ELynx.Sequence.Sequence

Creation date: Thu Oct 4 18:54:51 2018.

This module is to be imported qualified.

Types

type Name = ByteString

Names are just ByteStrings.

type Description = ByteString

The description of a sequence.

type Characters = Vector Character

The vector of characters of a sequence.

data Sequence

Sequences have a name, a possibly empty description, a code and hopefully a lot of data.

Constructors

Sequence

Fields

• name :: Name
• description :: Description
• alphabet :: Alphabet
• characters :: Characters

Instances

Show Sequence

Defined in ELynx.Sequence.Sequence

Methods

showsPrec :: Int -> Sequence -> ShowS

show :: Sequence -> String

showList :: [Sequence] -> ShowS

Eq Sequence

Defined in ELynx.Sequence.Sequence

Methods

(==) :: Sequence -> Sequence -> Bool

(/=) :: Sequence -> Sequence -> Bool

Input

fromByteString :: ByteString -> Characters

Convert byte string to sequence characters.

Output

toByteString :: Characters -> ByteString

Convert sequence characters to byte string.

header :: [Sequence] -> ByteString

A short description of the sequence.

summarize :: Sequence -> ByteString

Trim and show a Sequence.

summarizeSequences :: [Sequence] -> ByteString

Trim and show a list of Sequences.

body :: [Sequence] -> ByteString

Trim and show a list of Sequences.

Analysis

length :: Sequence -> Int

Calculate length of Sequence.

equalLength :: [Sequence] -> Bool

Check if all Sequences have equal length.

longest :: [Sequence] -> Sequence

Find the longest Sequence in a list.

Manipulation

trim :: Int -> Sequence -> Sequence

Trim to given length.

concat :: Sequence -> Sequence -> Sequence

Concatenate two sequences. Names have to match.

concatSequences :: [[Sequence]] -> [Sequence]

Concatenate a list of sequences, see concat.

Filtering

filterShorterThan :: Int -> [Sequence] -> [Sequence]

Only take Sequences that are shorter than a given number.

filterLongerThan :: Int -> [Sequence] -> [Sequence]

Only take Sequences that are longer than a given number.

filterStandard :: [Sequence] -> [Sequence]

Only take Sequences that contain at least on non-IUPAC character.