BioHMM 1.1.7 → 1.1.8

raw patch · 4 files changed

+30/−16 lines, 4 filesPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

API changes (from Hackage documentation)

Files

• BioHMM.cabal +3/−3
• changelog +4/−1
• src/Bio/HMMCompareResult.hs +9/−10
• src/Bio/HMMDraw.hs +14/−2

@@ -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.

@@ -1,4 +1,7 @@ -*-change-log-*-+1.1.8 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 8. June 2017+	* Minimal and simple visualisation now also support line mode+	* Added show instance for HMMCompareResult 1.1.7 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 7. June 2017 	* Improved placment of legend 1.1.6 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 23. May 2017@@ -8,7 +11,7 @@ 1.1.4 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 22. May 2017 	* Color scheme is now more robust for grayscale-printing 1.1.3 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 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 <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

@@ -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]

@@ -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