-- Hoogle documentation, generated by Haddock
-- See Hoogle, http://www.haskell.org/hoogle/


-- | Modify fasta (and CLIP) files in several optional ways
--   
--   Modify fasta (and CLIP) files in several optional ways
@package modify-fasta
@version 0.8.0.3

module Utility

-- | Adds the length of a sequence to the header of that sequence
addLengthHeader :: FastaSequence -> FastaSequence

-- | Adds filler germlines to normal fasta files
addFillerGermlines :: [FastaSequence] -> CloneMap
replaceChars :: Char -> Text -> Text -> Text

-- | Get the field of a fasta sequence, 1 indexed split by "|"
getField :: Int -> FastaSequence -> Text

module Types
data GeneticUnit
AminoAcid :: GeneticUnit
Nucleotide :: GeneticUnit
data FrameType
InFrame :: FrameType
OutFrame :: FrameType
type ID = Int
type Codon = Text
type CodonMut = Int
type Field = Int
type Start = Int
type Stop = Int
type Position = Int
type Frame = Int
type CloneEntry = (Germline, [FastaSequence])
type FillInValue = (Field, Start, Char)
type Mutation = (Char, Char)
type CountMap = Map (Position, Mutation) Int
type CodonMutations = [[(Position, Mutation)]]
instance GHC.Show.Show Types.FrameType
instance GHC.Read.Read Types.FrameType
instance GHC.Show.Show Types.GeneticUnit
instance GHC.Read.Read Types.GeneticUnit

module FilterFastaList
hasNoStops :: GeneticUnit -> Int -> FastaSequence -> Bool
isInFrame :: FastaSequence -> Bool
hasCustomFilter :: Bool -> Maybe Int -> Text -> FastaSequence -> Bool
hasAllCustomFilters :: Bool -> [(Maybe Int, Text)] -> FastaSequence -> Bool

module Print
printFasta :: CloneMap -> Text
printFastaNoGermline :: CloneMap -> Text
printSequenceCount :: Bool -> Int -> CloneMap -> Text

-- | Takes a clone entry and returns a formatted text with or without
--   germline
printCloneEntry :: Bool -> CloneEntry -> Text

module TransformFastaList

-- | Convert sequences to amino acids
convertToAminoAcidsFastaSequence :: FastaSequence -> FastaSequence
replaceChars :: Char -> Text -> Text -> Text

-- | Fill in the sequence with corrected nucleotides or amino acids
fillInSequence :: Field -> Start -> Char -> FastaSequence -> FastaSequence

-- | Change a field to a match, so a regex "ch.*_" to field 2 of
--   ">abc|brie_cheese_dude" would result in ">abc|cheese_". Useful
--   for getting specific properties from a field
changeField :: Maybe Field -> Text -> FastaSequence -> FastaSequence

-- | Change all fields to their matches based on changeField
changeAllFields :: FastaSequence -> [(Maybe Int, Text)] -> FastaSequence

-- | Get a region of a sequence, 1 indexed
getRegionSequence :: Maybe Start -> Maybe Stop -> FastaSequence -> FastaSequence

-- | Trim off extra nucleotides (or amino acids) from a fasta sequence. If
--   inframe and outframe are specified, instead cut off based on those
--   frames.
trimFasta :: GeneticUnit -> Maybe Frame -> Maybe Frame -> FastaSequence -> FastaSequence

-- | Convert non standard nucleotides to gaps
removeUnknownNucs :: FastaSequence -> FastaSequence

module FilterCloneList
filterHighlyMutatedEntry :: GeneticUnit -> CloneEntry -> CloneEntry

module Diversity
hamming :: Text -> Text -> Int
diversity :: (Ord b) => Double -> [b] -> Double
choose :: (Integral a) => a -> a -> a
rarefactionCurve :: (Eq a, Ord a) => [a] -> [Double]
rarefactionViable :: [Double] -> Double

module FilterCloneMap
isRight' :: Either a b -> Bool
listToMaybe' :: [a] -> Maybe [a]
filterHighlyMutated :: GeneticUnit -> CloneMap -> (CloneMap, Maybe String)
removeCodonMutCount :: CodonMut -> Text -> Text -> CloneMap -> CloneMap
removeStopsCloneMap :: GeneticUnit -> Int -> CloneMap -> (CloneMap, Maybe String)
removeDuplicatesCloneMap :: CloneMap -> CloneMap
removeOutOfFrameSeqs :: CloneMap -> CloneMap
removeCustomFilter :: Bool -> Bool -> Maybe Int -> Text -> CloneMap -> CloneMap
removeAllCustomFilters :: Bool -> Bool -> CloneMap -> [(Maybe Int, Text)] -> CloneMap
removeEmptyClone :: CloneMap -> CloneMap
convertToAminoAcidsCloneMap :: CloneMap -> (CloneMap, Maybe String)

module TransformCloneList
onlyMutations :: CodonMut -> Text -> Text -> CloneEntry -> CloneEntry
frequentMutations :: Maybe Int -> Maybe Int -> Maybe Double -> CloneEntry -> CloneEntry