On "java.lang.ArrayIndexOutOfBoundsException"

I try to assign the organism and pathway through arguments, but unexpectedly I got an exception: java.lang.ArrayIndexOutOfBoundsException. Having searched google I know it's caused because I try to index an empty array.
At first I didn't put in any arguments, so the argument array is empty. But I try to read in the organism name as well as pathway name from the empty arrays, then the exception is caused.

Now I have to try to find a better way to deal with the input arguments.

Highlight:
"java.lang.ArrayIndexOutOfBoundsException" is
Thrown to indicate that an array has been accessed with an illegal index. The index is either negative or greater than or equal to the size of the array.