Created two methods for BulgeGraph class.
1) get_stem_edge(self, stem, pos). Returns 0 if pos on 5' edge of stem, returns 1 if pos on 3' edge of stem.
2) shortest_path(self, e1, e2). Returns a list of the nodes along the shortest path between e1, and e2. The implementation might not be the most elegant, but it works on the structures I've tested it on.
I've tested these with bulge_graph.py in master fork.
Created two methods for BulgeGraph class. 1) get_stem_edge(self, stem, pos). Returns 0 if pos on 5' edge of stem, returns 1 if pos on 3' edge of stem. 2) shortest_path(self, e1, e2). Returns a list of the nodes along the shortest path between e1, and e2. The implementation might not be the most elegant, but it works on the structures I've tested it on.
I've tested these with bulge_graph.py in master fork.