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


-- | Libary for parsing ViennaRNA package output
--   
@package ViennaRNAParser
@version 1.0.1


-- | Parsers for Programs from the Vienna RNA Package this libary is
--   focused on Version > 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

-- | 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

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

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

-- | 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

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

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

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

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

-- | Data structure for individual interaction between a target and query
--   nucleic acid seqence
data RNAfold
RNAfold :: String -> String -> String -> Double -> RNAfold
sequenceIdentifier :: RNAfold -> String
foldSequence :: RNAfold -> String
foldSecondaryStructure :: RNAfold -> String
foldingEnergy :: RNAfold -> Double

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

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

-- | Data structure for individual interaction between a target and query
--   nucleic acid seqence
data RNAfold
RNAfold :: String -> String -> String -> Double -> RNAfold
sequenceIdentifier :: RNAfold -> String
foldSequence :: RNAfold -> String
foldSecondaryStructure :: RNAfold -> String
foldingEnergy :: RNAfold -> Double

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

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

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

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

-- | Data structure
data RNAdistance
RNAdistance :: Int -> RNAdistance
secondaryStructureDistance :: RNAdistance -> Int

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

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

-- | Data structure
data RNAdistance
RNAdistance :: Int -> RNAdistance
secondaryStructureDistance :: RNAdistance -> Int

-- | 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 -> 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 -> String

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

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

-- | 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 -> 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 -> String