Additional Parameters

[bryan-lunt]

There should be a facility in the ExprPar and ParFactory to hold more additional parameters, more easily. Perhaps a first step would be making the functions that convert between a std::vector<double> and an ExprPar virtual, so that it is easier to overwrite and add to them.

My suggestion is that each TF be allowed to have any number of parameters, and instead of storing them in vectors per parameter (column oriented) store them with the description of the TF (row oriented). When an ExprFunc is created, it can reformat them for its own use as it likes anyway.

Likewise, each promoter/enhancer should have its own parameters, with some facility for storing global parameters.

Similarly, in the ExprModel, we should have a more general facility for storing indicators, rather than the current ExprModel::actIndicators and ExprModel::repIndicators.

[bryan-lunt]

The new_storage branch deals with the first part. Arbitrary indicators aren't yet available. They probably aren't really needed, in the normal dynamic programming the difference between activators and repressors is just the bounds on their \alpha parameter.