This seems to be a question about the 3.0.0 MongoDB Java driver.
The general advice is to use Document/MongoCollection/MongoDatabase for new application development.
The DBObject/DBCollection/DB classes, however, remain in the 3.0.0 driver so that many existing applications that currently use the 2.x driver series have an upgrade path to the 3.0 driver. The driver authors (I'm one of them) tried to make this clear by deprecating the MongoClient.getDB method, which returns an instance of the DB class, in order to encourage use of the new MongoClient.getDatabase method, which returns an instance of MongoDatabase.
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