My first thing to check would be the fact that you have nested for-loops that may just be taking a very very very long time to run. If you have small files providing the data for @main and @annot, the for-loops will run quickly. If you have large files for both
, then the runtime of the innermost loop will be the main determiner of the runtime of the script. Given that you then have 2 more
nested for-loops in range_find(), your runtime is going to be on the order of O(n^4). This is usually considered to be poor.
The biggest suggestion I would have (after the obvious algorithmic improvement) is to pre-digest your data so that repetitive checks can be sped up or eliminated. The next thing would be to look at using a relational database (like MySQL or Oracle) and letting the power of relational calculus solve your problems.
My criteria for good software:
- Does it work?
- Can someone else come in, make a change, and be reasonably certain no bugs were introduced?