Compute costs matrix from phylogenetic tree and reorganise sources

src/classification.jl

@@ -0,0 +1,50 @@
+using Unicode
+
+mutable struct Classification
+    type::Symbol
+    name::Symbol
+    bio::String
+    children::Vector{Classification}
+    parent::Classification
+
+    function Classification(classif::Dict{String, Any})
+        children = [Classification(d) for d in get(classif, "children", [])]
+        type = Symbol(Unicode.normalize(classif["type"], casefold=true, stripmark=true))
+        name = Symbol(Unicode.normalize(classif["name"], casefold=true, stripmark=true))
+        classif = new(type, name, get(classif, "bio", ""), children)
+        for child in children
+            child.parent = classif
+        end
+        classif
+    end
+end
+
+function Base.show(io::IO, clf::Classification)
+    if length(clf.children) < 2
+        childrentext = " with $(length(clf.children)) child"
+    else
+        childrentext = " with $(length(clf.children)) children"
+    end
+    biotext = ""
+    if clf.bio != ""
+        biotext = " ($(clf.bio))"
+    end
+    print("Classification(", clf.type, " ", clf.name, biotext, childrentext, ")")
+end
+
+function getfirstparent(name::Symbol, classification::Classification)
+    if classification.name == name
+        parent = classification
+        while parent.parent.name != :god
+            parent = parent.parent
+        end
+        return parent
+    else
+        for child in classification.children
+            parent = getfirstparent(name, child)
+            if !isnothing(parent)
+                return parent
+            end
+        end
+    end
+end