Biobase.Secondary.Constraint

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

Documentation

class MkConstraint a where

We can create a constraint from different sources.

Minimal complete definition

mkConstraint

Methods

mkConstraint :: a -> Constraint

Instances

MkConstraint String

Methods

mkConstraint :: String -> Constraint

MkConstraint (Vector Char)

Methods

mkConstraint :: Vector Char -> Constraint

newtype Constraint

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

Constructors

Constraint

Fields

• unConstraint :: Vector (Char, Int)

Instances

Eq Constraint

Methods

(==) :: Constraint -> Constraint -> Bool

(/=) :: Constraint -> Constraint -> Bool

Read Constraint

Methods

readsPrec :: Int -> ReadS Constraint

readList :: ReadS [Constraint]

readPrec :: ReadPrec Constraint

readListPrec :: ReadPrec [Constraint]

Show Constraint

Methods

showsPrec :: Int -> Constraint -> ShowS

show :: Constraint -> String

showList :: [Constraint] -> ShowS

bonusCC :: Vector Char

nobonusCC :: Vector Char

bonusTable :: Double -> Double -> Constraint -> Unboxed ((Z :. Int) :. Int) Double

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)

Instances