-- 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,
--   mlocarna, cmalign
--   
--   Clustal tools are multiple sequence alignment tools for biological
--   sequence like DNA, RNA and Protein. For more information on clustal
--   Tools refer to <a>http://www.clustal.org/</a>.
--   
--   Mlocarna is a multiple sequence alignment tool for RNA sequences with
--   secondary structure output. For more information on mlocarna refer to
--   <a>http://www.bioinf.uni-freiburg.de/Software/LocARNA/</a>.
--   
--   Cmalign is a multiple sequence alignment program based on RNA family
--   models and produces ,among others, clustal output. It is part of
--   infernal <a>http://infernal.janelia.org/</a>.
@package ClustalParser
@version 1.3.0


-- | This module contains data structures for the Clustal tools For more
--   information on Clustal tools consult: <a>http://www.clustal.org/</a>
module Biobase.Clustal.Types

-- | Data type for clustal summary, containing information about the
--   alignment process, usually printed to STDOUT
data ClustalSummary
ClustalSummary :: Text -> Text -> [SequenceParameters] -> [PairwiseAlignmentSummary] -> Text -> Int -> [GroupSummary] -> Int -> Text -> ClustalSummary
[clustalw2version] :: ClustalSummary -> Text
[sequenceFormat] :: ClustalSummary -> Text
[parametersOfInputSequences] :: ClustalSummary -> [SequenceParameters]
[pairwiseAlignmentSummaries] :: ClustalSummary -> [PairwiseAlignmentSummary]
[guideTreeFileName] :: ClustalSummary -> Text
[groupNumber] :: ClustalSummary -> Int
[groupSummaries] :: ClustalSummary -> [GroupSummary]
[alignmentScore] :: ClustalSummary -> Int
[alignmentFileName] :: ClustalSummary -> Text
data SequenceParameters
SequenceParameters :: Int -> Text -> Int -> SequenceParameters
[inputSequenceIndex] :: SequenceParameters -> Int
[inputSequenceIdentifier] :: SequenceParameters -> Text
[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] -> Text -> ClustalAlignment
[alignmentEntries] :: ClustalAlignment -> [ClustalAlignmentEntry]
[conservationTrack] :: ClustalAlignment -> Text
showAlignment :: Int -> Int -> Int -> [ClustalAlignmentEntry] -> Text -> String
showAlignmentBlock :: Int -> Int -> [ClustalAlignmentEntry] -> Text -> String
showAlignmentLine :: Int -> Int -> ClustalAlignmentEntry -> String
data ClustalAlignmentEntry
ClustalAlignmentEntry :: Text -> Text -> ClustalAlignmentEntry
[entrySequenceIdentifier] :: ClustalAlignmentEntry -> Text
[entryAlignedSequence] :: ClustalAlignmentEntry -> Text
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] -> Text -> Double -> StructuralClustalAlignment
[structuralAlignmentEntries] :: StructuralClustalAlignment -> [ClustalAlignmentEntry]
[secondaryStructureTrack] :: StructuralClustalAlignment -> Text
[energy] :: StructuralClustalAlignment -> Double
data StructuralClustalAlignmentEntrySlice
StructuralClustalAlignmentEntrySlice :: String -> String -> StructuralClustalAlignmentEntrySlice
[structuralEntrySequenceSliceIdentifier] :: StructuralClustalAlignmentEntrySlice -> String
[structuralEntryAlignedSliceSequence] :: StructuralClustalAlignmentEntrySlice -> String
instance GHC.Classes.Eq Biobase.Clustal.Types.StructuralClustalAlignmentEntrySlice
instance GHC.Show.Show Biobase.Clustal.Types.StructuralClustalAlignmentEntrySlice
instance GHC.Classes.Eq Biobase.Clustal.Types.StructuralClustalAlignment
instance GHC.Classes.Eq Biobase.Clustal.Types.ClustalAlignmentSlice
instance GHC.Show.Show Biobase.Clustal.Types.ClustalAlignmentSlice
instance GHC.Classes.Eq Biobase.Clustal.Types.ClustalAlignmentEntrySlice
instance GHC.Show.Show Biobase.Clustal.Types.ClustalAlignmentEntrySlice
instance GHC.Classes.Eq Biobase.Clustal.Types.ClustalAlignment
instance GHC.Classes.Eq Biobase.Clustal.Types.ClustalAlignmentEntry
instance GHC.Show.Show Biobase.Clustal.Types.ClustalAlignmentEntry
instance GHC.Classes.Eq Biobase.Clustal.Types.ClustalSummary
instance GHC.Show.Show Biobase.Clustal.Types.ClustalSummary
instance GHC.Classes.Eq Biobase.Clustal.Types.GroupSummary
instance GHC.Show.Show Biobase.Clustal.Types.GroupSummary
instance GHC.Classes.Eq Biobase.Clustal.Types.PairwiseAlignmentSummary
instance GHC.Show.Show Biobase.Clustal.Types.PairwiseAlignmentSummary
instance GHC.Classes.Eq Biobase.Clustal.Types.SequenceParameters
instance GHC.Show.Show Biobase.Clustal.Types.SequenceParameters
instance GHC.Show.Show Biobase.Clustal.Types.StructuralClustalAlignment
instance GHC.Show.Show Biobase.Clustal.Types.ClustalAlignment


-- | Parse Clustal output For more information on Clustal tools consult:
--   <a>http://www.clustal.org/</a>
module Biobase.Clustal.Import

-- | 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)


-- | Types and functions for Clustal
module Biobase.Clustal