BiobaseXNA-0.10.0.0: Efficient RNA/DNA/Protein Primary/Secondary Structure

Biobase.Secondary.Constraint

Contents

Description

Simple oldstyle RNAfold constraints. A constraint yields a bonus or malus to energy.

Synopsis

# Documentation

class MkConstraint a where Source #

We can create a constraint from different sources.

Minimal complete definition

mkConstraint

Methods

Instances

 Source # Methods Source # Methods

newtype Constraint Source #

A constraint is nothing more than a vector of constraint characters together with a possible pairing for each character.

Constructors

 Constraint FieldsunConstraint :: Vector (Char, Int)

Instances

 Source # Methods Source # Methods Source # MethodsshowList :: [Constraint] -> ShowS #

Given a Constraint, create an NxN matrix with bonus energies. These energies can be included in all pair-creating functions and will disallow or strongly favor certain pairings, while others will receive neither bonus nor malus.

In case, a pair (i,j) is annotated as both, bonus- and malus-receiving, it will be set to receive a malus. This can happen, if something like "<" would give a bonus, but "x" gives a malus (and other cases).

TODO and again, we should parametrize over Energy, Score, etc (that is, Prim a)