-- Hoogle documentation, generated by Haddock -- See Hoogle, http://www.haskell.org/hoogle/ -- | Collection of types for bioinformatics -- @package BiobaseTypes @version 0.1.1.0 -- | Strand information. A newtyped version, complete with serialization, -- pattern synonyms, being a PrimitiveArray index type, etc. -- -- TODO will be expanded to encode biological sense information more -- clearly: -- http://en.wikipedia.org/wiki/Sense_%28molecular_biology%29. module Biobase.Types.Strand newtype Strand Strand :: Int -> Strand getStrand :: Strand -> Int instance Arbitrary Strand instance IndexStream Strand instance IndexStream z => IndexStream (z :. Strand) instance Index Strand instance Vector Vector Strand instance MVector MVector Strand instance Unbox Strand instance Eq Strand instance Ord Strand instance Generic Strand instance Datatype D1Strand instance Constructor C1_0Strand instance Selector S1_0_0Strand instance Hashable Strand instance FromJSON Strand instance ToJSON Strand instance Serialize Strand instance Binary Strand instance NFData Strand instance Enum Strand instance Bounded Strand instance Read Strand instance Show Strand -- | Discretized log-odds. module Biobase.Types.Odds -- | Discretized log-odds. -- -- The BLOSUM matrices, for example, store data in discretized log-odds -- form. -- -- TODO Might move up even higher into statistics modules. newtype DLO DLO :: Int -> DLO getDLO :: DLO -> Int instance NFData DLO instance ToJSON DLO instance FromJSON DLO instance Serialize DLO instance Binary DLO instance Vector Vector DLO instance MVector MVector DLO instance Unbox DLO instance Generic DLO instance Eq DLO instance Ord DLO instance Show DLO instance Read DLO instance Datatype D1DLO instance Constructor C1_0DLO instance Selector S1_0_0DLO module Biobase.Types.Index.Type -- | A linear Int-based index type. newtype Index (t :: Nat) Index :: Int -> Index getIndex :: Index -> Int -- | Turn an Int into an Index safely. index :: KnownNat t => Int -> Index t -- | Produce Just and Index or Nothing. maybeIndex :: KnownNat t => Int -> Maybe (Index t) instance Arbitrary (Index t) instance IndexStream (Index t) instance IndexStream z => IndexStream (z :. Index t) instance KnownNat t => Index (Index t) instance Vector Vector (Index t0) instance MVector MVector (Index t0) instance Unbox (Index t0) instance Show (Index t) instance Read (Index t) instance Eq (Index t) instance Ord (Index t) instance Generic (Index t) instance Ix (Index t) instance Datatype D1Index instance Constructor C1_0Index instance Selector S1_0_0Index instance Hashable (Index t) instance FromJSON (Index t) instance ToJSON (Index t) instance Serialize (Index t) instance Binary (Index t) instance NFData (Index t) instance KnownNat t => Num (Index t) -- | Biological sequence data is oftentimes indexed either 0- or -- 1-based. The Index type developed provides static -- guarantees that there is no confusion what index is in use. -- -- This module does not export the ctor Index. If you want to -- (unsafely) use it, import Biobase.Types.Index.Type directly. -- Use fromInt0 to make clear that you count from 0 and -- transform to an Index t. I.e. fromInt0 0 :: Index 1 -- yields the lowest 1-base index. module Biobase.Types.Index -- | Uses index to guarantee that the Index is ok. checkIndex :: KnownNat t => Index t -> Index t -- | Re-Index an index of type Index n as Index m. This -- is always safe, as 0 :: Index 0 gives 1 :: Index 1 -- for example. I.e. valid indices become valid indices. reIndex :: (KnownNat n, KnownNat m) => Index n -> Index m -- | Helper function that allows addition of an Index and -- an Int, with the Int on the right. (+.) :: KnownNat t => Index t -> Int -> Index t -- | Unsafe plus. unsafePlus :: KnownNat t => Index t -> Int -> Index t -- | Helper function that allows subtraction of an Index -- and an Int, with the Int on the right. (-.) :: KnownNat t => Index t -> Int -> Index t -- | Unsafe minus. unsafeMinus :: KnownNat t => Index t -> Int -> Index t -- | Return the index as an Int-style index that is zero-based. toInt0 :: KnownNat t => Index t -> Int -- | As an index from an Int-style zero-based one. -- -- TODO We might want to check that the argument is [0..]. fromInt0 :: KnownNat t => Int -> Index t -- | Zero-based indices. type I0 = Index 0 -- | One-based indices. type I1 = Index 1 getIndex :: Index t -> Int -- | Turn an Int into an Index safely. index :: KnownNat t => Int -> Index t -- | Produce Just and Index or Nothing. maybeIndex :: KnownNat t => Int -> Maybe (Index t) -- | A linear Int-based index type. data Index (t :: Nat) -- | For some values, we want to have different kind of extreme values. -- Consider a Double representing an energy. We want near -- infinities that do not lead to numeric problems. -- -- TODO benchmark different extremes and their interplay with algebraic -- operations. -- -- TODO consider the ieee754 package module Biobase.Types.NumericalExtremes -- | Very large and small numbers with some numerical safety to -- 1/0 or maxBound (depending on if we are -- Integral or RealFloat. -- -- We have: -- -- 
--   maxFinite >= extremelyLarge >= veryLarge
--
-- -- 
--   veryLarge >= verySmall
--
-- -- verySmall >= extremelySmall >= minFinite. -- -- TODO the small stuff should actually be around zero, but positive and -- go into NumericalEpsilon. Here we should actually use other -- names. class NumericalExtremes x maxFinite :: NumericalExtremes x => x minFinite :: NumericalExtremes x => x veryLarge :: NumericalExtremes x => x verySmall :: NumericalExtremes x => x extremelyLarge :: NumericalExtremes x => x extremelySmall :: NumericalExtremes x => x -- | Small numbers. class NumericalEpsilon x epsilon :: NumericalEpsilon x => x instance NumericalEpsilon Double instance NumericalExtremes Double instance NumericalExtremes Int -- | Different types of energies and conversion between. -- -- TODO enthalpy TODO entropy module Biobase.Types.Energy -- | Gibbs free energy change. -- -- For RNA structure, the change in energy from the unfolded structure to -- the given structure. -- -- In units of kcal / mol. -- -- TODO shall we phantom-type the actual units? newtype DeltaGibbs DG :: Double -> DeltaGibbs getDG :: DeltaGibbs -> Double -- | round $ DeltaGibbs / 100. newtype DeltaDekaGibbs DekaG :: Int -> DeltaDekaGibbs getDekaG :: DeltaDekaGibbs -> Int instance NumericalExtremes DeltaDekaGibbs instance Default DeltaDekaGibbs instance ToJSON DeltaDekaGibbs instance FromJSON DeltaDekaGibbs instance Serialize DeltaDekaGibbs instance Binary DeltaDekaGibbs instance Hashable DeltaDekaGibbs instance Vector Vector DeltaDekaGibbs instance MVector MVector DeltaDekaGibbs instance Unbox DeltaDekaGibbs instance NumericalEpsilon DeltaGibbs instance NumericalExtremes DeltaGibbs instance Eq DeltaDekaGibbs instance Ord DeltaDekaGibbs instance Num DeltaDekaGibbs instance Read DeltaDekaGibbs instance Show DeltaDekaGibbs instance Generic DeltaDekaGibbs instance Datatype D1DeltaDekaGibbs instance Constructor C1_0DeltaDekaGibbs instance Selector S1_0_0DeltaDekaGibbs instance Default DeltaGibbs instance ToJSON DeltaGibbs instance FromJSON DeltaGibbs instance Serialize DeltaGibbs instance Binary DeltaGibbs instance Hashable DeltaGibbs instance Vector Vector DeltaGibbs instance MVector MVector DeltaGibbs instance Unbox DeltaGibbs instance Eq DeltaGibbs instance Ord DeltaGibbs instance Num DeltaGibbs instance Fractional DeltaGibbs instance Read DeltaGibbs instance Show DeltaGibbs instance Generic DeltaGibbs instance Datatype D1DeltaGibbs instance Constructor C1_0DeltaGibbs instance Selector S1_0_0DeltaGibbs module Biobase.Types.Accession -- | The accession number is a unique identifier in bioinformatics. -- -- Depending on the source, accession numbers follow different -- alphanumeric formats! While letters-than-numbers is quite common, -- swissprot uses a mix. Hence, we just use a text string as accession. -- -- A phantom type is provided to enable type safety annotations. Helper -- functions provide smart construction from the Accession -- tagged generic type. newtype Accession t Accession :: Text -> Accession t _getAccession :: Accession t -> Text accession :: Stringable s => s -> Accession t tagAccession :: Accession f -> Accession t -- | nucleotide sequence data Nucleotide -- | protein sequence data Protein -- | Tag as being a clan. data Clan -- | Tag as being a Pfam model. data Pfam -- | Tag as being an Rfam model. Used for Stockholm and CM files. data Rfam -- | Species have an accession number, too. data Species instance Eq (Accession t) instance Ord (Accession t) instance Read (Accession t) instance Show (Accession t) instance Generic (Accession t) instance Datatype D1Accession instance Constructor C1_0Accession instance Selector S1_0_0Accession instance ToJSON (Accession t) instance Serialize (Accession t) instance Hashable (Accession t) instance FromJSON (Accession t) instance Binary (Accession t) instance IsString (Accession t)