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


-- | Libary for parsing Clustal tools output
--   
@package ClustalParser
@version 1.0.0


-- | Parse Clustal output
module Bio.ClustalParser

-- | Parse Clustal alignment (.aln) from String
parseClustalAlignment :: String -> Either ParseError ClustalAlignment

-- | Parse Clustal alignment (.aln) from filehandle
readClustalAlignment :: String -> IO (Either ParseError ClustalAlignment)

-- | Parse Clustal summary (printed to STDOUT) from String
parseClustalSummary :: String -> Either ParseError ClustalSummary

-- | Parse Clustal summary (printed to STDOUT) from file
readClustalSummary :: String -> IO (Either ParseError ClustalSummary)

-- | Data type for clustal summary, containing information about the
--   alignment process, usually printed to STDOUT
data ClustalSummary
ClustalSummary :: String -> String -> [SequenceParameters] -> [PairwiseAlignmentSummary] -> String -> Int -> [GroupSummary] -> Int -> String -> ClustalSummary
clustalw2version :: ClustalSummary -> String
sequenceFormat :: ClustalSummary -> String
parametersOfInputSequences :: ClustalSummary -> [SequenceParameters]
pairwiseAlignmentSummaries :: ClustalSummary -> [PairwiseAlignmentSummary]
guideTreeFileName :: ClustalSummary -> String
groupNumber :: ClustalSummary -> Int
groupSummaries :: ClustalSummary -> [GroupSummary]
alignmentScore :: ClustalSummary -> Int
alignmentFileName :: ClustalSummary -> String
data SequenceParameters
SequenceParameters :: Int -> String -> Int -> SequenceParameters
inputSequenceIndex :: SequenceParameters -> Int
inputSequenceIdentifier :: SequenceParameters -> String
inputSequenceLength :: SequenceParameters -> Int
data PairwiseAlignmentSummary
PairwiseAlignmentSummary :: Int -> Int -> Int -> PairwiseAlignmentSummary
firstSequenceIndex :: PairwiseAlignmentSummary -> Int
secondSequenceIndex :: PairwiseAlignmentSummary -> Int
pairwiseAlignmentScore :: PairwiseAlignmentSummary -> Int
data GroupSummary
GroupSummary :: Int -> Maybe Int -> Maybe Int -> GroupSummary
alignmentGroupIndex :: GroupSummary -> Int
numberOfAlignedSequences :: GroupSummary -> Maybe Int
groupScore :: GroupSummary -> Maybe Int

-- | Data structure for Clustal alignment format
data ClustalAlignment
ClustalAlignment :: [ClustalAlignmentEntry] -> String -> ClustalAlignment
alignmentEntries :: ClustalAlignment -> [ClustalAlignmentEntry]
conservationTrack :: ClustalAlignment -> String
data ClustalAlignmentEntry
ClustalAlignmentEntry :: String -> String -> ClustalAlignmentEntry
entrySequenceIdentifier :: ClustalAlignmentEntry -> String
entryAlignedSequence :: ClustalAlignmentEntry -> String
data ClustalAlignmentSlice
ClustalAlignmentSlice :: [ClustalAlignmentEntrySlice] -> String -> ClustalAlignmentSlice
entrySlices :: ClustalAlignmentSlice -> [ClustalAlignmentEntrySlice]
conservationTrackSlice :: ClustalAlignmentSlice -> String
data ClustalAlignmentEntrySlice
ClustalAlignmentEntrySlice :: String -> String -> Int -> ClustalAlignmentEntrySlice
entrySequenceSliceIdentifier :: ClustalAlignmentEntrySlice -> String
entryAlignedSliceSequence :: ClustalAlignmentEntrySlice -> String
spacerLength :: ClustalAlignmentEntrySlice -> Int
data ClustalGuideTree
ClustalGuideTree :: [ClustalGuideTreeEntry] -> ClustalGuideTree
guideTreeEntries :: ClustalGuideTree -> [ClustalGuideTreeEntry]
data ClustalGuideTreeEntry
ClustalGuideTreeEntry :: String -> Double -> ClustalGuideTreeEntry
entryDesignation :: ClustalGuideTreeEntry -> String
entryDistance :: ClustalGuideTreeEntry -> Double