The Maximum Expected Accuracy (MEA) secondary structure is the one holding the most base-pair probability weight as possible. It has to be computed in two Bellman's GAP runs:
getBPprob
is to access base-pairs computed in run 1) from within run 2).
Of course, code generation must be carefully orchestrated to combine both Bellman's GAP instances in the right way. See the makefile
of the program RNAshapes: Misc/Applications/RNAshapes/makefile.