty intercity rail transport into SF. If you want to take the train there from L.A., you can either take the Coast Starlight to Oakland, and then make your way over to the City either by an Amtrak-operated bus, or by BART, or you can take an alternative route that involves a bus to Bakersfield, then a train to Stockton, and then another bus to SF. But you can’t just step on a train in L.A. and ride directly to a station platform in S.F. proper. Given the geography of the area, that makes some sense, yet it’s hard to imagine that when intercity trains were the primary means of moving around the country, that you couldn’t take a train directly into S.F. Even though it would have meant going up a spur line into the Penninsula, and that back down around the Bay to continue either North or South–given the importance of S.F. it’s hard to believe it has always been bypassed in this way.

Are there any Northern California old timers who know the answers?

2

HUGE 1881 map showing the Central Pacific running to SF, and this shows the route of the San Francisco-Chicago journey in 1870.

3

Thanks, you Central African mountain dwelling knuckle-walking wild-lettuce-eating hominid. That’s a great link.

4

That map seems to suggest that there was a bridge between San Francisco & Oakland way back when…

The original transcontinental line ended at Sacramento. People wanted to go to San Francisco took riverboats the rest of the way. After a few more years the train went all the way to a pier in Oakland, where there was a train ferry to make the connection across to San Francisco.

http://home.comcast.net/~cable_car_guy/html/yesterday.htm

As the map suggests, until they built the Bay Bridge (originally there were train tracks on it) the only direct connection was via San Jose, a line which is still used by commuters to this day (http://www.caltrain.com/).