StockholmAlignment 1.0.4 → 1.1.0

raw patch · 3 files changed

+28/−14 lines, 3 filesPVP ok

version bump matches the API change (PVP)

API changes (from Hackage documentation)

Files

• StockholmAlignment.cabal +5/−5
• changelog +3/−0
• src/Bio/StockholmDraw.hs +20/−9

@@ -1,11 +1,11 @@ name:                StockholmAlignment-version:             1.0.4+version:             1.1.0 synopsis:            Libary for Stockholm aligmnent format description:         Libary containing parsing and visualisation functions and datastructures for Stockholm aligmnent 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@@ -21,8 +21,8 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/StockholmAlignment/tree/1.0.4-  tag:      1.0.4+  location: https://github.com/eggzilla/StockholmAlignment/tree/1.1.0+  tag:      1.1.0  library   -- Modules exported by the library.@@ -32,7 +32,7 @@                      Bio.StockholmFont    -- compiler-options:-  ghc-options:         -Wall -O2 -fno-warn-unused-do-bind+  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 >= 1.4

@@ -1,4 +1,7 @@ -*-change-log-*-+1.1.0 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 7. May 2017+	* Specific column labels are now passed as color vectors independent of model indices+	* Added consensus secondary structure to alignment visualisation 1.0.4 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 27. April 2017         * Added visualisation of consensus secondary structure if present 1.0.3 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 24. April 2017

@@ -10,6 +10,7 @@      drawStockholm,      convertWUSStoDotBracket,      extractGapfreeStructure,+     extractGapfreeIndexedStructure,      isGap     ) where @@ -23,8 +24,8 @@ import Graphics.SVGFonts import Bio.StockholmFont -drawStockholmLines :: Int -> Double -> V.Vector Int -> V.Vector (Int, V.Vector (Colour Double)) -> S.StockholmAlignment -> QDiagram Cairo V2 Double Any-drawStockholmLines entriesNumberCutoff maxWidth nodeAlignmentColIndices comparisonNodeLabels aln = alignmentBlocks+drawStockholmLines :: Int -> Double -> V.Vector (Int, V.Vector (Colour Double)) -> S.StockholmAlignment -> QDiagram Cairo V2 Double Any+drawStockholmLines entriesNumberCutoff maxWidth columnComparisonLabels aln = alignmentBlocks   where seqEntries = V.fromList (take entriesNumberCutoff (S.sequenceEntries aln))         --consensusStructureEntry = if null (S.columnAnnotations aln) then mempty else drawConsensusStructureEntry maxIdLength (S.columnAnnotations aln)         maybeConsensusStructureEntry = find ((T.pack "SS_cons"==) . S.tag) (S.columnAnnotations aln)@@ -37,9 +38,9 @@         letterWidth = 2.0 :: Double         availableLettersPerRow = maxWidth / letterWidth         blocks = makeLetterIntervals entryNumber availableLettersPerRow maxEntryLength-        colIndicescomparisonNodeLabels = V.zipWith (\a b -> (a,b)) nodeAlignmentColIndices comparisonNodeLabels-        sparseComparisonColLabels = V.map nodeToColIndices colIndicescomparisonNodeLabels-        fullComparisonColLabels = fillComparisonColLabels maxEntryLength sparseComparisonColLabels+        --colIndicescomparisonNodeLabels = V.zipWith (\a b -> (a,b)) nodeAlignmentColIndices comparisonNodeLabels+        --sparseComparisonColLabels = V.map nodeToColIndices colIndicescomparisonNodeLabels+        fullComparisonColLabels = fillComparisonColLabels maxEntryLength columnComparisonLabels         alignmentBlocks = vcat' with { _sep = 6.0 } (map (drawStockholmRowBlock maxIdLength vectorEntries maxEntryLength fullComparisonColLabels) blocks)            extractGapfreeStructure :: String -> String -> String@@ -55,6 +56,20 @@         gapfreeCompleteStructure = V.filter (\(i,_) -> notElem i sequencegaps) (V.indexed completeBPStructure)         entryStructure = map snd (V.toList  gapfreeCompleteStructure) ++extractGapfreeIndexedStructure :: String -> String -> [(Int,Char)]+extractGapfreeIndexedStructure alignedSequence regularStructure1 = indexedEntryStructure+  where regularsequence1 = map convertToRegularGap alignedSequence+        bpindicestest1 = basePairIndices regularStructure1 [] 0+        sequencegaps = elemIndices '-' regularsequence1+        -- convert incomplete basepairs to .+        incompleteBasepairs = filter (\(i,j) -> elem i sequencegaps || elem j sequencegaps) bpindicestest1+        incompleteIndicesCharacterPairs = concatMap (\(a,b) -> [(a,'.'),(b,'.')]) incompleteBasepairs+        completeBPStructure = V.update (V.fromList regularStructure1) (V.fromList incompleteIndicesCharacterPairs)+        -- remove gap character postitions from structure string+        gapfreeCompleteStructure = V.filter (\(i,_) -> notElem i sequencegaps) (V.indexed completeBPStructure)+        indexedEntryStructure = (V.toList gapfreeCompleteStructure)        + basePairIndices :: String -> [Int] -> Int -> [(Int,Int)] basePairIndices (x:xs) ys counter   | x == '(' = basePairIndices xs (counter:ys) (counter+1)@@ -98,10 +113,6 @@   | c == ':' = '.'   | c == ',' = '.'   | otherwise = c---nodeToColIndices :: (Int,(Int,V.Vector (Colour Double))) -> (Int,V.Vector (Colour Double))-nodeToColIndices (colIndex,(_,colors)) = (colIndex,colors)  fillComparisonColLabels :: Int ->  V.Vector (Int, V.Vector (Colour Double)) ->  V.Vector (Int, V.Vector (Colour Double)) fillComparisonColLabels maxEntryLength sparseComparisonColLabels = fullComparisonColLabels