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From the barbarians Improved Uncanny Dodge ability:
Improved Uncanny Dodge (Ex): At 5th level and higher, a barbarian can no longer be flanked. This defense denies a rogue the ability to sneak attack the barbarian by flanking her, unless the attacker has at least four more rogue levels than the target has barbarian levels.
If a character already has uncanny dodge (see above) from another class, the levels from the classes that grant uncanny dodge stack to determine the minimum rogue level required to flank the character.
Only the barbarian levels count.
In general, when something only specifies "levels" or "class level", it means levels in whatever class grants the ability. It they meant all class levels and hit dice, they would of said "character levels".
Besides, if it meant all levels/hit dice, the second part of Improved Uncanny Dodge would be useless. (The part about levels stacking to determine the rogue level to flank.)