Java software can be compile to native code with gcj, and basically removes the need of the presence of a Java Virtual Machine to run your Java code, such as based on BioJava. Now, in the past I have tried this now and then and read this official documentation, but I never found a really good tutorial aimed at bioinformatic. One that explains, for example, how that explains how to compile the source code into executables, not just with make, but also with Ant or Maven scripts. Or, how to compile BioJava as shared executable to which my own program dynamically links.
Therefore, what is your favorite gcj tutorial I should have a look at?
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Egon Willighagen
There are some good answers on Stackoverflow:
That post is actually quite inaccurate. I have asked about it on the #classpath channels, and the experts say the answers are nonsense. One issue, for example, is that no optimization is used when compiling to native code.
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Clearly, no one is using gcj in bioinformatics (yet) :(