cmv (empty) → 1.0.1
raw patch · 15 files changed
+2510/−0 lines, 15 filesdep +BioHMMdep +BiobaseInfernaldep +BiobaseTypessetup-changed
Dependencies added: BioHMM, BiobaseInfernal, BiobaseTypes, BiobaseXNA, ParsecTools, PrimitiveArray, SVGFonts, StockholmAlignment, aeson, base, bytestring, cmdargs, cmv, colour, containers, diagrams-cairo, diagrams-lib, directory, either-unwrap, filepath, mtl, parsec, template-haskell, text, vector
Files
- LICENSE +675/−0
- README.md +37/−0
- Setup.hs +2/−0
- changelog +3/−0
- cmv.cabal +86/−0
- src/Bio/CMCompareResult.hs +87/−0
- src/Bio/CMDraw.hs +845/−0
- src/cmcv/CMCVisualisation.hs +118/−0
- src/cmcv/cmctohmmc.hs +116/−0
- src/cmcv/cmcwsvtocmcv.hs +63/−0
- src/cmcv/hmmctocmc.hs +120/−0
- src/cmv/CMVJson.hs +44/−0
- src/cmv/CMVisualisation.hs +113/−0
- src/hmmcv/HMMCVisualisation.hs +107/−0
- src/hmmv/HMMVisualisation.hs +94/−0
+ LICENSE view
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Of course, your program's commands+might be different; for a GUI interface, you would use an "about box".++ You should also get your employer (if you work as a programmer) or school,+if any, to sign a "copyright disclaimer" for the program, if necessary.+For more information on this, and how to apply and follow the GNU GPL, see+<http://www.gnu.org/licenses/>.++ The GNU General Public License does not permit incorporating your program+into proprietary programs. If your program is a subroutine library, you+may consider it more useful to permit linking proprietary applications with+the library. If this is what you want to do, use the GNU Lesser General+Public License instead of this License. But first, please read+<http://www.gnu.org/philosophy/why-not-lgpl.html>.+
+ README.md view
@@ -0,0 +1,37 @@+ +=========+*cmv* is a collection of tools for the visualisation of Hidden Markov Models (*HMMV*) and RNA-family models (*CMV*).+Moreover it can visualise comparisons of these models (*HMMCV*,*CMCV*), and annotate linked regions in the structural alignments they were constructed from and via, 3rd party tools, in their consensus secondary structure.++They are available as a commandline tools and as a webservice [cmvs](http://rna.informatik.uni-freiburg.de/CMVS/).++The source code of *cmv* is open source and available via GitHub and Hackage (License GPL-3):++* [](https://github.com/eggzilla/cmv) [](https://travis-ci.org/eggzilla/cmv) [](https://hackage.haskell.org/package/cmv) [](https://anaconda.org/bioconda/cmv)++For instruction how to use *cmv* please see the [Help page.](192.52.2.124/cmvs/help)++### Optional Dependencies:+*cmv* creates output which can be visualised via following optional dependencies.+* [R2R](http://breaker.research.yale.edu/R2R/)+* [forna](http://rna.tbi.univie.ac.at/forna/)+ +### Installation via bioconda++*cmv* can be installed with all dependencies via [conda](https://conda.io/docs/install/quick.html). Once you have conda installed simply type:++ conda install -c bioconda cmv=1.0.0 ++### Installation via cabal-install++ cmv is implemented in Haskell and can be installed via the Haskell package distribution sytem [cabal](https://www.haskell.org/cabal/). Once you have cabal installed simply type:++ cabal install cmv++### Precompiled Executables++* Linux (ghc-8.0.1) [HMMV 1.0.0 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMV)+* Linux (ghc-8.0.1) [HMMCV 1.0.0 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMCV)+* Linux (ghc-8.0.1) [CMV 1.0.0 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMV)+* Linux (ghc-8.0.1) [CMCV 1.0.0 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCV)+
+ Setup.hs view
@@ -0,0 +1,2 @@+import Distribution.Simple+main = defaultMain
+ changelog view
@@ -0,0 +1,3 @@+-*-change-log-*-+1.0.0 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 16. June 2017+ * Initial release
+ cmv.cabal view
@@ -0,0 +1,86 @@+name: cmv+version: 1.0.1+synopsis: Detailed visualization of CMs, HMMs and their comparisions+description: cmv is a collection of tools for the visualisation of Hidden Markov Models (HMMV) and RNA-family models (CMV). Moreover it can visualise comparisons of these models (HMMCV,CMCV), and annotate linked regions in the structural alignments they were constructed from and via, 3rd party tools, in their consensus secondary structure.+license: GPL-3+license-file: LICENSE+author: Florian Eggenhofer+maintainer: egg@informatik.uni-freiburg.de+-- copyright: +category: Bioinformatics+build-type: Simple+cabal-version: >=1.8++extra-source-files:+ README.md changelog++source-repository head+ type: git+ location: https://github.com/eggzilla/cmv++source-repository this+ type: git+ location: https://github.com/eggzilla/cmv/tree/1.0.1+ tag: 1.0.1++library+ -- Modules exported by the library.+ exposed-modules: Bio.CMDraw+ Bio.CMCompareResult++ -- compiler-options:+ ghc-options: -Wall++ -- Other library packages from which modules are imported.+ build-depends: base >=4.5 && <5, parsec>=3.1.9, diagrams-lib, BiobaseInfernal, text, vector, ParsecTools, diagrams-cairo, filepath, colour, PrimitiveArray, BiobaseXNA, mtl, directory, either-unwrap, SVGFonts >= 1.6, BioHMM>=1.2.0, StockholmAlignment>=1.1.1, BiobaseTypes,containers+ + -- Directories containing source files.+ hs-source-dirs: src++executable CMCV+ Hs-Source-Dirs: ./src/cmcv/+ main-is: CMCVisualisation.hs+ ghc-options: -Wall+ build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.1++executable CMV+ Hs-Source-Dirs: ./src/cmv/+ main-is: CMVisualisation.hs+ ghc-options: -Wall + build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.1++executable CMCWStoCMCV+ Hs-Source-Dirs: ./src/cmcv/+ main-is: cmcwsvtocmcv.hs+ ghc-options: -Wall + build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath++executable CMCtoHMMC+ Hs-Source-Dirs: ./src/cmcv/+ main-is: cmctohmmc.hs+ ghc-options: -Wall + build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0++executable HMMCtoCMC+ Hs-Source-Dirs: ./src/cmcv/+ main-is: hmmctocmc.hs+ ghc-options: -Wall + build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0 ++executable CMVJson+ Hs-Source-Dirs: ./src/cmv/+ main-is: CMVJson.hs+ ghc-options: -Wall+ build-depends: base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, aeson++executable HMMCV+ Hs-Source-Dirs: ./src/hmmcv/+ main-is: HMMCVisualisation.hs+ ghc-options: -Wall+ build-depends: base >=4.5, cmdargs, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.1++executable HMMV+ Hs-Source-Dirs: ./src/hmmv/+ main-is: HMMVisualisation.hs+ ghc-options: -Wall+ build-depends: base >=4.5, cmdargs, diagrams-lib>=1.3.1.0, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.1
+ src/Bio/CMCompareResult.hs view
@@ -0,0 +1,87 @@+-- | Parse CMCompare output+-- parsing is done with parsec+-- For more information on CMCompare consult: <http://www.tbi.univie.ac.at/software/cmcompare/>++module Bio.CMCompareResult+ (+ CmcompareResult(..),+ getCmcompareResults,+ getModelsNames,+ getModelNames+ ) where++import Text.ParserCombinators.Parsec+import Data.List++-- | Datastructure for result strings of comparisons between covariance models by CMCompare+data CmcompareResult = CmcompareResult+ { model1Name :: String,+ model2Name :: String,+ linkscore1 :: Double,+ linkscore2 :: Double,+ linksequence :: String,+ model1structure :: String,+ model2structure :: String,+ model1matchednodes :: [Int],+ model2matchednodes :: [Int]+ } deriving ()++instance Show CmcompareResult where+ show (CmcompareResult _model1Name _model2Name _linkscore1 _linkscore2 _linksequence _model1structure _model2structure _model1matchednodes _model2matchednodes) = _model1Name ++ " " ++ _model2Name ++ " " ++ show _linkscore1 ++ " " ++ show _linkscore2 ++ " " ++ _linksequence ++ " " ++ _model1structure ++ " " ++ _model2structure ++ " " ++ formatMatchedNodes _model1matchednodes ++ " " ++ formatMatchedNodes _model2matchednodes ++ "\n"+ +formatMatchedNodes :: [Int] -> String+formatMatchedNodes nodes = "[" ++ intercalate "," (map show nodes) ++ "]"++readDouble :: String -> Double+readDouble = read++readInt :: String -> Int+readInt = read++-- | Parse a CMcompare result string+parseCmcompareResult :: GenParser Char st CmcompareResult+parseCmcompareResult = do+ name1 <- many1 (noneOf " ")+ _ <- many1 space+ name2 <- many1 (noneOf " ")+ _ <- many1 space+ score1 <- many1 (noneOf " ")+ _ <- many1 space+ score2 <- many1 (noneOf " ")+ _ <- many1 space+ linkseq <- many1 (oneOf "AGTCUagtcu")+ _ <- many1 space+ structure1 <- many1 (oneOf "(,.)")+ _ <- many1 space+ structure2 <- many1 (oneOf "(,.)")+ _ <- many1 space+ _ <- char '['+ nodes1 <- many1 parseMatchedNodes+ _ <- char ']'+ _ <- many1 space+ _ <- char '['+ nodes2 <- many1 parseMatchedNodes+ _ <- char ']'+ return $ CmcompareResult name1 name2 (readDouble score1) (readDouble score2) linkseq structure1 structure2 nodes1 nodes2++-- | Parse indices of matched nodes between models as integers+parseMatchedNodes :: GenParser Char st Int+parseMatchedNodes = do+ nodeNumber <- many1 digit+ optional (char ',')+ return (readInt nodeNumber)++-- | Parser for CMCompare result strings+getCmcompareResults :: FilePath -> IO [Either ParseError CmcompareResult]+getCmcompareResults filePath = let+ fp = filePath+ doParseLine' = parse parseCmcompareResult "parseCMCompareResults"+ in do+ fileContent <- fmap lines $ readFile fp+ return $ map doParseLine' fileContent++getModelsNames :: [CmcompareResult] -> [String]+getModelsNames models = concatMap getModelNames models++getModelNames :: CmcompareResult -> [String]+getModelNames model = [model1Name model,model2Name model]
+ src/Bio/CMDraw.hs view
@@ -0,0 +1,845 @@+-- | Drawing of covariance model (http://www.tbi.univie.ac.at/software/cmcompare/) guide trees and highlighting comparison results+-- Drawing is done with the diagrams package+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE FlexibleContexts #-}+{-# LANGUAGE TypeFamilies #-}+{-# LANGUAGE RankNTypes #-}++module Bio.CMDraw+ (+ drawSingleCMComparisons,+ drawSingleCMs,+ drawCM,+ text',+ svgsize,+ diagramName,+ printCM,+ NodeIndices,+ buildRowIndexStructure,+ buildTreeIndexStructure,+ mergedSecondaryStructureVisualisation,+ perModelSecondaryStructureVisualisation+ ) where++import Diagrams.Prelude+import Bio.CMCompareResult+import Data.List+import qualified Data.Text as T+import qualified Data.Vector as V+import Bio.StockholmData+import Bio.StockholmDraw+import Diagrams.Backend.Cairo+import qualified Data.Vector.Unboxed as VU+import qualified Data.PrimitiveArray.Index.PhantomInt as PI+import Biobase.Types.Bitscore (Bitscore(..), score2Prob)+import Text.Printf+--import qualified Data.Colour.SRGB.Linear as R+import qualified Data.Colour.SRGB as R+import Data.Maybe+import Control.Monad.State+import qualified Data.Char as C+import Graphics.SVGFonts+import Bio.StockholmFont+import qualified Biobase.SElab.CM.Types as CM+import qualified Biobase.SElab.CM.ModelStructure as CM+import Data.Either.Unwrap+import qualified Data.Map as M+import Data.Function ++-- | Draw one or more CM+drawSingleCMComparisons :: String -> Int -> Double -> String -> String -> Double -> Double -> [CM.CM] -> [Maybe StockholmAlignment] -> [CmcompareResult] -> [(QDiagram Cairo V2 Double Any,Maybe (QDiagram Cairo V2 Double Any))]+drawSingleCMComparisons modelDetail entryNumberCutoff transitionCutoff modelLayout emissiontype maxWidth scalef cms alns comparisons = diagrams+ where diagrams = map (drawCM modelDetail entryNumberCutoff transitionCutoff modelLayout emissiontype maxWidth scalef nameColorVector) zippedInput+ zippedInput = zip4 cms alns comparisonNodeLabels (V.toList colorVector)+ modelNumber = length cms+ comparisonNodeLabels = map (getComparisonNodeLabels comparisons nameColorVector) cms+ colorVector = makeColorVector modelNumber+ modelNames = V.fromList (map (T.unpack . CM._name) cms)+ nameColorVector = V.zipWith (\a b -> (a,b)) modelNames colorVector++-- | Draw one or more CM+drawSingleCMs :: String -> Int -> Double -> String -> String -> Double -> Double -> [CM.CM] -> [Maybe StockholmAlignment] -> [(QDiagram Cairo V2 Double Any,Maybe (QDiagram Cairo V2 Double Any))]+drawSingleCMs modelDetail entryNumberCutoff transitionCutoff modelLayout emissiontype maxWidth scalef cms alns = map (drawCM modelDetail entryNumberCutoff transitionCutoff modelLayout emissiontype maxWidth scalef emptyColorNameVector) zippedInput+ where zippedInput = zip4 cms alns comparisonNodeLabels colorList+ comparisonNodeLabels = map getBlankComparisonNodeLabels cms+ colorList = replicate (length cms) white+ emptyColorNameVector = V.empty++-- | Draw the guide Tree of a single CM+drawCM :: String -> Int -> Double -> String -> String -> Double -> Double -> V.Vector (String,Colour Double) -> (CM.CM,Maybe StockholmAlignment,V.Vector (Int,V.Vector (Colour Double)), Colour Double) -> (QDiagram Cairo V2 Double Any,Maybe (QDiagram Cairo V2 Double Any))+drawCM modelDetail entryNumberCutoff transitionCutoff modelLayout emissiontype maxWidth scalef nameColorVector (inputCM,aln,comparisonNodeLabels,modelColor)+ | modelLayout == "tree" = ((applyAll ([bg white]) modelTreeLayout),alignmentDiagram)+ | modelLayout == "flat" = ((applyAll ([bg white]) modelFlatLayout),alignmentDiagram)+ | otherwise = ((applyAll ([bg white])modelTreeLayout),alignmentDiagram)+ where cm = fromLeft (CM._cm inputCM) -- select Flexible Model+ nodes = V.fromList (M.elems (CM._fmNodes cm))+ nodeNumber = V.length nodes+ allStates = CM._fmStates cm+ boxlength = fromIntegral (length alphabetSymbols) + 2+ alphabetSymbols = ['A','U','C','G']+ indices = V.toList (V.iterateN (nodeNumber-1) (1+) 0)+ (indexStructure,_)= runState (buildTreeIndexStructure 1 nodes indices) startState+ modelName = CM._name inputCM+ modelFlatLayout = alignTL (vcat' with {_sep=0.1} [modelHeader,nodeTransitions]) # scale scalef+ modelTreeLayout = alignTL (vcat' with {_sep=0.1} [modelHeader,nodeTreeTransitions]) #scale scalef+ nodeTreeTransitions = applyAll (arrowList ++ labelList) nodesTree+ nodeTransitions = applyAll (arrowList ++ labelList) nodesFlat+ firstInterval = fromJust (find (\(_,p,_,_,_) -> p == 0) (fst indexStructure))+ nodesTree = drawCMNodeTree modelDetail alphabetSymbols emissiontype boxlength allStates comparisonNodeLabels nodes (fst indexStructure) firstInterval+ modelHeader = makeModelHeader (T.unpack modelName) modelColor nameColorVector+ nodeIndices = V.iterateN nodeNumber (1+) 0+ nodesFlat = vcat' with {_sep=0.01} (V.toList (V.map (drawCMNode modelDetail alphabetSymbols emissiontype boxlength (0 :: Int) nodeNumber nodeNumber allStates comparisonNodeLabels nodes) nodeIndices))+ allConnectedStates = makeAllConnectedStates allStates+ highConnectedStates = V.filter (\(_,_,w) -> w >= transitionCutoff) allConnectedStates+ connectedStates = V.filter (\(stateId,targetStateIndex,_) -> stateId /= targetStateIndex) highConnectedStates+ selfConnectedStates = V.filter (\(stateId,targetStateIndex,_) -> stateId == targetStateIndex) highConnectedStates+ arrowList = case modelDetail of+ "detailed" -> V.toList (V.map makeArrow connectedStates V.++ V.map makeSelfArrow selfConnectedStates)+ "interval"-> map (makeArrow . indexStructureToConnections) (filter (\(acc,emit,_,_,_)-> acc /= emit)(fst indexStructure))+ "minimal"-> V.toList (V.map makeArrow connectedStates)+ "simple"-> V.toList (V.map makeArrow connectedStates)+ _ -> []+ labelList = case modelDetail of+ "detailed" -> V.toList (V.map makeLabel connectedStates V.++ V.map makeSelfLabel selfConnectedStates)+ _ -> [] + alignmentDiagram = drawStockholmLinesComparisonLabel entryNumberCutoff maxWidth comparisonNodeLabels nodes aln++drawStockholmLinesComparisonLabel :: Int -> Double -> V.Vector (Int,V.Vector (Colour Double)) -> V.Vector CM.Node -> Maybe StockholmAlignment -> Maybe (QDiagram Cairo V2 Double Any)+drawStockholmLinesComparisonLabel entryNumberCutoff maxWidth comparisonNodeLabels nodes maybeAln+ | isJust maybeAln = Just alignmentVis+ | otherwise = Nothing+ where aln = fromJust maybeAln+ -- comparison labels do not include end nodes, but no root node.+ -- end nodes have no alignment columns associated+ columnComparisonLabels = getComparisonPerColumnLabels comparisonNodeLabels nodes+ alignmentVis = drawStockholmLines entryNumberCutoff maxWidth columnComparisonLabels aln+ +makeAllConnectedStates :: M.Map (PI.PInt () CM.StateIndex) CM.State -> V.Vector (String,String,Double)+makeAllConnectedStates allStates = allConnectedStates+ where indexStateTuples = M.assocs allStates+ allConnectedStates = V.fromList (concatMap makeStateConnections indexStateTuples)+ +makeStateConnections :: (PI.PInt () CM.StateIndex,CM.State) -> [(String,String,Double)]+makeStateConnections (pInt,currentState) = conns+ where stateId = show (PI.getPInt pInt)+ targetBitscoreVector = VU.toList (CM._stateTransitions currentState)+ conns = map (\(target,bitscore) -> (stateId,show(PI.getPInt target),score2Prob 1 bitscore)) targetBitscoreVector+++-- | Extracts consensus secondary structure from alignment and annotates cmcompare nodes for each model-model combination seperatly+perModelSecondaryStructureVisualisation :: String -> Double -> String -> [CM.CM] -> [Maybe StockholmAlignment] -> [CmcompareResult] -> [(String,String)]+perModelSecondaryStructureVisualisation selectedTool _ structureFilePath cms alns comparisons+ | selectedTool == "forna" = fornaVis+ | selectedTool == "r2r" = r2rVis+ | selectedTool == "fornaLink" = fornaLink+ | selectedTool == "r2rfornaLink" = fornaLink ++ r2rVis+ | selectedTool == "all" = fornaLink ++ r2rVis ++ fornaVis+ | otherwise = []+ where fornaVis = concatMap (buildFornaperModelInput structureFilePath) structureComparisonInfo+ fornaLink = concatMap (buildFornaLinksInput structureFilePath) structureComparisonInfo+ r2rVis = concatMap (buildR2RperModelInput structureFilePath) structureComparisonInfo+ modelNumber = length cms+ comparisonNodeLabels = map (getComparisonPerModelNodeLabels comparisons nameColorVector) cms+ colorVector = makeColorVector modelNumber+ modelNames = V.fromList (map (T.unpack . CM._name) cms)+ nameColorVector = V.zipWith (\a b -> (a,b)) modelNames colorVector+ structureComparisonInfo = zip3 cms alns comparisonNodeLabels++getComparisonPerModelNodeLabels :: [CmcompareResult] -> V.Vector (String, Colour Double) -> CM.CM -> V.Vector (String,Colour Double, V.Vector (Int,V.Vector (Colour Double)))+getComparisonPerModelNodeLabels comparsionResults colorVector model = modelComparisonLabels+ where modelName = T.unpack (CM._name model)+ relevantComparisons1 = filter ((modelName==) . model1Name) comparsionResults+ modelNodeInterval1 = map (\a -> (model2Name a,nub (model1matchednodes a))) relevantComparisons1 + relevantComparisons2 = filter ((modelName==) . model2Name) comparsionResults+ modelNodeInterval2 = map (\a -> (model1Name a,nub (model2matchednodes a))) relevantComparisons2+ modelNodeIntervals = V.fromList (modelNodeInterval1 ++ modelNodeInterval2)+ nodeNumber = (CM._nodesInModel model)+ modelComparisonLabels = V.map (getModelComparisonLabels modelName nodeNumber colorVector) modelNodeIntervals++getModelComparisonLabels :: String -> Int -> V.Vector (String, Colour Double) -> (String,[Int])-> (String,Colour Double,V.Vector (Int,V.Vector (Colour Double)))+getModelComparisonLabels _ nodeNumber colorVector (compModel,matchedNodes) = (compModel,modelColor,comparisonNodeLabels)+ where (modelColor,modelInterval) = modelToColor colorVector (compModel,matchedNodes)+ -- cm starts at node index 0 for root node and ends with end node+ -- cmcompare does not include root node, but end node + comparisonNodeLabels = V.generate (nodeNumber) (makeModelComparisonNodeLabel (modelColor,modelInterval))++makeModelComparisonNodeLabel :: (Colour Double,[Int]) -> Int -> (Int,V.Vector (Colour Double))+makeModelComparisonNodeLabel (modelColor, nodeInterval) nodeNumber + | elem nodeNumber nodeInterval = (nodeNumber,V.singleton modelColor)+ | otherwise = (nodeNumber,V.singleton white)++getComparisonPerColumnLabels :: V.Vector (Int,V.Vector (Colour Double)) -> V.Vector CM.Node -> V.Vector (Int, V.Vector (Colour Double))+getComparisonPerColumnLabels comparisonNodeLabels nodes = columnComparisonLabels where + unsortedColumnComparisonLabel = concatMap (nodeToColumnComparisonLabel nodes) (V.toList comparisonNodeLabels)+ columnComparisonLabels = V.fromList (sortBy (compare `on` fst) unsortedColumnComparisonLabel)++nodeToColumnComparisonLabel:: V.Vector CM.Node -> (Int, V.Vector (Colour Double)) -> [(Int,V.Vector (Colour Double))]+nodeToColumnComparisonLabel nodes (nodeIndex,colors) = colLabels+ where currentNode = (V.!) nodes (nodeIndex)+ colIndices = nub [CM._nodeColL currentNode,CM._nodeColR currentNode]+ colLabels = map (\a->(a,colors)) colIndices+ +--+buildR2RperModelInput :: String -> (CM.CM, Maybe StockholmAlignment,V.Vector (String,Colour Double,V.Vector (Int,V.Vector (Colour Double)))) -> [(String,String)]+buildR2RperModelInput structureFilePath (inputCM,maybeAln,comparisonNodeLabels)+ | isNothing maybeAln = []+ | otherwise = if V.null comparisonNodeLabels then singler2rInput else V.toList r2rComparisonInputs+ where cm = fromLeft (CM._cm inputCM) -- select Flexible Model+ modelName = T.unpack (CM._name inputCM)+ nodes = V.fromList (M.elems (CM._fmNodes cm))+ aln = fromJust maybeAln+ r2rInputPrefix = sHeader ++ sConsensusStructure ++ sConsensusSequence ++ sConsensusSequenceColor ++ sCovarianceAnnotation + allColumnAnnotations = columnAnnotations aln+ consensusSequenceList = map annotation (filter (\annotEntry -> tag annotEntry == T.pack "RF") allColumnAnnotations)+ consensusSequence = if null consensusSequenceList then "" else T.unpack (head consensusSequenceList)+ gapFreeConsensusSequence = map C.toUpper (filter (not . isGap) consensusSequence)+ consensusStructureList = map (convertWUSStoDotBracket . annotation) (filter (\annotEntry -> tag annotEntry == T.pack "SS_cons") allColumnAnnotations)+ consensusStructure = if null consensusStructureList then "" else T.unpack (head consensusStructureList)+ indexedGapFreeConsensusStructure = extractGapfreeIndexedStructure consensusSequence consensusStructure+ consensusStructureColIndices = map ((+1) . fst) indexedGapFreeConsensusStructure+ gapFreeConsensusStructure = map snd indexedGapFreeConsensusStructure+ --maxEntryLength = length consensusStructure+ --convert node to column labels as needed for consensus secondary structure+ columnComparisonLabels = V.map (\(mname,mcolor,comparisonNodePerModelLabels) -> (mname,mcolor,getComparisonPerColumnLabels comparisonNodePerModelLabels nodes)) comparisonNodeLabels+ --filter for labels that are part of consensus secondary structure by index+ consensusStructureColumnComparisonLabels = V.map (\(mname,mcolor,colLabels) -> (mname,mcolor,V.filter (\(i,_) -> elem i consensusStructureColIndices) colLabels)) columnComparisonLabels+ --consensusStructureColumnComparisonLabels = V.filter (\(i,_) -> elem i consensusStructureColIndices) columnComparisonLabels+ sHeader = "# STOCKHOLM 1.0\n"+ sConsensusStructure = "#=GC SS_cons " ++ gapFreeConsensusStructure ++ "\n"+ sConsensusSequence = "#=GC cons " ++ gapFreeConsensusSequence ++ "\n" -- ++ show consensusStructureColIndices ++ "\n" ++ show comparisonNodeLabels ++ "\n"+ sConsensusSequenceColor = "#=GC conss " ++ replicate (length gapFreeConsensusSequence) '2' ++ "\n"+ sCovarianceAnnotation = "#=GC cov_SS_cons " ++ replicate (length gapFreeConsensusSequence) '.' ++ "\n"+ singleFilePath = structureFilePath ++ modelName ++ ".r2r" + singler2rInput = [(singleFilePath,r2rInputPrefix)]+ -- for multiple comparisons we need to return different filenames and labels+ r2rComparisonInputs = V.map (buildR2RperModelComparisonInput modelName structureFilePath r2rInputPrefix) consensusStructureColumnComparisonLabels++buildR2RperModelComparisonInput :: String -> String -> String -> (String, Colour Double, V.Vector (Int, V.Vector (Colour Double))) -> (String,String)+buildR2RperModelComparisonInput modelName structureFilePath r2rInputPrefix (compModelName,modelColor,columnComparisonLabels) = (schemeFilePath,r2rInput)+ where schemeFilePath = structureFilePath ++ modelName ++ "." ++ compModelName ++ ".r2r"+ r2rLabels = map comparisonColLabelsToR2RLabel (V.toList columnComparisonLabels)+ sComparisonHighlight = "#=GC R2R_LABEL " ++ r2rLabels ++ "\n"+ backBoneColor = setBackboneColor modelColor+ sBackboneColorLabel = "#=GF R2R shade_along_backbone s rgb:" ++ backBoneColor ++ "\n"+ r2rInput = r2rInputPrefix ++ sComparisonHighlight ++ sBackboneColorLabel++setBackboneColor :: Colour Double -> String+setBackboneColor modelColor = show ((R.channelRed currentColor)* 255) ++ "," ++ show ((R.channelGreen currentColor) * 255) ++ "," ++ show ((R.channelBlue currentColor) * 255)+ where currentColor = R.toSRGB modelColor++buildFornaperModelInput :: String -> (CM.CM,Maybe StockholmAlignment,V.Vector (String,Colour Double,V.Vector (Int,V.Vector (Colour Double)))) -> [(String, String)]+buildFornaperModelInput structureFilePath (inputCM,maybeAln,comparisonNodeLabelsPerModels)+ | isNothing maybeAln = []+ | otherwise = fornaInput:colorSchemes+ where cm = fromLeft (CM._cm inputCM) -- select Flexible Model+ nodes = V.fromList (M.elems (CM._fmNodes cm))+ aln = fromJust maybeAln+ fornaString = ">" ++ modelName ++ "\n" ++ gapfreeConsensusSequence ++ "\n" ++ gapFreeConsensusStructure+ fornaFilePath = structureFilePath ++ modelName ++ ".forna"+ fornaInput = (fornaFilePath,fornaString)+ allColumnAnnotations = columnAnnotations aln+ consensusSequenceList = map annotation (filter (\annotEntry -> tag annotEntry == T.pack "RF") allColumnAnnotations)+ consensusSequence = if null consensusSequenceList then "" else T.unpack (head consensusSequenceList)+ gapfreeConsensusSequence = map C.toUpper (filter (not . isGap) consensusSequence)+ consensusStructureList = map (convertWUSStoDotBracket . annotation) (filter (\annotEntry -> tag annotEntry == T.pack "SS_cons") allColumnAnnotations)+ consensusStructure = if null consensusStructureList then "" else T.unpack (head consensusStructureList)+ indexedGapFreeConsensusStructure = extractGapfreeIndexedStructure consensusSequence consensusStructure+ consensusStructureColIndices = map ((+1) . fst) indexedGapFreeConsensusStructure+ gapFreeConsensusStructure = map snd indexedGapFreeConsensusStructure+ modelName = T.unpack (CM._name inputCM) + columnComparisonLabels = V.map (\(mname,mcolor,comparisonNodePerModelLabels) -> (mname,mcolor,getComparisonPerColumnLabels comparisonNodePerModelLabels nodes)) comparisonNodeLabelsPerModels+ --filter for labels that are part of consensus secondary structure by index+ consensusStructureColumnComparisonLabels = V.map (\(mname,mcolor,colLabels) -> (mname,mcolor,V.filter (\(i,_) -> elem i consensusStructureColIndices) colLabels)) columnComparisonLabels+ colorSchemes = V.toList (V.map (makeColorScheme modelName structureFilePath) consensusStructureColumnComparisonLabels)+ + +buildFornaLinksInput :: String -> (CM.CM,Maybe StockholmAlignment,V.Vector (String,Colour Double,V.Vector (Int,V.Vector (Colour Double)))) -> [(String, String)]+buildFornaLinksInput structureFilePath (inputCM,maybeAln,comparisonNodeLabelsPerModels)+ | isNothing maybeAln = []+ | otherwise = if V.null comparisonNodeLabelsPerModels then singleFornaLink else fornaComparisons+ where cm = fromLeft (CM._cm inputCM) -- select Flexible Model+ nodes = V.fromList (M.elems (CM._fmNodes cm))+ aln = fromJust maybeAln+ --http://nibiru.tbi.univie.ac.at/forna/forna.html?id=fasta&file=%3Eheader\nAACGUUAGUU\n(((....)))&colors=%3Eheader\n0\n0.1\n0.2\n0.3\n0.4\n0.5\n0.6\n0.7\n0.8\n0.9\n1+ fornaURLPrefix = "http://rna.tbi.univie.ac.at/forna/forna.html?id=fasta&file=%3Eheader\\n" ++ gapfreeConsensusSequence ++ "\\n" ++ gapFreeConsensusStructure+ singleFornaLink = [(fornaFilePath,fornaURLPrefix)]+ fornaFilePath = structureFilePath ++ modelName ++ ".fornalink"+ allColumnAnnotations = columnAnnotations aln+ consensusSequenceList = map annotation (filter (\annotEntry -> tag annotEntry == T.pack "RF") allColumnAnnotations)+ consensusSequence = if null consensusSequenceList then "" else T.unpack (head consensusSequenceList)+ gapfreeConsensusSequence = map C.toUpper (filter (not . isGap) consensusSequence)+ modelName = T.unpack (CM._name inputCM)+ consensusStructureList = map (convertWUSStoDotBracket . annotation) (filter (\annotEntry -> tag annotEntry == T.pack "SS_cons") allColumnAnnotations)+ consensusStructure = if null consensusStructureList then "" else T.unpack (head consensusStructureList)+ indexedGapFreeConsensusStructure = extractGapfreeIndexedStructure consensusSequence consensusStructure+ consensusStructureColIndices = map ((+1) . fst) indexedGapFreeConsensusStructure+ gapFreeConsensusStructure = map snd indexedGapFreeConsensusStructure + columnComparisonLabels = V.map (\(mname,mcolor,comparisonNodePerModelLabels) -> (mname,mcolor,getComparisonPerColumnLabels comparisonNodePerModelLabels nodes)) comparisonNodeLabelsPerModels+ --filter for labels that are part of consensus secondary structure by index+ consensusStructureColumnComparisonLabels = V.map (\(mname,mcolor,colLabels) -> (mname,mcolor,V.filter (\(i,_) -> elem i consensusStructureColIndices) colLabels)) columnComparisonLabels+ fornaComparisons = V.toList (V.map (makeFornaComparisonLink modelName structureFilePath fornaURLPrefix) consensusStructureColumnComparisonLabels)++makeFornaComparisonLink :: String -> String -> String -> (String,Colour Double,V.Vector (Int,V.Vector (Colour Double))) -> (String,String)+makeFornaComparisonLink modelName structureFilePath fornaURLPrefix (compModelName,_,comparisonColLabelsPerModel) = (comparisonPath,comparisonLink)+ where comparisonPath = structureFilePath ++ modelName ++ "." ++ compModelName ++ ".fornalink"+ comparisonLink = fornaURLPrefix ++ labelPrefix ++ singleColorLabels + labelPrefix = "&colors=%3Eheader\\n" + --forna only supports a single color per node, which has to be supplied as additional color scheme+ singleColorLabels = concatMap comparisonColLabelsToFornaLinkLabel (V.toList comparisonColLabelsPerModel)+ +comparisonColLabelsToFornaLinkLabel :: (Int, V.Vector (Colour Double)) -> String+comparisonColLabelsToFornaLinkLabel (_,colorVector)+ | V.null colorVector = ""+ | V.head colorVector /= white = "1\\n"+ | otherwise = "0\\n"+ +makeColorScheme :: String -> String -> (String,Colour Double,V.Vector (Int,V.Vector (Colour Double))) -> (String,String)+makeColorScheme modelName structureFilePath (compModelName,_,comparisonColLabelsPerModel) = (schemeFilePath,singleColorLabels)+ where schemeFilePath = structureFilePath ++ modelName ++ "." ++ compModelName ++ ".fornacolor"+ indexedComparisonColLabelsPerModel = V.indexed comparisonColLabelsPerModel+ --column indexes have to be mapped to gap free consensus sequence+ structureIndexedLabels = V.map (\(a,(_,c)) -> (a+1,c)) indexedComparisonColLabelsPerModel+ singleColorLabels = concatMap comparisonColLabelsToFornaLabel (V.toList structureIndexedLabels)+ +-- | Extracts consensus secondary structure from alignment and annotates cmcompare nodes for all comparisons in one merged output+mergedSecondaryStructureVisualisation :: String -> Double -> [CM.CM] -> [Maybe StockholmAlignment] -> [CmcompareResult] -> [(String,String)]+mergedSecondaryStructureVisualisation selectedTool _ cms alns comparisons+ | selectedTool == "forna" = fornaVis+ | selectedTool == "r2r" = r2rVis+ | otherwise = []+ where fornaVis = map buildMergedFornaInput structureComparisonInfo+ r2rVis = map buildMergedR2RInput structureComparisonInfo+ modelNumber = length cms+ comparisonNodeLabels = map (getComparisonNodeLabels comparisons nameColorVector) cms+ colorVector = makeColorVector modelNumber+ modelNames = V.fromList (map (T.unpack . CM._name) cms)+ nameColorVector = V.zipWith (\a b -> (a,b)) modelNames colorVector+ structureComparisonInfo = zip3 cms alns comparisonNodeLabels+ +buildMergedFornaInput :: (CM.CM,Maybe StockholmAlignment,V.Vector (Int, V.Vector (Colour Double))) -> (String, String)+buildMergedFornaInput (inputCM,maybeAln,comparisonNodeLabels)+ | isNothing maybeAln = ([],[])+ | otherwise = (fornaInput, colorScheme)+ where cm = fromLeft (CM._cm inputCM) -- select Flexible Model+ nodes = V.fromList (M.elems (CM._fmNodes cm))+ aln = fromJust maybeAln+ fornaInput = ">" ++ modelName ++ "\n" ++ gapfreeConsensusSequence ++ "\n" ++ gapFreeConsensusStructure+ allColumnAnnotations = columnAnnotations aln+ consensusSequenceList = map annotation (filter (\annotEntry -> tag annotEntry == T.pack "RF") allColumnAnnotations)+ consensusSequence = if null consensusSequenceList then "" else T.unpack (head consensusSequenceList)+ gapfreeConsensusSequence = map C.toUpper (filter (not . isGap) consensusSequence)+ modelName = T.unpack (CM._name inputCM)+ consensusStructureList = map (convertWUSStoDotBracket . annotation) (filter (\annotEntry -> tag annotEntry == T.pack "SS_cons") allColumnAnnotations)+ consensusStructure = if null consensusStructureList then "" else T.unpack (head consensusStructureList)+ indexedGapFreeConsensusStructure = extractGapfreeIndexedStructure consensusSequence consensusStructure+ --consensusStructureColIndices = map ((+1) . fst) indexedGapFreeConsensusStructure+ gapFreeConsensusStructure = map snd indexedGapFreeConsensusStructure+ columnComparisonLabels = getComparisonPerColumnLabels comparisonNodeLabels nodes+ --forna only supports a single color per node, which has to be supplied as additional color scheme+ singleColorLabels = concatMap comparisonColLabelsToFornaLabel (V.toList columnComparisonLabels)+ colorScheme = singleColorLabels++comparisonColLabelsToFornaLabel :: (Int, V.Vector (Colour Double)) -> String+comparisonColLabelsToFornaLabel (nodeNr,colorVector)+ | V.null colorVector = ""+ | V.head colorVector /= white = " " ++ show nodeNr ++ ":blue "+ | otherwise = ""+ +buildMergedR2RInput :: (CM.CM, Maybe StockholmAlignment,V.Vector (Int,V.Vector (Colour Double))) -> (String,String)+buildMergedR2RInput (inputCM,maybeAln,comparisonNodeLabels)+ | isNothing maybeAln = ([],[])+ | otherwise = (r2rInput,[])+ where cm = fromLeft (CM._cm inputCM) -- select Flexible Model+ nodes = V.fromList (M.elems (CM._fmNodes cm))+ aln = fromJust maybeAln+ r2rInput = sHeader ++ sConsensusStructure ++ sConsensusSequence ++ sConsensusSequenceColor ++ sCovarianceAnnotation ++ sComparisonHighlight ++ sBackboneColorLabel+ allColumnAnnotations = columnAnnotations aln+ consensusSequenceList = map annotation (filter (\annotEntry -> tag annotEntry == T.pack "RF") allColumnAnnotations)+ consensusSequence = if null consensusSequenceList then "" else T.unpack (head consensusSequenceList)+ gapFreeConsensusSequence = map C.toUpper (filter (not . isGap) consensusSequence)+ consensusStructureList = map (convertWUSStoDotBracket . annotation) (filter (\annotEntry -> tag annotEntry == T.pack "SS_cons") allColumnAnnotations)+ consensusStructure = if null consensusStructureList then "" else T.unpack (head consensusStructureList)+ indexedGapFreeConsensusStructure = extractGapfreeIndexedStructure consensusSequence consensusStructure+ --consensusStructureColIndices = map ((+1) . fst) indexedGapFreeConsensusStructure+ gapFreeConsensusStructure = map snd indexedGapFreeConsensusStructure+ columnComparisonLabels = getComparisonPerColumnLabels comparisonNodeLabels nodes+ r2rLabels = map comparisonColLabelsToR2RLabel (V.toList columnComparisonLabels)+ sHeader = "# STOCKHOLM 1.0\n"+ sConsensusStructure = "#=GC SS_cons " ++ gapFreeConsensusStructure ++ "\n"+ sConsensusSequence = "#=GC cons " ++ gapFreeConsensusSequence ++ "\n"+ sConsensusSequenceColor = "#=GC conss " ++ replicate (length gapFreeConsensusStructure) '2' ++ "\n"+ sCovarianceAnnotation = "#=GC cov_SS_cons " ++ replicate (length gapFreeConsensusStructure) '.' ++ "\n"+ sComparisonHighlight = "#=GC R2R_LABEL " ++ r2rLabels ++ "\n"+ sBackboneColorLabel = "#=GF R2R shade_along_backbone s rgb:200,0,0\n"++comparisonColLabelsToR2RLabel :: (Int, V.Vector (Colour Double)) -> Char+comparisonColLabelsToR2RLabel (_,colorVector)+ | V.null colorVector = '.'+ | V.head colorVector /= white = 's'+ | otherwise = '.'++-- 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+-- where fullComparisonColLabels = V.generate maxEntryLength (makeFullComparisonColLabel sparseComparisonColLabels)++-- makeFullComparisonColLabel :: V.Vector (Int, V.Vector (Colour Double)) -> Int -> (Int, V.Vector (Colour Double))+-- makeFullComparisonColLabel sparseComparisonColLabels colIndex = fullComparisonColLabel+-- where availableLabel = V.find (\(a,_)-> colIndex == a) sparseComparisonColLabels+-- fullComparisonColLabel = fromMaybe (colIndex,V.singleton white) availableLabel++indexStructureToConnections :: (Int, Int, String, Int, Int) -> (String,String,Double)+indexStructureToConnections (acc,emit,_,_,_) = (show emit,show acc,1)++data NodeIndices = S [Int] | L [Int] | R [Int]+ deriving (Show, Eq, Ord)++startState :: ([(Int,Int,String,Int,Int)],Int)+startState = ([],0::Int)++buildRowIndexStructure :: Int -> V.Vector CM.Node -> [Int] -> State ([(Int,Int,String,Int,Int)],Int) ([(Int,Int,String,Int,Int)],Int)+buildRowIndexStructure _ _ [] = do+ (a,b) <- get+ return (a,b)+buildRowIndexStructure row nodes (currentIndex:xs) = do+ (currentInterval,parentId) <- get+ let currentNode = nodes V.! currentIndex+ let currentEnd = getIndexEnd nodes (currentIndex:xs)+ let ntype = CM._nodeType currentNode+ case ntype of+ CM.Root -> put ((row,parentId,"S,",currentIndex,currentEnd):currentInterval,parentId) -- ROOT start tree + CM.BegL -> put ((row,parentId,"L,",currentIndex,currentEnd):currentInterval,parentId) -- BEGL set current label+ CM.BegR -> put ((row,parentId,"R,",currentIndex,currentEnd):currentInterval,parentId) -- BEGR set current label+ CM.Bif -> put (currentInterval,parentId+1)+ _ -> put (currentInterval,parentId)+ buildRowIndexStructure row nodes xs++buildTreeIndexStructure :: Int -> V.Vector CM.Node -> [Int] -> State ([(Int,Int,String,Int,Int)],Int) ([(Int,Int,String,Int,Int)],Int)+buildTreeIndexStructure intervalId nodes (currentIndex:xs) = do+ (currentInterval,parentId) <- get+ let currentNode = nodes V.! currentIndex+ let currentEnd = getIndexEnd nodes (currentIndex:xs)+ let ntype = CM._nodeType currentNode+ let maxId = if null currentInterval then 0 else maximum $ map (\(iid,_,_,_,_)-> iid) currentInterval+ let newId = maxId +1+ let nextId = setNextId ntype intervalId newId+ case ntype of+ CM.Root -> put ((intervalId,parentId,"S,",currentIndex,currentEnd):currentInterval,parentId)+ CM.BegL -> put ((newId,parentId,"L,",currentIndex,currentEnd):currentInterval,parentId)+ CM.BegR -> put ((newId,parentId,"R,",currentIndex,currentEnd):currentInterval,parentId)+ CM.Bif -> put (currentInterval,intervalId)+ _ -> put (currentInterval,parentId)+ buildTreeIndexStructure nextId nodes xs+buildTreeIndexStructure _ _ [] = do+ (a,b) <- get+ return (a,b)+ +setNextId :: CM.NodeType -> Int -> Int -> Int+setNextId ntype intervalId newId+ | ntype == CM.Root = newId+ | ntype == CM.BegL = newId+ | ntype == CM.BegR = newId+ | otherwise = intervalId++getIndexEnd :: V.Vector CM.Node -> [Int] -> Int+getIndexEnd nodes indices+ | null indices = length nodes -1+ | ntype == CM.End = currentIndex+ | ntype == CM.Bif = currentIndex+ | otherwise = getIndexEnd nodes remainingindices+ where currentIndex = head indices+ remainingindices = tail indices+ currentNode = nodes V.! currentIndex+ ntype = CM._nodeType currentNode++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 12 12 # lw 0.1 # fc modelColor # translate (r2 (negate 0, 5))) === strutY 1 === (strutX 30 ||| modelLegend)+ where modelLegend = makeModelLegend otherModelsNameColorVector+ otherModelsNameColorVector = V.filter ((/=mName) . fst) nameColorVector++makeModelLegend :: V.Vector (String,Colour Double) -> QDiagram Cairo V2 Double Any+makeModelLegend nameColorVector+ | V.null nameColorVector = mempty+ | otherwise = (legendHead === legendBody) <> rect boxX boxY # lw 0.1 # translate (r2 ((boxX/2)-1, negate (boxY/2) + 6))+ where legendHead = setLegendLabel "Legend:"+ legendBody = vcat (V.toList (V.map makeLegendEntry nameColorVector))+ nameLengths = V.map (length . fst) nameColorVector+ maxNameLength = fromIntegral $ V.maximum nameLengths+ entryNumber = fromIntegral $ V.length nameColorVector+ boxX = maxNameLength * 6+ boxY = entryNumber * 15 + 10++makeLegendEntry :: (String,Colour Double) -> QDiagram Cairo V2 Double Any+makeLegendEntry (mName,mColor) = setLegendLabel mName ||| strutX 0.5 ||| rect 4 4 # lw 0.1 # fc mColor # translate (r2 (negate 0, 2))++setLabel :: String -> QDiagram Cairo V2 Double Any+setLabel t = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False 2 2) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (negate 0.75, negate 0.25))+setTransition :: String -> QDiagram Cairo V2 Double Any+setTransition t = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False 2 2) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (negate 0.75, negate 0.75)) # rotate (1/4 @@ turn)+setState :: String -> Double -> Double -> QDiagram Cairo V2 Double Any+setState t x y = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False 3 3) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (x, y))+setNodeNumber :: String -> QDiagram Cairo V2 Double Any+setNodeNumber t = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False 5 5) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (negate 2, 0))+setNodeLabel :: String -> QDiagram Cairo V2 Double Any+setNodeLabel t = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False 6 6) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (negate 2, 0))+setLegendLabel :: String -> QDiagram Cairo V2 Double Any+setLegendLabel t = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False 10 10) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (negate 0.75, negate 0.75))+setModelName :: String -> QDiagram Cairo V2 Double Any+setModelName t = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False 20 20) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (negate 0.75, negate 0.75))++drawCMNodeTree :: String -> String -> String -> Int -> M.Map (PI.PInt () CM.StateIndex) CM.State -> V.Vector (Int, V.Vector (Colour Double))-> V.Vector CM.Node -> [(Int, Int, String, Int, Int)] -> (Int,Int,String,Int,Int) -> QDiagram Cairo V2 Double Any+drawCMNodeTree modelDetail alphabetSymbols emissiontype boxlength allStates comparisonNodeLabels nodes indexStructure (intervalId,parentId,intervalType,currentIndex,currentEnd) = nodeTree+ where nodeTree = currentIntervalDrawing === hcat' with {_sep = 20} (map (drawCMNodeTree modelDetail alphabetSymbols emissiontype boxlength allStates comparisonNodeLabels nodes indexStructure) nextIntervals)+ nextIntervals = filter (\(_,p,_,_,_) -> intervalId == p) indexStructure+ currentIntervalDrawing = drawCMNodeInterval modelDetail alphabetSymbols emissiontype boxlength currentIndex currentEnd currentEnd allStates comparisonNodeLabels nodes (intervalId,parentId,intervalType,currentIndex,currentEnd) --- ||| (text' (show intervalId ++ "I" ++ show indexStructure) <> rect 100 100)++--drawCMNodeRow :: String -> String -> String -> Int -> Int -> Int -> Int -> M.Map (PI.PInt () CM.StateIndex) CM.State -> V.Vector (Int, V.Vector (Colour Double))-> V.Vector CM.Node -> [(Int, Int, String, Int, Int)] -> QDiagram Cairo V2 Double Any+--drawCMNodeRow modelDetail alphabetSymbols emissiontype boxlength rowStart rowEnd lastIndex states comparisonNodeLabels nodes intervals = strutY 4 === hcat' with { _sep = 8 } (map (drawCMNodeInterval modelDetail alphabetSymbols emissiontype boxlength rowStart rowEnd lastIndex states comparisonNodeLabels nodes) intervals)++drawCMNodeInterval :: String -> String -> String -> Int -> Int -> Int -> Int -> M.Map (PI.PInt () CM.StateIndex) CM.State -> V.Vector (Int, V.Vector (Colour Double))-> V.Vector CM.Node -> (Int, Int, String, Int, Int) -> QDiagram Cairo V2 Double Any+drawCMNodeInterval modelDetail alphabetSymbols emissiontype boxlength rowStart rowEnd lastIndex states comparisonNodeLabels nodes (intervalId,_,_,currentIndex,currentEnd)+ | modelDetail == "interval" = intervalVis+ | otherwise = nodeVis+ where intervalVis = rect 20 0 # named ("a" ++ intervalIdString) # lw 0.0 === (rect 20 40 # lw 0.1 <> text' (show currentIndex ++ "-" ++ show currentEnd)) === rect 20 0 # named ("e" ++ intervalIdString) # lw 0.0 === strutY 5.0+ intervalIdString = show intervalId+ nodeVis = strutY 4 ===vcat' with { _sep = nodespacer } (map (drawCMNode modelDetail alphabetSymbols emissiontype boxlength rowStart rowEnd lastIndex states comparisonNodeLabels nodes) currentInterval)+ currentInterval = [currentIndex..currentEnd]+ nodespacer = if modelDetail == "detailed" then (0 :: Double) else (0.5 :: Double)++getCMNodeType :: CM.Node -> String+getCMNodeType node+ | ntype == CM.Bif = "BIF"+ | ntype == CM.MatP = "MATP"+ | ntype == CM.MatL = "MATL"+ | ntype == CM.MatR = "MATR"+ | ntype == CM.BegL = "BEGL"+ | ntype == CM.BegR = "BEGR"+ | ntype == CM.Root = "ROOT"+ | ntype == CM.End = "END"+ | otherwise = "NA"+ where ntype = CM._nodeType node++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))++--textWithSize' :: String -> Double -> QDiagram Cairo V2 Double Any+--textWithSize' t si = textSVG_ (TextOpts linLibertineFont INSIDE_H KERN False si si) t # fc black # fillRule EvenOdd # lw 0.0 # translate (r2 (negate siOffset, negate siOffset))+-- where siOffset = si/2++-- | Transform covariance model node labels to colors+--labelToColor :: String -> Colour Double+--labelToColor label+-- | label == "MATP" = sRGB24 211 211 211 -- P+-- | label == "MATL" = sRGB24 211 211 211 -- L+-- | label == "MATR" = sRGB24 211 211 211 -- R+-- | label == "BIF" = sRGB24 255 069 064 -- B+-- | label == "ROOT" = sRGB24 245 245 245 -- S+-- | label == "BEGL" = sRGB24 211 211 211 -- S+-- | label == "BEGR" = sRGB24 211 211 211 -- S +-- | label == "END" = sRGB24 245 245 245 -- E+--labelToColor _ = sRGB24 245 245 245++drawCMNode :: String -> String -> String -> Int -> Int -> Int -> Int -> M.Map (PI.PInt () CM.StateIndex) CM.State -> V.Vector (Int, V.Vector (Colour Double)) -> V.Vector CM.Node -> Int -> QDiagram Cairo V2 Double Any+drawCMNode modelDetail alphabetSymbols emissiontype boxlength _ _ _ states comparisonNodeLabels nodes nodeIndex+ | modelDetail == "minimal" = drawCMMinimalNodeBox alphabetSymbols emissiontype boxlength states comparisonNodeLabels node nodeIndex+ | modelDetail == "simple" = drawCMSimpleNodeBox alphabetSymbols emissiontype boxlength states comparisonNodeLabels node nodeIndex+ | otherwise = detailedNodeBox+ where node = nodes V.! nodeIndex+ --idNumber = nodeIndex+ --nId = show idNumber+ detailedNodeBox = drawCMDetailedNodeBox alphabetSymbols emissiontype boxlength states comparisonNodeLabels node nodeIndex+ --nodeType = getCMNodeType node+ --nodeLabels = V.toList (snd (comparisonNodeLabels V.! idNumber))++colorBox :: Double -> Colour Double -> QDiagram Cairo V2 Double Any+colorBox singleBoxYLength colColour = rect 5 singleBoxYLength # fc colColour # lw 0.1++drawCMMinimalNodeBox :: String -> String -> Int -> M.Map (PI.PInt () CM.StateIndex) CM.State -> V.Vector (Int, V.Vector (Colour Double)) -> CM.Node -> Int -> QDiagram Cairo V2 Double Any+drawCMMinimalNodeBox alphabetSymbols emissiontype boxlength currentStates comparisonNodeLabels node nodeIndex+ | ntype == CM.Bif = minimalNode === splitStatesBox -- bifNode + | ntype == CM.BegL = splitStatesBox === minimalNode -- begLNode + | ntype == CM.BegR = splitStatesBox === minimalNode -- begRNode + | otherwise = minimalNode+ where ntype = CM._nodeType node+ idNumber = nodeIndex+ nId = show idNumber+ stateIndices = V.toList (CM._nodeStates node)+ minimalNode = rect 5 5 # lw 0.1 # lc black <> text' nId # fontSize 2 <> wheel 2 nodeLabels # lw 0.1 # lc black+ splitStatesBox = hcat (map (drawCMSimpleStateBox nId alphabetSymbols emissiontype boxlength currentStates) stateIndices)+ --nodeType = getCMNodeType node+ nodeLabels = V.toList (snd (comparisonNodeLabels V.! idNumber))+ --boxNumber = fromIntegral $ length nodeLabels+ --totalBoxYlength = 5 + --singleBoxYLength = totalBoxYlength / boxNumber+ --colourBoxes = vcat (map (colorBox singleBoxYLength) nodeLabels)++drawCMSimpleNodeBox :: String -> String -> Int -> M.Map (PI.PInt () CM.StateIndex) CM.State -> V.Vector (Int, V.Vector (Colour Double)) -> CM.Node -> Int -> QDiagram Cairo V2 Double Any+drawCMSimpleNodeBox alphabetSymbols emissiontype boxlength currentStates comparisonNodeLabels node nodeIndex+ | ntype == CM.Bif = simpleNode === splitStatesBox -- bifNode + | ntype == CM.BegL = splitStatesBox === simpleNode -- begLNode + | ntype == CM.BegR = splitStatesBox === simpleNode -- begRNode + | otherwise = simpleNode+ where ntype = CM._nodeType node+ idNumber = nodeIndex + nId = show idNumber+ stateIndices = V.toList (CM._nodeStates node)+ simpleNode = rect 10 5 # lw 0.1 # lc black <> ((text' nId # translate (r2 (negate 7.5,0)) <> colourBoxes # translate (r2 (negate 7.5, boxYoffset))) ||| text' nodeType # translate (r2 (14,0)))+ splitStatesBox = hcat (map (drawCMSimpleStateBox nId alphabetSymbols emissiontype boxlength currentStates) stateIndices)+ nodeType = getCMNodeType node+ nodeLabels = V.toList (snd (comparisonNodeLabels V.! idNumber))+ boxNumber = fromIntegral $ length nodeLabels+ totalBoxYlength = 5 + singleBoxYLength = totalBoxYlength / boxNumber+ -- concatenated colorboxes are placed atop the simplenode box with the first colorbox+ boxYoffset = totalBoxYlength/2 - singleBoxYLength/2+ colourBoxes = vcat (map (colorBox singleBoxYLength) nodeLabels)++drawCMSimpleStateBox :: String -> String -> String -> Int -> M.Map (PI.PInt () CM.StateIndex) CM.State -> PI.PInt () CM.StateIndex -> QDiagram Cairo V2 Double Any+drawCMSimpleStateBox _ _ _ _ currentStates sIndex+ | stype == CM.S = sState + | stype == CM.B = bState + | otherwise = mempty+ where currentState = currentStates M.! sIndex+ stype = CM._stateType currentState+ stateIndx = show (PI.getPInt sIndex)+ sState = rect 1 0.001 # lw 0 # named ("a" ++ stateIndx)+ bState = rect 1 0.001 # lw 0 # named ("e" ++ stateIndx)++drawCMDetailedNodeBox :: String -> String -> Int -> M.Map (PI.PInt () CM.StateIndex) CM.State -> V.Vector (Int, V.Vector (Colour Double)) -> CM.Node -> Int -> QDiagram Cairo V2 Double Any+drawCMDetailedNodeBox alphabetSymbols emissiontype boxlength currentStates comparisonNodeLabels node nodeIndex+ | ntype == CM.Bif = bifNode # translate (r2 (negate 25,25)) <> nodeBox+ | ntype == CM.MatP = matPNode # translate (r2 (negate 25,25)) <> nodeBox+ | ntype == CM.MatL = matLNode # translate (r2 (negate 25,25)) <> nodeBox+ | ntype == CM.MatR = matRNode # translate (r2 (negate 25,25)) <> nodeBox+ | ntype == CM.BegL = begLNode # translate (r2 (negate 25,25)) <> nodeBox+ | ntype == CM.BegR = begRNode # translate (r2 (negate 25,25)) <> nodeBox+ | ntype == CM.Root = rootNode # translate (r2 (negate 25,25)) <> nodeBox+ | ntype == CM.End = endNode # translate (r2 (negate 25,25)) <> nodeBox+ | otherwise = endNode <> nodeBox+ where ntype = CM._nodeType node+ idNumber = nodeIndex+ nId = show idNumber+ nodeLabels = V.toList (snd (comparisonNodeLabels V.! idNumber))+ stateIndices = V.toList (CM._nodeStates node)+ splitStatesBox = hcat' with { _sep = 0.01 } (map (drawCMSplitStateBox nId alphabetSymbols emissiontype boxlength currentStates) stateIndices)+ insertStatesBox = hcat (map (drawCMInsertStateBox nId alphabetSymbols emissiontype boxlength currentStates) stateIndices)+ -- bif b+ bifNode = (idBox nId "BIF" nodeLabels # rotate (1/4 @@ turn) # translate (r2 (1, negate 17)) ||| strutX 0.5 ||| splitStatesBox) === strutY 5.0 === insertStatesBox+ -- matP mp ml mr d il ir+ matPNode = (idBox nId "MATP" nodeLabels # rotate (1/4 @@ turn) # translate (r2 (1, negate 17)) ||| strutX 0.5||| splitStatesBox) === strutY 5.0 === insertStatesBox+ -- matL ml d il+ matLNode = (idBox nId "MATL" nodeLabels # rotate (1/4 @@ turn) # translate (r2 (1, negate 17)) ||| strutX 0.5 ||| splitStatesBox) === strutY 5.0 === insertStatesBox+ -- matR mr d ir+ matRNode = (idBox nId "MATR" nodeLabels # rotate (1/4 @@ turn) # translate (r2 (1, negate 17)) ||| strutX 0.5||| splitStatesBox) === strutY 5.0 === insertStatesBox+ -- begL s+ begLNode = (idBox nId "BEGL" nodeLabels # rotate (1/4 @@ turn) # translate (r2 (1, negate 17)) ||| strutX 0.5 ||| splitStatesBox) === strutY 5.0 === insertStatesBox+ -- begR s il+ begRNode = (idBox nId "BEGR" nodeLabels # rotate (1/4 @@ turn) # translate (r2 (1, negate 17)) ||| strutX 0.5||| splitStatesBox) === strutY 5.0 === insertStatesBox+ -- root s il ir+ rootNode = (idBox nId "ROOT" nodeLabels # rotate (1/4 @@ turn) # translate (r2 (1, negate 17)) ||| strutX 0.5||| splitStatesBox) === strutY 5.0 === insertStatesBox+ -- end e+ endNode = (idBox nId "END" nodeLabels # rotate (1/4 @@ turn) # translate (r2 (1, negate 17)) ||| strutX 0.5 ||| splitStatesBox) === strutY 5.0 === insertStatesBox++idBox :: String -> String -> [Colour Double] -> QDiagram Cairo V2 Double Any+idBox nId nType nodeLabels = (setNodeNumber nId # translate (r2 (negate ((fromIntegral (length nId))/2), 0)) <> wheel 4 nodeLabels # lw 0.1 # translate (r2 (0, 1)) <> rect 3 3 # lw 0) ||| strutX 1.0 ||| setNodeLabel nType+nodeBox :: QDiagram Cairo V2 Double Any+nodeBox = rect 60 60 # lw 0.1++wheel :: Double -> [Colour Double] -> QDiagram Cairo V2 Double Any+wheel wsize colors = wheel' # rotate r+ where+ wheel' = mconcat $ zipWith fc colors (iterateN n (rotate a) w)+ n = length colors+ a = 1 / fromIntegral n @@ turn+ w = wedge wsize xDir a # lwG 0+ r = (1/4 @@ turn) ^-^ (1/(2*fromIntegral n) @@ turn)++drawCMSplitStateBox :: String -> String -> String -> Int -> M.Map (PI.PInt () CM.StateIndex) CM.State -> PI.PInt () CM.StateIndex -> QDiagram Cairo V2 Double Any+drawCMSplitStateBox _ _ emissiontype _ currentStates sIndex+ | stype == CM.D = dState # translate (r2 (negate 3,negate 1)) <> statebox 8.0 20.0 stateIndx+ | stype == CM.MP = mpState # translate (r2 (negate 7,negate 1)) <> statebox 16.0 20.0 stateIndx+ | stype == CM.ML = mlState # translate (r2 (negate 3,negate 1)) <> statebox 8.0 20.0 stateIndx+ | stype == CM.MR = mrState # translate (r2 (negate 3,negate 1)) <> statebox 8.0 20.0 stateIndx+ | stype == CM.S = sState # translate (r2 (negate 3,negate 1)) <> statebox 8.0 20.0 stateIndx+ | stype == CM.E = eState # translate (r2 (negate 3,negate 1)) <> statebox 8.0 20.0 stateIndx+ | stype == CM.B = bState # translate (r2 (negate 3,negate 1)) <> statebox 8.0 20.0 stateIndx+ | stype == CM.EL = elState # translate (r2 (negate 3,negate 1)) <> statebox 8.0 20.0 stateIndx+ | otherwise = mempty+ where currentState = currentStates M.! sIndex+ stype = CM._stateType currentState+ stateIndx = show (PI.getPInt sIndex)+ singleEmissionBitscores = CM._stateEmissions currentState+ singleEmissionEntries = setEmissions emissiontype 4 singleEmissionBitscores+ singleSymbolsAndEmissions = zip ["A","U","G","C"] (VU.toList singleEmissionEntries)+ pairEmissionBitscores = CM._stateEmissions currentState+ pairEmissionEntries = setEmissions emissiontype 16 pairEmissionBitscores+ pairSymbolsAndEmissions = zip ["AA","AU","AG","AC","UU","UA","UG","UC","GG","GA","GU","GC","CC","CA","CU","CG"] (VU.toList pairEmissionEntries)+ pairSymbolsAndEmissions1 = take 8 pairSymbolsAndEmissions+ pairSymbolsAndEmissions2 = drop 8 pairSymbolsAndEmissions+ dState = setState ("D" ++ stateIndx) (negate 0.5) (negate 1) === strutY 1 + mpState = setState ("MP" ++ stateIndx) (negate 0.5) (negate 1) === strutY 1 === (vcat (map (emissionEntry emissiontype) pairSymbolsAndEmissions1) ||| strutX 0.5 ||| vcat (map (emissionEntry emissiontype) pairSymbolsAndEmissions2))+ mlState = setState ("ML" ++ stateIndx) (negate 0.5) (negate 1) === strutY 1 === vcat (map (emissionEntry emissiontype) singleSymbolsAndEmissions)+ mrState = setState ("MR" ++ stateIndx) (negate 0.5) (negate 1) === strutY 1 === vcat (map (emissionEntry emissiontype) singleSymbolsAndEmissions)+ sState = setState ("S" ++ stateIndx) (negate 0.5) (negate 1) === strutY 1+ eState = setState ("E" ++ stateIndx) (negate 0.5) (negate 1) === strutY 1+ bState = setState ("B" ++ stateIndx) (negate 0.5) (negate 1) === strutY 1+ elState = setState ("EL" ++ stateIndx) (negate 0.5) (negate 1) === strutY 1++drawCMInsertStateBox :: String -> String -> String -> Int -> M.Map (PI.PInt () CM.StateIndex) CM.State -> PI.PInt () CM.StateIndex -> QDiagram Cairo V2 Double Any+drawCMInsertStateBox _ _ emissiontype _ currentStates sIndex+ | stype == CM.IL = ((ilState # translate (r2 (negate 3,negate 1))) <> statebox 8.0 20.0 stateIndx) ||| strutX 38+ | stype == CM.IR = (irState # translate (r2 (negate 3,negate 1))) <> inverseStatebox 8.0 20.0 stateIndx+ | otherwise = mempty+ where currentState = currentStates M.! sIndex+ stype = CM._stateType currentState+ stateIndx = show (PI.getPInt sIndex)+ singleEmissionBitscores = CM._stateEmissions currentState+ singleEmissionEntries = setEmissions emissiontype 4 singleEmissionBitscores+ singleSymbolsAndEmissions = zip ["A","U","G","C"] (VU.toList singleEmissionEntries)+ ilState = setState ("IL" ++ stateIndx) (negate 0.5) (negate 1) === strutY 1 === vcat (map (emissionEntry emissiontype) singleSymbolsAndEmissions)+ irState = setState ("IR" ++ stateIndx) (negate 0.5) (negate 1) === strutY 1 === vcat (map (emissionEntry emissiontype) singleSymbolsAndEmissions)++setEmissions :: String -> Double -> VU.Vector Bitscore -> VU.Vector Double+setEmissions emissiontype normalizationFactor emissions+ | emissiontype == "score" = scoreentries+ | emissiontype == "probability" = propentries+ | emissiontype == "bar" = barentries+ | otherwise = barentries+ where scoreentries = VU.map bitScore2Double emissions+ propentries = VU.map ((/normalizationFactor) . score2Prob 1) emissions+ barentries = VU.map ((/normalizationFactor) . score2Prob 1) emissions++--wrap :: a -> [a]+--wrap x = [x]++emissionEntry :: String -> (String,Double) -> QDiagram Cairo V2 Double Any+emissionEntry emissiontype (symbol,emission)+ | emissiontype == "probability" = textentry+ | emissiontype == "score" = textentry+ | emissiontype == "bar" = barentry+ | otherwise = barentry+ where textentry = setLabel (symbol ++ " " ++ printf "%.3f" emission)+ barentry = setLabel symbol ||| strutX 0.2 ||| bar emission++bar :: Double -> QDiagram Cairo V2 Double Any+bar emission = rect (4 * emission) 1 # lw 0 # fc black # translate (r2 (negate (2 - (4 * emission/2)),0)) <> rect 4 1 # lw 0.03++--makeSingleEmissionIndices index = V.fromList [PAI.Z PAI.:. index PAI.:. A,PAI.Z PAI.:. index PAI.:. U,PAI.Z PAI.:. index PAI.:. G,PAI.Z PAI.:. index PAI.:. C]++--makePairEmissionIndices cindex = V.fromList [PAI.Z PAI.:. cindex PAI.:. A PAI.:. A,PAI.Z PAI.:. cindex PAI.:. A PAI.:. U,PAI.Z PAI.:. cindex PAI.:. A PAI.:. G,PAI.Z PAI.:. cindex PAI.:. A PAI.:. C,PAI.Z PAI.:. cindex PAI.:. U PAI.:. U,PAI.Z PAI.:. cindex PAI.:. U PAI.:. A,PAI.Z PAI.:. cindex PAI.:. U PAI.:. G,PAI.Z PAI.:. cindex PAI.:. U PAI.:. C,PAI.Z PAI.:. cindex PAI.:. G PAI.:. G,PAI.Z PAI.:. cindex PAI.:. G PAI.:. A,PAI.Z PAI.:. cindex PAI.:. G PAI.:. U,PAI.Z PAI.:. cindex PAI.:. G PAI.:. C,PAI.Z PAI.:. cindex PAI.:. C PAI.:. C,PAI.Z PAI.:. cindex PAI.:. C PAI.:. A,PAI.Z PAI.:. cindex PAI.:. C PAI.:. U,PAI.Z PAI.:. cindex PAI.:. C PAI.:.G]++statebox :: Double -> Double -> String -> QDiagram Cairo V2 Double Any+statebox x y si = (rect 0.05 0.1 # lw 0 # named ("s" ++ si) ||| rect 1 0.1 # lw 0 # named ("a" ++ si) ||| rect 2 0.1 # lw 0 ||| rect 0.05 0.1 # lw 0 # named ("z" ++ si)) === rect x y # lw 0.1 === rect 1 0 # lw 0 # named ("e" ++ si)++inverseStatebox :: Double -> Double -> String -> QDiagram Cairo V2 Double Any+inverseStatebox x y si = (rect 0.05 0.1 # lw 0 # named ("s" ++ si) ||| rect 1 0.1 # lw 0 # named ("a" ++ si) ||| rect 2 0.1 # lw 0 ||| rect 0.05 0.1 # lw 0 # named ("z" ++ si)) === rect x y # lw 0.1 === rect 1 0 # lw 0 # named ("e" ++ si)++--scaling+-- | Specifies the size of the diagram. Absolute adapts to overall size according to subdiagrams+svgsize :: SizeSpec V2 Double+svgsize = mkSizeSpec2D Nothing Nothing++-- | Check for available cairo output formats+diagramName :: String -> String -> Either String String+diagramName filename fileformat+ | fileformat == "pdf" = Right (filename ++ "." ++ fileformat )+ | fileformat == "svg" = Right (filename ++ "." ++ fileformat )+ | fileformat == "png" = Right (filename ++ "." ++ fileformat )+ | fileformat == "ps" = Right (filename ++ "." ++ fileformat )+ | otherwise = Left "Unsupported output format requested (use svg, pdf, ps, png)"+ +printCM :: FilePath -> SizeSpec V2 Double -> QDiagram Cairo V2 Double Any -> IO ()+printCM outputName = renderCairo outputName++getBlankComparisonNodeLabels :: CM.CM -> V.Vector (Int, V.Vector (Colour Double))+getBlankComparisonNodeLabels model = comparisonNodeLabels+ where comparisonNodeLabels = V.generate (nodeNumber ) makeBlankComparisonNodeLabel+ nodeNumber = (CM._nodesInModel model) ++makeBlankComparisonNodeLabel :: Int -> (Int,V.Vector (Colour Double))+makeBlankComparisonNodeLabel nodeNumber = (nodeNumber,V.singleton white)++getComparisonNodeLabels :: [CmcompareResult] -> V.Vector (String, Colour Double) -> CM.CM -> V.Vector (Int, V.Vector (Colour Double))+getComparisonNodeLabels comparsionResults colorVector model = comparisonNodeLabels+ where modelName = T.unpack (CM._name model)+ relevantComparisons1 = filter ((modelName==) . model1Name) comparsionResults+ modelNodeInterval1 = map (\a -> (model2Name a,model1matchednodes a)) relevantComparisons1 + relevantComparisons2 = filter ((modelName==) . model2Name) comparsionResults+ modelNodeInterval2 = map (\a -> (model1Name a,model2matchednodes a)) relevantComparisons2+ modelNodeIntervals = V.fromList (modelNodeInterval1 ++ modelNodeInterval2)+ colorNodeIntervals = V.map (modelToColor colorVector) modelNodeIntervals+ nodeNumber = (CM._nodesInModel model)+ comparisonNodeLabels = V.generate (nodeNumber ) (makeComparisonNodeLabel colorNodeIntervals)++modelToColor :: V.Vector (String,Colour Double) -> (String,[Int]) -> (Colour Double,[Int])+modelToColor colorVector (mName,nInterval) = nColorInterval+ where nColorInterval = (snd (fromJust entry),nInterval)+ --nColorInterval = maybe Nothing (\a -> Just (snd a,nInterval)) entry+ entry = V.find (\(a,_)-> mName == a) colorVector++makeComparisonNodeLabel :: V.Vector (Colour Double,[Int]) -> Int -> (Int,V.Vector (Colour Double))+makeComparisonNodeLabel colorNodeIntervals nodeNumber = comparisonNodeLabel+ where relevantColorNodeIntervals = V.filter (\(_,b) -> elem nodeNumber b) colorNodeIntervals+ modelColors = V.map fst relevantColorNodeIntervals+ comparisonNodeLabel = if null modelColors then (nodeNumber,V.singleton white) else (nodeNumber,modelColors)++-- First colors are picked from http://colorbrewer2.org, scheme. Comparisons up to+-- 4 models are colorblind safe+makeColorVector :: Int -> V.Vector (Colour Double)+makeColorVector modelNumber = V.take modelNumber colorVector+ where colorVector = V.fromList [R.sRGB24read "#a6cee3", R.sRGB24read "#1f78b4", R.sRGB24read "#b2df8a", R.sRGB24read "#33a02c", R.sRGB24read "#ffff99", R.sRGB24read "#cab2d6", R.sRGB24read "#6a3d9a", R.sRGB24read "#b15928", R.sRGB24read "#fb9a99", R.sRGB24read "#e31a1c", R.sRGB24read "#fdbf6f", R.sRGB24read "#ff7f00", 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]++makeArrow :: ([Char], [Char], Double) -> QDiagram Cairo V2 Double Any -> QDiagram Cairo V2 Double Any+makeArrow (lab1,lab2,weight) = connectOutside' arrowStyle1 ("e" ++ lab1) ("a" ++ lab2)+ where arrowStyle1 = with & arrowHead .~ spike & shaftStyle %~ lw (local 0.1) & headLength .~ local 0.01 & shaftStyle %~ dashingG [weight, 0.1] 0 & headStyle %~ fc black . opacity (weight * 2)++makeSelfArrow :: ([Char], [Char], Double) -> QDiagram Cairo V2 Double Any -> QDiagram Cairo V2 Double Any +makeSelfArrow (lab1,_,weight) = connectPerim' arrowStyle ("s" ++ lab1) ("z" ++ lab1) (5/12 @@ turn) (8/12 @@ turn)+ where arrowStyle = with & arrowHead .~ spike & arrowShaft .~ shaft' & arrowTail .~ lineTail & tailTexture .~ solid black & shaftStyle %~ lw (local 0.1) & headLength .~ local 0.01 & tailLength .~ 0 & shaftStyle %~ dashingG [weight, 0.3] 0 & headStyle %~ fc black . opacity (weight * 2)+ shaft' = wedge 3 xDir (2/4 @@ turn)++makeLabel :: (String, String, Double) -> QDiagram Cairo V2 Double Any -> QDiagram Cairo V2 Double Any+makeLabel (n1,n2,weight) =+ withName ("a" ++ n1) $ \b1 ->+ withName ("s" ++ n2) $ \b2 ->+ let v = location b2 .-. location b1+ midpoint = location b1 .+^ (v ^/ 2)+ (xOffset,yOffset) = setLabelOffset (location b1 ^. _x) (location b2 ^. _x) (location b1 ^. _y) (location b2 ^. _y)+ in+ Diagrams.Prelude.atop (position [(midpoint # translateX xOffset # translateY yOffset, setTransition ((show (roundPos 3 weight))))])+ --Diagrams.Prelude.atop (position [(midpoint # translateX xOffset # translateY yOffset, setTransition (lclass ++"," ++ (show (roundPos 3 weight))))]) + --Diagrams.Prelude.atop (position [(midpoint # translateX xOffset # translateY yOffset, setTransition (n1 ++"," ++ n2 ++"," ++lclass ++"," ++ (show (roundPos 3 weight))))]) ++setLabelOffset :: Double -> Double -> Double -> Double -> (Double,Double)+setLabelOffset x1 x2 y1 y2+ -- + | ydiff < 2 = (0,0)+ | xdiff < 2 = (negate 1,negate 1)+ -- + | x1 > x2 && (ydiff > 30) = (negate 1,negate 10)+ -- + | x1 < x2 && (ydiff > 30) = (1,negate 10) + -- between split and insert state of same node - left upper(A)+ | x1 > x2 && (ydiff < 30) = (negate 1,negate 12)+ -- between split and insert state of same node - right upper (B)+ | x1 < x2 && (ydiff < 30) = (0,negate 12)+ -- between same split states of different nodes (C)+ | otherwise = (0,0)+ where ydiff = abs (abs y1 - abs y2)+ xdiff = abs (abs x1 - abs x2)+ +makeSelfLabel :: (String, String, Double) -> QDiagram Cairo V2 Double Any -> QDiagram Cairo V2 Double Any+makeSelfLabel (n1,_,weight)+ | weight == 0 = mempty+ | otherwise = withName ("e" ++ n1) $ \b1 ->+ let midpoint = location b1+ in+ Diagrams.Prelude.atop (position [(midpoint # translateX (negate 0.25) # translateY 22, setTransition (show (roundPos 3 weight)))])++roundPos :: (RealFrac a) => Int -> a -> a+roundPos positions number = fromInteger (round $ number * (10^positions)) / (10.0^^positions)++bitScore2Double :: Bitscore -> Double+bitScore2Double (Bitscore x) = x
+ src/cmcv/CMCVisualisation.hs view
@@ -0,0 +1,118 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE RankNTypes #-}+{-# LANGUAGE FlexibleContexts #-}++-- | Visualize detailed comparsions of Infernal Covariance Models+-- Datastructures and parsing of covariance models is provided by Biobase+-- Visualization is accomplished with diagrams-svg+-- For more information on Infernal consult <http://eddylab.org/infernal/>++module Main where++import Bio.CMCompareResult+import Bio.CMDraw+import qualified Biobase.SElab.CM as CM+import Biobase.SElab.CM.Import (cmFromFile)+import System.Console.CmdArgs+import Data.Either+import qualified Data.Either.Unwrap as E+import System.Directory+import qualified Data.Text as T+import qualified Bio.StockholmParser as SP+import Paths_cmv (version)+import Data.Version (showVersion)+import Data.List (intercalate)+import Control.Monad+import Data.Maybe++options :: Options+data Options = Options+ { cmcompareResultFile :: String,+ modelsFile :: String,+ alignmentFile :: String,+ modelDetail :: String,+ modelLayout :: String,+ emissionLayout :: String,+ alignmentEntries :: Int,+ transitionCutoff :: Double,+ maxWidth :: Double,+ scalingFactor :: Double,+ comparisonAlignment :: String,+ outputFormat :: String,+ outputDirectoryPath :: String,+ secondaryStructureVisTool :: String,+ modelNameToggle :: Bool+ } deriving (Show,Data,Typeable)++options = Options+ { cmcompareResultFile = def &= name "r" &= help "Path to CMCompare result file",+ modelsFile = def &= name "m" &= help "Path to covariance model file",+ alignmentFile = "" &= name "s" &= help "Path to stockholm alignment file",+ modelDetail = "detailed" &= name "d" &= help "Set verbosity of drawn models: minimal, simple, detailed",+ modelLayout = "tree" &= name "l" &= help "Set layout of drawn models: flat, tree",+ emissionLayout = "box" &= name "e" &= help "Set layout of drawn models: score, probability, box (Default: box)",+ alignmentEntries = (50 :: Int) &= name "n" &= help "Set cutoff for included stockholm alignment entries (Default: 50)",+ transitionCutoff = (0.01 :: Double) &= name "t" &= help "Minimal value for a transition probability to be displayed (Default: 0.01)",+ maxWidth = (200 :: Double) &= name "w" &= help "Set maximal width of result figure (Default: 100)",+ scalingFactor = (2 :: Double) &= name "c" &= help "Set uniform scaling factor for image size (Default: 2)",+ comparisonAlignment = "model" &= name "a" &= help "Set layout of drawn models: model, comparison",+ outputFormat = "pdf" &= name "f" &= help "Output image format: pdf, svg, png, ps (Default: pdf)",+ outputDirectoryPath = "" &= name "p" &= help "Output directory path (Default: none)",+ secondaryStructureVisTool = "" &= name "x" &= help "Select tool for secondary structure visualisation: forna, r2r (Default: none)",+ modelNameToggle = False &= name "b" &= help "Write all comma separted model names to modelNames file (Default: False)"+ } &= summary ("CMCV " ++ toolVersion) &= help "Florian Eggenhofer - 2013-2017" &= verbosity++main :: IO ()+main = do+ Options{..} <- cmdArgs options+ --Validate input+ modelFileExists <- doesFileExist modelsFile+ cmcFileExists <- doesFileExist cmcompareResultFile+ if modelFileExists && cmcFileExists+ then do+ cms <- cmFromFile modelsFile+ cmcResultParsed <- getCmcompareResults cmcompareResultFile+ let comparisons = rights cmcResultParsed+ alnInput <- SP.readExistingStockholm alignmentFile+ Control.Monad.when (isLeft alnInput) $ print (E.fromLeft alnInput)+ --let outputName = diagramName "cmcv" outputFormat+ let modelNumber = length cms+ let alns = if isRight alnInput then map (\a -> Just a) (E.fromRight alnInput) else replicate modelNumber Nothing+ let currentModelNames = map (T.unpack . CM._name) cms+ currentWD <- getCurrentDirectory+ let dirPath = if null outputDirectoryPath then currentWD else outputDirectoryPath+ writeModelNameFile modelNameToggle dirPath currentModelNames+ let modelFileNames = map (\m -> m ++ "." ++ outputFormat) currentModelNames+ let alignmentFileNames = map (\m -> m ++ ".aln" ++ "." ++ outputFormat) currentModelNames+ setCurrentDirectory dirPath+ let (modelVis,alignmentVis) = unzip $ drawSingleCMComparisons modelDetail alignmentEntries transitionCutoff modelLayout emissionLayout maxWidth scalingFactor cms alns comparisons+ mapM_ (\(a,b) -> printCM a svgsize b) (zip modelFileNames modelVis)+ mapM_ (\(alnPath,stockholm) -> if isJust stockholm then printCM alnPath svgsize (fromJust stockholm) else return ()) (zip alignmentFileNames alignmentVis)+ let structureVisType = "perModel"+ if structureVisType == "perModel"+ then do+ let structureFilePath = dirPath ++ "/"+ let structureVisInputs = perModelSecondaryStructureVisualisation secondaryStructureVisTool maxWidth structureFilePath cms alns comparisons+ mapM_ (\(structureFileName,structureVis) -> writeFile structureFileName structureVis) structureVisInputs+ setCurrentDirectory currentWD+ else do+ let structureFilePaths = map (\m -> dirPath ++ "/" ++ m ++ "." ++ secondaryStructureVisTool) currentModelNames+ let structureVisInputs = mergedSecondaryStructureVisualisation secondaryStructureVisTool maxWidth cms alns comparisons+ mapM_ (\(structureFileName,(structureVis,_)) -> writeFile structureFileName structureVis) (zip structureFilePaths structureVisInputs)+ mapM_ (\(structureFileName,(_,colorScheme)) -> writeFile (structureFileName ++"Color") colorScheme) (zip structureFilePaths structureVisInputs)+ else do+ Control.Monad.unless modelFileExists $ putStrLn "Model file not found"+ Control.Monad.unless cmcFileExists $ putStrLn "Comparison file not found"++toolVersion :: String+toolVersion = showVersion version++writeModelNameFile :: Bool -> String -> [String] -> IO ()+writeModelNameFile toggle outputDirectoryPath modelNames =+ if toggle+ then do+ let modelNamesString = intercalate "," modelNames+ writeFile (outputDirectoryPath ++ "modelNames") modelNamesString+ else return ()
+ src/cmcv/cmctohmmc.hs view
@@ -0,0 +1,116 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE RankNTypes #-}+{-# LANGUAGE FlexibleContexts #-}++-- | ++module Main where++import Bio.CMCompareResult+import qualified Biobase.SElab.CM.Types as CM+import qualified Biobase.SElab.CM.ModelStructure as CM+import Biobase.SElab.CM.Import (cmFromFile)+import qualified Bio.HMMParser as HM+import System.Console.CmdArgs+import Data.Either+import qualified Data.Either.Unwrap as E+import System.Directory+import qualified Data.Text as T+import Paths_cmv (version)+import Data.Version (showVersion)+import Data.List (intercalate)+import Control.Monad+import Data.Maybe+import qualified Data.Map as M+import qualified Bio.HMMCompareResult as HC+import qualified Data.Vector as V+import Data.List++options :: Options+data Options = Options+ { cmcompareResultFile :: String,+ cmmodelsFile :: String,+ hmmmodelsFile :: String+ } deriving (Show,Data,Typeable)++options = Options+ { cmcompareResultFile = def &= name "r" &= help "Path to CMCompare result file",+ cmmodelsFile = def &= name "c" &= help "Path to covariance model file",+ hmmmodelsFile = def &= name "h" &= help "Path to hmm model file"+ } &= summary ("CMCtoHMMC " ++ toolVersion) &= help "Florian Eggenhofer - 2013-2017" &= verbosity++main :: IO ()+main = do+ Options{..} <- cmdArgs options+ --Validate input+ cmmodelFileExists <- doesFileExist cmmodelsFile+ hmmmodelFileExists <- doesFileExist hmmmodelsFile+ cmcFileExists <- doesFileExist cmcompareResultFile+ if cmmodelFileExists && hmmmodelFileExists && cmcFileExists+ then do+ cms <- cmFromFile cmmodelsFile+ inputhmms <- HM.readHMMER3 hmmmodelsFile+ let hmms = E.fromRight inputhmms+ cmcResultParsed <- getCmcompareResults cmcompareResultFile+ let comparisons = rights cmcResultParsed+ let cmVector = V.fromList cms+ let hmmVector = V.fromList hmms+ --let modelNumber = length cms+ let cmModelNames = map (T.unpack . CM._name) cms+ let hmmModelNames = map HM.name hmms+ --currentWD <- getCurrentDirectory+ --let dirPath = if null outputDirectoryPath then currentWD else outputDirectoryPath+ --setCurrentDirectory dirPath+ let hmmcs = map (cmctohmmc cmModelNames hmmModelNames cmVector hmmVector) comparisons+ mapM_ (putStr . show) hmmcs+ else do+ Control.Monad.unless cmmodelFileExists $ putStrLn "CM Model file not found"+ Control.Monad.unless hmmmodelFileExists $ putStrLn "HMM Model file not found"+ Control.Monad.unless cmcFileExists $ putStrLn "Comparison file not found"++toolVersion :: String+toolVersion = showVersion version++cmctohmmc :: [String] -> [String] -> V.Vector CM.CM -> V.Vector HM.HMMER3 -> CmcompareResult -> HC.HMMCompareResult +cmctohmmc cmModelNames hmmModelNames cmVector hmmVector comparison = hmmcompare+ where cm1Index = fromJust (elemIndex (model1Name comparison) cmModelNames)+ cm2Index = fromJust (elemIndex (model2Name comparison) cmModelNames)+ inputCM1 = cmVector V.! cm1Index+ cm1 = E.fromLeft (CM._cm inputCM1) + inputCM2 = cmVector V.! cm2Index+ cm2 = E.fromLeft (CM._cm inputCM2)+ hmm1Index = fromJust (elemIndex (model1Name comparison) hmmModelNames)+ hmm2Index = fromJust (elemIndex (model2Name comparison) hmmModelNames)+ hmm1 = hmmVector V.! hmm1Index+ hmm2 = hmmVector V.! hmm2Index+ cm1nodeIndices = nub (model1matchednodes comparison)+ cm2nodeIndices = nub (model2matchednodes comparison)+ cm1nodes = (M.elems (CM._fmNodes cm1))+ cm2nodes = (M.elems (CM._fmNodes cm2))+ hmm1nodes = HM.nodes hmm1+ hmm2nodes = HM.nodes hmm2+ --filter cmnodes+ intervalcm1nodes = map (\i -> nodeToColumnIndices (cm1nodes !! i)) cm1nodeIndices+ intervalcm2nodes = map (\i -> nodeToColumnIndices(cm2nodes !! i)) cm2nodeIndices+ aln1colIndices = concat intervalcm1nodes+ aln2colIndices = concat intervalcm2nodes + linkedhmm1nodes = V.filter (\node -> elem (fromJust (HM.nma node)) aln1colIndices) hmm1nodes+ linkedhmm2nodes = V.filter (\node -> elem (fromJust (HM.nma node)) aln2colIndices) hmm2nodes+ hmm1interval = V.map HM.nodeId linkedhmm1nodes+ hmm2interval = V.map HM.nodeId linkedhmm2nodes+ hmmcompare = HC.HMMCompareResult (model1Name comparison) (model2Name comparison) (linkscore1 comparison) (linkscore2 comparison) (linksequence comparison) (V.toList hmm1interval) (V.toList hmm2interval)++nodeToColumnIndices:: CM.Node -> [Int]+nodeToColumnIndices currentNode = nub [CM._nodeColL currentNode,CM._nodeColR currentNode]+-- where currentNode = (V.!) nodes (nodeIndex)+-- colIndices = nub [CM._nodeColL currentNode,CM._nodeColR currentNode]++writeModelNameFile :: Bool -> String -> [String] -> IO ()+writeModelNameFile toggle outputDirectoryPath modelNames =+ if toggle+ then do+ let modelNamesString = intercalate "," modelNames+ writeFile (outputDirectoryPath ++ "modelNames") modelNamesString+ else return ()
+ src/cmcv/cmcwsvtocmcv.hs view
@@ -0,0 +1,63 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE RankNTypes #-}+{-# LANGUAGE FlexibleContexts #-}++-- | Visualize detailed comparsions of Infernal Covariance Models+-- Datastructures and parsing of covariance models is provided by Biobase+-- Visualization is accomplished with diagrams-svg+-- For more information on Infernal consult <http://eddylab.org/infernal/>++module Main where++import Bio.CMCompareResult+import qualified Biobase.SElab.CM as CM+import Biobase.SElab.CM.Import (cmFromFile)+import System.Console.CmdArgs+import Data.Either+import System.Directory+import qualified Data.Text as T+import Paths_cmv (version)+import Data.Version (showVersion)++options :: Options+data Options = Options+ { cmcompareResultFile :: String,+ modelsFile :: String+ } deriving (Show,Data,Typeable)++options = Options+ { cmcompareResultFile = def &= name "r" &= help "Path to CMCompare result file",+ modelsFile = def &= name "m" &= help "Path to covariance model file"+ } &= summary ("cmcwstocmcv " ++ toolVersion ++ "Converts CMcompare webserver output and used model file to comparison file useable by cmcv") &= help "Florian Eggenhofer - 2017" &= verbosity++main :: IO ()+main = do+ Options{..} <- cmdArgs options+ --Validate input+ modelFileExists <- doesFileExist modelsFile+ cmcFileExists <- doesFileExist cmcompareResultFile+ if modelFileExists && cmcFileExists+ then do+ cms <- cmFromFile modelsFile+ cmcResultParsed <- getCmcompareResults cmcompareResultFile+ let comparisons = rights cmcResultParsed+ let currentModelNames = map (T.unpack . CM._name) cms+ let nameTuples = makeNameTuple currentModelNames+ let zippednameTuplesComparisons = zip nameTuples comparisons+ let namedComparisons = concatMap makeNamedComparison zippednameTuplesComparisons+ putStr namedComparisons+ else print "Input files not found\n"++makeNamedComparison :: ((String,String),CmcompareResult) -> String +makeNamedComparison ((name1,name2),comparison) = show (comparison { model1Name = name1, model2Name = name2 })++makeNameTuple :: [String] -> [(String,String)]+makeNameTuple [] = []+makeNameTuple (mname:mnames)+ | null mnames = []+ | otherwise = ntuples ++ makeNameTuple mnames+ where ntuples = map (\a -> (mname,a)) mnames+toolVersion :: String+toolVersion = showVersion version
+ src/cmcv/hmmctocmc.hs view
@@ -0,0 +1,120 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE RankNTypes #-}+{-# LANGUAGE FlexibleContexts #-}++-- | ++module Main where++import Bio.CMCompareResult+import qualified Biobase.SElab.CM.Types as CM+import qualified Biobase.SElab.CM.ModelStructure as CM+import Biobase.SElab.CM.Import (cmFromFile)+import qualified Bio.HMMParser as HM+import System.Console.CmdArgs+import Data.Either+import qualified Data.Either.Unwrap as E+import System.Directory+import qualified Data.Text as T+import Paths_cmv (version)+import Data.Version (showVersion)+import Data.List (intercalate)+import Control.Monad+import Data.Maybe+import qualified Data.Map as M+import qualified Bio.HMMCompareResult as HC+import qualified Data.Vector as V+import Data.List++options :: Options+data Options = Options+ { hmmcompareResultFile :: String,+ cmmodelsFile :: String,+ hmmmodelsFile :: String+ } deriving (Show,Data,Typeable)++options = Options+ { hmmcompareResultFile = def &= name "r" &= help "Path to HMMCompare result file",+ cmmodelsFile = def &= name "c" &= help "Path to covariance model file",+ hmmmodelsFile = def &= name "h" &= help "Path to hmm model file"+ } &= summary ("HMMCtoCMC " ++ toolVersion) &= help "Florian Eggenhofer - 2013-2017" &= verbosity++main :: IO ()+main = do+ Options{..} <- cmdArgs options+ --Validate input+ cmmodelFileExists <- doesFileExist cmmodelsFile+ hmmmodelFileExists <- doesFileExist hmmmodelsFile+ cmcFileExists <- doesFileExist hmmcompareResultFile+ if cmmodelFileExists && hmmmodelFileExists && cmcFileExists+ then do+ cms <- cmFromFile cmmodelsFile+ inputhmms <- HM.readHMMER3 hmmmodelsFile+ let hmms = E.fromRight inputhmms+ hmmcResultParsed <- HC.getHMMCompareResults hmmcompareResultFile+ let comparisons = rights hmmcResultParsed+ let comparisonse = lefts hmmcResultParsed+ print comparisonse+ let cmVector = V.fromList cms+ let hmmVector = V.fromList hmms+ --let modelNumber = length cms+ let cmModelNames = map (T.unpack . CM._name) cms+ let hmmModelNames = map HM.name hmms+ --currentWD <- getCurrentDirectory+ --let dirPath = if null outputDirectoryPath then currentWD else outputDirectoryPath+ --setCurrentDirectory dirPath+ let cmcs = map (hmmctocmc cmModelNames hmmModelNames cmVector hmmVector) comparisons+ mapM_ (putStr . show) cmcs+ else do+ Control.Monad.unless cmmodelFileExists $ putStrLn "CM Model file not found"+ Control.Monad.unless hmmmodelFileExists $ putStrLn "HMM Model file not found"+ Control.Monad.unless cmcFileExists $ putStrLn "Comparison file not found"++toolVersion :: String+toolVersion = showVersion version++hmmctocmc :: [String] -> [String] -> V.Vector CM.CM -> V.Vector HM.HMMER3 -> HC.HMMCompareResult -> CmcompareResult+hmmctocmc cmModelNames hmmModelNames cmVector hmmVector comparison = cmcompare+ where cm1Index = fromJust (elemIndex (HC.model1Name comparison) cmModelNames)+ cm2Index = fromJust (elemIndex (HC.model2Name comparison) cmModelNames)+ inputCM1 = cmVector V.! cm1Index+ cm1 = E.fromLeft (CM._cm inputCM1) + inputCM2 = cmVector V.! cm2Index+ cm2 = E.fromLeft (CM._cm inputCM2)+ hmm1Index = fromJust (elemIndex (HC.model1Name comparison) hmmModelNames)+ hmm2Index = fromJust (elemIndex (HC.model2Name comparison) hmmModelNames)+ hmm1 = hmmVector V.! hmm1Index+ hmm2 = hmmVector V.! hmm2Index+ hmm1nodeIndices = nub (HC.model1matchednodes comparison)+ hmm2nodeIndices = nub (HC.model2matchednodes comparison)+ cm1nodes = (M.elems (CM._fmNodes cm1))+ cm2nodes = (M.elems (CM._fmNodes cm2))+ hmm1nodes = HM.nodes hmm1+ hmm2nodes = HM.nodes hmm2+ --filter cmnodes+ aln1colIndices = map (\i -> fromJust $ HM.nma (hmm1nodes V.! (i-1))) hmm1nodeIndices+ aln2colIndices = map (\i -> fromJust $ HM.nma (hmm2nodes V.! (i-1))) hmm2nodeIndices+ -- aln1colIndices = concatMap nodeToColumnIndices cm1nodes+ -- aln2colIndices = concatMap nodeToColumnIndices cm2nodes+ -- linkedcm1nodes = V.filter (\node -> elem (fromJust (HM.nma node)) aln1colIndices) cm1nodes+ -- linkedcm2nodes = V.filter (\node -> elem (fromJust (HM.nma node)) aln2colIndices) cm2nodes+ -- cm1interval = V.map HM.nodeId linkedcm1nodes+ -- cm2interval = V.map HM.nodeId linkedcm2nodes+ cm1interval = findIndices (\n -> or $ map (\i -> elem i aln1colIndices) (nodeToColumnIndices n)) cm1nodes+ cm2interval = findIndices (\n -> or $ map (\i -> elem i aln2colIndices) (nodeToColumnIndices n)) cm2nodes+ cmcompare = CmcompareResult (HC.model1Name comparison) (HC.model2Name comparison) (HC.linkscore1 comparison) (HC.linkscore2 comparison) (HC.linksequence comparison) (replicate (length cm1interval) '.') (replicate (length cm2interval) '.') cm1interval cm2interval++nodeToColumnIndices:: CM.Node -> [Int]+nodeToColumnIndices currentNode = nub [CM._nodeColL currentNode,CM._nodeColR currentNode]+-- where currentNode = (V.!) nodes (nodeIndex)+-- colIndices = nub [CM._nodeColL currentNode,CM._nodeColR currentNode]++writeModelNameFile :: Bool -> String -> [String] -> IO ()+writeModelNameFile toggle outputDirectoryPath modelNames =+ if toggle+ then do+ let modelNamesString = intercalate "," modelNames+ writeFile (outputDirectoryPath ++ "modelNames") modelNamesString+ else return ()
+ src/cmv/CMVJson.hs view
@@ -0,0 +1,44 @@+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE DeriveDataTypeable #-}+-- | TaxIds2Tree+-- dist/build/CMVJson/CMVJson -i input.cm+module Main where++import Prelude +import System.Console.CmdArgs+--import qualified Biobase.SElab.CM as CM+import Biobase.SElab.CM.Import (cmFromFile)+--import Data.Either.Unwrap+--import qualified Data.Vector as V+--import qualified Data.ByteString.Lazy.Char8 as L+--import Data.Char+--import qualified Data.Aeson.Encode as E+import qualified Data.Aeson as E+--------------------------------------------------------++data Options = Options + { inputModelFile :: String,+ outputDirectoryPath :: String+ } deriving (Show,Data,Typeable)++options :: Options+options = Options+ { inputModelFile = def &= name "m" &= help "Path to input",+ outputDirectoryPath = def &= name "o" &= help "Path to output directory"+ } &= summary "CMVJson - CM is converted into a graphical tree representation via .json (via d3js)" &= help "Florian Eggenhofer - 2017" &= verbosity ++main :: IO ()+main = do+ Options{..} <- cmdArgs options+ cms <- cmFromFile inputModelFile+ if not (null cms)+ then do + let jsonCM = E.encode (head cms)+ print jsonCM+ else print "No models"++--generateJsonOutput :: String -> Gr SimpleTaxon Double -> IO ()+--generateJsonOutput outputDirectoryPath inputGraph = do+-- let jsonOutput = E.encode (grev inputGraph)+-- L.writeFile (outputDirectoryPath ++ "model.json") jsonOutput+
+ src/cmv/CMVisualisation.hs view
@@ -0,0 +1,113 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE RankNTypes #-}+{-# LANGUAGE FlexibleContexts #-}++-- | Visualize Infernal Covariance Models+-- Datastructures and parsing of covariance models is provided by Biobase+-- Visualization is accomplished with diagrams-svg+-- For more information on Infernal consult <http://eddylab.org/infernal/>++module Main where++import Bio.CMDraw+import qualified Biobase.SElab.CM as CM+import Biobase.SElab.CM.Import (cmFromFile)+import System.Console.CmdArgs+import System.Directory+import Data.Either.Unwrap+import qualified Bio.StockholmParser as SP+import qualified Data.Text as T+import Paths_cmv (version)+import Data.Version (showVersion)+import Data.List (intercalate)+import Control.Monad+import Data.Maybe++options :: Options+data Options = Options+ { modelFile :: String,+ alignmentFile :: String,+ modelDetail :: String,+ modelLayout :: String,+ emissionLayout :: String,+ alignmentEntries :: Int,+ transitionCutoff :: Double,+ maxWidth :: Double,+ scalingFactor :: Double,+ outputFormat :: String,+ outputDirectoryPath :: String,+ secondaryStructureVisTool :: String,+ modelNameToggle :: Bool+ } deriving (Show,Data,Typeable)++options = Options+ { modelFile = def &= name "m" &= help "Path to covariance model file",+ alignmentFile = "" &= name "s" &= help "Path to stockholm alignment file",+ modelDetail = "detailed" &= name "d" &= help "Set verbosity of drawn models: minimal, simple, detailed",+ modelLayout = "tree" &= name "l" &= help "Set layout of drawn models: flat, tree",+ emissionLayout = "box" &= name "e" &= help "Set layout of drawn models: score, probability, box (Default: box)",+ alignmentEntries = (50 :: Int) &= name "n" &= help "Set cutoff for included stockholm alignment entries (Default: 50)",+ transitionCutoff = (0.01 :: Double) &= name "t" &= help "Minimal value for a transition probability to be displayed (Default: 0.01)",+ maxWidth = (200 :: Double) &= name "w" &= help "Set maximal width of result figure (Default: 100)",+ scalingFactor = (2.0 :: Double) &= name "c" &= help "Set uniform scaling factor for image size (Default: 2)",+ outputFormat = "pdf" &= name "f" &= help "Output image format: pdf, svg, png, ps (Default: pdf)",+ outputDirectoryPath = "" &= name "p" &= help "Output directory path (Default: none)",+ secondaryStructureVisTool = "" &= name "x" &= help "Select tool for secondary structure visualisation: forna, r2r (Default: none)",+ modelNameToggle = False &= name "b" &= help "Write all comma separted model names to modelNames file (Default: False)"+ } &= summary ("CMV " ++ toolVersion) &= help "Florian Eggenhofer - 2013-2016" &= verbosity++main :: IO ()+main = do+ Options{..} <- cmdArgs options+ modelFileExists <- doesFileExist modelFile+ if modelFileExists+ then do+ cms <- cmFromFile modelFile+ if not (null cms)+ then do+ alnInput <- SP.readExistingStockholm alignmentFile+ Control.Monad.when (isLeft alnInput) $ print (fromLeft alnInput)+ --let outputName = diagramName "cmv" outputFormat+ let modelNumber = length cms+ let alns = if isRight alnInput then map (\a -> Just a) (fromRight alnInput) else replicate modelNumber Nothing+ let currentModelNames = map (T.unpack . CM._name) cms+ currentWD <- getCurrentDirectory+ let dirPath = if null outputDirectoryPath then currentWD else outputDirectoryPath+ writeModelNameFile modelNameToggle dirPath currentModelNames+ let modelFileNames = map (\m -> m ++ "." ++ outputFormat) currentModelNames+ let alignmentFileNames = map (\m -> m ++ ".aln" ++ "." ++ outputFormat) currentModelNames+ setCurrentDirectory dirPath+ let (modelVis,alignmentVis)= unzip $ drawSingleCMs modelDetail alignmentEntries transitionCutoff modelLayout emissionLayout maxWidth scalingFactor cms alns+ mapM_ (\(a,b) -> printCM a svgsize b) (zip modelFileNames modelVis)+ mapM_ (\(alnPath,stockholm) -> if isJust stockholm then printCM alnPath svgsize (fromJust stockholm) else return ()) (zip alignmentFileNames alignmentVis)+ let structureVisType = "perModel"+ if structureVisType == "perModel"+ then do+ let structureFilePath = dirPath ++ "/"+ let structureVisInputs = perModelSecondaryStructureVisualisation secondaryStructureVisTool maxWidth structureFilePath cms alns []+ mapM_ (\(structureFileName,structureVis) -> writeFile structureFileName structureVis) structureVisInputs+ setCurrentDirectory currentWD+ else do+ let structureFilePaths = map (\m -> dirPath ++ "/" ++ m ++ "." ++ secondaryStructureVisTool) currentModelNames+ let structureVisInputs = mergedSecondaryStructureVisualisation secondaryStructureVisTool maxWidth cms alns []+ mapM_ (\(structureFileName,(structureVis,_)) -> writeFile structureFileName structureVis) (zip structureFilePaths structureVisInputs)+ mapM_ (\(structureFileName,(_,colorScheme)) -> writeFile (structureFileName ++"Color") colorScheme) (zip structureFilePaths structureVisInputs)+ setCurrentDirectory currentWD+ + else+ print "Could not read covariance models from input file"+ else+ putStrLn "Input model file not found"++toolVersion :: String+toolVersion = showVersion version++writeModelNameFile :: Bool -> String -> [String] -> IO ()+writeModelNameFile toggle outputDirectoryPath modelNames =+ if toggle+ then do+ let modelNamesString = intercalate "," modelNames+ writeFile (outputDirectoryPath ++ "modelNames") modelNamesString+ else return ()
+ src/hmmcv/HMMCVisualisation.hs view
@@ -0,0 +1,107 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE RankNTypes #-}+{-# LANGUAGE FlexibleContexts #-}++-- | Visualize detailed comparsions of HMMER3 models+-- For more information on Infernal consult <http://hmmer.org/>++module Main where++import Bio.HMMCompareResult+import Bio.HMMDraw+import qualified Bio.HMMParser as HM+import System.Console.CmdArgs+import Data.Either+import qualified Data.Either.Unwrap as E+import System.Directory+import qualified Bio.StockholmParser as SP+import Paths_cmv (version)+import Data.Version (showVersion)+import Data.List (intercalate)+import Control.Monad+import Data.Maybe++options :: Options+data Options = Options+ { hmmCompareResultFile :: String,+ modelsFile :: String,+ alignmentFile :: String,+ modelDetail :: String,+ emissionLayout :: String,+ alignmentEntries :: Int,+ maxWidth :: Double,+ scalingFactor :: Double,+ transitionCutoff :: Double,+ comparisonAlignment :: String,+ outputFormat :: String,+ outputDirectoryPath :: String,+ modelNameToggle :: Bool+ } deriving (Show,Data,Typeable)++options = Options+ { hmmCompareResultFile = def &= name "r" &= help "Path to HMMCompare result file",+ modelsFile = def &= name "m" &= help "Path to covariance model file",+ alignmentFile = "" &= name "s" &= help "Path to stockholm alignment file",+ modelDetail = "detailed" &= name "d" &= help "Set verbosity of drawn models: minimal, simple, detailed",+ emissionLayout = "box" &= name "e" &= help "Set layout of drawn models: score, probability, box (Default: box)",+ alignmentEntries = (50 :: Int) &= name "n" &= help "Set cutoff for included stockholm alignment entries (Default: 50)",+ maxWidth = (55 :: Double) &= name "w" &= help "Set maximal width of result figure (Default: 100)",+ scalingFactor = (2 :: Double) &= name "c" &= help "Set uniform scaling factor for image size (Default: 2)",+ transitionCutoff = (0.01 :: Double) &= name "t" &= help "Minimal value for a transition probability to be displayed (Default: 0.01)",+ comparisonAlignment = "model" &= name "a" &= help "Set layout of drawn models: model, comparison",+ outputFormat = "pdf" &= name "f" &= help "Output image format: pdf, svg, png, ps (Default: pdf)",+ outputDirectoryPath = "" &= name "p" &= help "Output directory path (Default: none)",+ modelNameToggle = False &= name "b" &= help "Write all comma separted model names to modelNames file (Default: False)"+ } &= summary ("HMMCV " ++ toolVersion) &= help "Florian Eggenhofer - 2013-2016" &= verbosity++main :: IO ()+main = do+ Options{..} <- cmdArgs options+ --Validate input+ modelFileExists <- doesFileExist modelsFile+ hmmCFileExists <- doesFileExist hmmCompareResultFile+ alnFileExists <- doesFileExist alignmentFile+ if modelFileExists && hmmCFileExists && alnFileExists+ then do+ inputModels <- HM.readHMMER3 modelsFile+ if isRight inputModels+ then do+ let models = E.fromRight inputModels+ hmmCResultParsed <- getHMMCompareResults hmmCompareResultFile+ let modelNumber = length models+ alnInput <- SP.readExistingStockholm alignmentFile+ Control.Monad.when (isLeft alnInput) $ print (E.fromLeft alnInput)+ let alns = if isRight alnInput then map (\a -> Just a) (E.fromRight alnInput) else replicate modelNumber Nothing+ let currentModelNames = map HM.name models+ currentWD <- getCurrentDirectory+ let dirPath = if null outputDirectoryPath then currentWD else outputDirectoryPath+ if and $ map isRight hmmCResultParsed+ then do+ let rightHMMCResultsParsed = rights hmmCResultParsed+ --let outputName = diagramName "hmmcv" outputFormat+ setCurrentDirectory dirPath+ let modelFileNames = map (\m -> m ++ "." ++ outputFormat) currentModelNames+ let alignmentFileNames = map (\m -> m ++ ".aln" ++ "." ++ outputFormat) currentModelNames+ writeModelNameFile modelNameToggle dirPath currentModelNames+ let (modelVis,alignmentVis) = unzip $ drawSingleHMMComparison modelDetail alignmentEntries transitionCutoff emissionLayout maxWidth scalingFactor models alns rightHMMCResultsParsed+ mapM_ (\(a,b) -> printHMM a svgsize b) (zip modelFileNames modelVis)+ mapM_ (\(alnPath,stockholm) -> if isJust stockholm then printHMM alnPath svgsize (fromJust stockholm) else return ()) (zip alignmentFileNames alignmentVis)+ setCurrentDirectory currentWD+ else print (lefts hmmCResultParsed)+ else print (E.fromLeft inputModels)+ else do+ Control.Monad.unless modelFileExists $ putStrLn "Model file not found"+ Control.Monad.unless hmmCFileExists $ putStrLn "Comparison file not found"++toolVersion :: String+toolVersion = showVersion version++writeModelNameFile :: Bool -> String -> [String] -> IO ()+writeModelNameFile toggle outputDirectoryPath modelNames =+ if toggle+ then do+ let modelNamesString = intercalate "," modelNames+ writeFile (outputDirectoryPath ++ "modelNames") modelNamesString+ else return ()
+ src/hmmv/HMMVisualisation.hs view
@@ -0,0 +1,94 @@+{-# LANGUAGE DeriveDataTypeable #-}+{-# LANGUAGE NoMonomorphismRestriction #-}+{-# LANGUAGE RecordWildCards #-}+{-# LANGUAGE RankNTypes #-}+{-# LANGUAGE FlexibleContexts #-}++-- | Visualize Hidden Markov Models++module Main where++import qualified Bio.HMMParser as HM+import Bio.HMMDraw+import System.Console.CmdArgs+import Data.Either.Unwrap+import System.Directory+import qualified Bio.StockholmParser as SP+import Paths_cmv (version)+import Data.Version (showVersion)+import Data.List (intercalate)+import Control.Monad+import Data.Maybe++options :: Options+data Options = Options+ { modelFile :: String,+ alignmentFile :: String,+ modelDetail :: String,+ emissionLayout :: String,+ alignmentEntries :: Int,+ maxWidth :: Double,+ scalingFactor :: Double,+ transitionCutoff :: Double,+ outputFormat :: String,+ outputDirectoryPath :: String,+ modelNameToggle :: Bool+ } deriving (Show,Data,Typeable)+++options = Options+ { modelFile = def &= name "m" &= help "Path to hidden Markov model file",+ alignmentFile = "" &= name "s" &= help "Path to stockholm alignment file",+ modelDetail = "detailed" &= name "d" &= help "Set verbosity of drawn models: minimal, simple, detailed",+ emissionLayout = "box" &= name "e" &= help "Set layout of drawn models: score, probability, box (Default: box)",+ alignmentEntries = (50 :: Int) &= name "n" &= help "Set cutoff for included stockholm alignment entries (Default: 50)",+ maxWidth = (55:: Double) &= name "w" &= help "Set maximal width of result figure (Default: 55)",+ scalingFactor = (2 :: Double) &= name "c" &= help "Set uniform scaling factor for image size (Default: 2)",+ transitionCutoff = (0.01 :: Double) &= name "t" &= help "Minimal value for a transition probability to be displayed (Default: 0.01)",+ outputFormat = "pdf" &= name "f" &= help "Output image format: pdf, svg, png, ps (Default: pdf)",+ outputDirectoryPath = "" &= name "p" &= help "Output directory path (Default: none)",+ modelNameToggle = False &= name "b" &= help "Write all comma separted model names to modelNames file (Default: False)"+ } &= summary ("HMMV " ++ toolVersion) &= help "Florian Eggenhofer - 2016-2017" &= verbosity++main :: IO ()+main = do+ Options{..} <- cmdArgs options+ modelFileExists <- doesFileExist modelFile+ if modelFileExists+ then do+ inputModels <- HM.readHMMER3 modelFile+ if isRight inputModels+ then do+ alnInput <- SP.readExistingStockholm alignmentFile+ Control.Monad.when (isLeft alnInput) $ print (fromLeft alnInput)+ -- cairo outputFormat check+ --let outputName = diagramName "hmmv" outputFormat+ let currentModels = fromRight inputModels+ let modelNumber = length currentModels+ let alns = if isRight alnInput then map (\a -> Just a) (fromRight alnInput) else replicate modelNumber Nothing+ let currentModelNames = map HM.name currentModels+ currentWD <- getCurrentDirectory+ let dirPath = if null outputDirectoryPath then currentWD else outputDirectoryPath+ setCurrentDirectory dirPath+ let modelFileNames = map (\m -> m ++ "." ++ outputFormat) currentModelNames+ let alignmentFileNames = map (\m -> m ++ ".aln" ++ "." ++ outputFormat) currentModelNames+ writeModelNameFile modelNameToggle dirPath currentModelNames+ let (modelVis,alignmentVis) = unzip $ drawSingleHMMER3s modelDetail alignmentEntries transitionCutoff maxWidth scalingFactor emissionLayout currentModels alns+ mapM_ (\(a,b) -> printHMM a svgsize b) (zip modelFileNames modelVis)+ mapM_ (\(alnPath,stockholm) -> if isJust stockholm then printHMM alnPath svgsize (fromJust stockholm) else return ()) (zip alignmentFileNames alignmentVis)+ setCurrentDirectory currentWD+ else+ print (fromLeft inputModels)+ else+ putStrLn "Input model file not found"++toolVersion :: String+toolVersion = showVersion version++writeModelNameFile :: Bool -> String -> [String] -> IO ()+writeModelNameFile toggle outputDirectoryPath modelNames =+ if toggle+ then do+ let modelNamesString = intercalate "," modelNames+ writeFile (outputDirectoryPath ++ "modelNames") modelNamesString+ else return ()