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It's better to work with the original source than to try to decompile a class file.

I'm talking about finding out why the code outputs only 0's. I find it easier to use small files for testing. The debug print outs will be smaller.
It depends on the app and the data. It's up to...

Make a smaller one for easier testing.

Try debugging the code by adding calls to the println() method to print out the values in the arrays before and after they are changed by the different methods to see where the values are being...

Can you also post the contents of the console window from when the program is executed?

Try doing some debugging by printing out the values of the array as it is created to see why its values are...

How did you read the contents of the .dat file so you could copy its contents and pasted it here?
If you used a simple editor to read the file and were able to see what is posted here, it looks the...