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


-- | Libary for Stockholm aligmnent format
--   
--   Libary containing parsing and visualisation functions and
--   datastructures for Stockholm aligmnent format
@package StockholmAlignment
@version 1.0.4


-- | Module exporting SVG Font for visualising Stockholm alignments
module Bio.StockholmFont
linLibertineFont :: PreparedFont Double


-- | Datastructures for Stockholm alignments
module Bio.StockholmData

-- | Data structure for a Stockholm format alignment
data StockholmAlignment
StockholmAlignment :: Text -> [AnnotationEntry] -> [AnnotationEntry] -> [SequenceEntry] -> StockholmAlignment
[version] :: StockholmAlignment -> Text
[fileAnnotations] :: StockholmAlignment -> [AnnotationEntry]
[columnAnnotations] :: StockholmAlignment -> [AnnotationEntry]
[sequenceEntries] :: StockholmAlignment -> [SequenceEntry]
data SequenceEntry
SequenceEntry :: Text -> Text -> [AnnotationEntry] -> [AnnotationEntry] -> SequenceEntry
[sequenceId] :: SequenceEntry -> Text
[entrySequence] :: SequenceEntry -> Text
[sequenceAnnotation] :: SequenceEntry -> [AnnotationEntry]
[residueAnnotation] :: SequenceEntry -> [AnnotationEntry]
data AnnotationEntry
AnnotationEntry :: Text -> Text -> AnnotationEntry
[tag] :: AnnotationEntry -> Text
[annotation] :: AnnotationEntry -> Text
data StockholmToken
TokFileA :: Text -> Text -> StockholmToken
[fTag] :: StockholmToken -> Text
[fInfo] :: StockholmToken -> Text
TokColA :: Text -> Text -> StockholmToken
[cTag] :: StockholmToken -> Text
[cInfo] :: StockholmToken -> Text
TokResA :: Text -> Text -> Text -> StockholmToken
[rId] :: StockholmToken -> Text
[rTag] :: StockholmToken -> Text
[rInfo] :: StockholmToken -> Text
TokSeqA :: Text -> Text -> Text -> StockholmToken
[aId] :: StockholmToken -> Text
[aTag] :: StockholmToken -> Text
[aInfo] :: StockholmToken -> Text
TokSeq :: Text -> Text -> StockholmToken
[sId] :: StockholmToken -> Text
[sSeq] :: StockholmToken -> Text
instance GHC.Classes.Eq Bio.StockholmData.StockholmToken
instance GHC.Show.Show Bio.StockholmData.StockholmToken
instance GHC.Classes.Eq Bio.StockholmData.StockholmAlignment
instance GHC.Show.Show Bio.StockholmData.StockholmAlignment
instance GHC.Classes.Eq Bio.StockholmData.SequenceEntry
instance GHC.Show.Show Bio.StockholmData.SequenceEntry
instance GHC.Classes.Eq Bio.StockholmData.AnnotationEntry
instance GHC.Show.Show Bio.StockholmData.AnnotationEntry


-- | Functions for visualising Stockholm alignments
module Bio.StockholmDraw
drawStockholmLines :: Int -> Double -> Vector Int -> Vector (Int, Vector (Colour Double)) -> StockholmAlignment -> QDiagram Cairo V2 Double Any
drawStockholm :: Int -> StockholmAlignment -> QDiagram Cairo V2 Double Any
convertWUSStoDotBracket :: Text -> Text
extractGapfreeStructure :: String -> String -> String
isGap :: Char -> Bool


-- | Functions for parsing Stockholm alignments
module Bio.StockholmParser
readExistingStockholm :: String -> IO (Either String [StockholmAlignment])

-- | parse
parseStockholm :: String -> Either ParseError [StockholmAlignment]

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