I just started Shader programming(GLSL) and created a few with RenderMonkey. Now I want to use this Shaders in my java code. Are there any simple examples of how I do that?
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I don't have any myself, but if I have a problem along these lines I have often found the best place for 3D programming and Java advice is over at JavaGaming.org - I've not been there for a while, but it was always a helpful and knowledgeable community.
The new version of Jogl adds as an Utility shader loading/compiling and Uniform setting/getting calls. Have a look at the API for the selection of methods.
You could look at ogre4j, a Java wrapper/port of the popular open-source Ogre3D graphics engine. It might be a bit heavy-weight for your needs, but for a proper 3D project, worth a look for sure.
I have found a very simple example