cmv 1.0.6 → 1.0.7

raw patch · 6 files changed

+79/−57 lines, 6 filesdep ~StockholmAlignmentPVP: major bump suggested

API removals or changes: PVP suggests a major version bump

Dependency ranges changed: StockholmAlignment

API changes (from Hackage documentation)

Files

• README.md +16/−12
• changelog +3/−0
• cmv.cabal +9/−9
• src/Bio/CMDraw.hs +43/−34
• src/cmcv/CMCVisualisation.hs +4/−1
• src/cmv/CMVisualisation.hs +4/−1

@@ -9,20 +9,24 @@  *   [![GitHub](https://img.shields.io/github/tag/eggzilla/cmv.svg)](https://github.com/eggzilla/cmv) [![Build Status](https://travis-ci.org/eggzilla/cmv.svg?branch=master)](https://travis-ci.org/eggzilla/cmv) [![Hackage](https://img.shields.io/hackage/v/cmv.svg)](https://hackage.haskell.org/package/cmv) [![Bioconda](https://anaconda.org/bioconda/cmv/badges/version.svg)](https://anaconda.org/bioconda/cmv) [![Docker Repository on Quay](https://quay.io/repository/biocontainers/cmv/status "Docker Repository on Quay")](https://quay.io/repository/repository/biocontainers/cmv) -For instruction how to use *cmv* please see the [Help page.](192.52.2.124/cmvs/help)--### Usage via biocontainer (docker)--*cmv* can be retrieved and used as docker container with all dependencies via [docker](https://docs.docker.com/engine/installation/). Once you have docker installed simply type:+For instruction how to use *cmv* please see the [Help page.](http://www.gapjunction.eu/cmvs/help) -       docker run -i -t quay.io/biocontainers/cmv:1.0.5--0 /bin/bash+## Installation+For Linux we recommend installation via bioconda, for macOS usage of the docker container.+The example input files used in the webservice (EGF, Piwi, Hammerhead Clan, tRNA Clan) can be retrieved here: [Example input](http://www.gapjunction.eu/data/cmvs/exampleInput.zip) -### Installation via bioconda+### Installation via bioconda - Linux  *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 -c conda-forge cmv        +### Usage via biocontainer docker - MacOS++*cmv* can be retrieved and used as docker container with all dependencies via [docker](https://docs.docker.com/engine/installation/). Once you have docker installed simply type:++       docker run -i -t quay.io/biocontainers/cmv:1.0.7--0 /bin/bash+ ### 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/). CMV is implemented in Haskell and can be installed via the Haskell package distribution sytem cabal. Additionally to cabal you require [cairo](https://cairographics.org/), [pango](http://www.pango.org/), [happy](https://www.haskell.org/happy/) and [alex](https://www.haskell.org/alex/) which can be installed via the distribution package manager e.g. Ubuntu: @@ -40,9 +44,9 @@  ### Precompiled Executables -* Linux (ghc-8.0.2) [HMMV 1.0.3 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMV)-* Linux (ghc-8.0.2) [HMMCV 1.0.3 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMCV)-* Linux (ghc-8.0.2) [CMV 1.0.2 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMV)-* Linux (ghc-8.0.2) [CMCV 1.0.2 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCV)-* Linux (ghc-8.0.2) [CMCV 1.0.2 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCWStoCMCV)+* Linux (ghc-8.2.2) [HMMV 1.0.7 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMV)+* Linux (ghc-8.2.2) [HMMCV 1.0.7 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/HMMCV)+* Linux (ghc-8.2.2) [CMV 1.0.7 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMV)+* Linux (ghc-8.2.2) [CMCV 1.0.7 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCV)+* Linux (ghc-8.2.2) [CMCV 1.0.7 x86_64](http://www.bioinf.uni-freiburg.de/~egg/cmvs/bin/CMCWStoCMCV)    

@@ -1,4 +1,7 @@ -*-change-log-*-+1.0.7 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 15. January 2018+	* Improved placment of index labels+	* Prepared for layout direction extension 1.0.6 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 26. September 2017 	* Fixed a missing output bug in HMMCV 1.0.5 Florian Eggenhofer <egg@informatik.uni-freiburg.de> 18. September 2017

@@ -1,12 +1,12 @@ name:                cmv-version:             1.0.6+version:             1.0.7 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-Tested-With: GHC == 8.0.2, GHC == 8.2.1          +Tested-With: GHC == 8.0.2, GHC == 8.2.2 category:            Bioinformatics build-type:          Simple cabal-version:       >=1.8@@ -20,8 +20,8 @@  source-repository this   type:     git-  location: https://github.com/eggzilla/cmv/tree/1.0.6-  tag:      1.0.6+  location: https://github.com/eggzilla/cmv/tree/1.0.7+  tag:      1.0.7  library   -- Modules exported by the library.@@ -32,7 +32,7 @@   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>=1.6.0.2, BioHMM>=1.2.0, StockholmAlignment>=1.1.1, BiobaseTypes,containers,diagrams-core+  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>=1.6.0.2, BioHMM>=1.2.0, StockholmAlignment>=1.1.2, BiobaseTypes,containers,diagrams-core      -- Directories containing source files.   hs-source-dirs:      src@@ -41,13 +41,13 @@   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>=1.4.1.2, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.1+  build-depends:       base >=4.5, cmdargs, BiobaseInfernal==0.8.1.0, BiobaseXNA, diagrams-lib>=1.4.1.2, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.2  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, parsec, colour, containers, bytestring, template-haskell, text, vector, directory, cmv, either-unwrap, filepath, StockholmAlignment>=1.1.1+  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>=1.1.2  executable CMCWStoCMCV   Hs-Source-Dirs:      ./src/cmcv/@@ -77,10 +77,10 @@   Hs-Source-Dirs:      ./src/hmmcv/   main-is:	       HMMCVisualisation.hs   ghc-options:         -Wall-  build-depends:       base >=4.5, cmdargs, diagrams-lib, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.1+  build-depends:       base >=4.5, cmdargs, diagrams-lib, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.2  executable HMMV   Hs-Source-Dirs:      ./src/hmmv/   main-is:	       HMMVisualisation.hs   ghc-options:         -Wall-  build-depends:       base >=4.5, cmdargs, diagrams-lib, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.1+  build-depends:       base >=4.5, cmdargs, diagrams-lib, parsec, colour, containers, bytestring, text, vector, directory, cmv, either-unwrap, filepath, BioHMM>=1.2.0, StockholmAlignment>=1.1.2

@@ -47,9 +47,9 @@ 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+drawSingleCMComparisons :: String -> String -> Int -> Double -> String -> String -> Double -> Double -> [CM.CM] -> [Maybe StockholmAlignment] -> [CmcompareResult] -> [(QDiagram Cairo V2 Double Any,Maybe (QDiagram Cairo V2 Double Any))]+drawSingleCMComparisons layoutDirection modelDetail entryNumberCutoff transitionCutoff modelLayout emissiontype maxWidth scalef cms alns comparisons = diagrams+  where diagrams = map (drawCM layoutDirection 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@@ -58,16 +58,16 @@         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+drawSingleCMs :: String -> String -> Int -> Double -> String -> String -> Double -> Double -> [CM.CM] -> [Maybe StockholmAlignment] -> [(QDiagram Cairo V2 Double Any,Maybe (QDiagram Cairo V2 Double Any))]+drawSingleCMs layoutDirection modelDetail entryNumberCutoff transitionCutoff modelLayout emissiontype maxWidth scalef cms alns = map (drawCM layoutDirection 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)+drawCM :: String -> 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 layoutDirection 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)@@ -80,15 +80,16 @@          indices = V.toList (V.iterateN (nodeNumber-1) (1+) 0)          (indexStructure,_)= runState (buildTreeIndexStructure 1 nodes indices) startState          modelName = CM._name inputCM+         currentCat = if layoutDirection == "vertical" then vcat' with {_sep=0.01} else hcat' with {_sep=0.01}          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+         nodesTree = drawCMNodeTree layoutDirection 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))+         nodesFlat = currentCat (V.toList (V.map (drawCMNode layoutDirection 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@@ -489,22 +490,28 @@ 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)+drawCMNodeTree :: String -> 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 layoutDirection modelDetail alphabetSymbols emissiontype boxlength allStates comparisonNodeLabels nodes indexStructure (intervalId,parentId,intervalType,currentIndex,currentEnd) = nodeTree+  where nodeTree = if layoutDirection == "vertical" then verticalNodeTree else horizontalNodeTree+        verticalNodeTree = currentIntervalDrawing === hcat' with {_sep = 20} (map (drawCMNodeTree layoutDirection modelDetail alphabetSymbols emissiontype boxlength allStates comparisonNodeLabels nodes indexStructure) nextIntervals)+        horizontalNodeTree = currentIntervalDrawing ||| vcat' with {_sep = 20} (map (drawCMNodeTree layoutDirection 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)+        currentIntervalDrawing = drawCMNodeInterval layoutDirection 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)+drawCMNodeInterval :: String -> 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 layoutDirection 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+  where intervalVis = if layoutDirection == "vertical" then verticalIntervalVis else horizontalIntervalVis+        verticalIntervalVis = 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+        horizontalIntervalVis = 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 ||| strutX 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)+        nodeVis = if layoutDirection == "vertical" then verticalNodeVis else horizontalNodeVis+        verticalNodeVis = strutY 4  === vcat' with { _sep = nodespacer } (map (drawCMNode layoutDirection modelDetail alphabetSymbols emissiontype boxlength rowStart rowEnd lastIndex states comparisonNodeLabels nodes) currentInterval)+        horizontalNodeVis = strutX 5 ||| hcat' with { _sep = nodespacer } (map (drawCMNode layoutDirection 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) @@ -541,30 +548,31 @@ --   | 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+drawCMNode :: String -> 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 layoutDirection modelDetail alphabetSymbols emissiontype boxlength _ _ _ states comparisonNodeLabels nodes nodeIndex+  | modelDetail == "minimal" = drawCMMinimalNodeBox layoutDirection alphabetSymbols emissiontype boxlength states comparisonNodeLabels node nodeIndex+  | modelDetail == "simple" = drawCMSimpleNodeBox layoutDirection 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+        detailedNodeBox = drawCMDetailedNodeBox layoutDirection 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 +drawCMMinimalNodeBox :: String -> 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 layoutDirection alphabetSymbols emissiontype boxlength currentStates comparisonNodeLabels node nodeIndex+  | ntype == CM.Bif = currentCat minimalNode  splitStatesBox -- bifNode +  | ntype == CM.BegL = currentCat splitStatesBox minimalNode -- begLNode +  | ntype == CM.BegR = currentCat splitStatesBox minimalNode -- begRNode    | otherwise = minimalNode     where ntype = CM._nodeType node           idNumber = nodeIndex           nId = show idNumber+          currentCat = if layoutDirection == "vertical" then (===) else (|||)           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)@@ -575,15 +583,16 @@           --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 +drawCMSimpleNodeBox :: String -> 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 layoutDirection alphabetSymbols emissiontype boxlength currentStates comparisonNodeLabels node nodeIndex+  | ntype == CM.Bif = currentCat simpleNode splitStatesBox -- bifNode +  | ntype == CM.BegL = currentCat splitStatesBox simpleNode -- begLNode +  | ntype == CM.BegR = currentCat splitStatesBox simpleNode -- begRNode    | otherwise = simpleNode     where ntype = CM._nodeType node           idNumber = nodeIndex            nId = show idNumber+          currentCat = if layoutDirection == "vertical" then (===) else (|||)           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)@@ -607,8 +616,8 @@           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+drawCMDetailedNodeBox :: String -> 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 layoutDirection 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

@@ -32,6 +32,7 @@   { cmcompareResultFile :: String,     modelsFile :: String,     alignmentFile :: String,+--    layoutDirection :: String,     modelDetail :: String,     modelLayout :: String,     emissionLayout :: String,@@ -50,6 +51,7 @@   { 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",+--    layoutDirection = "vertical" &= name "g" &= help "Set in which direction the model is drawn: vertical, horizontal (Default: vertical)",     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)",@@ -79,6 +81,7 @@        Control.Monad.when (isLeft alnInput) $ print (E.fromLeft alnInput)        --let outputName = diagramName "cmcv" outputFormat        let modelNumber = length cms+       let layoutDirection = "vertical"        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@@ -87,7 +90,7 @@        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+       let (modelVis,alignmentVis) = unzip $ drawSingleCMComparisons layoutDirection 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"

@@ -29,6 +29,7 @@ data Options = Options   { modelFile :: String,     alignmentFile :: String,+--    layoutDirection :: String,     modelDetail :: String,     modelLayout :: String,     emissionLayout :: String,@@ -45,6 +46,7 @@ options = Options   { modelFile = def &= name "m" &= help "Path to covariance model file",     alignmentFile = "" &= name "s" &= help "Path to stockholm alignment file",+--    layoutDirection = "vertical" &= name "g" &= help "Set in which direction the model is drawn: vertical, horizontal (Default: vertical)",     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)",@@ -71,6 +73,7 @@           Control.Monad.when (isLeft alnInput) $ print (fromLeft alnInput)           --let outputName = diagramName "cmv" outputFormat           let modelNumber = length cms+	  let layoutDirection = "vertical"           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@@ -79,7 +82,7 @@           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+          let (modelVis,alignmentVis)= unzip $ drawSingleCMs layoutDirection 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"