ELynx.Data.Sequence.Sequence

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

Types

type SequenceName = ByteString

For now, SequenceNames are just ByteStrings.

type SequenceCharacters = Vector Character

The vector of characters of a sequence.

data Sequence

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

Constructors

Sequence SequenceName Alphabet SequenceCharacters

Instances

Eq Sequence

Defined in ELynx.Data.Sequence.Sequence

Methods

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

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

Show Sequence

Defined in ELynx.Data.Sequence.Sequence

Methods

showsPrec :: Int -> Sequence -> ShowS

show :: Sequence -> String

showList :: [Sequence] -> ShowS

Lenses

name :: Lens' Sequence SequenceName

alphabet :: Lens' Sequence Alphabet

characters :: Lens' Sequence SequenceCharacters

Input

toCharacters :: ByteString -> SequenceCharacters

Convert byte string to sequence characters.

Output

fromCharacters :: SequenceCharacters -> ByteString

Convert sequence characters to byte string.

showSequence :: Sequence -> ByteString

Show a Sequence, untrimmed.

showSequenceList :: [Sequence] -> ByteString

Show a list of Sequences, untrimmed.

sequenceListHeader :: ByteString

Header printed before Sequence list.

summarizeSequence :: Sequence -> ByteString

Trim and show a Sequence.

summarizeSequenceList :: [Sequence] -> ByteString

Trim and show a list of Sequences.

summarizeSequenceListBody :: [Sequence] -> ByteString

Trim and show a list of Sequences.

Analysis

lengthSequence :: 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

trimSequence :: Int -> Sequence -> Sequence

Trim to given length.

concatenate :: Sequence -> Sequence -> Sequence

Concatenate two sequences. SequenceNames have to match.

concatenateSeqs :: [[Sequence]] -> [Sequence]

Concatenate a list of sequences, see concatenate.

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.