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what do you mean programatically? file type assocations are generally held within the level of a file manager app of a desktop environment like gnome or kde. you'd need to look at your DE of choice as there's no accross the board mechanism that you'd use.
The association of a file with a program is not a responsibility of operating system. Thus, there is no such association which will work, so to say, on "Linux". This criteria is a responsibility of Desktop environment the user is working in.
In Windows, there is only one desktop environment. On Linux, some may use KDE, other may use Gnome, and still other may use Fluxbox, or Windowmaker, or any number of choices available. All these have different approach for any problem, and there is no standard. As of now there is no standard way to associate a file with a program. What you may do however, is to write something for KDE and Gnome. These are most popular DEs, and in case user is using something else, you can pretty much assume that he does not need such associations.