Is there a way to "embed" -Xmx command into program

Hi fellow members,
I have been working on a program to analyze web page structural similarity and has been posting on this forum for some help recently. At the moment I manage to parse html into DOM tree and perform tree edit distance analysis.
But I'm facing a problem which is heap memory running out. More complex web pages run up to >1000 nodes and the recursive comparing which has a time complexity of N^2 will cause outofmemory error. I have already reduced the number of nodes such as excluding text nodes as I'm primarily concerned with the structural similarity.
By using -Xmx to increase the heap memory helps to solve the problem partially. I would prefer to embed this command into the program so that user does not need to type it out every time. Is there a way to do this?
Thanks in advance.

I see, thanks a lot guys, I will read up on batch file processing.
But I'm wondering if I'm going to make it into a .exe file which will include the GUI in the near future, will I still need to write a batch file or any swing component can set the memory?
One more wild question, is there a way to set heap memory to be dynamic, as in increasing according to the program needs?

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