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


-- | Detailed visualization of CMs, HMMs and their comparisions
--   
--   cmv is a collection of tools for the visualisation of Hidden Markov
--   Models (HMMV) and RNA-family models (CMV). Moreover it can visualise
--   comparisons of these models (HMMCV,CMCV), and annotate linked regions
--   in the structural alignments they were constructed from and via, 3rd
--   party tools, in their consensus secondary structure.
@package cmv
@version 1.0.2


-- | Parse CMCompare output parsing is done with parsec For more
--   information on CMCompare consult:
--   <a>http://www.tbi.univie.ac.at/software/cmcompare/</a>
module Bio.CMCompareResult

-- | Datastructure for result strings of comparisons between covariance
--   models by CMCompare
data CmcompareResult
CmcompareResult :: String -> String -> Double -> Double -> String -> String -> String -> [Int] -> [Int] -> CmcompareResult
[model1Name] :: CmcompareResult -> String
[model2Name] :: CmcompareResult -> String
[linkscore1] :: CmcompareResult -> Double
[linkscore2] :: CmcompareResult -> Double
[linksequence] :: CmcompareResult -> String
[model1structure] :: CmcompareResult -> String
[model2structure] :: CmcompareResult -> String
[model1matchednodes] :: CmcompareResult -> [Int]
[model2matchednodes] :: CmcompareResult -> [Int]

-- | Parser for CMCompare result strings
getCmcompareResults :: FilePath -> IO [Either ParseError CmcompareResult]
getModelsNames :: [CmcompareResult] -> [String]
getModelNames :: CmcompareResult -> [String]
instance GHC.Show.Show Bio.CMCompareResult.CmcompareResult


-- | Drawing of covariance model
--   (http:/<i>www.tbi.univie.ac.at</i>software<i>cmcompare</i>) guide
--   trees and highlighting comparison results Drawing is done with the
--   diagrams package
module Bio.CMDraw

-- | Draw one or more CM
drawSingleCMComparisons :: String -> Int -> Double -> String -> String -> Double -> Double -> [CM] -> [Maybe StockholmAlignment] -> [CmcompareResult] -> [(QDiagram Cairo V2 Double Any, Maybe (QDiagram Cairo V2 Double Any))]

-- | Draw one or more CM
drawSingleCMs :: String -> Int -> Double -> String -> String -> Double -> Double -> [CM] -> [Maybe StockholmAlignment] -> [(QDiagram Cairo V2 Double Any, Maybe (QDiagram Cairo V2 Double Any))]

-- | Draw the guide Tree of a single CM
drawCM :: String -> Int -> Double -> String -> String -> Double -> Double -> Vector (String, Colour Double) -> (CM, Maybe StockholmAlignment, Vector (Int, Vector (Colour Double)), Colour Double) -> (QDiagram Cairo V2 Double Any, Maybe (QDiagram Cairo V2 Double Any))
text' :: String -> QDiagram Cairo V2 Double Any

-- | Specifies the size of the diagram. Absolute adapts to overall size
--   according to subdiagrams
svgsize :: SizeSpec V2 Double

-- | Check for available cairo output formats
diagramName :: String -> String -> Either String String
printCM :: FilePath -> SizeSpec V2 Double -> QDiagram Cairo V2 Double Any -> IO ()
data NodeIndices
buildRowIndexStructure :: Int -> Vector Node -> [Int] -> State ([(Int, Int, String, Int, Int)], Int) ([(Int, Int, String, Int, Int)], Int)
buildTreeIndexStructure :: Int -> Vector Node -> [Int] -> State ([(Int, Int, String, Int, Int)], Int) ([(Int, Int, String, Int, Int)], Int)

-- | Extracts consensus secondary structure from alignment and annotates
--   cmcompare nodes for all comparisons in one merged output
mergedSecondaryStructureVisualisation :: String -> Double -> [CM] -> [Maybe StockholmAlignment] -> [CmcompareResult] -> [(String, String)]

-- | Extracts consensus secondary structure from alignment and annotates
--   cmcompare nodes for each model-model combination seperatly
perModelSecondaryStructureVisualisation :: String -> Double -> String -> [CM] -> [Maybe StockholmAlignment] -> [CmcompareResult] -> [(String, String)]
instance GHC.Classes.Ord Bio.CMDraw.NodeIndices
instance GHC.Classes.Eq Bio.CMDraw.NodeIndices
instance GHC.Show.Show Bio.CMDraw.NodeIndices