1 files changed, 1 insertions, 20 deletions
diff --git a/bin/cluster.hs b/bin/cluster.hs
index 7da6810..6b0d917 100644
--- a/bin/cluster.hs
+++ b/bin/cluster.hs
@@ -88,22 +88,6 @@ model xs = do
 -- Tabulate list
 tabulate xs = M.elems $ M.fromListWith (+) [(c, 1) | c <- xs]
 
--- Draws a phylogeny to DOT format
-drawGraph :: FilePath -> [[Double]] -> [Int] -> IO ()
-drawGraph path ps cl = writeFile path $ "digraph{" <> edges <> "}"
-  where
-    edges = concatMap calcEdges [1 .. length tab - 1]
-    calcEdges idx = fmt (parent idx) <> "->" <> fmt idx <> ";"
-    fmt i = "\"" <> intercalate "," (map fmtDbl $ ps' !! i) <> " " <> show (tab !! i) <> "\""
-    tab = tabulate cl
-    parent = flip div 2 . (\x -> x - 1)
-    fmtDbl = show . (/ 10) . fromIntegral . round . (* 1000)
-    ps' = transpose $ map norm ps
-
-    -- Normalise to frequency of parent
-    norm :: [Double] -> [Double]
-    norm xxs@(x : xs) = x : zipWith (\i y -> y / xxs !! parent i) [1 ..] xs
-
 -- Command line args
 data Options = Options
   { seed :: Int,
@@ -111,8 +95,7 @@ data Options = Options
     mhfrac :: Double,
     input :: FilePath,
     propsPath :: FilePath,
-    clusterPath :: FilePath,
-    dotPath :: FilePath
+    clusterPath :: FilePath
   }
 
 main = run =<< execParser opts
@@ -128,7 +111,6 @@ main = run =<< execParser opts
         <*> argument str (metavar "INPUT")
         <*> argument str (metavar "PROPS")
         <*> argument str (metavar "TREE")
-        <*> strOption (long "dot" <> short 'd' <> help "draw graph of phylogeny in dot format" <> value "" <> metavar "PATH")
 
     probability = eitherReader $ \arg -> case reads arg of
       [(r, "")] -> if r <= 1 && r > 0 then Right r else Left "mhfrac not a valid probability"
@@ -142,7 +124,6 @@ run opts = do
   ((ps, cl), _) <- foldl1' (\a c -> if mml a < mml c then a else c) . take (nsamples opts) <$> mh (mhfrac opts) 0.5 (model $ getCompact parsed)
   writeFile (propsPath opts) . unlines $ map (intercalate "," . map show) ps
   writeFile (clusterPath opts) . unlines $ map show cl
-  when (dotPath opts /= "") $ drawGraph (dotPath opts) ps cl
   where
     mml ((ps, cl), lik) = sum' (sum' (log . (+ 1))) ps + sum' (log . (+ 1)) tab - sum' (ln . stirling) tab - ln lik
       where