internal and external nodes

README.md

@@ -45,7 +45,7 @@ Branches have `Float64` lengths
 We can quickly look at the nodes present in our `Tree`:
 
     > collect(exampletree.nodes)
-    
+
     [unattached node]
     [branch 1]-->[internal node]-->[branch 2]
     [branch 2]-->[leaf node]                 
@@ -64,13 +64,13 @@ There are many other functions available that are helpful when dealing with tree
 `outdegree`,
 `isroot`,
 `isleaf`,
-`isnode`,
+`isinternal`,
 `findroots`,
 `findleaves`,
-`findnodes`,
+`findinternal`,
 `findnonroots`,
 `findnonleaves`,
-`findnonnodes`,
+`findexternal`,
 `areconnected`,
 `nodepath`,
 `branchpath`,

src/PhyloTrees.jl

@@ -37,14 +37,14 @@ module PhyloTrees
     outdegree,
     isroot,
     isleaf,
-    isnode,
+    isinternal,
     findroots,
     findroot,
     findleaves,
-    findnodes,
+    findinternals,
+    findexternals,
     findnonroots,
     findnonleaves,
-    findnonnodes,
     areconnected,
     nodepath,
     branchpath,

src/utilities.jl

@@ -61,13 +61,13 @@ end
 
 
 """
-isnode(tree::Tree,
-       node::Int64)
+isinternal(tree::Tree,
+           node::Int64)
 
 Determine if a `Node` is an internal `Node`
 """
-function isnode(tree::Tree,
-                node::Int64)
+function isinternal(tree::Tree,
+                    node::Int64)
   if outdegree(tree, node) > 0 && indegree(tree, node) == 1
     return true
   else
@@ -145,14 +145,14 @@ end
 
 
 """
-findnodes(tree::Tree)
+findinternals(tree::Tree)
 
 Find the internal `Node`s of a `Tree`
 """
-function findnodes(tree::Tree)
+function findinternals(tree::Tree)
   nodes = Int64[]
   for i in keys(tree.nodes)
-    if isnode(tree, i)
+    if isinternal(tree, i)
       push!(nodes, i)
     end
   end
@@ -202,21 +202,21 @@ end
 
 
 """
-findnonnodes(tree::Tree)
+findexternals(tree::Tree)
 
-Find the non-internal `Node`s of a `Tree`
+Find the external `Node`s of a `Tree`
 """
-function findnonnodes(tree::Tree)
-  nonnodes = Int64[]
+function findexternals(tree::Tree)
+  externals = Int64[]
   for i in keys(tree.nodes)
-    if !isnode(tree, i)
-      push!(nonnodes, i)
+    if !isinternal(tree, i)
+      push!(externals, i)
     end
   end
-  if length(nonnodes) == 0
-    warn("No non-internal nodes detected")
+  if length(externals) == 0
+    warn("No external nodes detected")
   end
-  return nonnodes
+  return externals
 end
 
 
@@ -312,7 +312,7 @@ nodepath(tree::Tree,
 function nodepath(tree::Tree,
                   node::Int64)
   path = [node]
-  while isleaf(tree, path[end]) || isnode(tree, path[end])
+  while isleaf(tree, path[end]) || isinternal(tree, path[end])
     push!(path, parentnode(tree, path[end]))
   end
   return path
@@ -414,7 +414,7 @@ Branch pathway through which a specified node connects to a root
 function branchpath(tree::Tree,
                     node::Int64)
   path = Int64[]
-  while isleaf(tree, node) || isnode(tree, node)
+  while isleaf(tree, node) || isinternal(tree, node)
     push!(path, tree.nodes[node].in[1])
     node = tree.branches[path[end]].source
   end

test/runtests.jl

@@ -8,7 +8,7 @@ branch!(g, 1, 5.0)
 branch!(g, 2, 20.0)
 
 @test length(findroots(g)) == 1
-@test length(findleaves(g)) - 1 == length(findnodes(g))
+@test length(findleaves(g)) - 1 == length(findinternals(g))
 
 for i = 1:length(g.nodes)
   @test length(g.nodes[i].out) <= 2
@@ -22,4 +22,4 @@ end
 @test distance(g, 1, 4) == 30.0
 @test distance(g, 4, 3) == 35.0
 
-@test sum(distance(g)) > 0. 
+@test sum(distance(g)) > 0.