add name2taxids

src/Taxonomy.jl

@@ -10,7 +10,7 @@ export current_db, current_db!,
        AbstractTaxon, Taxon, UnclassifiedTaxon,
        Lineage, isreformatted,
        print_tree,
-       taxid, name, rank, parent, get, children, lca, source,
+       taxid, name, rank, parent, get, name2taxids, children, lca, source,
        reformat, namedtuple, print_lineage, isdescendant, isancestor, 
        All, Between, Cols,
        From, Until,

src/taxon.jl

@@ -15,24 +15,18 @@ struct Taxon <: AbstractTaxon
         return new(idx, db)
     end
 end
+Taxon(idx::Int) = Taxon(idx, current_db())
 
 """
-    Taxon(name::AbstractString, db::Taxonomy.DB)
-    Taxon(name::AbstractString)
+    name2taxids(name::AbstractString, db::Taxonomy.DB)
+    name2taxids(name::AbstractString)
 
-Construct a `Taxon` from its `name`. `name` must match to the scientific name exactly.
-Throws an error if there is no match or multiple candidates.
+Return a `Vector` of taxid from its `name`. `name` must match to the scientific name exactly.
+If multiple hits are found, return a multi-element `Vector`. If not, 1- or 0-element `Vector`. 
 Omitting `db` automatically calls `current_db()`, which is usually the database that was last created.
 """
-function Taxon(name::String, db::DB)
-    taxid_canditates = findall(isequal(name), db.names)
-    length(taxid_canditates) == 0 && error("There is no candidate for $name")
-    length(taxid_canditates) == 1 && return Taxon(only(taxid_canditates), db)
-    length(taxid_canditates) > 1 && error("There are several candidates for $name. Candidates: $taxid_canditates")
-end 
-
-Taxon(idx::Int) = Taxon(idx, current_db())
-Taxon(name::String) = Taxon(name, current_db())
+name2taxids(name::AbstractString, db::DB) = findall(isequal(name), db.names)
+name2taxids(name::AbstractString) = name2taxids(name, current_db())
 
 """
     taxid(taxon::Taxon)

test/runtests.jl

@@ -23,7 +23,7 @@ db = Taxonomy.DB("db/nodes.dmp", "db/names.dmp")
     @test @inferred(sprint(io -> show(io, human))) == "9606 [species] Homo sapiens"
 
     @test @inferred(Nothing, get(db, 9606, nothing)) == human
-    @test Taxon("Homo", db) == Taxon(9605, db)
+    @test @inferred(name2taxids("Homo", db)) == [9605]
 
     @test @inferred(Nothing, AbstractTrees.parent(human)) == Taxon(9605,db)
     @test @inferred(Set(children(human))) == Set([Taxon(63221,db), Taxon(741158, db)])