biojava | source project dedicated to providing a Java library | Genomics library

Summary:

I have a program I want to ship as a single jar file.

It depends on three big resource files (700MB each) in a binary format. The file content can easily be accessed via indexing, my parser therefore reads these files as RandomAccessFile-objects.

So my goal is to access resource files from a jar via File objects.

My problem:

When accessing the resource files from my file system, there is no issue, but I aim to pack them into the jar file of the program, so the user does not need to handle these files themselves.

The only way I found so far to access a file packed in a jar is via InputStream (generated by class.getResourceAsStream()), which is totally useless for my application as it would be much too slow reading these files from start to end instead of using RandomAccessFile.

Copying the file content into a file, reading it and deleting it in runtime is no option eigher for the same reason.

Can someone confirm that there is no way to achieve my goal or provide a solution (or a hint so I can work it out myself)?

What I found so far:

I found this answer and if I understand the answer it says that there is no way to solve my problem:

Resources in a .jar file are not files in the sense that the OS can access them directly via normal file access APIs.

And since java.io.File represents exactly that kind of file (i.e. a thing that looks like a file to the OS), it can't be used to refer to anything in a .jar file.

A possible workaround is to extract the resource to a temporary file and refer to that with a File.

I think I can follow the reasoning behind it, but it is over eight years old now and while I am not very educated when it comes to file systems and archives, I know that the Java language has evolved quite much since then, so maybe there is hope? :)

Probably useless background information:

The files are genomes in the 2bit format and I use the TwoBitParser from biojava via the wrapper class TwoBitFacade?. The Javadocs can be found here and here.