Totally different thing. The java program encodes each decision and computation that it performs directly.
It's just that a brain alters it's behavior and structure as a result of processing inputs (development).
We don't (normally) write Java programs to change their behavior as they process information from their environment during execution.
Translation: translating Lord of the Rings into Chinese.
Development: hearing a short plot synopsis of Lord of the Rings and writing your own fantasy novel based on the same theme.
Development really does do something analogous to that. It takes a collection of proteins and rules and, through embodiment within the laws of physics, constructs the phenotype. The phenotype contains vastly more information than the genotype, and two identical genotypes will not produce absolutely identical phenotypes.
There is something fundamental about development that we do not understand. This is widely acknowledged in the developmental biology, evo-devo, and evolutionary computation fields. A closer analogy than the loose one above might be some of the behaviors we see with fractals and cellular automata, though development is less deterministic than that.
Evolution and development are somehow related. We don't quite get that either. But both processes add vast amounts of information and both involve adaptation.