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

.gitignore

@@ -118,3 +118,12 @@ doc/book/wolf_data/Release-253/ncbitaxo/readme.txt
 doc/book/results/toto.tasta
 sample/.DS_Store
 GO
+ncbitaxo/citations.dmp
+ncbitaxo/delnodes.dmp
+ncbitaxo/division.dmp
+ncbitaxo/gc.prt
+ncbitaxo/gencode.dmp
+ncbitaxo/merged.dmp
+ncbitaxo/names.dmp
+ncbitaxo/nodes.dmp
+ncbitaxo/readme.txt

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 {
+	if node.HasScientificName() {
 		return fmt.Sprintf("%s:%v [%s]",
 			taxonomyCode,
 			*node.id,
 			node.ScientificName())
+	}
+
+	return fmt.Sprintf("%s:%v",
+		taxonomyCode,
+		*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),
 	}
 }
 

pkg/obitools/obifind/iterator.go

@@ -1,7 +1,6 @@
 package obifind
 
 import (
-	"bytes"
 	"fmt"
 
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
@@ -22,11 +21,7 @@ func IFilterRankRestriction() func(*obitax.ITaxon) *obitax.ITaxon {
 }
 
 func ITaxonNameMatcher() (func(string) *obitax.ITaxon, error) {
-	taxonomy, err := CLILoadSelectedTaxonomy()
+	taxonomy := obitax.DefaultTaxonomy()
-
-	if err != nil {
-		return nil, err
-	}
 
 	fun := func(name string) *obitax.ITaxon {
 		return taxonomy.IFilterOnName(name, __fixed_pattern__)
@@ -53,27 +48,25 @@ func ITaxonRestrictions() (func(*obitax.ITaxon) *obitax.ITaxon, error) {
 }
 
 func TaxonAsString(taxon *obitax.Taxon, pattern string) string {
-	text := taxon.ScientificName()
+	// var text string
+	// if __with_path__ {
+	// 	var bf bytes.Buffer
+	// 	path := taxon.Path()
 
-	if __with_path__ {
+	// 	bf.WriteString(path.Get(path.Len() - 1).ScientificName())
-		var bf bytes.Buffer
-		path := taxon.Path()
 
-		bf.WriteString(path.Get(path.Len() - 1).ScientificName())
+	// 	for i := path.Len() - 2; i >= 0; i-- {
+	// 		fmt.Fprintf(&bf, ":%s", path.Get(i).ScientificName())
+	// 	}
 
-		for i := path.Len() - 2; i >= 0; i-- {
+	// 	text = bf.String()
-			fmt.Fprintf(&bf, ":%s", path.Get(i).ScientificName())
+	// }
-		}
 
-		text = bf.String()
+	return fmt.Sprintf("%-20s | %10s | %10s | %-20s",
-	}
-
-	return fmt.Sprintf("%-20s | %10s | %10s | %-20s | %s",
 		pattern,
 		taxon.String(),
 		taxon.Parent().String(),
-		taxon.Rank(),
+		taxon.Rank())
-		text)
 }
 
 func TaxonWriter(itaxa *obitax.ITaxon, pattern string) {

pkg/obitools/obifind/options.go

@@ -1,17 +1,14 @@
 package obifind
 
 import (
-	"errors"
+	"fmt"
 
-	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiformats/ncbitaxdump"
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obioptions"
 	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
 	"github.com/DavidGamba/go-getoptions"
 )
 
-var __taxdump__ = ""
-var __alternative_name__ = false
 var __rank_list__ = false
-var __selected_taxonomy__ = (*obitax.Taxonomy)(nil)
 var __taxonomical_restriction__ = make([]string, 0)
 
 var __fixed_pattern__ = false
@@ -20,24 +17,6 @@ var __taxid_path__ = "NA"
 var __taxid_sons__ = "NA"
 var __restrict_rank__ = ""
 
-func LoadTaxonomyOptionSet(options *getoptions.GetOpt, required, alternatiive bool) {
-	if required {
-		options.StringVar(&__taxdump__, "taxdump", "",
-			options.Alias("t"),
-			options.Required(),
-			options.Description("Points to the directory containing the NCBI Taxonomy database dump."))
-	} else {
-		options.StringVar(&__taxdump__, "taxdump", "",
-			options.Alias("t"),
-			options.Description("Points to the directory containing the NCBI Taxonomy database dump."))
-	}
-	if alternatiive {
-		options.BoolVar(&__alternative_name__, "alternative-names", false,
-			options.Alias("a"),
-			options.Description("Enable the search on all alternative names and not only scientific names."))
-	}
-}
-
 func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {
 	options.BoolVar(&__rank_list__, "rank-list", false,
 		options.Alias("l"),
@@ -48,31 +27,23 @@ func FilterTaxonomyOptionSet(options *getoptions.GetOpt) {
 		options.Description("Restrict output to some subclades."))
 }
 
-func CLISelectedNCBITaxDump() string {
-	return __taxdump__
-}
-
-func CLIHasSelectedTaxonomy() bool {
-	return __taxdump__ != ""
-}
-
-func CLIAreAlternativeNamesSelected() bool {
-	return __alternative_name__
-}
-
 func CLITaxonomicalRestrictions() (*obitax.TaxonSet, error) {
-	taxonomy, err := CLILoadSelectedTaxonomy()
+	taxonomy := obitax.DefaultTaxonomy()
 
-	if err != nil {
+	if taxonomy == nil {
-		return nil, err
+		return nil, fmt.Errorf("no taxonomy loaded")
 	}
 
 	ts := taxonomy.NewTaxonSet()
 	for _, taxid := range __taxonomical_restriction__ {
 		tx := taxonomy.Taxon(taxid)
 
-		if err != nil {
+		if tx == nil {
-			return nil, err
+			return nil, fmt.Errorf(
+				"cannot find taxon %s in taxonomy %s",
+				taxid,
+				taxonomy.Name(),
+			)
 		}
 
 		ts.InsertTaxon(tx)
@@ -81,24 +52,8 @@ func CLITaxonomicalRestrictions() (*obitax.TaxonSet, error) {
 	return ts, nil
 }
 
-func CLILoadSelectedTaxonomy() (*obitax.Taxonomy, error) {
-	if CLISelectedNCBITaxDump() != "" {
-		if __selected_taxonomy__ == nil {
-			var err error
-			__selected_taxonomy__, err = ncbitaxdump.LoadNCBITaxDump(CLISelectedNCBITaxDump(),
-				!CLIAreAlternativeNamesSelected())
-			if err != nil {
-				return nil, err
-			}
-		}
-		return __selected_taxonomy__, nil
-	}
-
-	return nil, errors.New("no NCBI taxdump selected using option -t|--taxdump")
-}
-
 func OptionSet(options *getoptions.GetOpt) {
-	LoadTaxonomyOptionSet(options, true, true)
+	obioptions.LoadTaxonomyOptionSet(options, true, true)
 	FilterTaxonomyOptionSet(options)
 	options.BoolVar(&__fixed_pattern__, "fixed", false,
 		options.Alias("F"),