where does the saying originate

Possibly a substitution for "cup of Java" another expression coming from a coffee source.

i always thought of "java" as being a cup of tea

No, around these parts Java is always coffee. I think the shift from Java to 'joe' is correct.

Cup of Joe

Josephus Daniels (18 May 1862-15 January 1948) was appointed Secretary of the Navy by President Woodrow Wilson in 1913. Among his reforms of the Navy were inaugurating the practice of making 100 Sailors from the Fleet eligible for entrance into the Naval Academy, the introduction of women into the service, and the abolishment of the officers' wine mess. From that time on, the strongest drink aboard Navy ships could only be coffee and over the years, a cup of coffee became known as "a cup of Joe".

http://en.wiktionary.org/wiki/cup_of_joe

Oh yes.

As zomebody once zaid, data is not the plural of anecdote.

Cheer up, Mac. It's possible, you know, that although the phrase 'cup of joe' had been around for quite a while, Jesephus Daniels' edict helped to popularize it, while its putative antecedent 'cuppa Java' fell into relative disuse.

I love coffee, I love tea
I love the the Java Jive and it loves me
Coffee and tea and the java and me
A cup, a cup, a cup, a cup, a cup (Boy)

I love java, sweet and hot
Whoops Mr. Moto, I'm a coffee pot
Shoot the pot and I'll pour me a shot
A cup, a cup, a cup, a cup, a cup

Oh slip me a slug from the wonderful mug
And I'll cut a rug just snug in a jug
A sliced up onion and a raw one
Draw one -
Waiter, waiter, percolator

The Manhatten Transfer recorded this some time back....very talented

After some thought it occurred to me that asking for a cuppa joe was more of a 40s -50s phrase in American films. If I want coffee when I'm in a restaurant I ask for high test, so they don't pour decaf. I don't think I've ever heard an actual person ask for a cup of joe.