BioHMM 1.1.8 → 1.2.0
raw patch · 4 files changed
+11/−7 lines, 4 filesPVP ok
version bump matches the API change (PVP)
API changes (from Hackage documentation)
Files
- BioHMM.cabal +3/−3
- changelog +5/−0
- src/Bio/HMMCompareResult.hs +0/−1
- src/Bio/HMMDraw.hs +3/−3
BioHMM.cabal view
@@ -1,5 +1,5 @@ name: BioHMM-version: 1.1.8+version: 1.2.0 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/1.1.8- tag: 1.1.8+ location: https://github.com/eggzilla/BioHMM/tree/1.2.0+ tag: 1.2.0 library -- Modules exported by the library.
changelog view
@@ -1,4 +1,9 @@ -*-change-log-*-+1.2.0 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 9. June 2017+ * Fixed a bug where comparison nodes from the other model were used+ * Fixed alignment width+1.1.9 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 9. June 2017+ * Changed HMMCompare parsing for more similarity to CMCompare parsing 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
src/Bio/HMMCompareResult.hs view
@@ -72,7 +72,6 @@ _ <- char '[' nodes2 <- many1 parseMatchedNodes _ <- char ']'- newline return $ HMMCompareResult name1 name2 (readDouble score1) (readDouble score2) linkseq nodes1 nodes2 -- | Parse indices of matched nodes between models as integers
src/Bio/HMMDraw.hs view
@@ -81,7 +81,7 @@ simpleNodesHeader = alignTL (vcat' with { _sep = 5 } [modelHeader,simpleNodes]) verboseNodesHeader = alignTL (vcat' with { _sep = 5 } [modelHeader,verboseNodes]) modelHeader = makeModelHeader (HM.name model) modelColor nameColorVector- alignmentDiagram = drawStockholmLinesComparisonLabel entryNumberCutoff maxWidth comparisonNodeLabels currentNodes aln + alignmentDiagram = drawStockholmLinesComparisonLabel entryNumberCutoff (200 :: Double) comparisonNodeLabels currentNodes aln drawStockholmLinesComparisonLabel :: Int -> Double -> V.Vector (Int,V.Vector (Colour Double)) -> V.Vector HM.HMMER3Node -> Maybe S.StockholmAlignment -> Maybe (QDiagram Cairo V2 Double Any) drawStockholmLinesComparisonLabel entryNumberCutoff maxWidth comparisonNodeLabels nodes maybeAln@@ -408,9 +408,9 @@ getComparisonNodeLabels comparsionResults colorVector model = comparisonNodeLabels where modelName = HM.name model relevantComparisons1 = filter ((modelName==) . model1Name) comparsionResults- modelNodeInterval1 = map (\a -> (model2Name a,model2matchednodes a)) relevantComparisons1+ modelNodeInterval1 = map (\a -> (model2Name a,model1matchednodes a)) relevantComparisons1 relevantComparisons2 = filter ((modelName==) . model2Name) comparsionResults- modelNodeInterval2 = map (\a -> (model1Name a,model1matchednodes a)) relevantComparisons2+ modelNodeInterval2 = map (\a -> (model1Name a,model2matchednodes a)) relevantComparisons2 modelNodeIntervals = V.fromList (modelNodeInterval1 ++ modelNodeInterval2) colorNodeIntervals = V.map (modelToColor colorVector) modelNodeIntervals nodeNumber = V.length (HM.nodes model)