-- Hoogle documentation, generated by Haddock
-- See Hoogle, http://www.haskell.org/hoogle/


-- | (deprecated) Ring class, with several instances.
--   
--   Provides an algebraic ring class and instances for Gibbs free energy,
--   partition function probabilities, and scores. Conversion between
--   different entities is provided by a convert function. All entities are
--   ready for the vector library.
--   
--   <ul>
--   <li>Ignore everything except the Ring itself!</li>
--   </ul>
@package BiobaseTypes
@version 0.0.2.2


-- | Algebraic ring structure. Very similar to others found throughout
--   hackage.
--   
--   TODO maybe use on of the already-written packages?
module Biobase.Types.Ring

-- | Define the basic operations on a ring.
class (Eq a, Ord a) => Ring a
(.+.) :: Ring a => a -> a -> a
(.*.) :: Ring a => a -> a -> a
(.^.) :: Ring a => a -> Int -> a
(.^^.) :: Ring a => a -> Double -> a
neg :: Ring a => a -> a
one :: Ring a => a
zero :: Ring a => a
isZero :: Ring a => a -> Bool

module Biobase.Types.Energy

-- | Some default instances. Left out the Num one, so that you have to
--   explicitly instanciate if you want to go around the Ring structure.
newtype Energy
Energy :: Int -> Energy
unEnergy :: Energy -> Int
instance Prim Energy
instance Unbox Energy
instance Vector Vector Energy
instance MVector MVector Energy
instance Show Energy
instance Read Energy
instance Eq Energy
instance Ord Energy
instance Ring Energy

module Biobase.Types.Score

-- | Some default instances. Left out the Num one, so that you have to
--   explicitly instanciate if you want to go around the Ring structure.
newtype Score
Score :: Int -> Score
unScore :: Score -> Int
instance Prim Score
instance Unbox Score
instance Vector Vector Score
instance MVector MVector Score
instance Show Score
instance Read Score
instance Eq Score
instance Ord Score
instance Ring Score

module Biobase.Types.Partition

-- | Some default instances. Left out the Num one, so that you have to
--   explicitly instanciate if you want to go around the Ring structure.
newtype Partition
Partition :: Double -> Partition
unPartition' :: Partition -> Double
mkPartition :: Double -> Partition
unPartition :: Partition -> Double
logSum :: Double -> Double -> Double
log1p :: Double -> Double
expm1 :: Double -> Double
instance Prim Partition
instance Unbox Partition
instance Vector Vector Partition
instance MVector MVector Partition
instance Show Partition
instance Read Partition
instance Eq Partition
instance Ord Partition
instance Ring Partition


-- | Provides a converting function between different types. Most useful
--   conversions are instanced here.
module Biobase.Types.Convert

-- | How to convert between different values.
class Convert a b c
convert :: Convert a b c => a -> b -> c

-- | From (Gibbs free) energy to partition function values.
--   
--   TODO temperature is running around here: move to some library later on
newtype Kelvin
Kelvin :: Double -> Kelvin
unKelvin :: Kelvin -> Double
instance Convert Kelvin Energy Partition