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


-- | Libary for parsing ViennaRNA package output
--   
@package ViennaRNAParser
@version 1.2.0


-- | This module contains a data structure for RNAup output For more
--   information on RNAup consult:
--   <a>http://www.tbi.univie.ac.at/RNA/RNAup.html</a>
module Bio.RNAupData

-- | Data structure for individual interaction between a target and query
--   nucleic acid seqence, contains all (sub)-optimal interactions
data RNAupInteraction
RNAupInteraction :: String -> String -> [RNAupInteractionRegion] -> RNAupInteraction
upQueryIdentifier :: RNAupInteraction -> String
upTargetIdentifier :: RNAupInteraction -> String
upInteractions :: RNAupInteraction -> [RNAupInteractionRegion]

-- | Data structure for (sub-) optimal interaction region
data RNAupInteractionRegion
RNAupInteractionRegion :: String -> Int -> Int -> Int -> Int -> Double -> Maybe Double -> Maybe Double -> Maybe Double -> String -> String -> Maybe String -> RNAupInteractionRegion
upSecondaryStructure :: RNAupInteractionRegion -> String
upQueryDuplexBegin :: RNAupInteractionRegion -> Int
upQueryDuplexEnd :: RNAupInteractionRegion -> Int
upTargetDuplexBegin :: RNAupInteractionRegion -> Int
upTargetDuplexEnd :: RNAupInteractionRegion -> Int
upDuplexEnergy :: RNAupInteractionRegion -> Double
upDuplexEnergyWithoutAccessiblity :: RNAupInteractionRegion -> Maybe Double
upQueryAccessiblity :: RNAupInteractionRegion -> Maybe Double
upTargetAccessibility :: RNAupInteractionRegion -> Maybe Double
upQuerySequence :: RNAupInteractionRegion -> String
upTargetSequence :: RNAupInteractionRegion -> String
upOutputFileName :: RNAupInteractionRegion -> Maybe String
instance Show RNAupInteractionRegion
instance Eq RNAupInteractionRegion
instance Show RNAupInteraction
instance Eq RNAupInteraction


-- | Parse RNAup interaction_first output For more information on RNAup
--   consult: <a>http://www.tbi.univie.ac.at/RNA/RNAup.html</a>
module Bio.RNAupParser

-- | parse RNAupOutput from input string
parseRNAup :: [Char] -> Either ParseError [RNAupInteraction]

-- | parse from input filePath
readRNAup :: String -> IO (Either ParseError [RNAupInteraction])


-- | This module contains a data structure for RNAdistance output For more
--   information on RNAdistance consult: &lt;&gt;
module Bio.RNAdistanceData

-- | Data structure
data RNAdistance
RNAdistance :: Int -> RNAdistance
secondaryStructureDistance :: RNAdistance -> Int
instance Show RNAdistance
instance Eq RNAdistance


-- | Parse RNAdistance output For more information on RNAdistance consult:
--   &lt;&gt;
module Bio.RNAdistanceParser

-- | parse RNAdistance output from input string
parseRNAdistance :: [Char] -> Either ParseError RNAdistance

-- | parse RNAdistance output from input filePath
readRNAdistance :: String -> IO (Either ParseError RNAdistance)


-- | This module contains a data structure for RNAalifold output For more
--   information on RNAalifold consult: &lt;&gt;
module Bio.RNAalifoldData

-- | Data structure corrsponds with alifoldoutput redirected to file.
--   Output written directly to commandline also contains number of
--   sequences and length of consensus sequence
data RNAalifold
RNAalifold :: String -> String -> Double -> Double -> Double -> RNAalifold
alignmentConsensusSequence :: RNAalifold -> String
alignmentConsensusDotBracket :: RNAalifold -> String
alignmentConsensusMinimumFreeEnergy :: RNAalifold -> Double
alignmentConsensusInitialMinimumFreeEnergy :: RNAalifold -> Double
alignmentConsensusEnergyCovarianceContributions :: RNAalifold -> Double
instance Show RNAalifold
instance Eq RNAalifold


-- | Parse RNAalifold output For more information on RNAalifold consult:
--   &lt;&gt;
module Bio.RNAalifoldParser
systemRNAalifold :: String -> String -> String -> IO ExitCode

-- | parse RNAalifold output from input string
parseRNAalifold :: [Char] -> Either ParseError RNAalifold

-- | parse RNAalifold output from input filePath
readRNAalifold :: String -> IO (Either ParseError RNAalifold)


-- | This module contains a data structure for RNAfold output For more
--   information on RNAplex consult:
--   <a>http://www.tbi.univie.ac.at/RNA/RNAfold.html</a>
module Bio.RNAfoldData

-- | Data structure for RNAfold
data RNAfold
RNAfold :: String -> String -> String -> Double -> RNAfold
sequenceIdentifier :: RNAfold -> String
foldSequence :: RNAfold -> String
foldSecondaryStructure :: RNAfold -> String
foldingEnergy :: RNAfold -> Double
instance Show RNAfold
instance Eq RNAfold


-- | Parse RNAfold output For more information on RNAfold consult:
--   <a>http://www.tbi.univie.ac.at/RNA/RNAfold</a>
module Bio.RNAfoldParser

-- | Run external RNAfold command and read the output into the
--   corresponding datatype
systemRNAfold :: String -> String -> IO ExitCode

-- | parse RNAfold output from input string
parseRNAfold :: [Char] -> Either ParseError RNAfold

-- | parse RNAfold output from input filePath
readRNAfold :: String -> IO (Either ParseError RNAfold)


-- | This module contains a hierarchical data structure for RNAz output For
--   more information on RNAz consult:
--   <a>http://www.tbi.univie.ac.at/~wash/RNAz/</a>
module Bio.RNAzData

-- | All elements of RNAz output are contained in this datatype
data RNAz
RNAz :: String -> Int -> Int -> String -> Double -> Double -> Double -> Double -> Double -> Double -> Double -> Double -> Double -> Double -> String -> String -> Double -> Double -> String -> [RNAzResult] -> RNAzConsensus -> RNAz
version :: RNAz -> String
sequenceNumber :: RNAz -> Int
columnNumber :: RNAz -> Int
readingDirection :: RNAz -> String
meanPairwiseIdentity :: RNAz -> Double
shannonEntropy :: RNAz -> Double
gcContent :: RNAz -> Double
meanSingleSequenceMinimumFreeEnergy :: RNAz -> Double
consensusMinimumFreeEnergy :: RNAz -> Double
energyContribution :: RNAz -> Double
covarianceContribution :: RNAz -> Double
combinationsPair :: RNAz -> Double
meanZScore :: RNAz -> Double
structureConservationIndex :: RNAz -> Double
backgroundModel :: RNAz -> String
decisionModel :: RNAz -> String
svmDecisionValue :: RNAz -> Double
svmRNAClassProbability :: RNAz -> Double
prediction :: RNAz -> String
rnazResults :: RNAz -> [RNAzResult]
rnazConsensus :: RNAz -> RNAzConsensus

-- | Datatype contains all result elements for each member of the input
--   alignment
data RNAzResult
RNAzResult :: String -> String -> String -> Double -> Double -> Char -> RNAzResult
header :: RNAzResult -> String
resultSequence :: RNAzResult -> String
dotBracket :: RNAzResult -> String
minimumFreeEnergy :: RNAzResult -> Double
zScore :: RNAzResult -> Double
zscoreCalculationApproach :: RNAzResult -> Char

-- | Datatype contains all elements for the consenus result of input
--   alignment
data RNAzConsensus
RNAzConsensus :: String -> String -> RNAzConsensus
consensusSequence :: RNAzConsensus -> String
consensusDotBracket :: RNAzConsensus -> String
instance Show RNAzResult
instance Eq RNAzResult
instance Show RNAzConsensus
instance Eq RNAzConsensus
instance Show RNAz
instance Eq RNAz


-- | Parse RNAz output For more information on RNAz consult:
--   &lt;<a>http://www.tbi.univie.ac.at/~wash/RNAz</a>
module Bio.RNAzParser

-- | Run external RNAz command and read the output into the corresponding
--   datatype
systemRNAz :: String -> String -> IO ExitCode

-- | parse RNAz from input string
parseRNAz :: [Char] -> Either ParseError RNAz

-- | parse from input filePath
readRNAz :: String -> IO (Either ParseError RNAz)


-- | This module contains a hierarchical data structure for RNAplex output
--   For more information on RNAplex consult:
--   <a>http://www.bioinf.uni-leipzig.de/Software/RNAplex/</a>
module Bio.RNAplexData

-- | Data structure for individual interaction between a target and query
--   nucleic acid seqence
data RNAplexInteraction
RNAplexInteraction :: String -> String -> String -> Int -> Int -> Int -> Int -> Double -> Maybe Double -> Maybe Double -> Maybe Double -> RNAplexInteraction
targetIdentifier :: RNAplexInteraction -> String
queryIdentifier :: RNAplexInteraction -> String
plexSecondaryStructure :: RNAplexInteraction -> String
targetDuplexBegin :: RNAplexInteraction -> Int
targetDuplexEnd :: RNAplexInteraction -> Int
queryDuplexBegin :: RNAplexInteraction -> Int
queryDuplexEnd :: RNAplexInteraction -> Int
duplexEnergy :: RNAplexInteraction -> Double
duplexEnergyWithoutAccessiblity :: RNAplexInteraction -> Maybe Double
queryAccessiblity :: RNAplexInteraction -> Maybe Double
targetAccessibility :: RNAplexInteraction -> Maybe Double
instance Show RNAplexInteraction
instance Eq RNAplexInteraction


-- | Parse RNAplex output For more information on RNAplex consult:
--   <a>http://www.bioinf.uni-leipzig.de/Software/RNAplex/</a>
module Bio.RNAplexParser

-- | parse RNAplexOutput from input string
parseRNAplex :: [Char] -> Either ParseError [RNAplexInteraction]

-- | parse from input filePath
readRNAplex :: String -> IO (Either ParseError [RNAplexInteraction])


-- | This module contains a data structure for RNAcofold output For more
--   information on RNAcofold consult:
--   <a>http://www.tbi.univie.ac.at/RNA/RNAcofold.html</a>
module Bio.RNAcofoldData

-- | Data structure for cofolding of 2 nucleic acid sequences
data RNAcofold
RNAcofold :: String -> String -> String -> String -> Double -> RNAcofold
coFoldSequence1 :: RNAcofold -> String
coFoldSequence2 :: RNAcofold -> String
coFoldSecondaryStructure1 :: RNAcofold -> String
coFoldSecondaryStructure2 :: RNAcofold -> String
coFoldingEnergy :: RNAcofold -> Double
instance Show RNAcofold
instance Eq RNAcofold


-- | Parse RNAfold output For more information on RNAcofold consult:
--   <a>http://www.tbi.univie.ac.at/RNA/RNAcofold.html</a>
module Bio.RNAcofoldParser

-- | Run external RNAcofold command
systemRNAcofold :: String -> String -> IO ExitCode

-- | parse RNAcofold output from input string
parseRNAcofold :: [Char] -> Either ParseError RNAcofold

-- | parse RNAcofold output from input filePath
readRNAcofold :: String -> IO (Either ParseError RNAcofold)


-- | Parsers for Programs from the Vienna RNA Package this libary is
--   focused on Version &gt; 2.0 For more information on the Vienna
--   RNAPackage consult: <a>http://www.tbi.univie.ac.at/~ivo/RNA/</a> or
--   the homepage of the current maintainer:
--   <a>http://www.tbi.univie.ac.at/~ronny/RNA/index.html</a>
module Bio.ViennaRNAParser