Changes to be committed:

modified:   .gitignore
	new file:   pkg/obitax/default_taxonomy.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonnode.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonset.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obifind/iterator.go
	modified:   pkg/obitools/obifind/options.go

pkg/obitax/default_taxonomy.go

@@ -0,0 +1,29 @@
+package obitax
+
+import "log"
+
+var __defaut_taxonomy__ *Taxonomy
+
+func (taxonomy *Taxonomy) SetAsDefault() {
+	__defaut_taxonomy__ = taxonomy
+}
+
+func (taxonomy *Taxonomy) OrDefault(panicOnNil bool) *Taxonomy {
+	if taxonomy == nil {
+		return __defaut_taxonomy__
+	}
+
+	if panicOnNil && taxonomy == nil {
+		log.Panic("Cannot deal with nil taxonomy")
+	}
+
+	return taxonomy
+}
+
+func IsDefaultTaxonomyDefined() bool {
+	return __defaut_taxonomy__ != nil
+}
+
+func DefaultTaxonomy() *Taxonomy {
+	return __defaut_taxonomy__
+}

pkg/obitax/taxon.go

@@ -30,6 +30,10 @@ func (taxon *Taxon) String() string {
 	return taxon.Node.String(taxon.Taxonomy.code)
 }
 
+func (taxon *Taxon) HasScientificName() bool {
+	return taxon != nil && taxon.Node.HasScientificName()
+}
+
 // ScientificName returns the scientific name of the Taxon.
 // It retrieves the scientific name from the underlying TaxNode associated with the taxon.
 //

pkg/obitax/taxonnode.go

@@ -35,10 +35,17 @@ type TaxNode struct {
 // Returns:
 //   - A formatted string representing the TaxNode in the form "taxonomyCode:id [scientificName]".
 func (node *TaxNode) String(taxonomyCode string) string {
-	return fmt.Sprintf("%s:%v [%s]",
+	if node.HasScientificName() {
+		return fmt.Sprintf("%s:%v [%s]",
+			taxonomyCode,
+			*node.id,
+			node.ScientificName())
+	}
+
+	return fmt.Sprintf("%s:%v",
 		taxonomyCode,
-		*node.id,
-		node.ScientificName())
+		*node.id)
+
 }
 
 // Id returns the unique identifier of the TaxNode.
@@ -59,6 +66,10 @@ func (node *TaxNode) ParentId() *string {
 	return node.parent
 }
 
+func (node *TaxNode) HasScientificName() bool {
+	return node != nil && node.scientificname != nil
+}
+
 // ScientificName returns the scientific name of the TaxNode.
 // It dereferences the pointer to the scientific name string associated with the taxon node.
 //

pkg/obitax/taxonomy.go

@@ -86,6 +86,12 @@ func NewTaxonomy(name, code, codeCharacters string) *Taxonomy {
 //   - The taxon identifier as a *string corresponding to the provided taxid.
 //   - An error if the taxid is not valid or cannot be converted.
 func (taxonomy *Taxonomy) Id(taxid string) (*string, error) {
+	taxonomy = taxonomy.OrDefault(false)
+
+	if taxonomy == nil {
+		return nil, fmt.Errorf("Cannot extract Id from nil Taxonomy")
+	}
+
 	matches := taxonomy.matcher.FindStringSubmatch(taxid)
 
 	if matches == nil {
@@ -106,6 +112,8 @@ func (taxonomy *Taxonomy) Id(taxid string) (*string, error) {
 //   - A string representing the taxon node in the format "taxonomyCode:id [scientificName]",
 //     or an error if the taxon node with the specified ID does not exist in the taxonomy.
 func (taxonomy *Taxonomy) TaxidSting(id string) (string, error) {
+	taxonomy = taxonomy.OrDefault(false)
+
 	pid, err := taxonomy.Id(id)
 
 	if err != nil {
@@ -132,6 +140,8 @@ func (taxonomy *Taxonomy) TaxidSting(id string) (string, error) {
 //   - A pointer to the Taxon instance associated with the provided taxid.
 //   - If the taxid is unknown, the method will log a fatal error.
 func (taxonomy *Taxonomy) Taxon(taxid string) *Taxon {
+	taxonomy = taxonomy.OrDefault(false)
+
 	id, err := taxonomy.Id(taxid)
 
 	if err != nil {
@@ -155,6 +165,12 @@ func (taxonomy *Taxonomy) Taxon(taxid string) *Taxon {
 // Returns:
 //   - A pointer to the TaxonSet representing the collection of taxon nodes in the taxonomy.
 func (taxonomy *Taxonomy) AsTaxonSet() *TaxonSet {
+	taxonomy = taxonomy.OrDefault(false)
+
+	if taxonomy == nil {
+		return nil
+	}
+
 	return taxonomy.nodes
 }
 
@@ -164,6 +180,12 @@ func (taxonomy *Taxonomy) AsTaxonSet() *TaxonSet {
 // Returns:
 //   - An integer representing the total count of taxa in the taxonomy.
 func (taxonomy *Taxonomy) Len() int {
+	taxonomy = taxonomy.OrDefault(false)
+
+	if taxonomy == nil {
+		return 0
+	}
+
 	return taxonomy.nodes.Len()
 }
 
@@ -181,14 +203,14 @@ func (taxonomy *Taxonomy) Len() int {
 //   - A pointer to the newly created Taxon instance.
 //   - An error if the taxon cannot be added (e.g., it already exists and replace is false).
 func (taxonomy *Taxonomy) AddTaxon(taxid, parent string, rank string, isRoot bool, replace bool) (*Taxon, error) {
+	taxonomy = taxonomy.OrDefault(false)
 
 	parentid, perr := taxonomy.Id(parent)
-	id, err := taxonomy.Id(taxid)
-
 	if perr != nil {
 		return nil, fmt.Errorf("error in parsing parent taxid %s: %v", parent, perr)
 	}
 
+	id, err := taxonomy.Id(taxid)
 	if err != nil {
 		return nil, fmt.Errorf("error in parsing taxid %s: %v", taxid, err)
 	}
@@ -228,6 +250,8 @@ func (taxonomy *Taxonomy) AddTaxon(taxid, parent string, rank string, isRoot boo
 //   - A pointer to the Taxon associated with the oldtaxid.
 //   - An error if the alias cannot be added (e.g., the old taxon does not exist).
 func (taxonomy *Taxonomy) AddAlias(newtaxid, oldtaxid string, replace bool) (*Taxon, error) {
+	taxonomy = taxonomy.OrDefault(false)
+
 	newid, err := taxonomy.Id(newtaxid)
 
 	if err != nil {
@@ -261,6 +285,12 @@ func (taxonomy *Taxonomy) AddAlias(newtaxid, oldtaxid string, replace bool) (*Ta
 // Returns:
 //   - A slice of strings containing the ranks of the taxa.
 func (taxonomy *Taxonomy) RankList() []string {
+	taxonomy = taxonomy.OrDefault(false)
+
+	if taxonomy == nil {
+		return make([]string, 0)
+	}
+
 	return taxonomy.ranks.Slice()
 }
 
@@ -270,6 +300,12 @@ func (taxonomy *Taxonomy) RankList() []string {
 // Returns:
 //   - A pointer to the map that indexes taxa in the taxonomy.
 func (taxonomy *Taxonomy) Index() *map[*string]*TaxonSet {
+	taxonomy = taxonomy.OrDefault(false)
+
+	if taxonomy == nil {
+		return nil
+	}
+
 	return &(taxonomy.index)
 }
 
@@ -278,6 +314,7 @@ func (taxonomy *Taxonomy) Index() *map[*string]*TaxonSet {
 // Returns:
 //   - A string representing the name of the taxonomy.
 func (taxonomy *Taxonomy) Name() string {
+	taxonomy = taxonomy.OrDefault(true)
 	return taxonomy.name
 }
 
@@ -286,6 +323,7 @@ func (taxonomy *Taxonomy) Name() string {
 // Returns:
 //   - A string representing the unique code of the taxonomy.
 func (taxonomy *Taxonomy) Code() string {
+	taxonomy = taxonomy.OrDefault(true)
 	return taxonomy.code
 }
 
@@ -295,6 +333,7 @@ func (taxonomy *Taxonomy) Code() string {
 // Parameters:
 //   - root: A pointer to the Taxon instance to be set as the root.
 func (taxonomy *Taxonomy) SetRoot(root *Taxon) {
+	taxonomy = taxonomy.OrDefault(true)
 	taxonomy.root = root.Node
 }
 
@@ -304,6 +343,8 @@ func (taxonomy *Taxonomy) SetRoot(root *Taxon) {
 // Returns:
 //   - A pointer to the Taxon instance representing the root of the taxonomy.
 func (taxonomy *Taxonomy) Root() *Taxon {
+	taxonomy = taxonomy.OrDefault(true)
+
 	return &Taxon{
 		Taxonomy: taxonomy,
 		Node:     taxonomy.root,
@@ -315,5 +356,6 @@ func (taxonomy *Taxonomy) Root() *Taxon {
 // Returns:
 //   - A boolean indicating whether the Taxonomy has a root node (true) or not (false).
 func (taxonomy *Taxonomy) HasRoot() bool {
-	return taxonomy.root != nil
+	taxonomy = taxonomy.OrDefault(false)
+	return taxonomy != nil && taxonomy.root != nil
 }

pkg/obitax/taxonset.go

@@ -32,7 +32,7 @@ func (taxonomy *Taxonomy) NewTaxonSet() *TaxonSet {
 	return &TaxonSet{
 		set:      make(map[*string]*TaxNode),
 		nalias:   0,
-		taxonomy: taxonomy,
+		taxonomy: taxonomy.OrDefault(true),
 	}
 }
 
@@ -68,6 +68,9 @@ func (set *TaxonSet) Get(id *string) *Taxon {
 // Returns:
 //   - An integer representing the count of unique taxa in the TaxonSet.
 func (set *TaxonSet) Len() int {
+	if set == nil {
+		return 0
+	}
 	return len(set.set) - set.nalias
 }
 
@@ -81,11 +84,17 @@ func (set *TaxonSet) Len() int {
 // 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(node *TaxNode) {
+func (set *TaxonSet) Insert(node *TaxNode) *TaxonSet {
+	if set == nil {
+		log.Panic("Cannot insert node into nil TaxonSet")
+	}
+
 	if old := set.set[node.id]; old != nil && old.id != node.id {
 		set.nalias--
 	}
 	set.set[node.id] = node
+
+	return set
 }
 
 // InsertTaxon adds a Taxon to the TaxonSet. It verifies that the Taxon belongs
@@ -94,7 +103,11 @@ func (set *TaxonSet) Insert(node *TaxNode) {
 //
 // Parameters:
 //   - taxon: A pointer to the Taxon instance to be added to the TaxonSet.
-func (set *TaxonSet) InsertTaxon(taxon *Taxon) {
+func (set *TaxonSet) InsertTaxon(taxon *Taxon) *TaxonSet {
+	if set == nil {
+		set = taxon.Taxonomy.NewTaxonSet()
+	}
+
 	if set.taxonomy != taxon.Taxonomy {
 		log.Fatalf(
 			"Cannot insert taxon %s into taxon set belonging to %s taxonomy",
@@ -102,6 +115,8 @@ func (set *TaxonSet) InsertTaxon(taxon *Taxon) {
 			set.taxonomy.name,
 		)
 	}
+
+	return set.Insert(taxon.Node)
 }
 
 // Taxonomy returns a pointer to the Taxonomy instance that this TaxonSet belongs to.
@@ -109,6 +124,10 @@ func (set *TaxonSet) InsertTaxon(taxon *Taxon) {
 // Returns:
 //   - A pointer to the Taxonomy instance that this TaxonSet belongs to.
 func (set *TaxonSet) Taxonomy() *Taxonomy {
+	if set == nil {
+		return nil
+	}
+
 	return set.taxonomy
 }
 
@@ -124,6 +143,10 @@ func (set *TaxonSet) Taxonomy() *Taxonomy {
 //   - 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, taxon *Taxon) {
+	if set == nil {
+		log.Panic("Cannot add alias to a nil TaxonSet")
+	}
+
 	original := set.Get(taxon.Node.id)
 	if original == nil {
 		log.Fatalf("Original taxon %v is not part of taxon set", id)

pkg/obitax/taxonslice.go

@@ -40,7 +40,7 @@ type TaxonSlice struct {
 func (taxonomy *Taxonomy) NewTaxonSlice(size, capacity int) *TaxonSlice {
 	return &TaxonSlice{
 		slice:    make([]*TaxNode, size, capacity),
-		taxonomy: taxonomy,
+		taxonomy: taxonomy.OrDefault(true),
 	}
 }