Bio.Sequence.Alignment

Documentation

type Substitution a = a -> a -> Int

Substitution function for a values comparison

type Gap = Int

Gap type

class Alignment a where

Introduces all useful methods to create an alignment

Minimal complete definition

gap, substitution, conditions, inits, selector, additional

Methods

gap :: a -> Gap

substitution :: a -> Substitution Char

conditions :: a -> Conditions

inits :: a -> Int -> Int

selector :: a -> StartSelector

additional :: a -> Int

alignment :: Alignment a => a -> ByteString -> ByteString -> (Int, (ByteString, ByteString))

mkGlobal :: Substitution Char -> Gap -> SimpleAlignment

mkLocal :: Substitution Char -> Gap -> SimpleAlignment

mkSemiglobal :: Substitution Char -> Gap -> SimpleAlignment

mkEditDistance :: EditDistance