Judge Alsup - who really wishes Oracle and Google had settled so he wouldn't have to hear the Java trial - is proposing to decide whether APIs are copyrightable himself and not have the jury wade into that legal brier patch.
However, he is also proposing to instruct the jury that the structure, sequence and organization of the asserted Java APIs are copyrightable, which between you, me and those angels dancing on the head of a pin over there is the same as saying the APIs are copyrighted.
The good judge is going to wait for the jury to come home with a verdict on whether Google infringed the Java APIs - and the overwhelming evidence presented at trial suggests it did - before he says whether or not they are copyrightable and springs that tiger out of its cage.

He's taking this route in an attempt to level the proverbial playing field for all concerned, according to what FOSS Patents says about Oracle and Google's "midnight filings" Wednesday.
FOSS says Judge Alsup told Google: "I've already said that I'm going to instruct the jury, subject to a motion under Rule 50 [motion for judgment as a matter of law, i.e., a decision by the judge himself] later at the end of the case. I'm going to instruct the jury that the copyrights extend to the Structure, Sequence, and Organization.
"Now, I'm reserving on that ultimately. I see both arguments on that point, but we ought to get the verdict on that. If you were to win on fair use, for example, then the judge doesn't have to decide those hard questions."
Google doesn't want the judge to be quite so explicit. It would prefer the jury be told to assume copyrightability and we'll sort the wash out later.
FOSS quotes Google telling the judge that telling "the jury that a fundamental premise of Google's defense case is wrong (rather than simply undecided)" would "leave the jury wondering what Google and its witnesses have been talking about for the past two weeks" and "prejudice the jury against Google on the issues the jury will actually decide."
The other alternative, however, could prejudice Oracle's position.
FOSS says "if the judge [ultimately] rules against copyrightability, the whole API copyright issue works out in Google's favor, but if he rules in favor of copyrightability, he would, in retrospect, simply have told the jury the truth - even if prematurely, or one might say presciently."
"In the scenario of Oracle being right on copyrightability, there would, however, be very significant prejudice for Oracle if the jury decided on infringement, fair use and Google's equitable defenses based on considerably uncertainty over whether the material at issue is even protected at all. If that prejudice was outcome-determinative, Oracle would never know how the judge would have decided on copyrightability - because in that case, he'll say that the finder of fact determined there was no infringement, rendering moot any questions of copyrightability. The only way Oracle could get a decision on copyrightability in that scenario would be a judicial decision overruling the jury, or a new jury trial with a different outcome."
See www.fosspatents.com/2012/04/judge-plans-to-inform-jury-that.html.