Add some missing Show instances

Author: MaybeJustJames

src/Bio/Phylogeny/Internal/PhyloXml.purs

@@ -49,6 +49,20 @@ newtype XmlNode = XmlNode
 
 derive instance eqXmlNode :: Eq XmlNode
 
+instance showXmlNode :: Show XmlNode where
+  show (XmlNode { name, value: Just v }) = name <> "=\"" <> v <> "\""
+  show (XmlNode { name, attributes })
+    | M.isEmpty attributes = name
+    | otherwise = name <> ": " <> myShow attributes
+        where
+        myShow :: M.Map String Attribute -> String
+        myShow attrs = "{"
+          <>
+            ( foldl (\acc (k /\ v) -> acc <> " " <> k <> ": " <> show v) "" $
+                (M.toUnfoldable attrs :: Array (Tuple String Attribute))
+            )
+          <> "}"
+
 parsePhyloXml :: String -> Either ParseError Phylogeny
 parsePhyloXml input = runParser input phyloXmlParser
 
@@ -57,15 +71,14 @@ phyloXmlParser = do
   tree' <- phyloxml
   case convert tree' of
     Right { meta, trees } -> do
+      let withRefs = foldl updateRefs mempty trees
       pure
-        $ toAnnotatedPhylogeny meta
-        $ foldl
-            ( \acc@(PartialPhylogeny { maxRef }) p ->
-                acc <> interpretIntermediate (maxRef + 1) p
-            )
-            mempty
-            trees
+        $ toAnnotatedPhylogeny meta withRefs
     Left err -> fail err
+  where
+  updateRefs :: PartialPhylogeny -> Tree PartialNode -> PartialPhylogeny
+  updateRefs acc@(PartialPhylogeny { maxRef }) p =
+    acc <> interpretIntermediate (maxRef + 1) p
 
 branchLength :: M.Map String Attribute -> Maybe Number
 branchLength attrs =

src/Bio/Phylogeny/Internal/Types.purs

@@ -32,7 +32,7 @@ import Data.List as L
 import Data.Map as M
 import Data.Maybe (Maybe(..), fromMaybe)
 import Data.Traversable (class Traversable, sequenceDefault, traverse)
-import Data.Tuple (Tuple, uncurry)
+import Data.Tuple (Tuple(..))
 import Data.Tuple.Nested ((/\))
 import Parsing (ParserT)
 
@@ -43,7 +43,7 @@ data Event
   | LateralGeneTransfer
   | Recombination
 
-derive instance eqNodeType :: Eq Event
+derive instance eqEvent :: Eq Event
 
 eventToString :: Event -> String
 eventToString Clade = "Clade"
@@ -52,6 +52,9 @@ eventToString Hybrid = "Hybrid"
 eventToString LateralGeneTransfer = "LateralGeneTransfer"
 eventToString Recombination = "Recombination"
 
+instance showEvent :: Show Event where
+  show = eventToString
+
 type NodeName = String
 
 type NodeIdentifier = Int
@@ -137,6 +140,13 @@ data Tree a
 
 derive instance eqTree :: Eq a => Eq (Tree a)
 
+instance showTree :: Show a => Show (Tree a) where
+  show (Leaf l) = "L: " <> show l
+  show (Internal v children) = "(I:" <> show v <> toStr children <> ")"
+    where
+    toStr :: forall x. Show x => Array x -> String
+    toStr xs = foldl (\acc x -> acc <> " " <> show x) "" xs
+
 instance functorTree :: Functor Tree where
   map f (Leaf n) = Leaf (f n)
   map f (Internal p cs) = Internal (f p) (map (map f) cs)
@@ -238,12 +248,12 @@ toPhylogeny (PartialPhylogeny phylogeny) =
 
 toAnnotatedPhylogeny :: Array Metadata -> PartialPhylogeny -> Phylogeny
 toAnnotatedPhylogeny metadata (PartialPhylogeny phylogeny) =
-  { metadata: uncurry mergeMetadata <$> A.zip metadata phylogeny.metadata
+  { metadata: mergeMetadata <$> A.zip metadata phylogeny.metadata
   , network: fromMap phylogeny.network
   }
   where
-  mergeMetadata :: Metadata -> Metadata -> Metadata
-  mergeMetadata a b =
+  mergeMetadata :: Tuple Metadata Metadata -> Metadata
+  mergeMetadata (Tuple a b) =
     { name: a.name <|> b.name
     , parent: max a.parent b.parent
     , rooted: a.rooted || b.rooted