Akismet learning from comments marked as spam?

Hi, I have read that while using Akismet, if an admin marks a comment as ‘Spam’, the Akismet server will learn from that while filtering comments in the future. My question is, if a comment is programmatically marked as ‘Spam’ via a filter in functions.php or a plugin or something, will Akismet note that also and block similar comment entries in the future, or does a comment need to be *manually* marked as Spam to be noted?