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


-- | Unsupervized construction of RNA family models
--   
--   RNAlien is a tool for automatic construction of RNAfamily models from
--   a single sequence.
--   
--   It is available as a commandline tool, for testing or construction of
--   few sequences the webservice can be used.
--   
--   The source code of RNAlien, as well as the webserver is open source
--   and available via GitHub (License GPL-3):
--   
--   <ul>
--   <li><a>RNAlien</a></li>
--   <li><a>AlienServer</a></li>
--   </ul>
--   
--   TaxonomyTools which can be used to visualise the organisms included in
--   a RNAlien result can be found here (License GPL-3):
--   
--   <ul>
--   <li><a>TaxonomyTools-Github</a></li>
--   <li><a>TaxonomyTools-Hackage</a></li>
--   </ul>
--   
--   For instruction how to use RNAlien please see the <a>Help page</a>.
--   
--   Dependencies:
--   
--   <ul>
--   <li><a>Infernal</a></li>
--   <li><a>Locarna</a></li>
--   <li><a>RNAz</a></li>
--   <li><a>RNAcode</a></li>
--   <li><a>ViennaRNA package</a></li>
--   </ul>
--   
--   Installation via cabal-install:
--   
--   <pre>
--   cabal install RNAlien
--   </pre>
@package RNAlien
@version 1.6.0


-- | Interface for the RNAcentral REST webservice.
module Biobase.RNAlien.RNAcentralHTTP

-- | Function for querying the RNAcentral REST interface.
rnaCentralHTTP :: String -> IO (Either String RNAcentralEntryResponse)

-- | Build a query from a input sequence
--   
--   TODO [chzs] consider using strict bytestring as long as possible.
--   
--   TODO [chzs] consider giving useful typelevel names to the types in
--   <tt>Fasta</tt>. One may give a type-level name to the sequence
--   identifier, and an identifier (like <tt>DNA</tt>) to the biosequence
--   type.
buildSequenceViaMD5Query :: Fasta () () -> String
buildStringViaMD5Query :: String -> String
getRNACentralEntries :: [String] -> IO [Either String RNAcentralEntryResponse]
showRNAcentralAlienEvaluation :: [Either String RNAcentralEntryResponse] -> String

-- | Data structure for RNAcentral entry response
data RNAcentralEntryResponse
RNAcentralEntryResponse :: Int -> Maybe Text -> Maybe Text -> [RNAcentralEntry] -> RNAcentralEntryResponse
[count] :: RNAcentralEntryResponse -> Int
[next] :: RNAcentralEntryResponse -> Maybe Text
[previous] :: RNAcentralEntryResponse -> Maybe Text
[results] :: RNAcentralEntryResponse -> [RNAcentralEntry]
data RNAcentralEntry
RNAcentralEntry :: Text -> Text -> Text -> Text -> Int -> Text -> Text -> RNAcentralEntry
[url] :: RNAcentralEntry -> Text
[rnacentral_id] :: RNAcentralEntry -> Text
[md5] :: RNAcentralEntry -> Text
[sequence] :: RNAcentralEntry -> Text
[length] :: RNAcentralEntry -> Int
[xrefs] :: RNAcentralEntry -> Text
[publications] :: RNAcentralEntry -> Text
instance GHC.Generics.Generic Biobase.RNAlien.RNAcentralHTTP.RNAcentralEntryResponse
instance GHC.Classes.Eq Biobase.RNAlien.RNAcentralHTTP.RNAcentralEntryResponse
instance GHC.Show.Show Biobase.RNAlien.RNAcentralHTTP.RNAcentralEntryResponse
instance GHC.Generics.Generic Biobase.RNAlien.RNAcentralHTTP.RNAcentralEntry
instance GHC.Classes.Eq Biobase.RNAlien.RNAcentralHTTP.RNAcentralEntry
instance GHC.Show.Show Biobase.RNAlien.RNAcentralHTTP.RNAcentralEntry
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.RNAlien.RNAcentralHTTP.RNAcentralEntryResponse
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.RNAlien.RNAcentralHTTP.RNAcentralEntryResponse
instance Data.Aeson.Types.ToJSON.ToJSON Biobase.RNAlien.RNAcentralHTTP.RNAcentralEntry
instance Data.Aeson.Types.FromJSON.FromJSON Biobase.RNAlien.RNAcentralHTTP.RNAcentralEntry


-- | This module contains data structures for RNAlien
module Biobase.RNAlien.Types

-- | Static construction options
data StaticOptions
StaticOptions :: String -> String -> Double -> Maybe Int -> Bool -> String -> Int -> Bool -> Bool -> Bool -> Int -> Maybe String -> Maybe String -> Bool -> Bool -> StaticOptions
[tempDirPath] :: StaticOptions -> String
[sessionID] :: StaticOptions -> String
[nSCICutoff] :: StaticOptions -> Double
[userTaxId] :: StaticOptions -> Maybe Int
[singleHitperTaxToggle] :: StaticOptions -> Bool
[querySelectionMethod] :: StaticOptions -> String
[queryNumber] :: StaticOptions -> Int
[lengthFilterToggle] :: StaticOptions -> Bool
[coverageFilterToggle] :: StaticOptions -> Bool
[blastSoftmaskingToggle] :: StaticOptions -> Bool
[cpuThreads] :: StaticOptions -> Int
[blastDatabase] :: StaticOptions -> Maybe String
[taxRestriction] :: StaticOptions -> Maybe String
[verbositySwitch] :: StaticOptions -> Bool
[offline] :: StaticOptions -> Bool

-- | Keeps track of model construction
data ModelConstruction
ModelConstruction :: Int -> [Fasta () ()] -> [TaxonomyRecord] -> Maybe Int -> Maybe Taxon -> Double -> Bool -> [Fasta () ()] -> [SearchResult] -> ModelConstruction
[iterationNumber] :: ModelConstruction -> Int
[inputFasta] :: ModelConstruction -> [Fasta () ()]
[taxRecords] :: ModelConstruction -> [TaxonomyRecord]
[upperTaxonomyLimit] :: ModelConstruction -> Maybe Int
[taxonomicContext] :: ModelConstruction -> Maybe Taxon
[evalueThreshold] :: ModelConstruction -> Double
[alignmentModeInfernal] :: ModelConstruction -> Bool
[selectedQueries] :: ModelConstruction -> [Fasta () ()]
[potentialMembers] :: ModelConstruction -> [SearchResult]
data TaxonomyRecord
TaxonomyRecord :: Int -> [SequenceRecord] -> TaxonomyRecord
[recordTaxonomyId] :: TaxonomyRecord -> Int
[sequenceRecords] :: TaxonomyRecord -> [SequenceRecord]
data SequenceRecord
SequenceRecord :: Fasta () () -> Int -> ByteString -> SequenceRecord
[nucleotideSequence] :: SequenceRecord -> Fasta () ()
[aligned] :: SequenceRecord -> Int
[recordDescription] :: SequenceRecord -> ByteString

data CMsearch
CMsearch :: String -> String -> String -> [CMsearchHit] -> CMsearch
[queryCMfile] :: CMsearch -> String
[targetSequenceDatabase] :: CMsearch -> String
[numberOfWorkerThreads] :: CMsearch -> String
[cmsearchHits] :: CMsearch -> [CMsearchHit]

data CMsearchHit
CMsearchHit :: Int -> Char -> Double -> Double -> Double -> ByteString -> Int -> Int -> Char -> ByteString -> ByteString -> Double -> ByteString -> CMsearchHit
[hitRank] :: CMsearchHit -> Int
[hitSignificance] :: CMsearchHit -> Char
[hitEvalue] :: CMsearchHit -> Double
[hitScore] :: CMsearchHit -> Double
[hitBias] :: CMsearchHit -> Double
[hitSequenceHeader] :: CMsearchHit -> ByteString
[hitStart] :: CMsearchHit -> Int
[hitEnd] :: CMsearchHit -> Int
[hitStrand] :: CMsearchHit -> Char
[hitModel] :: CMsearchHit -> ByteString
[hitTruncation] :: CMsearchHit -> ByteString
[hitGCContent] :: CMsearchHit -> Double
[hitDescription] :: CMsearchHit -> ByteString
data SearchResult
SearchResult :: [(Fasta () (), Int, ByteString)] -> Maybe Double -> SearchResult
[candidates] :: SearchResult -> [(Fasta () (), Int, ByteString)]
[blastDatabaseSize] :: SearchResult -> Maybe Double

data CMstat
CMstat :: Int -> String -> String -> Int -> Double -> Int -> Int -> Int -> Int -> String -> Double -> Double -> CMstat
[statIndex] :: CMstat -> Int
[statName] :: CMstat -> String
[statAccession] :: CMstat -> String
[statSequenceNumber] :: CMstat -> Int
[statEffectiveSequences] :: CMstat -> Double
[statConsensusLength] :: CMstat -> Int
[statW] :: CMstat -> Int
[statBasepairs] :: CMstat -> Int
[statBifurcations] :: CMstat -> Int
[statModel] :: CMstat -> String
[relativeEntropyCM] :: CMstat -> Double
[relativeEntropyHMM] :: CMstat -> Double
instance GHC.Read.Read Biobase.RNAlien.Types.CMstat
instance GHC.Classes.Eq Biobase.RNAlien.Types.CMstat
instance GHC.Read.Read Biobase.RNAlien.Types.CMsearch
instance GHC.Classes.Eq Biobase.RNAlien.Types.CMsearch
instance GHC.Show.Show Biobase.RNAlien.Types.CMsearch
instance GHC.Read.Read Biobase.RNAlien.Types.CMsearchHit
instance GHC.Classes.Eq Biobase.RNAlien.Types.CMsearchHit
instance GHC.Show.Show Biobase.RNAlien.Types.CMsearchHit
instance GHC.Show.Show Biobase.RNAlien.Types.StaticOptions
instance GHC.Show.Show Biobase.RNAlien.Types.CMstat
instance GHC.Show.Show Biobase.RNAlien.Types.ModelConstruction
instance GHC.Show.Show Biobase.RNAlien.Types.SearchResult
instance GHC.Show.Show Biobase.RNAlien.Types.TaxonomyRecord
instance GHC.Show.Show Biobase.RNAlien.Types.SequenceRecord


-- | This module contains parsing functions for Infernal programs
module Biobase.RNAlien.InfernalParser

-- | parse from input filePath
readCMSearch :: String -> IO (Either ParseError CMsearch)

-- | parse from input filePath
readCMSearches :: String -> IO (Either ParseError CMsearch)

-- | parse from input filePath
parseCMSearch :: String -> Either ParseError CMsearch

-- | parse from input filePath
parseCMSearches :: String -> Either ParseError CMsearch

-- | parse from input filePath
parseCMstat :: String -> Either ParseError CMstat

-- | parse from input filePath
readCMstat :: String -> IO (Either ParseError CMstat)


-- | This module contains functions for RNAlien
module Biobase.RNAlien.Library

-- | Create session id for RNAlien
createSessionID :: Maybe String -> IO String
logMessage :: String -> String -> IO ()
logEither :: Show a => Either a b -> String -> IO ()

-- | Initial RNA family model construction - generates iteration number,
--   seed alignment and model
modelConstructer :: StaticOptions -> ModelConstruction -> IO ModelConstruction
constructTaxonomyRecordsCSVTable :: ModelConstruction -> String

-- | Used for passing progress to Alien server
resultSummary :: ModelConstruction -> StaticOptions -> IO ()
setVerbose :: Verbosity -> Bool
logToolVersions :: String -> String -> IO ()
checkTools :: [String] -> String -> String -> IO (Either String String)

-- | Run CMsearch
systemCMsearch :: Int -> String -> String -> String -> String -> IO ExitCode

-- | parse from input filePath
readCMSearch :: String -> IO (Either ParseError CMsearch)

-- | parse from input filePath
readCMSearches :: String -> IO (Either ParseError CMsearch)
compareCM :: String -> String -> String -> IO (Either String Double)

-- | parse from input filePath
parseCMSearch :: String -> Either ParseError CMsearch

-- | Extract a substring with coordinates from cmsearch, first nucleotide
--   has index 1
cmSearchsubString :: Int -> Int -> String -> String
setInitialTaxId :: Bool -> Int -> Maybe String -> String -> Maybe Int -> Fasta () () -> IO (Maybe Int)
evaluateConstructionResult :: StaticOptions -> ModelConstruction -> IO String

-- | parse from input filePath
readCMstat :: String -> IO (Either ParseError CMstat)

-- | parse from input filePath
parseCMstat :: String -> Either ParseError CMstat

-- | Check if alien can connect to NCBI
checkNCBIConnection :: IO (Either String String)
preprocessClustalForRNAz :: String -> String -> Int -> Double -> Double -> Bool -> IO (Either String (String, String))

-- | Call for external preprocessClustalForRNAz
preprocessClustalForRNAzExternal :: String -> String -> Int -> Int -> Int -> Bool -> IO (Either String (String, String))

-- | Call for external preprocessClustalForRNAcode - RNAcode additionally
--   to RNAz requirements does not accept pipe,underscore, doublepoint
--   symbols
preprocessClustalForRNAcodeExternal :: String -> String -> Int -> Int -> Int -> Bool -> IO (Either String (String, String))
rnaZEvalOutput :: Either ParseError RNAz -> String
reformatFasta :: Fasta () () -> Fasta () ()
checkTaxonomyRestriction :: Maybe String -> Maybe String

-- | Partitions sequences by containing a cmsearch hit and extracts the hit
--   region as new sequence
evaluePartitionTrimCMsearchHits :: Double -> [(CMsearch, (Fasta () (), Int, ByteString))] -> ([(CMsearch, (Fasta () (), Int, ByteString))], [(CMsearch, (Fasta () (), Int, ByteString))], [(CMsearch, (Fasta () (), Int, ByteString))])
readFastaFile :: String -> IO [Fasta () ()]
writeFastaFile :: String -> [Fasta () ()] -> IO ()