While Obama did pass the America Invents Act, nothing in the act addressed software patents. Software patents have been under heated debate for years. The debate is over where the line should be in terms of what software is patentable, whether saying software patents are too abstract is fair, and if innovation is encouraged or not by patents on software.
Currently in the US, patent law disallows any patents with abstract ideas, which generally applies to most potential patents involving software. Thus, computer software companies have a difficult time patenting their products. Promoters of software patents say that it will be good for research and development, protection, and cause economic benefit. Those against software patents believe copyright is sufficient, software patents will hinder research and development, and that software is a different breed in the sense that they are designed differently, because it is based off function as opposed to physical structure. In other words, patents on software essentially grant rights to concepts and not tangible creations. Here is an interesting article involving Apple that discusses how there is not a high enough standard for granting patents. I found the picture above amusing.