Documentation

Space-efficient RNAfold structure. RNAfold allows a DNA input, but this is not allowed in this data structure. If you want that, keep the original input string around.

This structure provides only Getter's. Only the sequenceID can be updated via sequenceIDlens. This is to prevent accidental updates of fields that are actually interdependent.

Missing parts are sloppily encoded by bogus values and empty strings. All Folded structures and derived values are lazy. In case rnafold was used to construct the structure, calculations are deferred until needed.

TODO newtype the sequence id.

TODO temperature. How to encode? Kelvin? In BiobaseTypes! Could use (Nat)SciTypes!

TODO complete BP probability array

TODO lazy fields for computation on demand!

TODO Wrapped via Maybe?

Fold a sequence.

This function is threadsafe via the viennaRNA-mutex.

TODO add temperature parameter

TODO consider creating a "super-lens" that updates whenever _input or _temperature change.

Parsing for RNAfold. This should parse all variants that RNAfold produces.

The parser for a Folded structure has to deal with different "energy" types. The different energies are bracketed by different types of brackets.

mfe        (((...))) ( -1.20)
ensemble   (((...))) [ -1.41]
centroid   (((...))) { -1.20 d=1.06}

TODO Move into submodule.

TODO pipes-based streaming parser

TODO how to handle parsing the BP probability array, if known?

TODO I think it is possible to figure the line type based on the energy and the brackets around the energy.