Wgs84 coordinate system to J2000

You can look at the frames documentation.

What you need is to first build the two frames (itrf which is equivalent to wgs84 and eme2000), compute the transform between these two frames, and finally apply the transform Something along these lines (beware I just wrote this in the forum, there may be some typos):

Frame         itrf         = FramesFactory.getITRF(IERESConventions.IERS_2010, false);
Frame         eme2000      = FramesFactory.getEME2000();
Transfrom     itrf2Eme2000 = itrf.getTransformTo(eme2000, date);
PVCoordinates pvEME2000    = itrf2Eme2000.transformPVCoordinates(pvItrf);
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