Biobase.Primary.Letter

A newtype with an attached phenotype which allows us to encode nucleotides and amino acids. Actual seqence-specific functions can be founds in the appropriate modules AA and Nuc.

Documentation

newtype Letter t

A Letter together with its phantom type t encodes bio-sequences.

Constructors

Letter

Fields

getLetter :: Int

Instances

IsostericityLookup ExtPair

For extended basepairs, we take the default mapping and go from there.

TODO inClass missing

IsostericityLookup Pair

Normal basepairs are assumed to have cWW basepairing.

TODO inClass missing

Vector Vector (Letter a)

MVector MVector (Letter a)

Bounded (Letter RNA)

Bounded (Letter DNA)

Bounded (Letter XNA)

Bounded (Letter DEG)

Enum (Letter Unknown)

Enum (Letter RNA)

Enum (Letter DNA)

Enum (Letter XNA)

Enum (Letter DEG)

Enum (Letter AA)

Eq (Letter t)

Ord (Letter t)

Read (Letter Unknown)

Read (Letter RNA)

Read (Letter DNA)

Read (Letter XNA)

Read (Letter AA)

Show (Letter Unknown)

Show (Letter RNA)

Show (Letter DNA)

Show (Letter XNA)

Show (Letter DEG)

Show (Letter AA)

Ix (Letter t)

IsString [Letter RNA]

IsString [Letter DNA]

IsString [Letter XNA]

IsString [Letter DEG]

(Unbox (Letter t), IsString [Letter t]) => IsString (Vector (Letter t))

Generic (Letter t)

Index (Letter l)

IndexStream (Letter l)

ToJSON (Letter t)

FromJSON (Letter t)

Binary (Letter t)

Serialize (Letter t)

NFData (Letter t)

Hashable (Letter t)

Unbox (Letter a)

Degenerate (Letter RNA)

Degenerate (Letter DNA)

Degenerate (Letter XNA)

Complement (Letter RNA) (Letter RNA)

Complement (Letter RNA) (Letter DNA)

Complement (Letter DNA) (Letter RNA)

Complement (Letter DNA) (Letter DNA)

IndexStream z => IndexStream ((:.) z (Letter l))

MkViennaPair (Letter RNA, Letter RNA)

data MVector s0 (Letter a0) = MV_Letter (MVector s Int)

type Rep (Letter t)

data Vector (Letter a0) = V_Letter (Vector Int)

type Primary t = Vector (Letter t)

class MkPrimary n t where

Conversion from a large number of sequence-like inputs to primary sequences.

Methods

primary :: n -> Primary t

Instances

MkPrimary (Vector Char) t => MkPrimary String t

MkPrimary (Vector Char) t => MkPrimary ByteString t

MkPrimary (Vector Char) t => MkPrimary ByteString t

MkPrimary (Vector Char) t => MkPrimary Text t

MkPrimary (Vector Char) t => MkPrimary Text t

MkPrimary (Vector Char) RNA

MkPrimary (Vector Char) DNA

MkPrimary (Vector Char) XNA

MkPrimary (Vector Char) DEG

MkPrimary (Vector Char) AA

MkPrimary (Vector Int) Unknown

Instances for Letter.