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


-- | Collection of types for bioinformatics
--   
--   Types used in a number of bioinformatics libraries.
--   
--   <ul>
--   <li>linear indices</li>
--   <li>energies</li>
--   <li>numerics</li>
--   <li>biostring wrappers</li>
--   </ul>
@package BiobaseTypes
@version 0.1.3.0


-- | Wrappers for structural data. Encoded as bytestrings. This differs
--   from <tt>BiobaseXNA</tt>, where specialized encodings are used. These
--   structures are supposedly "short", they need to fit into a strict
--   bytestring.
--   
--   TODO Consider where to move each type. There are merge possibilities
--   between BiobaseXNA and BiobaseTypes.
module Biobase.Types.Structure

-- | Secondary structure using <tt>()</tt> for paired elements, and
--   <tt>.</tt> for unpaired ones. It is assumed that the <tt>()</tt> match
--   up. These structures from a Monoid.
newtype RNAss
RNAss :: ByteString -> RNAss
[_rnass] :: RNAss -> ByteString
rnass :: Iso' RNAss ByteString

-- | Ensemble structure encoding. *Very* different type ctor name chosen!
--   The structure of this string makes verification much more complicated.
--   
--   TODO describe encoding used by RNAfold for the ensemble string.
newtype RNAensembleStructure
RNAes :: ByteString -> RNAensembleStructure
[_rnaes] :: RNAensembleStructure -> ByteString
rnaes :: Iso' RNAensembleStructure ByteString

-- | Cofolded structure.
data RNAds
RNAds :: !ByteString -> !ByteString -> RNAds
[_rnadsL] :: RNAds -> !ByteString
[_rnadsR] :: RNAds -> !ByteString
rnadsR :: Lens' RNAds ByteString
rnadsL :: Lens' RNAds ByteString

-- | A Prism that turns ByteStrings with a single <tt>&amp;</tt> into
--   <tt>RNAds</tt>.
rnads :: Prism' ByteString RNAds

-- | Isomorphism from <tt>RNAds</tt> to <tt>(RNAss,RNAss)</tt>. The
--   <tt>RNAss</tt> are only legal if taken both: <tt>rnassFromDimer .
--   both</tt>.
rnads2rnassPair :: Iso' RNAds (RNAss, RNAss)

-- | Try to create a dimeric structure.
mkRNAds :: (Monad m, MonadError RNAStructureError m) => ByteString -> m RNAds

-- | Capture what might be wrong with the RNAss.
data RNAStructureError
RNAStructureError :: String -> ByteString -> RNAStructureError
[_rnaStructureError] :: RNAStructureError -> String
[_rnaOffender] :: RNAStructureError -> ByteString

-- | Verifies that the given RNAss is properly formatted. Otherwise, error
--   out.
--   
--   TODO Implement! Check with BiobaseXNA and the stack effort in there.
--   This might influence if the verification goes into BiobaseXNA and
--   happens via an <tt>Iso'</tt>.
verifyRNAss :: (Monad m, MonadError RNAStructureError m) => RNAss -> m RNAss
newtype RNApset
RNApset :: Set (Int, Int) -> RNApset
[_rnapset] :: RNApset -> Set (Int, Int)
rnapset :: Iso' RNApset (Set (Int, Int))

-- | Transform an <a>RNAss</a> into a set of base pairs <tt>(i,j)</tt>. The
--   pairs are 0-based.
rnassPairSet :: (MonadError String m) => RNAss -> m RNApset

-- | RNA pair set, but a transformation error calls <tt>error</tt>.
rnassPairSet' :: RNAss -> RNApset

-- | Calculates the number of different base pairs betwwen two structures.
pairDist :: RNApset -> RNApset -> Int
instance Control.DeepSeq.NFData Biobase.Types.Structure.RNApset
instance GHC.Generics.Generic Biobase.Types.Structure.RNApset
instance GHC.Classes.Ord Biobase.Types.Structure.RNApset
instance GHC.Classes.Eq Biobase.Types.Structure.RNApset
instance GHC.Show.Show Biobase.Types.Structure.RNApset
instance GHC.Read.Read Biobase.Types.Structure.RNApset
instance GHC.Generics.Generic Biobase.Types.Structure.RNAStructureError
instance GHC.Show.Show Biobase.Types.Structure.RNAStructureError
instance Control.DeepSeq.NFData Biobase.Types.Structure.RNAds
instance Control.DeepSeq.NFData Biobase.Types.Structure.RNAStructureError
instance GHC.Generics.Generic Biobase.Types.Structure.RNAds
instance Data.Data.Data Biobase.Types.Structure.RNAds
instance GHC.Read.Read Biobase.Types.Structure.RNAds
instance GHC.Show.Show Biobase.Types.Structure.RNAds
instance GHC.Classes.Ord Biobase.Types.Structure.RNAds
instance GHC.Classes.Eq Biobase.Types.Structure.RNAds
instance Control.DeepSeq.NFData Biobase.Types.Structure.RNAensembleStructure
instance GHC.Generics.Generic Biobase.Types.Structure.RNAensembleStructure
instance Data.Data.Data Biobase.Types.Structure.RNAensembleStructure
instance GHC.Read.Read Biobase.Types.Structure.RNAensembleStructure
instance GHC.Show.Show Biobase.Types.Structure.RNAensembleStructure
instance GHC.Classes.Ord Biobase.Types.Structure.RNAensembleStructure
instance GHC.Classes.Eq Biobase.Types.Structure.RNAensembleStructure
instance Control.DeepSeq.NFData Biobase.Types.Structure.RNAss
instance GHC.Base.Monoid Biobase.Types.Structure.RNAss
instance GHC.Generics.Generic Biobase.Types.Structure.RNAss
instance Data.Data.Data Biobase.Types.Structure.RNAss
instance GHC.Read.Read Biobase.Types.Structure.RNAss
instance GHC.Show.Show Biobase.Types.Structure.RNAss
instance GHC.Classes.Ord Biobase.Types.Structure.RNAss
instance GHC.Classes.Eq Biobase.Types.Structure.RNAss


-- | Strand information. A newtyped version, complete with serialization,
--   pattern synonyms, being a <tt>PrimitiveArray</tt> index type, etc.
--   
--   TODO will be expanded to encode biological sense information more
--   clearly:
--   <a>http://en.wikipedia.org/wiki/Sense_%28molecular_biology%29</a>.
module Biobase.Types.Strand
newtype Strand
Strand :: Int -> Strand
[getStrand] :: Strand -> Int
instance Data.Vector.Unboxed.Base.Unbox Biobase.Types.Strand.Strand
instance Data.Vector.Generic.Mutable.Base.MVector Data.Vector.Unboxed.Base.MVector Biobase.Types.Strand.Strand
instance Data.Vector.Generic.Base.Vector Data.Vector.Unboxed.Base.Vector Biobase.Types.Strand.Strand
instance Data.PrimitiveArray.Index.Class.Index Biobase.Types.Strand.Strand
instance Data.PrimitiveArray.Index.Class.IndexStream z => Data.PrimitiveArray.Index.Class.IndexStream (z Data.PrimitiveArray.Index.Class.:. Biobase.Types.Strand.Strand)
instance Data.PrimitiveArray.Index.Class.IndexStream Biobase.Types.Strand.Strand
instance Test.QuickCheck.Arbitrary.Arbitrary Biobase.Types.Strand.Strand
instance GHC.Generics.Generic Biobase.Types.Strand.Strand
instance GHC.Classes.Ord Biobase.Types.Strand.Strand
instance GHC.Classes.Eq Biobase.Types.Strand.Strand
instance GHC.Show.Show Biobase.Types.Strand.Strand
instance GHC.Read.Read Biobase.Types.Strand.Strand
instance GHC.Enum.Bounded Biobase.Types.Strand.Strand
instance GHC.Enum.Enum Biobase.Types.Strand.Strand
instance Data.Binary.Class.Binary Biobase.Types.Strand.Strand
instance Data.Serialize.Serialize Biobase.Types.Strand.Strand
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.Types.Strand.Strand
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.Types.Strand.Strand
instance Data.Hashable.Class.Hashable Biobase.Types.Strand.Strand
instance Control.DeepSeq.NFData Biobase.Types.Strand.Strand


-- | Wrappers around biosequences.
module Biobase.Types.Sequence

-- | A sequence identifier. Just a newtype wrapped text field. Because we
--   can never know what people are up to, this is utf8-encoded.
--   
--   TODO Provide <tt>Iso'</tt> for <tt>Text</tt>, too?
newtype SequenceID
SequenceID :: ByteString -> SequenceID
[_sequenceID] :: SequenceID -> ByteString
sequenceID :: Iso' SequenceID ByteString

-- | Convert to a string in a unicode-aware manner.
sequenceIDstring :: Iso' SequenceID String

-- | A short RNA sequence.
--   
--   It is an instance of <a>Ixed</a> to allow <tt>RNAseq (BS.pack "cag")
--   ^? ix 2 == Just <tt>g</tt></tt>.
newtype RNAseq
RNAseq :: ByteString -> RNAseq
[_rnaseq] :: RNAseq -> ByteString
rnaseq :: Iso' RNAseq ByteString
mkRNAseq :: ByteString -> RNAseq

-- | A short DNA sequence.
--   
--   Note everything really long should be handled by specialized libraries
--   with streaming capabilities.
newtype DNAseq
DNAseq :: ByteString -> DNAseq
[_dnaseq] :: DNAseq -> ByteString
dnaseq :: Iso' DNAseq ByteString
mkDNAseq :: ByteString -> DNAseq

-- | Simple case translation from <tt>U</tt> to <tt>T</tt>. with upper and
--   lower-case awareness.
rna2dna :: Char -> Char

-- | Single character RNA complement.
rnaComplement :: Char -> Char

-- | Simple case translation from <tt>T</tt> to <tt>U</tt> with upper- and
--   lower-case awareness.
dna2rna :: Char -> Char

-- | Single character DNA complement.
dnaComplement :: Char -> Char

-- | Transcribes a DNA sequence into an RNA sequence. Note that
--   <a>transcribe</a> is actually very generic. We just define its
--   semantics to be that of biomolecular transcription.
--   
--   <a>transcribe</a> makes the assumption that, given <tt>DNA -&gt;
--   RNA</tt>, we transcribe the coding strand.
--   <a>http://hyperphysics.phy-astr.gsu.edu/hbase/Organic/transcription.html</a>
--   
--   @<tt> DNAseq <a>ACGT</a> ^. transcribe == RNAseq <a>ACGU</a> RNAseq
--   <a>ACGU</a> ^. transcribe == DNAseq <a>ACGT</a> RNAseq <a>ACGU</a> ^.
--   from transcribe :: DNAseq == DNAseq <a>ACGT</a> </tt>@
class Transcribe f where type TranscribeTo f :: * where {
    type family TranscribeTo f :: *;
}
transcribe :: Transcribe f => Iso' f (TranscribeTo f)

-- | Transcribe a DNA sequence into an RNA sequence. This does not
--   <tt>reverse</tt> the sequence!

-- | Transcribe a RNA sequence into an DNA sequence. This does not
--   <tt>reverse</tt> the sequence!

-- | The complement of a biosequence.
class Complement f
complement :: Complement f => Iso' f f
instance Control.Lens.Internal.Iso.Reversing Biobase.Types.Sequence.DNAseq
instance Control.DeepSeq.NFData Biobase.Types.Sequence.DNAseq
instance Control.Lens.At.Ixed Biobase.Types.Sequence.DNAseq
instance Data.String.IsString Biobase.Types.Sequence.DNAseq
instance Biobase.Types.Sequence.Transcribe Biobase.Types.Sequence.DNAseq
instance Biobase.Types.Sequence.Transcribe Biobase.Types.Sequence.RNAseq
instance Biobase.Types.Sequence.Complement Biobase.Types.Sequence.DNAseq
instance Biobase.Types.Sequence.Complement Biobase.Types.Sequence.RNAseq
instance GHC.Show.Show Biobase.Types.Sequence.DNAseq
instance GHC.Read.Read Biobase.Types.Sequence.DNAseq
instance GHC.Classes.Ord Biobase.Types.Sequence.DNAseq
instance GHC.Classes.Eq Biobase.Types.Sequence.DNAseq
instance GHC.Generics.Generic Biobase.Types.Sequence.DNAseq
instance Data.Data.Data Biobase.Types.Sequence.DNAseq
instance Control.Lens.Internal.Iso.Reversing Biobase.Types.Sequence.RNAseq
instance Control.DeepSeq.NFData Biobase.Types.Sequence.RNAseq
instance Control.Lens.At.Ixed Biobase.Types.Sequence.RNAseq
instance Data.String.IsString Biobase.Types.Sequence.RNAseq
instance GHC.Show.Show Biobase.Types.Sequence.RNAseq
instance GHC.Read.Read Biobase.Types.Sequence.RNAseq
instance GHC.Classes.Ord Biobase.Types.Sequence.RNAseq
instance GHC.Classes.Eq Biobase.Types.Sequence.RNAseq
instance GHC.Generics.Generic Biobase.Types.Sequence.RNAseq
instance Data.Data.Data Biobase.Types.Sequence.RNAseq
instance Control.DeepSeq.NFData Biobase.Types.Sequence.SequenceID
instance Data.String.IsString Biobase.Types.Sequence.SequenceID
instance GHC.Show.Show Biobase.Types.Sequence.SequenceID
instance GHC.Read.Read Biobase.Types.Sequence.SequenceID
instance GHC.Classes.Ord Biobase.Types.Sequence.SequenceID
instance GHC.Classes.Eq Biobase.Types.Sequence.SequenceID
instance GHC.Generics.Generic Biobase.Types.Sequence.SequenceID
instance Data.Data.Data Biobase.Types.Sequence.SequenceID


-- | 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 Data.Vector.Unboxed.Base.Unbox Biobase.Types.Odds.DLO
instance Data.Vector.Generic.Mutable.Base.MVector Data.Vector.Unboxed.Base.MVector Biobase.Types.Odds.DLO
instance Data.Vector.Generic.Base.Vector Data.Vector.Unboxed.Base.Vector Biobase.Types.Odds.DLO
instance Data.Binary.Class.Binary Biobase.Types.Odds.DLO
instance Data.Serialize.Serialize Biobase.Types.Odds.DLO
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.Types.Odds.DLO
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.Types.Odds.DLO
instance Data.Hashable.Class.Hashable Biobase.Types.Odds.DLO
instance Control.DeepSeq.NFData Biobase.Types.Odds.DLO
instance GHC.Read.Read Biobase.Types.Odds.DLO
instance GHC.Show.Show Biobase.Types.Odds.DLO
instance GHC.Classes.Ord Biobase.Types.Odds.DLO
instance GHC.Classes.Eq Biobase.Types.Odds.DLO
instance GHC.Generics.Generic Biobase.Types.Odds.DLO


-- | For some values, we want to have different kind of extreme values.
--   Consider a <tt>Double</tt> representing an energy. We want <tt>near
--   infinities</tt> that do not lead to numeric problems.
--   
--   TODO benchmark different extremes and their interplay with algebraic
--   operations.
--   
--   TODO consider the <tt>ieee754</tt> package
module Biobase.Types.NumericalExtremes

-- | Very large and small numbers with some numerical safety to
--   <tt>1/0</tt> or <tt>maxBound</tt> (depending on if we are
--   <tt>Integral</tt> or <tt>RealFloat</tt>.
--   
--   We have:
--   
--   <pre>
--   maxFinite &gt;= maxExtreme &gt;= maxLarge
--   </pre>
--   
--   <pre>
--   maxLarge &gt;= minLarge
--   </pre>
--   
--   <tt>minLarge &gt;= minExtreme &gt;= minFinite</tt>.
class NumericalExtremes x
maxFinite :: NumericalExtremes x => x
minFinite :: NumericalExtremes x => x
maxExtreme :: NumericalExtremes x => x
minExtreme :: NumericalExtremes x => x
maxLarge :: NumericalExtremes x => x
minLarge :: NumericalExtremes x => x

-- | Small numbers.
class NumericalEpsilon x
epsilon :: NumericalEpsilon x => x
instance Biobase.Types.NumericalExtremes.NumericalExtremes GHC.Types.Int
instance Biobase.Types.NumericalExtremes.NumericalExtremes GHC.Types.Double
instance Biobase.Types.NumericalExtremes.NumericalEpsilon GHC.Types.Double

module Biobase.Types.Names.Internal
speciesNameBimap :: IORef (Bimap (HashMap Text Int) (Vector Text))

-- | Add <tt>Text</tt> and return <tt>Int</tt> key. Will return key for
--   existing string and thereby serves for lookup in left-to-right
--   direction.
speciesNameBimapAdd :: Text -> Int

-- | Lookup the <tt>InternedMultiChar</tt> based on an <tt>Int</tt> key.
--   Unsafe totality assumption.
speciesNameBimapLookupInt :: Int -> Text


-- | Names for biological things.
--   
--   Species names are internalized and represented as an <tt>Int</tt>.
--   This allows using them in structures like an <tt>IntMap</tt>.
--   
--   For other names, we newtype-wrap normal text internalization.
module Biobase.Types.Names

-- | A species name. Represented with an <tt>Int</tt>, but behaves like a
--   <tt>Text</tt>.
newtype SpeciesName
SpeciesName :: Int -> SpeciesName
[getSpeciesNameRep] :: SpeciesName -> Int

-- | Smart constructor that performs the correct internalization.
speciesName :: Text -> SpeciesName

-- | The taxonomic rank. This encodes the name for a given rank.
newtype TaxonomicRank
TaxonomicRank :: InternedText -> TaxonomicRank
[getTaxonomicRank] :: TaxonomicRank -> InternedText
instance GHC.Generics.Generic Biobase.Types.Names.TaxonomicRank
instance GHC.Show.Show Biobase.Types.Names.TaxonomicRank
instance GHC.Classes.Ord Biobase.Types.Names.TaxonomicRank
instance GHC.Classes.Eq Biobase.Types.Names.TaxonomicRank
instance Data.String.IsString Biobase.Types.Names.TaxonomicRank
instance Data.Vector.Unboxed.Base.Unbox Biobase.Types.Names.SpeciesName
instance Data.Vector.Generic.Mutable.Base.MVector Data.Vector.Unboxed.Base.MVector Biobase.Types.Names.SpeciesName
instance Data.Vector.Generic.Base.Vector Data.Vector.Unboxed.Base.Vector Biobase.Types.Names.SpeciesName
instance GHC.Classes.Ord Biobase.Types.Names.SpeciesName
instance Data.String.IsString Biobase.Types.Names.SpeciesName
instance GHC.Show.Show Biobase.Types.Names.SpeciesName
instance GHC.Read.Read Biobase.Types.Names.SpeciesName
instance Data.Hashable.Class.Hashable Biobase.Types.Names.SpeciesName
instance Data.String.Conversions.ConvertibleStrings Data.Text.Internal.Text Biobase.Types.Names.SpeciesName
instance Data.String.Conversions.ConvertibleStrings Biobase.Types.Names.SpeciesName Data.Text.Internal.Text
instance Control.DeepSeq.NFData Biobase.Types.Names.SpeciesName
instance Data.Binary.Class.Binary Biobase.Types.Names.SpeciesName
instance Data.Serialize.Serialize Biobase.Types.Names.SpeciesName
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.Types.Names.SpeciesName
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.Types.Names.SpeciesName
instance Control.DeepSeq.NFData Biobase.Types.Names.TaxonomicRank
instance Data.String.Conversions.ConvertibleStrings Data.Text.Internal.Text Biobase.Types.Names.TaxonomicRank
instance Data.String.Conversions.ConvertibleStrings Biobase.Types.Names.TaxonomicRank Data.Text.Internal.Text
instance Data.Hashable.Class.Hashable Biobase.Types.Names.TaxonomicRank
instance GHC.Read.Read Biobase.Types.Names.TaxonomicRank
instance Data.Binary.Class.Binary Biobase.Types.Names.TaxonomicRank
instance Data.Serialize.Serialize Biobase.Types.Names.TaxonomicRank
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.Types.Names.TaxonomicRank
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.Types.Names.TaxonomicRank
instance GHC.Generics.Generic Biobase.Types.Names.SpeciesName
instance GHC.Classes.Eq Biobase.Types.Names.SpeciesName

module Biobase.Types.Index.Type

-- | A linear <tt>Int</tt>-based index type.
newtype Index (t :: Nat)
Index :: Int -> Index
[getIndex] :: Index -> Int

-- | Turn an <a>Int</a> into an <a>Index</a> safely.
index :: forall t. KnownNat t => Int -> Index t

-- | Produce <a>Just</a> and <a>Index</a> or <a>Nothing</a>.
maybeIndex :: forall t. KnownNat t => Int -> Maybe (Index t)
instance Data.Vector.Unboxed.Base.Unbox (Biobase.Types.Index.Type.Index t0)
instance Data.Vector.Generic.Mutable.Base.MVector Data.Vector.Unboxed.Base.MVector (Biobase.Types.Index.Type.Index t0)
instance Data.Vector.Generic.Base.Vector Data.Vector.Unboxed.Base.Vector (Biobase.Types.Index.Type.Index t0)
instance GHC.TypeLits.KnownNat t => Data.PrimitiveArray.Index.Class.Index (Biobase.Types.Index.Type.Index t)
instance Data.PrimitiveArray.Index.Class.IndexStream z => Data.PrimitiveArray.Index.Class.IndexStream (z Data.PrimitiveArray.Index.Class.:. Biobase.Types.Index.Type.Index t)
instance Data.PrimitiveArray.Index.Class.IndexStream (Biobase.Types.Index.Type.Index t)
instance Test.QuickCheck.Arbitrary.Arbitrary (Biobase.Types.Index.Type.Index t)
instance GHC.Arr.Ix (Biobase.Types.Index.Type.Index t)
instance GHC.Generics.Generic (Biobase.Types.Index.Type.Index t)
instance GHC.Classes.Ord (Biobase.Types.Index.Type.Index t)
instance GHC.Classes.Eq (Biobase.Types.Index.Type.Index t)
instance GHC.Read.Read (Biobase.Types.Index.Type.Index t)
instance GHC.Show.Show (Biobase.Types.Index.Type.Index t)
instance GHC.TypeLits.KnownNat t => GHC.Num.Num (Biobase.Types.Index.Type.Index t)
instance Control.DeepSeq.NFData (Biobase.Types.Index.Type.Index t)
instance Data.Binary.Class.Binary (Biobase.Types.Index.Type.Index t)
instance Data.Serialize.Serialize (Biobase.Types.Index.Type.Index t)
instance Data.Aeson.Types.ToJSON.ToJSON (Biobase.Types.Index.Type.Index t)
instance Data.Aeson.Types.FromJSON.FromJSON (Biobase.Types.Index.Type.Index t)
instance Data.Hashable.Class.Hashable (Biobase.Types.Index.Type.Index t)


-- | Biological sequence data is oftentimes indexed either <tt>0-</tt> or
--   <tt>1-</tt>based. The <tt>Index</tt> type developed provides static
--   guarantees that there is no confusion what index is in use.
--   
--   This module does not export the ctor <tt>Index</tt>. If you want to
--   (unsafely) use it, import <tt>Biobase.Types.Index.Type</tt> directly.
--   Use <tt>fromInt0</tt> to make clear that you count from 0 and
--   transform to an <tt>Index t</tt>. I.e. <tt>fromInt0 0 :: Index 1</tt>
--   yields the lowest 1-base index.
module Biobase.Types.Index

-- | Uses <a>index</a> to guarantee that the <a>Index</a> is ok.
checkIndex :: forall t. KnownNat t => Index t -> Index t

-- | Re-Index an index of type <tt>Index n</tt> as <tt>Index m</tt>. This
--   is always safe, as <tt>0 :: Index 0</tt> gives <tt>1 :: Index 1</tt>
--   for example. I.e. valid indices become valid indices.
reIndex :: forall n m. (KnownNat n, KnownNat m) => Index n -> Index m

-- | Helper function that allows <tt>addition</tt> of an <a>Index</a> and
--   an <a>Int</a>, with the <a>Int</a> on the right.
(+.) :: forall t. KnownNat t => Index t -> Int -> Index t

-- | Unsafe plus.
unsafePlus :: forall t. KnownNat t => Index t -> Int -> Index t

-- | Helper function that allows <tt>subtraction</tt> of an <a>Index</a>
--   and an <a>Int</a>, with the <a>Int</a> on the right.
(-.) :: forall t. KnownNat t => Index t -> Int -> Index t

-- | Delta between two <a>Index</a> points.
delta :: forall t. KnownNat t => Index t -> Index t -> Int

-- | Unsafe minus.
unsafeMinus :: forall t. KnownNat t => Index t -> Int -> Index t

-- | Return the index as an <tt>Int</tt>-style index that is zero-based.
toInt0 :: forall t. KnownNat t => Index t -> Int

-- | As an index from an <tt>Int</tt>-style zero-based one.
--   
--   TODO We might want to check that the argument is <tt>[0..]</tt>.
fromInt0 :: forall t. 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 <a>Int</a> into an <a>Index</a> safely.
index :: forall t. KnownNat t => Int -> Index t

-- | Produce <a>Just</a> and <a>Index</a> or <a>Nothing</a>.
maybeIndex :: forall t. KnownNat t => Int -> Maybe (Index t)

-- | A linear <tt>Int</tt>-based index type.
data Index (t :: Nat)


-- | Encode the number of hits to expect. This is typically dependent on
--   some "database size". Evalues are bounded by <tt>[0,infinity)</tt>.
--   
--   TODO Evalues close to zero are more interesting. We should strongly
--   consider log-conversion here.
module Biobase.Types.Evalue

-- | Type-safe wrapper for e-values.
newtype Evalue
Evalue :: Double -> Evalue
[getEvalue] :: Evalue -> Double

-- | By default, we expect no hits.
instance Data.Vector.Unboxed.Base.Unbox Biobase.Types.Evalue.Evalue
instance Data.Vector.Generic.Mutable.Base.MVector Data.Vector.Unboxed.Base.MVector Biobase.Types.Evalue.Evalue
instance Data.Vector.Generic.Base.Vector Data.Vector.Unboxed.Base.Vector Biobase.Types.Evalue.Evalue
instance Data.Default.Class.Default Biobase.Types.Evalue.Evalue
instance Biobase.Types.NumericalExtremes.NumericalExtremes Biobase.Types.Evalue.Evalue
instance GHC.Generics.Generic Biobase.Types.Evalue.Evalue
instance GHC.Num.Num Biobase.Types.Evalue.Evalue
instance GHC.Show.Show Biobase.Types.Evalue.Evalue
instance GHC.Read.Read Biobase.Types.Evalue.Evalue
instance GHC.Classes.Ord Biobase.Types.Evalue.Evalue
instance GHC.Classes.Eq Biobase.Types.Evalue.Evalue
instance Data.Binary.Class.Binary Biobase.Types.Evalue.Evalue
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.Types.Evalue.Evalue
instance Data.Hashable.Class.Hashable Biobase.Types.Evalue.Evalue
instance Data.Serialize.Serialize Biobase.Types.Evalue.Evalue
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.Types.Evalue.Evalue
instance Control.DeepSeq.NFData Biobase.Types.Evalue.Evalue


-- | 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 <tt>kcal / mol</tt>.
--   
--   TODO shall we phantom-type the actual units?
newtype DG
DG :: Double -> DG
[dG] :: DG -> Double

-- | <tt>round $ DG / 100</tt>.
newtype DeltaDekaGibbs
DekaG :: Int -> DeltaDekaGibbs
[getDekaG] :: DeltaDekaGibbs -> Int
instance Biobase.Types.NumericalExtremes.NumericalExtremes Biobase.Types.Energy.DeltaDekaGibbs
instance Data.Vector.Unboxed.Base.Unbox Biobase.Types.Energy.DeltaDekaGibbs
instance Data.Vector.Generic.Mutable.Base.MVector Data.Vector.Unboxed.Base.MVector Biobase.Types.Energy.DeltaDekaGibbs
instance Data.Vector.Generic.Base.Vector Data.Vector.Unboxed.Base.Vector Biobase.Types.Energy.DeltaDekaGibbs
instance Data.Hashable.Class.Hashable Biobase.Types.Energy.DeltaDekaGibbs
instance Data.Binary.Class.Binary Biobase.Types.Energy.DeltaDekaGibbs
instance Data.Serialize.Serialize Biobase.Types.Energy.DeltaDekaGibbs
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.Types.Energy.DeltaDekaGibbs
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.Types.Energy.DeltaDekaGibbs
instance Control.DeepSeq.NFData Biobase.Types.Energy.DeltaDekaGibbs
instance Data.Default.Class.Default Biobase.Types.Energy.DeltaDekaGibbs
instance GHC.Generics.Generic Biobase.Types.Energy.DeltaDekaGibbs
instance GHC.Show.Show Biobase.Types.Energy.DeltaDekaGibbs
instance GHC.Read.Read Biobase.Types.Energy.DeltaDekaGibbs
instance GHC.Num.Num Biobase.Types.Energy.DeltaDekaGibbs
instance GHC.Classes.Ord Biobase.Types.Energy.DeltaDekaGibbs
instance GHC.Classes.Eq Biobase.Types.Energy.DeltaDekaGibbs
instance Biobase.Types.NumericalExtremes.NumericalExtremes Biobase.Types.Energy.DG
instance Biobase.Types.NumericalExtremes.NumericalEpsilon Biobase.Types.Energy.DG
instance Data.Vector.Unboxed.Base.Unbox Biobase.Types.Energy.DG
instance Data.Vector.Generic.Mutable.Base.MVector Data.Vector.Unboxed.Base.MVector Biobase.Types.Energy.DG
instance Data.Vector.Generic.Base.Vector Data.Vector.Unboxed.Base.Vector Biobase.Types.Energy.DG
instance Data.Hashable.Class.Hashable Biobase.Types.Energy.DG
instance Data.Binary.Class.Binary Biobase.Types.Energy.DG
instance Data.Serialize.Serialize Biobase.Types.Energy.DG
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.Types.Energy.DG
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.Types.Energy.DG
instance Control.DeepSeq.NFData Biobase.Types.Energy.DG
instance Data.Default.Class.Default Biobase.Types.Energy.DG
instance Data.Data.Data Biobase.Types.Energy.DG
instance GHC.Generics.Generic Biobase.Types.Energy.DG
instance GHC.Show.Show Biobase.Types.Energy.DG
instance GHC.Read.Read Biobase.Types.Energy.DG
instance GHC.Real.Fractional Biobase.Types.Energy.DG
instance GHC.Num.Num Biobase.Types.Energy.DG
instance GHC.Classes.Ord Biobase.Types.Energy.DG
instance GHC.Classes.Eq Biobase.Types.Energy.DG


-- | Bit scores as used by different algorithms in bioinformatics,
--   linguistics, and probably elsewhere.
--   
--   Basically, the base-2 logarithm of the probability of the input given
--   the model vs the probability of the input given the null model.
--   
--   <pre>
--   S = log_2 (P(seq|model) / P(seq|null))
--   </pre>
module Biobase.Types.Bitscore

-- | Bit score; behaves like a double (deriving Num). In particular, the
--   algebraic operations behave as expected <tt>Bitscore a + Bitscore b ==
--   Bitscore (a+b)</tt>.
--   
--   Currently geared towards use as in <tt>Infernal</tt> and
--   <tt>HMMER</tt>.
--   
--   Infernal users guide, p.42: log-odds score in log_2 (aka bits).
newtype Bitscore
Bitscore :: Double -> Bitscore
[getBitscore] :: Bitscore -> Double

-- | A default bitscore of "-infinity", but with <tt>10-1</tt> wiggle room.
--   
--   TODO Check out the different "defaults" Infernal uses

-- | Given a null model and a probability, calculate the corresponding
--   <tt>BitScore</tt>.
--   
--   TODO <tt>x&lt;=epsilon</tt> ?
prob2Score :: Double -> Double -> Bitscore

-- | Given a null model and a <tt>BitScore</tt> return the corresponding
--   probability.
score2Prob :: Double -> Bitscore -> Double
instance Data.Vector.Unboxed.Base.Unbox Biobase.Types.Bitscore.Bitscore
instance Data.Vector.Generic.Mutable.Base.MVector Data.Vector.Unboxed.Base.MVector Biobase.Types.Bitscore.Bitscore
instance Data.Vector.Generic.Base.Vector Data.Vector.Unboxed.Base.Vector Biobase.Types.Bitscore.Bitscore
instance Data.Default.Class.Default Biobase.Types.Bitscore.Bitscore
instance GHC.Generics.Generic Biobase.Types.Bitscore.Bitscore
instance GHC.Real.Fractional Biobase.Types.Bitscore.Bitscore
instance GHC.Num.Num Biobase.Types.Bitscore.Bitscore
instance GHC.Show.Show Biobase.Types.Bitscore.Bitscore
instance GHC.Read.Read Biobase.Types.Bitscore.Bitscore
instance GHC.Classes.Ord Biobase.Types.Bitscore.Bitscore
instance GHC.Classes.Eq Biobase.Types.Bitscore.Bitscore
instance Biobase.Types.NumericalExtremes.NumericalExtremes Biobase.Types.Bitscore.Bitscore
instance Data.Binary.Class.Binary Biobase.Types.Bitscore.Bitscore
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.Types.Bitscore.Bitscore
instance Data.Hashable.Class.Hashable Biobase.Types.Bitscore.Bitscore
instance Data.Serialize.Serialize Biobase.Types.Bitscore.Bitscore
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.Types.Bitscore.Bitscore
instance Control.DeepSeq.NFData Biobase.Types.Bitscore.Bitscore


-- | Accession numbers. These <i>numbers</i> are not really numbers because
--   they they are made up of alphanumeric characters.
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 <tt>Accession</tt>
--   tagged generic type.
newtype Accession t
Accession :: Text -> Accession t
[_getAccession] :: Accession t -> Text

-- | Generate an accession with an explicit phantom type: <tt>accession'
--   Nucleotide <a>Bla</a></tt> has type <tt>:: Accession Nucleotide</tt>.
accession' :: ConvertibleStrings s Text => t -> s -> Accession t

-- | Generate an accession when the type <tt>Accession t</tt> is clear from
--   the context.
accession :: ConvertibleStrings s Text => s -> Accession t

-- | Retag an accession
retagAccession :: Accession f -> Accession t

-- | nucleotide sequence
data Nucleotide
Nucleotide :: Nucleotide

-- | protein sequence
data Protein
Protein :: Protein

-- | Tag as being a clan.
data Clan
Clan :: Clan

-- | Tag as being a Pfam model.
data Pfam
Pfam :: Pfam

-- | Tag as being an Rfam model. Used for Stockholm and CM files.
data Rfam
Rfam :: Rfam

-- | Species have an accession number, too.
data Species
Species :: Species

-- | Guess the type of accession number. Returns <tt>Nothing</tt> if
--   unknown structure.
guessAccessionType :: Accession t -> Maybe Text
instance GHC.Generics.Generic (Biobase.Types.Accession.Accession t)
instance GHC.Show.Show (Biobase.Types.Accession.Accession t)
instance GHC.Read.Read (Biobase.Types.Accession.Accession t)
instance GHC.Classes.Ord (Biobase.Types.Accession.Accession t)
instance GHC.Classes.Eq (Biobase.Types.Accession.Accession t)
instance Data.String.IsString (Biobase.Types.Accession.Accession t)
instance Data.Binary.Class.Binary (Biobase.Types.Accession.Accession t)
instance Data.Aeson.Types.FromJSON.FromJSON (Biobase.Types.Accession.Accession t)
instance Data.Hashable.Class.Hashable (Biobase.Types.Accession.Accession t)
instance Data.Serialize.Serialize (Biobase.Types.Accession.Accession t)
instance Data.Aeson.Types.ToJSON.ToJSON (Biobase.Types.Accession.Accession t)
instance Control.DeepSeq.NFData (Biobase.Types.Accession.Accession t)


-- | Biological classification of species.
module Biobase.Types.Taxonomy

-- | Taxonomic classification. <tt>Enum</tt> together with a final
--   <tt>Unknown</tt> is somewhat fishy.
data Classification
Kingdom :: Classification
Phylum :: Classification
Class :: Classification
Order :: Classification
SubOrder :: Classification
Family :: Classification
Genus :: Classification
Species :: Classification
Unknown :: Classification

-- | A somewhat generic representation of a species within a taxonomic
--   context.
data Taxon
Taxon :: !SpeciesName -> !(Accession Species) -> !(Vector (TaxonomicRank, Classification)) -> Taxon

-- | the full, formal name of a species
[species] :: Taxon -> !SpeciesName

-- | the accession for the species (or <tt>""</tt> if unknown)
[accession] :: Taxon -> !(Accession Species)

-- | vector with classification information
[classification] :: Taxon -> !(Vector (TaxonomicRank, Classification))
instance GHC.Generics.Generic Biobase.Types.Taxonomy.Taxon
instance GHC.Show.Show Biobase.Types.Taxonomy.Taxon
instance GHC.Read.Read Biobase.Types.Taxonomy.Taxon
instance GHC.Classes.Eq Biobase.Types.Taxonomy.Taxon
instance Data.Vector.Unboxed.Base.Unbox Biobase.Types.Taxonomy.Classification
instance Data.Vector.Generic.Mutable.Base.MVector Data.Vector.Unboxed.Base.MVector Biobase.Types.Taxonomy.Classification
instance Data.Vector.Generic.Base.Vector Data.Vector.Unboxed.Base.Vector Biobase.Types.Taxonomy.Classification
instance Data.Binary.Class.Binary Biobase.Types.Taxonomy.Taxon
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.Types.Taxonomy.Taxon
instance Data.Serialize.Serialize Biobase.Types.Taxonomy.Taxon
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.Types.Taxonomy.Taxon
instance Control.DeepSeq.NFData Biobase.Types.Taxonomy.Taxon
instance Data.Hashable.Class.Hashable Biobase.Types.Taxonomy.Taxon
instance GHC.Generics.Generic Biobase.Types.Taxonomy.Classification
instance GHC.Enum.Enum Biobase.Types.Taxonomy.Classification
instance GHC.Show.Show Biobase.Types.Taxonomy.Classification
instance GHC.Read.Read Biobase.Types.Taxonomy.Classification
instance GHC.Classes.Ord Biobase.Types.Taxonomy.Classification
instance GHC.Classes.Eq Biobase.Types.Taxonomy.Classification
instance Data.Binary.Class.Binary Biobase.Types.Taxonomy.Classification
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.Types.Taxonomy.Classification
instance Data.Hashable.Class.Hashable Biobase.Types.Taxonomy.Classification
instance Data.Serialize.Serialize Biobase.Types.Taxonomy.Classification
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.Types.Taxonomy.Classification
instance Control.DeepSeq.NFData Biobase.Types.Taxonomy.Classification