Consolidate find_bulge_loop, shortest_bg_loop and find_multiloop_loops somehow.

ViennaRNA / forgi

An RNA manipulation library.

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Consolidate find_bulge_loop, shortest_bg_loop and find_multiloop_loops somehow. #10

Closed Bernhard10 closed 5 years ago

Bernhard10 commented 8 years ago

A bulge graph has the member functions

find_bulge_loop
shortest_bg_loop
find_multiloop_loops, which depends on shorthest_bg_loop

There are no tests for find_bulge_loop.

Is there a reason we need to maintain both functions?

Bernhard10 commented 8 years ago

There is also get_multiloop_nucleotides which seems to be unused.

pkerpedjiev commented 8 years ago

From what I can tell, get_shortest_bg_loop operates on nucleotides whereas find_bulge_loop operates on cg elements. find_multiloop_loops seems to find all multiloop loops.

So they're all slightly different, but could probably be consolidated somehow.

Bernhard10 commented 5 years ago

Forgi 2.0 now has

find_bulge_loop for the shortest loop involving the element (can contain interior loops), on the level of elements.
find_mlonly_multiloops for the shortest loop containing only m, t and f segments, for all loops.

And some convenience functions which are thin wrappers around find_mlonly_multiloops:

shortest_mlonly_multiloop for the shortest loop involving one element, containing only m, t and f segments
junctions - property, to list all regular multiloops