Bio.CMDraw

Drawing of covariance model (http:/www.tbi.univie.ac.atsoftwarecmcompare) guide trees and highlighting comparison results Drawing is done with the diagrams package

Documentation

drawSingleCMComparisons :: String -> 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 -> String -> Int -> Double -> String -> String -> Double -> Double -> [CM] -> [Maybe StockholmAlignment] -> [(QDiagram Cairo V2 Double Any, Maybe (QDiagram Cairo V2 Double Any))]

Draw one or more CM

drawCM :: String -> 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))

Draw the guide Tree of a single CM

text' :: String -> QDiagram Cairo V2 Double Any

svgsize :: SizeSpec V2 Double

Specifies the size of the diagram. Absolute adapts to overall size according to subdiagrams

diagramName :: String -> String -> Either String String

Check for available cairo output formats

printCM :: FilePath -> SizeSpec V2 Double -> QDiagram Cairo V2 Double Any -> IO ()

data NodeIndices

Instances

Eq NodeIndices

Methods

(==) :: NodeIndices -> NodeIndices -> Bool

(/=) :: NodeIndices -> NodeIndices -> Bool

Ord NodeIndices

Methods

compare :: NodeIndices -> NodeIndices -> Ordering

(<) :: NodeIndices -> NodeIndices -> Bool

(<=) :: NodeIndices -> NodeIndices -> Bool

(>) :: NodeIndices -> NodeIndices -> Bool

(>=) :: NodeIndices -> NodeIndices -> Bool

max :: NodeIndices -> NodeIndices -> NodeIndices

min :: NodeIndices -> NodeIndices -> NodeIndices

Show NodeIndices

Methods

showsPrec :: Int -> NodeIndices -> ShowS

show :: NodeIndices -> String

showList :: [NodeIndices] -> ShowS

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)

mergedSecondaryStructureVisualisation :: String -> Double -> [CM] -> [Maybe StockholmAlignment] -> [CmcompareResult] -> [(String, String)]

Extracts consensus secondary structure from alignment and annotates cmcompare nodes for all comparisons in one merged output

perModelSecondaryStructureVisualisation :: String -> Double -> String -> [CM] -> [Maybe StockholmAlignment] -> [CmcompareResult] -> [(String, String)]

Extracts consensus secondary structure from alignment and annotates cmcompare nodes for each model-model combination seperatly