Added suboptimal folding for t22:
- Uses same Expansion struct as for randomised traceback
- Pairs are handled explicitly in the State rather than implicitly like in t04 by looking at the DP tables (for DP_P)
Added SHAPE support for t22:
- add pf_paired and pf_unpaired vectors to the energy model - these are pseudofree energy penalties for each nucleotide
- Each substructure handles paired pseudofree energy for its opening pair.
- Closing pairs are the opening pair of the next substructure, and are handled by it.
- Unlike RNAstructure:
- unpaired pseudofree energy is applied for special hairpins hairpins.
- paired pseudofree energy is not double counted inside helices or missed for lonely pairs
- paired pseudofree energy is counted across a size 1 bulge loop