BioHMM 1.0.8 → 1.0.9

raw patch · 3 files changed

+12/−13 lines, 3 filesdep ~StockholmAlignmentPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependency ranges changed: StockholmAlignment

API changes (from Hackage documentation)

Files

• BioHMM.cabal +5/−5
• changelog +2/−0
• src/Bio/HMMDraw.hs +5/−8

@@ -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

@@ -1,4 +1,6 @@ -*-change-log-*-+1.0.9 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 13. April 2017+	* Improved handling of missing stockholm input 1.0.8 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 7. April 2017 	* Fixed a bug with a missing structure parameter character 1.0.7 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 19. March 2017

@@ -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