I have to read the co-ordinates of a 3D object from the txt file and store it in an array. But I need to store it in a JAR file so that I can view the final product in my visualizer (Jmol). How do I get about in doing that?

Sorry I meant, after storing the co-ordinates in the array, I need it to undergo some processes such as rotation & translation and finally, the final product would be a JAR file.

There are classes for writing jar files. See JarOutputStream for example.
Try google for sample code.

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