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You can approach rendering 3D graphics in several different ways.
Use OpenGL Directly
Many programmers find using OpenGL (via JOGL or LWJGL) directly the only way they can get the exact low level control they need. OpenGL provides primitive functions that allow you to render graphics with special attention given to 3D scenes. There's a wealth of tutorials at NeHe which have mostly been ported to Java.
Use a scenegraph or engine
Engines and Scenegraph abstract rendering in to APIs that allow you to construct scenes without worrying about the details of rendering. Scenegraphs allow you to build of tree of "nodes" describing your scene and then ask the engine to render it for you. Generally these engines handle culling of non-viewable geometry from the scene, transparency sorting and state management. Notable Java engines/scenegraphs are Java3D, JME, Agency9, Xith3D and JPCT.
Use 2D methods to render your own scene
Theres only three reasons you'd want to do this. Either you want to learn about how 3D rendering works, you are extremely worried about having dependencies on libraries or you're a glutton for punishment.
-- Main.kevglass - 24 Oct 2005
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