BioHMM 1.1.2 → 1.1.3

raw patch · 3 files changed

+28/−22 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• BioHMM.cabal +3/−3
• changelog +2/−0
• src/Bio/HMMDraw.hs +23/−19

@@ -1,5 +1,5 @@ name:                BioHMM-version:             1.1.2+version:             1.1.3 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/1.1.2-  tag:      1.1.2+  location: https://github.com/eggzilla/BioHMM/tree/1.1.3+  tag:      1.1.3  library   -- Modules exported by the library.

@@ -1,4 +1,6 @@ -*-change-log-*-+1.1.3 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 9. May 2017+	* Now using same simplified label color scheme as CMDraw  1.1.2 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 7. May 2017 	* Labels for columns are now passed to alignment visualisation instead of nodes 	* Improved mapping node to column labels

@@ -24,7 +24,7 @@ import qualified Data.Vector as V import Bio.HMMCompareResult import Bio.StockholmDraw-import qualified Data.Colour.SRGB.Linear as R+--import qualified Data.Colour.SRGB.Linear as R import Data.List import Graphics.SVGFonts import Bio.StockholmFont@@ -425,26 +425,30 @@ makeBlankComparisonNodeLabel nodeNumber = (nodeNumber,V.singleton white)  makeColorVector :: Int -> V.Vector (Colour Double)-makeColorVector modelNumber = V.map (\(a,b,c) -> R.rgb a b c) modelRGBTupel-   where indexVector = V.iterateN modelNumber (1+) 0-         stepSize = (765 :: Double) / fromIntegral modelNumber-         modelRGBTupel = V.map (makeRGBTupel stepSize) indexVector+makeColorVector modelNumber = V.take modelNumber colorVector+   where colorVector = V.fromList [crimson, moccasin, lime, seagreen, aqua ,darkorange ,blue, blueviolet ,brown ,burlywood ,cadetblue ,chartreuse ,chocolate ,coral ,cornflowerblue ,cornsilk ,cyan ,darkblue ,darkcyan ,darkgoldenrod ,darkgray ,darkgreen ,darkgrey ,darkkhaki ,darkmagenta ,darkolivegreen ,darkorchid ,darkred ,darksalmon ,darkseagreen ,darkslateblue ,darkslategray ,darkslategrey ,darkturquoise ,darkviolet ,deeppink ,deepskyblue ,dimgray ,dimgrey ,dodgerblue ,firebrick ,forestgreen ,fuchsia ,gainsboro ,gold ,goldenrod ,gray ,grey ,green ,greenyellow ,honeydew ,hotpink ,indianred,indigo ,ivory ,khaki ,lavender ,lavenderblush ,lawngreen ,lemonchiffon ,lime ,limegreen ,linen ,magenta ,maroon ,mediumaquamarine ,mediumblue ,mediumorchid ,mediumpurple ,mediumseagreen ,mediumslateblue ,mediumspringgreen ,mediumturquoise ,mediumvioletred ,midnightblue ,mintcream ,mistyrose ,navy ,oldlace ,olive ,olivedrab ,orange ,orangered ,orchid ,papayawhip ,peachpuff ,peru ,pink ,plum ,powderblue ,purple ,red ,rosybrown ,royalblue ,saddlebrown ,salmon ,sandybrown ,seagreen] -makeRGBTupel :: Double -> Int -> (Double,Double,Double)-makeRGBTupel stepSize modelNumber = (normA,normB,normC)-  where  totalSize = fromIntegral modelNumber * stepSize-         a = rgbBoundries (totalSize  - 510)-         b = rgbBoundries (totalSize - 255)-         c = rgbBoundries totalSize -         normA = a/255 -         normB = b/255-         normC = c/255 +--makeColorVector :: Int -> V.Vector (Colour Double)+--makeColorVector modelNumber = V.map (\(a,b,c) -> R.rgb a b c) modelRGBTupel+--   where indexVector = V.iterateN modelNumber (1+) 0+--         stepSize = (765 :: Double) / fromIntegral modelNumber+--         modelRGBTupel = V.map (makeRGBTupel stepSize) indexVector -rgbBoundries :: Double -> Double-rgbBoundries rgbValue-  | rgbValue>240 = 240-  | rgbValue<10 = 10-  | otherwise = rgbValue+--makeRGBTupel :: Double -> Int -> (Double,Double,Double)+-- makeRGBTupel stepSize modelNumber = (normA,normB,normC)+--   where  totalSize = fromIntegral modelNumber * stepSize+--          a = rgbBoundries (totalSize  - 510)+--          b = rgbBoundries (totalSize - 255)+--          c = rgbBoundries totalSize +--          normA = a/255 +--          normB = b/255+--          normC = c/255 ++-- rgbBoundries :: Double -> Double+-- rgbBoundries rgbValue+--   | rgbValue>240 = 240+--   | rgbValue<10 = 10+--   | otherwise = rgbValue  text' :: String -> QDiagram Cairo V2 Double Any text' t = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False 3 3) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (negate 0.75, negate 0.75))