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


-- | Libary for parsing Clustal tools output
--   
--   Currently contains parsers and datatypes for: clustalw2, clustalo
--   
--   For more information on clustal Tools refer to
--   <a>http://www.clustal.org/</a>
--   
--   ClustalW2 is a general purpose DNA or protein multiple sequence
--   alignment program for three or more sequences.
--   
--   Clustal Omega is a new multiple sequence alignment program that uses
--   seeded guide trees and HMM profile-profile techniques to generate
--   alignments between three or more sequences.
@package ClustalParser
@version 1.0.1


-- | Parse Clustal output For more information on Clustal tools consult:
--   <a>http://www.clustal.org/</a>
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 alignment (.aln) with secondary structure in dot-bracket
--   notation from String (as produced by mlocarna)
parseStructuralClustalAlignment :: String -> Either ParseError StructuralClustalAlignment

-- | Parse Clustal alignment (.aln) with secondary structure in dot-bracket
--   notation from filehandle (as produced by mlocarna)
readStructuralClustalAlignment :: String -> IO (Either ParseError StructuralClustalAlignment)

-- | 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 structure for structural Clustal alignment format
data StructuralClustalAlignment
StructuralClustalAlignment :: [ClustalAlignmentEntry] -> String -> Double -> StructuralClustalAlignment
structuralAlignmentEntries :: StructuralClustalAlignment -> [ClustalAlignmentEntry]
secondaryStructureTrack :: StructuralClustalAlignment -> String
energy :: StructuralClustalAlignment -> Double
data StructuralClustalAlignmentSlice
StructuralClustalAlignmentSlice :: [StructuralClustalAlignmentEntrySlice] -> StructuralClustalAlignmentSlice
structuralEntrySlices :: StructuralClustalAlignmentSlice -> [StructuralClustalAlignmentEntrySlice]
data StructuralClustalAlignmentEntrySlice
StructuralClustalAlignmentEntrySlice :: String -> String -> StructuralClustalAlignmentEntrySlice
structuralEntrySequenceSliceIdentifier :: StructuralClustalAlignmentEntrySlice -> String
structuralEntryAlignedSliceSequence :: StructuralClustalAlignmentEntrySlice -> String