Hi,
I'm learning javascript in college and i was wondering if i could use it in AGS, would AGS recognize java or not?
No.
Although the syntax that AGS uses is somewhat similar.
First of all, be careful. You just mixed up "Java" and "JavaScript", two completely different scripting languages from different companies/backgrounds made for two different purposes.
Learning any object-oriented scripting language would put you in good preparation for coding in AGS. C# would be my best suggestion for AGS, and for having a coding career.