The Java API uses the REST Application services on MarkLogic which is fully HTTP 1.1 compliant and TCP/IP.
Not sure what else you are asking for.
For programs written in Java the Java API is the recommended API for most uses
http://developer.marklogic.com/products/java
You can also use the REST services directly, but the Java API adds a lot of Best Practice and exposes a higher level of abstraction to make coding simplier.
You can use the REST API from any application that can do HTTP
http://docs.marklogic.com/guide/rest-dev/intro
But its a bit more work as you have to construct your HTTP messages directly.
You can also create your own HTTP interface and access it through TCP/IP (HTTP) by making an HTTP App Server (written in XQuery).
Finally if you want very low level but effecient access, using Java or .NET you can use the XCC interface which is more tedious to use but provides a lower level feature for advanced users. This requires the Java or .NET library as the protocol is not documented.
https://developer.marklogic.com/products/xcc
What language are you going to be using and what kinds of operations ? That can help focus on which API is best for you.
-David Lee