diff --git a/BioHMM.cabal b/BioHMM.cabal --- a/BioHMM.cabal +++ b/BioHMM.cabal @@ -1,5 +1,5 @@ name: BioHMM -version: 1.1.7 +version: 1.1.8 synopsis: Libary for Hidden Markov Models in HMMER3 format. description: Libary containing parsing and visualisation functions and datastructures for Hidden Markov Models in HMMER3 format. license: GPL-3 @@ -20,8 +20,8 @@ source-repository this type: git - location: https://github.com/eggzilla/BioHMM/tree/1.1.7 - tag: 1.1.7 + location: https://github.com/eggzilla/BioHMM/tree/1.1.8 + tag: 1.1.8 library -- Modules exported by the library. diff --git a/changelog b/changelog --- a/changelog +++ b/changelog @@ -1,4 +1,7 @@ -*-change-log-*- +1.1.8 Florian Eggenhofer 8. June 2017 + * Minimal and simple visualisation now also support line mode + * Added show instance for HMMCompareResult 1.1.7 Florian Eggenhofer 7. June 2017 * Improved placment of legend 1.1.6 Florian Eggenhofer 23. May 2017 @@ -8,7 +11,7 @@ 1.1.4 Florian Eggenhofer 22. May 2017 * Color scheme is now more robust for grayscale-printing 1.1.3 Florian Eggenhofer 9. May 2017 - * Now using same simplified label color scheme as CMDraw + * Now using same simplified label color scheme as CMDraw 1.1.2 Florian Eggenhofer 7. May 2017 * Labels for columns are now passed to alignment visualisation instead of nodes * Improved mapping node to column labels diff --git a/src/Bio/HMMCompareResult.hs b/src/Bio/HMMCompareResult.hs --- a/src/Bio/HMMCompareResult.hs +++ b/src/Bio/HMMCompareResult.hs @@ -2,23 +2,16 @@ module Bio.HMMCompareResult ( - HMMCompareResult, + HMMCompareResult(..), parseHMMCompareResult, readHMMCompareResult, - model1Name, - model2Name, - linkscore1, - linkscore2, - linksequence, - model1matchednodes, - model2matchednodes, getHMMCompareResults, getModelsNames, getModelNames ) where import Text.ParserCombinators.Parsec ---import Control.Monad +import Data.List -- | Datastructure for result strings of comparisons between covariance models by HMMCompare data HMMCompareResult = HMMCompareResult @@ -29,7 +22,13 @@ linksequence :: String, model1matchednodes :: [Int], model2matchednodes :: [Int] - } deriving (Show) + } deriving () + +instance Show HMMCompareResult where + show (HMMCompareResult _model1Name _model2Name _linkscore1 _linkscore2 _linksequence _model1matchednodes _model2matchednodes) = _model1Name ++ " " ++ _model2Name ++ " " ++ show _linkscore1 ++ " " ++ show _linkscore2 ++ " " ++ _linksequence ++ " " ++ formatMatchedNodes _model1matchednodes ++ " " ++ formatMatchedNodes _model2matchednodes ++ "\n" + +formatMatchedNodes :: [Int] -> String +formatMatchedNodes nodes = "[" ++ intercalate "," (map show nodes) ++ "]" -- | parse HMMCompareResult model from input string parseHMMCompareResult :: String -> Either ParseError [HMMCompareResult] diff --git a/src/Bio/HMMDraw.hs b/src/Bio/HMMDraw.hs --- a/src/Bio/HMMDraw.hs +++ b/src/Bio/HMMDraw.hs @@ -72,8 +72,10 @@ nodeWidth = 6.0 :: Double nodeNumberPerRow = floor (maxWidth / nodeWidth - 2) nodesIntervals = makeNodeIntervals nodeNumberPerRow nodeNumber - minimalNodes = hcat (V.toList (V.map (drawHMMNodeMinimal comparisonNodeLabels)currentNodes)) # scale scalef - simpleNodes = hcat (V.toList (V.map (drawHMMNodeSimple alphabetSymbols emissiontype boxlength comparisonNodeLabels) currentNodes)) # scale scalef + --minimalNodes = hcat (V.toList (V.map (drawHMMNodeMinimal comparisonNodeLabels)currentNodes)) # scale scalef + --simpleNodes = hcat (V.toList (V.map (drawHMMNodeSimple alphabetSymbols emissiontype boxlength comparisonNodeLabels) currentNodes)) # scale scalef + minimalNodes = vcat' with { _sep = 3 } (V.toList (V.map (drawMinimalNodeRow currentNodes comparisonNodeLabels) nodesIntervals)) + simpleNodes = vcat' with { _sep = 3 } (V.toList (V.map (drawSimpleNodeRow alphabetSymbols emissiontype boxlength currentNodes comparisonNodeLabels) nodesIntervals)) verboseNodes = vcat' with { _sep = 3 } (V.toList (V.map (drawDetailedNodeRow alphabetSymbols emissiontype boxlength transitionCutoff nodeNumber currentNodes comparisonNodeLabels) nodesIntervals)) minimalNodesHeader = alignTL (vcat' with { _sep = 5 } [modelHeader,minimalNodes]) simpleNodesHeader = alignTL (vcat' with { _sep = 5 } [modelHeader,simpleNodes]) @@ -138,6 +140,16 @@ rowLength = nodeNumberPerRow safeLength = if rowStart + rowLength >= nodeNumber then nodeNumber - rowStart else rowLength +drawMinimalNodeRow :: V.Vector HM.HMMER3Node -> V.Vector (Int,V.Vector (Colour Double)) -> (Int, Int) -> QDiagram Cairo V2 Double Any +drawMinimalNodeRow allNodes comparisonNodeLabels (currentIndex,nodeSliceLength) = simpleNodes + where currentNodes = V.slice currentIndex nodeSliceLength allNodes + simpleNodes = hcat (V.toList (V.map (drawHMMNodeMinimal comparisonNodeLabels) currentNodes)) + +drawSimpleNodeRow :: String -> String -> Double -> V.Vector HM.HMMER3Node -> V.Vector (Int,V.Vector (Colour Double)) -> (Int, Int) -> QDiagram Cairo V2 Double Any +drawSimpleNodeRow alphabetSymbols emissiontype boxLength allNodes comparisonNodeLabels (currentIndex,nodeSliceLength) = simpleNodes + where currentNodes = V.slice currentIndex nodeSliceLength allNodes + simpleNodes = hcat (V.toList (V.map (drawHMMNodeSimple alphabetSymbols emissiontype boxLength comparisonNodeLabels) currentNodes)) + drawDetailedNodeRow :: String -> String -> Double -> Double -> Int -> V.Vector HM.HMMER3Node -> V.Vector (Int,V.Vector (Colour Double)) -> (Int, Int) -> QDiagram Cairo V2 Double Any drawDetailedNodeRow alphabetSymbols emissiontype boxLength transitionCutoff lastIndex allNodes comparisonNodeLabels (currentIndex,nodeSliceLength) = detailedRow where currentNodes = V.slice currentIndex nodeSliceLength allNodes