Fisrt step in the obitax rewriting

pkg/obitax/taxonset.go

@@ -1,15 +1,126 @@
 package obitax
 
-type TaxonSet map[int]*TaxNode
+import log "github.com/sirupsen/logrus"
 
-func (set *TaxonSet) Get(i int) *TaxNode {
-	return (*set)[i]
+// TaxonSet represents a collection of taxa within a taxonomy.
+// It holds a mapping of taxon identifiers to their corresponding TaxNode instances,
+// as well as a reference to the associated Taxonomy.
+//
+// Fields:
+//   - set: A map that associates taxon identifiers of type T with their corresponding TaxNode[T] instances.
+//   - taxonomy: A pointer to the Taxonomy[T] instance that this TaxonSet belongs to.
+type TaxonSet struct {
+	set      map[string]*TaxNode
+	nalias   int
+	taxonomy *Taxonomy
 }
 
+// Get retrieves the TaxNode[T] associated with the specified taxon identifier.
+// It returns the TaxNode if it exists in the TaxonSet; otherwise, it returns nil.
+//
+// Parameters:
+//   - i: The taxon identifier of type T for which the TaxNode is to be retrieved.
+//
+// Returns:
+//   - A pointer to the TaxNode[T] associated with the provided identifier, or nil
+//     if no such taxon exists in the set.
+func (set *TaxonSet) Get(i string) *TaxNode {
+	return set.set[i]
+}
+
+// Len returns the number of unique taxa in the TaxonSet.
+// It calculates the count by subtracting the number of aliases from the total
+// number of entries in the set.
+//
+// Returns:
+//   - An integer representing the count of unique taxa in the TaxonSet.
 func (set *TaxonSet) Len() int {
-	return len(*set)
+	return len(set.set) - set.nalias
 }
 
-func (set *TaxonSet) Inserts(taxon *TaxNode) {
-	(*set)[taxon.taxid] = taxon
+// Insert adds a TaxNode[T] to the TaxonSet. If a taxon with the same identifier
+// already exists in the set, it updates the reference. If the existing taxon was
+// an alias, its alias count is decremented.
+//
+// Parameters:
+//   - taxon: A pointer to the TaxNode[T] instance to be added to the TaxonSet.
+//
+// Behavior:
+//   - If a taxon with the same identifier already exists and is different from the
+//     new taxon, the alias count is decremented.
+func (set *TaxonSet) Insert(taxon *TaxNode) {
+	if old := set.set[taxon.id]; old != nil && old.id != taxon.id {
+		set.nalias--
+	}
+	set.set[taxon.id] = taxon
+}
+
+// Taxonomy returns a pointer to the Taxonomy[T] instance that this TaxonSet belongs to.
+//
+// Returns:
+//   - A pointer to the Taxonomy[T] instance that this TaxonSet belongs to
+func (set *TaxonSet) Taxonomy() *Taxonomy {
+	return set.taxonomy
+}
+
+// Alias associates a given alias string with a specified TaxNode in the TaxonSet.
+// It first converts the alias to its corresponding identifier using the Id method.
+// If the original taxon is not part of the taxon set, it logs a fatal error and terminates the program.
+//
+// Parameters:
+//   - alias: A string representing the alias to be associated with the taxon node.
+//   - node: A pointer to the TaxNode[T] instance that the alias will refer to.
+//
+// Behavior:
+//   - If the original taxon corresponding to the alias is not part of the taxon set,
+//     the method will log a fatal error and terminate the program.
+func (set *TaxonSet) Alias(id string, node *TaxNode) {
+	original := set.Get(node.id)
+	if original != nil {
+		log.Fatalf("Original taxon %v is not part of taxon set", id)
+	}
+	set.set[id] = node
+	set.nalias++
+}
+
+// IsAlias checks if the given identifier corresponds to an alias in the TaxonSet.
+// It retrieves the TaxNode associated with the identifier and returns true if the
+// node exists and its identifier is different from the provided identifier; otherwise, it returns false.
+//
+// Parameters:
+//   - id: The identifier of type T to be checked for alias status.
+//
+// Returns:
+//   - A boolean indicating whether the identifier corresponds to an alias in the set.
+func (set *TaxonSet) IsAlias(id string) bool {
+	node := set.Get(id)
+	return node != nil && node.id != id
+}
+
+// IsATaxon checks if the given ID corresponds to a valid taxon node in the TaxonSet.
+// It returns true if the node exists and its ID matches the provided ID; otherwise, it returns false.
+// id corresponding to alias returns false.
+//
+// Parameters:
+//   - id: The identifier of the taxon to check.
+//
+// Returns:
+//   - A boolean indicating whether the specified ID corresponds to a valid taxon node.
+func (set *TaxonSet) IsATaxon(id string) bool {
+	node := set.Get(id)
+	return node != nil && node.id == id
+}
+
+// Contains checks if the TaxonSet contains a taxon node with the specified ID.
+// It returns true if the node exists in the set; otherwise, it returns false.
+// id corresponding to alias or true taxa returns true.
+//
+// Parameters:
+//   - id: The identifier of the taxon to check for presence in the set.
+//
+// Returns:
+//   - A boolean indicating whether the TaxonSet contains a taxon node with the specified ID.
+func (set *TaxonSet) Contains(id string) bool {
+	node := set.Get(id)
+	return node != nil
 }