BiobaseXNA-0.9.2.1: Efficient RNA/DNA representations

Safe HaskellNone
LanguageHaskell2010

Biobase.Primary.Letter

Contents

Description

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.

Synopsis

Documentation

newtype Letter t Source

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

Constructors

Letter 

Fields

getLetter :: Int
 

Instances

IsostericityLookup ExtPair Source

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

TODO inClass missing

IsostericityLookup Pair Source

Normal basepairs are assumed to have cWW basepairing.

TODO inClass missing

Vector Vector (Letter a) Source 
MVector MVector (Letter a) Source 
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) Source 
Ord (Letter t) Source 
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) Source 
IsString [Letter RNA] 
IsString [Letter DNA] 
IsString [Letter XNA] 
IsString [Letter DEG] 
(Unbox (Letter t), IsString [Letter t]) => IsString (Vector (Letter t)) Source 
Generic (Letter t) Source 
Index (Letter l) Source 
IndexStream (Letter l) Source 
ToJSON (Letter t) Source 
FromJSON (Letter t) Source 
Binary (Letter t) Source 
Serialize (Letter t) Source 
NFData (Letter t) Source 
Hashable (Letter t) Source 
Unbox (Letter a) Source 
Degenerate (Letter RNA) Source 
Degenerate (Letter DNA) Source 
Degenerate (Letter XNA) Source 
Complement (Letter RNA) (Letter RNA) Source 
Complement (Letter RNA) (Letter DNA) Source 
Complement (Letter DNA) (Letter RNA) Source 
Complement (Letter DNA) (Letter DNA) Source 
IndexStream z => IndexStream ((:.) z (Letter l)) Source 
MkViennaPair (Letter RNA, Letter RNA) Source 
data MVector s0 (Letter a0) = MV_Letter (MVector s Int) Source 
type Rep (Letter t) Source 
data Vector (Letter a0) = V_Letter (Vector Int) Source 

type Primary t = Vector (Letter t) Source

class MkPrimary n t where Source

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

Methods

primary :: n -> Primary t Source

Instances

Instances for Letter.