Fine-tuning simple structure simulation by nested intervals

[cerebis]

This new approach uses recursion to generating nested intervals across a given replicon, where the number of size range are constrained.

Size The constraint on size range is currently proportional to the entire replicon length. For large bacterial chromosomes, this choice appears ok. However, for smaller replicons, the proportionate constraint may be inappropriate. The ultimate capacity to fold (ignoring interaction forces) would ultimately be an inherrent property of DNA (flexibility).

Recursion Recursion creates the nested intervals. Currently, a depth of two produces reasonable detail that appears qualitatively similar to experimental results. Deeper recursion, which generates increasingly smaller intervals results in a washed out and blurry main-diagonal in the contact map. The finer detail appearing lost. I suspect this is entirely due to how selection probability is assigned to the interval hierarchy.

Relates to #39

[cerebis]

The only remaining thing left to do here is how best to assign probability across the levels. I don't think my current strategy is perfect.