diff --git a/BioHMM.cabal b/BioHMM.cabal --- a/BioHMM.cabal +++ b/BioHMM.cabal @@ -1,11 +1,11 @@ name: BioHMM -version: 1.0.8 +version: 1.0.9 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 license-file: LICENSE author: Florian Eggenhofer -maintainer: egg@tbi.univie.ac.at +maintainer: egg@informatik.uni-freiburg.de -- copyright: category: Bioinformatics build-type: Simple @@ -20,8 +20,8 @@ source-repository this type: git - location: https://github.com/eggzilla/BioHMM/tree/1.0.8 - tag: 1.0.8 + location: https://github.com/eggzilla/BioHMM/tree/1.0.9 + tag: 1.0.9 library -- Modules exported by the library. @@ -34,7 +34,7 @@ ghc-options: -Wall -fno-warn-unused-do-bind -- Other library packages from which modules are imported. - build-depends: base >=4.5 && <5, parsec>=3.1.9, diagrams-lib>=1.3, text, vector, ParsecTools, diagrams-cairo>=1.3, filepath, colour, directory, either-unwrap, SVGFonts >= 1.6, StockholmAlignment + build-depends: base >=4.5 && <5, parsec>=3.1.9, diagrams-lib>=1.3, text, vector, ParsecTools, diagrams-cairo>=1.3, filepath, colour, directory, either-unwrap, SVGFonts >= 1.6, StockholmAlignment>=1.0.2 -- Directories containing source files. hs-source-dirs: src diff --git a/changelog b/changelog --- a/changelog +++ b/changelog @@ -1,4 +1,6 @@ -*-change-log-*- +1.0.9 Florian Eggenhofer 13. April 2017 + * Improved handling of missing stockholm input 1.0.8 Florian Eggenhofer 7. April 2017 * Fixed a bug with a missing structure parameter character 1.0.7 Florian Eggenhofer 19. March 2017 diff --git a/src/Bio/HMMDraw.hs b/src/Bio/HMMDraw.hs --- a/src/Bio/HMMDraw.hs +++ b/src/Bio/HMMDraw.hs @@ -5,15 +5,12 @@ {-# LANGUAGE RankNTypes #-} module Bio.HMMDraw - ( - --drawHMMER3s, - drawHMMER3, + ( drawHMMER3, drawSingleHMMER3s, svgsize, diagramName, printHMM, getComparisonsHighlightParameters, - --drawHMMComparison, drawSingleHMMComparison ) where @@ -32,7 +29,7 @@ import Graphics.SVGFonts import Bio.StockholmFont -drawSingleHMMComparison :: String -> Int -> Double -> String -> Double -> Double -> [HM.HMMER3] -> [Maybe S.StockholmAlignment] -> [HMMCompareResult] -> [(QDiagram Cairo V2 Double Any,QDiagram Cairo V2 Double Any)] +drawSingleHMMComparison :: String -> Int -> Double -> String -> Double -> Double -> [HM.HMMER3] -> [Maybe S.StockholmAlignment] -> [HMMCompareResult] -> [(QDiagram Cairo V2 Double Any,Maybe (QDiagram Cairo V2 Double Any))] drawSingleHMMComparison modelDetail entryNumberCutoff transitionCutoff emissiontype maxWidth scalef hmms alns comparisons | modelDetail == "minimal" = map (drawHMMER3 modelDetail entryNumberCutoff transitionCutoff maxWidth scalef emissiontype nameColorVector) zippedInput | modelDetail == "simple" = map (drawHMMER3 modelDetail entryNumberCutoff transitionCutoff maxWidth scalef emissiontype nameColorVector) zippedInput @@ -45,7 +42,7 @@ nameColorVector = V.zipWith (\a b -> (a,b)) modelNames colorVector comparisonNodeLabels = map (getComparisonNodeLabels comparisons nameColorVector) hmms -drawSingleHMMER3s :: String -> Int -> Double -> Double -> Double -> String -> [HM.HMMER3] -> [Maybe S.StockholmAlignment] -> [(QDiagram Cairo V2 Double Any,QDiagram Cairo V2 Double Any)] +drawSingleHMMER3s :: String -> Int -> Double -> Double -> Double -> String -> [HM.HMMER3] -> [Maybe S.StockholmAlignment] -> [(QDiagram Cairo V2 Double Any,Maybe (QDiagram Cairo V2 Double Any))] drawSingleHMMER3s modelDetail entryNumberCutoff transitionCutoff maxWidth scalef emissiontype hmms alns | modelDetail == "minimal" = map (drawHMMER3 modelDetail entryNumberCutoff transitionCutoff maxWidth scalef emissiontype emptyColorNameVector) zippedInput | modelDetail == "simple" = map (drawHMMER3 modelDetail entryNumberCutoff transitionCutoff maxWidth scalef emissiontype emptyColorNameVector) zippedInput @@ -57,7 +54,7 @@ emptyColorNameVector = V.empty -- | -drawHMMER3 :: String -> Int -> Double -> Double -> Double -> String -> V.Vector (String,Colour Double) -> (HM.HMMER3,Maybe S.StockholmAlignment, V.Vector (Int,V.Vector (Colour Double)), Colour Double) -> (QDiagram Cairo V2 Double Any,QDiagram Cairo V2 Double Any) +drawHMMER3 :: String -> Int -> Double -> Double -> Double -> String -> V.Vector (String,Colour Double) -> (HM.HMMER3,Maybe S.StockholmAlignment, V.Vector (Int,V.Vector (Colour Double)), Colour Double) -> (QDiagram Cairo V2 Double Any,Maybe (QDiagram Cairo V2 Double Any)) drawHMMER3 modelDetail entriesNumberCutoff transitionCutoff maxWidth scalef emissiontype nameColorVector (model,aln,comparisonNodeLabels,modelColor) | modelDetail == "minimal" = ((applyAll ([bg white]) minimalNodesHeader) # scale scalef,alignmentDiagram) | modelDetail == "simple" = ((applyAll ([bg white]) simpleNodesHeader) # scale scalef,alignmentDiagram) @@ -80,7 +77,7 @@ simpleNodesHeader = alignTL (vcat' with { _sep = 5 } [modelHeader,simpleNodes]) verboseNodesHeader = alignTL (vcat' with { _sep = 5 } [modelHeader,verboseNodes]) modelHeader = makeModelHeader (HM.name model) modelColor nameColorVector - alignmentDiagram = maybe mempty (drawStockholmLines entriesNumberCutoff maxWidth nodeAlignmentColIndices comparisonNodeLabels) aln + alignmentDiagram = maybe Nothing (\a -> Just (drawStockholmLines entriesNumberCutoff maxWidth nodeAlignmentColIndices comparisonNodeLabels a)) aln makeModelHeader :: String -> Colour Double -> V.Vector (String,Colour Double) -> QDiagram Cairo V2 Double Any makeModelHeader mName modelColor nameColorVector = strutX 2 ||| setModelName mName ||| strutX 1 ||| rect 6 6 # lw 0.1 # fc modelColor # translate (r2 (negate 0, 3)) ||| strutX 30 ||| modelLegend