There are two usecases for compiling RNA programs from this package:
- You combine existing components or your new components to implement an algorithm for a new problem; or you simply want to directly get your hands on manual execution of
gapc
. Passing command line argument into this programs is not necessary, because you are happy with some defaults.
- You developed some instances and want to deploy them with the ability to accept some arguments.
To serve both usecases "rnaoptions_defaults.hh" comes with defaults for all arguments, as well as the functions to pass them into the generated recursions. What to use can be set by a -D g++ flag WITH_RNAOPTIONS
. To ensure that one or the other is used, "rnaoptions_defaults.hh" is imported by Extensions/singlefold.hh and Extensions/alifold.hh; one of which must be imported by your program.