03 cobra battery issue

OK, I have a 69 fastback and I was using my 03 cobra to jump it...the next day i was driving and my cobra started burbling and died, took it to the shop and found the battery was dead..charged the battery, car starts and runs fine, I thought that I fried my alternator but a buddy of mine said that it should have a "fused link" between the alternator and starter that should have saved my alternator. is this true? do i need a new alternator to battery cable or is my alternator toast? looked in my hanes manual and it didnt help at all..also would the fused link cable be the red(positive) or the black(negative) cable? any help would be awesome

so replace the cable and I should be fine..?

I checked the entire cable running from my power distribution box to my alternator and there is no fuse..I took out my alternator and am going get it checked out....if there is a fuse its not in the cable and all the fuses in my power dist box are good.