seqloc-0.6.1.1: Handle sequence locations for bioinformatics

Safe HaskellSafe
LanguageHaskell2010

Bio.SeqLoc.SeqLike

Documentation

class SeqLike s where #

Minimal complete definition

length, ntAt, subseq, subseqPad, concat

Methods

length :: Integral n => s -> n #

Length of sequence data

ntAt :: Integral n => s -> n -> Maybe Char #

Just the nucleotide at a specified sequence data offset, given in 0-based coordinates, or Nothing if the offset is beyond the bounds of the data

subseq :: (Integral n, Integral m) => n -> m -> s -> Maybe s #

Just the nucleotides in subsequence of the sequence data, or Nothing if the region extends beyond the bounds of the sequence.

subseqPad :: (Integral n, Integral m) => n -> m -> s -> s #

Nucleotides in a subsequence of the sequence data, padded with N when the region extends beyond the bounds of the sequence.

concat :: [s] -> s #

Instances

SeqLike ByteString # 
SeqLike ByteString # 
SeqLike [Char] # 

Methods

length :: Integral n => [Char] -> n #

ntAt :: Integral n => [Char] -> n -> Maybe Char #

subseq :: (Integral n, Integral m) => n -> m -> [Char] -> Maybe [Char] #

subseqPad :: (Integral n, Integral m) => n -> m -> [Char] -> [Char] #

concat :: [[Char]] -> [Char] #