Allow retention of internal nodes with only one outbound connection a…

…fter droptips!().

codemeta.json

@@ -4,7 +4,7 @@
  "applicationCategory": "ecology",
  "codeRepository": "https://github.com/EcoJulia/Phylo.jl",
  "dateCreated": "2017-04-21",
- "dateModified": "2024-10-13",
+ "dateModified": "2024-10-14",
  "datePublished": "2018-08-11",
  "description": "Package for creating and manipulating phylogenies in Julia",
  "downloadUrl": "https://github.com/EcoJulia/Phylo.jl/archive/refs/tags/v0.6.0.tar.gz",

src/trim.jl

@@ -13,22 +13,26 @@ include tips or root.
 getinternalnodes(t::AbstractTree) = collect(nodenamefilter(isinternal, t))
 
 """
- droptips!(tree::AbstractTree{OneTree}, tips)
+ droptips!(tree::AbstractTree{OneTree}, tips; keep = false)
 
 Function to drop tips from a phylogenetic tree `tree`, which are found in
-the vector of tips or tip names, `tips`.
+the vector of tips or tip names, `tips`. `keep` determines whether to keep
+internal and root nodes that now only have one child (default is `false`).
+Internal nodes with no children will always be removed.
 """
 function droptips! end
 @traitfn function droptips!(tree::T,
- tips::AbstractVector{N}) where
- {N, RT,
- T <: AbstractTree{OneTree, RT, N}; !MatchNodeType{T, N}}
- return isempty(tips) ? N[] :
- droptips!(tree, [getnode(tree, tip) for tip in tips])
+ tips::AbstractVector{N};
+ keep = false) where
+ {N, RT, NL,
+ T <: AbstractTree{OneTree, RT, NL}; !MatchNodeType{T, N}}
+ return isempty(tips) ? NL[] :
+ droptips!(tree, [getnode(tree, tip) for tip in tips], keep = keep)
 end
 
 @traitfn function droptips!(tree::T,
- tips::AbstractVector{N}) where
+ tips::AbstractVector{N};
+ keep = false) where
  {N, RT, NL,
  T <: AbstractTree{OneTree, RT, NL}; MatchNodeType{T, N}}
  keep_tips = N[tip for tip in getleaves(tree) if tip ∉ tips]
@@ -45,26 +49,28 @@ end
  map(x -> deletenode!(tree, x), nodes)
  end
 
- # Merge internal nodes that no longer have multiple children
- while any(map(x -> length(getchildren(tree, x)) .< 2,
- getinternalnodes(tree)))
- inner_nodes = getinternalnodes(tree)
- remove_nodes = findall(map(x -> length(getchildren(tree, x)) .< 2,
- inner_nodes))
- for i in remove_nodes
- parent = getparent(tree, inner_nodes[i])
- parentbranch = getinbound(tree, inner_nodes[i])
+ if !keep
+ # Merge internal nodes that no longer have multiple children
+ while any(map(x -> length(getchildren(tree, x)) .< 2,
+ getinternalnodes(tree)))
+ inner_nodes = getinternalnodes(tree)
+ remove_nodes = findall(map(x -> length(getchildren(tree, x)) .< 2,
+ inner_nodes))
+ for i in remove_nodes
+ parent = getparent(tree, inner_nodes[i])
+ parentbranch = getinbound(tree, inner_nodes[i])
 
- child = getchildren(tree, inner_nodes[i])[1]
- childbranch = getoutbounds(tree, getnode(tree, inner_nodes[i]))[1]
+  child = getchildren(tree, inner_nodes[i])[1]
+  childbranch = getoutbounds(tree, getnode(tree, inner_nodes[i]))[1]
 
- len = distance(tree, parent, child)
+  len = distance(tree, parent, child)
 
- deletebranch!(tree, parentbranch)
- deletebranch!(tree, childbranch)
- deletenode!(tree, inner_nodes[i])
+  deletebranch!(tree, parentbranch)
+  deletebranch!(tree, childbranch)
+  deletenode!(tree, inner_nodes[i])
 
- createbranch!(tree, parent, child, len)
+ createbranch!(tree, parent, child, len)
+ end
  end
  end