I’ve just finished my masters thesis for artificial intelligence. Coding was mostly processing java, some data wrangling with python and awk. Charts were made python and spreadsheet.
I actually wanted to write about doing a larger project with processing. First thing I would consider is whether to use processing ide or eclipse IDE or similar that is actually designed to handle large projects. 1000+ lines gets a bit rough to handle in processing ide. And with that amount of code you will most likely do some sort of refactoring (ie. renaming method, moving methods from class to another etc) and eclipse is better suited to that.
Another thing is code division. Use classes. It helps to handle and remember the program structure. It helps to keep methods short and understandable. Short and understandable means less errors and easier to find errors. Classes ease the load on you mind. You don’t have to remember or search that much of your code, when it’s well structured and minor details are hidden in class methods.
I would also recommend to use data structures from Collections, unless you want to put your code to web. I started my code with processing tables, but they were too slow for my use at least.
And finally know your processing. It has extensive and easy to use set of functions. If you do things ‘processing way’ you don’t have to worry about exceptions or loads of other cumbersome stuff.