Copyright | (c) Dominik Schrempf 2018 |
---|---|
License | GPL-3 |
Maintainer | dominik.schrempf@gmail.com |
Stability | unstable |
Portability | portable |
Safe Haskell | None |
Language | Haskell2010 |
Creation date: Thu Oct 4 18:54:51 2018.
Synopsis
- type SequenceName = ByteString
- type SequenceCharacters = Vector Character
- data Sequence = Sequence SequenceName Alphabet SequenceCharacters
- name :: Lens' Sequence SequenceName
- alphabet :: Lens' Sequence Alphabet
- characters :: Lens' Sequence SequenceCharacters
- toCharacters :: ByteString -> SequenceCharacters
- fromCharacters :: SequenceCharacters -> ByteString
- showSequence :: Sequence -> ByteString
- showSequenceList :: [Sequence] -> ByteString
- sequenceListHeader :: ByteString
- summarizeSequence :: Sequence -> ByteString
- summarizeSequenceList :: [Sequence] -> ByteString
- summarizeSequenceListBody :: [Sequence] -> ByteString
- lengthSequence :: Sequence -> Int
- equalLength :: [Sequence] -> Bool
- longest :: [Sequence] -> Sequence
- trimSequence :: Int -> Sequence -> Sequence
- concatenate :: Sequence -> Sequence -> Sequence
- concatenateSeqs :: [[Sequence]] -> [Sequence]
- filterShorterThan :: Int -> [Sequence] -> [Sequence]
- filterLongerThan :: Int -> [Sequence] -> [Sequence]
Types
type SequenceName = ByteString Source #
For now, SequenceName
s are just ByteString
s.
type SequenceCharacters = Vector Character Source #
The vector of characters of a sequence.
Sequences have a name, a code and hopefully a lot of data.
Lenses
Input
toCharacters :: ByteString -> SequenceCharacters Source #
Convert byte string to sequence characters.
Output
fromCharacters :: SequenceCharacters -> ByteString Source #
Convert sequence characters to byte string.
showSequence :: Sequence -> ByteString Source #
Show a Sequence
, untrimmed.
showSequenceList :: [Sequence] -> ByteString Source #
Show a list of Sequence
s, untrimmed.
sequenceListHeader :: ByteString Source #
Header printed before Sequence
list.
summarizeSequence :: Sequence -> ByteString Source #
Trim and show a Sequence
.
summarizeSequenceList :: [Sequence] -> ByteString Source #
Trim and show a list of Sequence
s.
summarizeSequenceListBody :: [Sequence] -> ByteString Source #
Trim and show a list of Sequence
s.
Analysis
Manipulation
concatenate :: Sequence -> Sequence -> Sequence Source #
Concatenate two sequences. SequenceName
s have to match.
concatenateSeqs :: [[Sequence]] -> [Sequence] Source #
Concatenate a list of sequences, see concatenate
.