You may also be interested in the write-up from Sun, as part of the standard JSSE documentation:
http://docs.oracle.com/javase/8/docs/technotes/guides/security/jsse/JSSERefGuide.html#Stores
Typically, the trust store is used to store only public keys, for verification purposes, such as with X.509 authentication. For manageability purposes, it's quite common for admins or developers to simply conflate the two into a single store.