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


-- | Libary for Hidden Markov Models in HMMER3 format.
--   
--   Libary containing parsing and visualisation functions and
--   datastructures for Hidden Markov Models in HMMER3 format.
@package BioHMM
@version 1.1.2


-- | Datastructures for nHMMER hidden Markov models, representing RNA
--   families For more information on nHMMER consult
--   <a>http://eddylab.org/infernal/</a>
module Bio.HMMData

-- | Data structure for HMMER
data HMMER3
HMMER3 :: String -> String -> String -> Maybe String -> Int -> Maybe Int -> String -> Bool -> Bool -> Bool -> Bool -> Bool -> String -> Maybe String -> Int -> Double -> Int -> Maybe (Double, Double) -> Maybe (Double, Double) -> Maybe (Double, Double) -> Maybe String -> Maybe String -> (Double, Double) -> (Double, Double) -> (Double, Double) -> String -> HMMER3Composite -> HMMER3Node -> Vector HMMER3Node -> HMMER3
[version] :: HMMER3 -> String
[name] :: HMMER3 -> String
[acc] :: HMMER3 -> String
[desc] :: HMMER3 -> Maybe String
[leng] :: HMMER3 -> Int
[maxl] :: HMMER3 -> Maybe Int
[alpha] :: HMMER3 -> String
[rf] :: HMMER3 -> Bool
[mm] :: HMMER3 -> Bool
[cons] :: HMMER3 -> Bool
[cs] :: HMMER3 -> Bool
[map] :: HMMER3 -> Bool
[date] :: HMMER3 -> String
[com] :: HMMER3 -> Maybe String
[nseq] :: HMMER3 -> Int
[effn] :: HMMER3 -> Double
[cksum] :: HMMER3 -> Int
[ga] :: HMMER3 -> Maybe (Double, Double)
[tc] :: HMMER3 -> Maybe (Double, Double)
[nc] :: HMMER3 -> Maybe (Double, Double)
[bm] :: HMMER3 -> Maybe String
[sm] :: HMMER3 -> Maybe String
[localmsv] :: HMMER3 -> (Double, Double)
[localviterbi] :: HMMER3 -> (Double, Double)
[localforward] :: HMMER3 -> (Double, Double)
[hmm] :: HMMER3 -> String
[compo] :: HMMER3 -> HMMER3Composite
[begin] :: HMMER3 -> HMMER3Node
[nodes] :: HMMER3 -> Vector HMMER3Node

-- | Data structure for the HMMER3 node
data HMMER3Node
HMMER3Node :: Int -> Vector Double -> Maybe Int -> Maybe Char -> Maybe Char -> Bool -> Maybe Char -> Vector Double -> Maybe Double -> Maybe Double -> Maybe Double -> Maybe Double -> Maybe Double -> Maybe Double -> Maybe Double -> HMMER3Node
[nodeId] :: HMMER3Node -> Int
[matchEmissions] :: HMMER3Node -> Vector Double
[nma] :: HMMER3Node -> Maybe Int
[ncr] :: HMMER3Node -> Maybe Char
[nra] :: HMMER3Node -> Maybe Char
[nmv] :: HMMER3Node -> Bool
[ncs] :: HMMER3Node -> Maybe Char
[insertEmissions] :: HMMER3Node -> Vector Double
[m2m] :: HMMER3Node -> Maybe Double
[m2i] :: HMMER3Node -> Maybe Double
[m2d] :: HMMER3Node -> Maybe Double
[i2m] :: HMMER3Node -> Maybe Double
[i2i] :: HMMER3Node -> Maybe Double
[d2m] :: HMMER3Node -> Maybe Double
[d2d] :: HMMER3Node -> Maybe Double

-- | Data structure for the HMMER3 overall probabilities
data HMMER3Composite
HMMER3Composite :: Vector Double -> HMMER3Composite
[compositeMatchEmissions] :: HMMER3Composite -> Vector Double
instance GHC.Classes.Eq Bio.HMMData.HMMER3
instance GHC.Show.Show Bio.HMMData.HMMER3
instance GHC.Classes.Eq Bio.HMMData.HMMER3Composite
instance GHC.Show.Show Bio.HMMData.HMMER3Composite
instance GHC.Classes.Eq Bio.HMMData.HMMER3Node
instance GHC.Show.Show Bio.HMMData.HMMER3Node


-- | Parse HMM models Currently contains a parser for HMMER3 models For
--   more information on HMMER consult: <a>http://hmmer.org</a>
module Bio.HMMParser

-- | parse HMMER3 model from input string
parseHMMER3 :: [Char] -> Either ParseError [HMMER3]

-- | parse HMMER3 from input filePath
readHMMER3 :: String -> IO (Either ParseError [HMMER3])
alphabetToSymbols :: String -> String


-- | Parse HMMCompare output
module Bio.HMMCompareResult

-- | Datastructure for result strings of comparisons between covariance
--   models by HMMCompare
data HMMCompareResult

-- | parse HMMCompareResult model from input string
parseHMMCompareResult :: String -> Either ParseError [HMMCompareResult]

-- | parse HMMCompareResult from input filePath
readHMMCompareResult :: String -> IO (Either ParseError [HMMCompareResult])
model1Name :: HMMCompareResult -> String
model2Name :: HMMCompareResult -> String
linkscore1 :: HMMCompareResult -> Double
linkscore2 :: HMMCompareResult -> Double
linksequence :: HMMCompareResult -> String
model1matchednodes :: HMMCompareResult -> [Int]
model2matchednodes :: HMMCompareResult -> [Int]

-- | Parser for HMMCompare result strings
getHMMCompareResults :: FilePath -> IO [Either ParseError HMMCompareResult]
getModelsNames :: [HMMCompareResult] -> [String]
getModelNames :: HMMCompareResult -> [String]
instance GHC.Show.Show Bio.HMMCompareResult.HMMCompareResult


module Bio.HMMDraw
drawHMMER3 :: String -> Int -> Double -> Double -> Double -> String -> Vector (String, Colour Double) -> (HMMER3, Maybe StockholmAlignment, Vector (Int, Vector (Colour Double)), Colour Double) -> (QDiagram Cairo V2 Double Any, Maybe (QDiagram Cairo V2 Double Any))
drawSingleHMMER3s :: String -> Int -> Double -> Double -> Double -> String -> [HMMER3] -> [Maybe StockholmAlignment] -> [(QDiagram Cairo V2 Double Any, Maybe (QDiagram Cairo V2 Double Any))]
svgsize :: SizeSpec V2 Double

-- | Check for available cairo output formats
diagramName :: String -> String -> Either String String
printHMM :: String -> SizeSpec V2 Double -> QDiagram Cairo V2 Double Any -> IO ()
getComparisonsHighlightParameters :: [HMMER3] -> [HMMCompareResult] -> [(Int, Int, Int, Int, Int, Int, Int, Int)]
drawSingleHMMComparison :: String -> Int -> Double -> String -> Double -> Double -> [HMMER3] -> [Maybe StockholmAlignment] -> [HMMCompareResult] -> [(QDiagram Cairo V2 Double Any, Maybe (QDiagram Cairo V2 Double Any))]