bio-0.4.6: A bioinformatics library Source code Contents Index

Bio.Sequence.HashWord

Synopsis

data HashF k = HF { hash :: SeqData -> Offset -> Maybe k hashes :: SeqData -> [(k, Offset)] ksort :: [k] -> [k] } genkeys :: HashF k -> HashF k contigous :: Integral k => Int -> HashF k rcontig :: Integral k => Int -> HashF k compact :: SeqData -> [SeqData] rcpacked :: Integral k => Int -> HashF k type Shape = String gapped :: Integral k => Shape -> HashF k isN :: Char -> Bool n2k :: Integral k => Int -> SeqData -> k n2i' :: Num a => a -> SeqData -> a k2n :: Integral k => Int -> k -> SeqData val :: Num t => Char -> t unval :: Num a => a -> Char complement :: Char -> Char

Documentation

data HashF k Source

This is a struct for containing a set of hashing functions Constructors HF hash :: SeqData -> Offset -> Maybe k calculates the hash at a given offset in the sequence hashes :: SeqData -> [(k, Offset)] calculate all hashes from a sequence, and their indices ksort :: [k] -> [k] for sorting hashes

genkeys :: HashF k -> HashF k Source

Adds a default hashes function to a HashF, when hash is defined.

contigous :: Integral k => Int -> HashF k Source

Contigous constructs an int/eger from a contigous k-word.

rcontig :: Integral k => Int -> HashF k Source

Like contigous, but returns the same hash for a word and its reverse complement.

compact :: SeqData -> [SeqData] Source

rcpacked :: Integral k => Int -> HashF k Source

Like rcontig, but ignoring monomers (i.e. arbitrarily long runs of a single nucelotide are treated the same a single nucleotide.

type Shape = String Source

gapped :: Integral k => Shape -> HashF k Source

isN :: Char -> Bool Source

n2k :: Integral k => Int -> SeqData -> k Source

n2i' :: Num a => a -> SeqData -> a Source

k2n :: Integral k => Int -> k -> SeqData Source

val :: Num t => Char -> t Source

unval :: Num a => a -> Char Source

complement :: Char -> Char Source

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