fix print_lineage internal

docs/src/man/usage.md

@@ -6,7 +6,7 @@
 # Load the package
 julia> using Taxonomy
 
-# Construct a Taxonomy.DB objext from the path to each file
+# Construct a Taxonomy.DB object from the path to each file
 julia> db = Taxonomy.DB("db/nodes.dmp","db/names.dmp")
 Taxonomy.DB("db/nodes.dmp","db/names.dmp")
 
@@ -67,7 +67,7 @@ julia> collect(AbastractTrees.PreOrderDFS(human))
  741158 [subspecies] Homo sapiens subsp. 'Denisova'
  63221 [subspecies] Homo sapiens neanderthalensis
 
-# print subtree
+# Print subtree
 julia> print_tree(Taxon(9604))
 9604 [family] Hominidae
 ├─ 2922387 [no rank] unclassified Hominidae

src/DataAPI.jl

@@ -8,4 +8,4 @@ struct Until{T <: Union{Int, Symbol}}
     last::T
 end
 
-Until(x::AbstractString) = Until(Symbol(x))
+Until(x::AbstractString) = Until(Symbol(x))

src/Taxonomy.jl

@@ -24,4 +24,4 @@ include("rank.jl")
 include("lineage.jl")
 include("lca.jl")
 
-end
+end

src/lca.jl

@@ -13,4 +13,4 @@ end
 function lca(taxa::Taxon...)
     l = getindex(Taxon, taxa...)
     return lca(l)
-end
+end

src/lineage.jl

@@ -174,7 +174,6 @@ This function is useful for converting `Lineage` to `DataFrame`, for example.
 function namedtuple(l::Lineage; fill_by_missing::Bool=false)
     ranks = first.(collect(l.index))
     values = getindex.(Ref(l), ranks)
-
     if fill_by_missing
         values = map(values) do val
             val isa UnclassifiedTaxon ? missing : val
@@ -196,28 +195,18 @@ Print a formatted representation of the lineage to the given `IO` object.
 * `skip::Bool = false` - If `true`, skip printing `UnclassifiedTaxon` and delimiter.
 """
 function print_lineage(io::IO, lineage::Lineage; delim::AbstractString=";", fill::Bool=false, skip::Bool=false)
-    name_line = String[] 
-    for taxon in lineage
-        if typeof(taxon) == UnclassifiedTaxon
-            if skip
-                continue
-            end
+    taxa = collect(lineage)
+    skip && filter!(taxon -> !(taxon isa UnclassifiedTaxon), taxa)
 
-            if fill
-                push!(name_line, name(taxon))
-            else
-                push!(name_line, "")
-            end
+    names = map(taxa) do taxon
+        if taxon isa UnclassifiedTaxon
+            fill ? name(taxon) : ""
         else
-            push!(name_line, name(taxon))
+            name(taxon)
         end
     end
 
-    if isempty(name_line)
-        return nothing
-    end
-
-    l = foldl((x,y) -> x*delim*y, name_line)
+    l = join(names, delim)
     print(io, l)
     return nothing
 end
@@ -240,4 +229,4 @@ AbstractTrees.isdescendant(descendant::Taxon, ancestor::Taxon) = ancestor in Lin
 
 Return `true` if the former taxon is an ancestor of the latter taxon.
 """
-isancestor(ancestor::Taxon, descendant::Taxon) = AbstractTrees.isdescendant(descendant, ancestor)
+isancestor(ancestor::Taxon, descendant::Taxon) = AbstractTrees.isdescendant(descendant, ancestor)

src/rank.jl

@@ -77,4 +77,4 @@ function Base.isless(x1::AbstractTaxon, x2::CanonicalRank)
     end
 end
 
-Base.:<=(x1::AbstractTaxon, x2::CanonicalRank) = Rank(x1) == x2 ? true : x1 < x2
+Base.:<=(x1::AbstractTaxon, x2::CanonicalRank) = Rank(x1) == x2 ? true : x1 < x2

src/taxon.jl

@@ -131,4 +131,4 @@ Base.show(io::IO, taxon::UnclassifiedTaxon) = print(io, "Unclassified [$(rank(ta
 rank(taxon::UnclassifiedTaxon) = taxon.rank
 name(taxon::UnclassifiedTaxon) = taxon.name
 
-source(taxon::UnclassifiedTaxon) = taxon.source
+source(taxon::UnclassifiedTaxon) = taxon.source