Changes to be committed:

modified:   cmd/obitools/obitag/main.go
	modified:   cmd/obitools/obitag2/main.go
	modified:   go.mod
	modified:   go.sum
	modified:   pkg/obiformats/ncbitaxdump/read.go
	modified:   pkg/obioptions/version.go
	modified:   pkg/obiseq/attributes.go
	modified:   pkg/obiseq/taxonomy_lca.go
	modified:   pkg/obiseq/taxonomy_methods.go
	modified:   pkg/obiseq/taxonomy_predicate.go
	modified:   pkg/obitax/inner.go
	modified:   pkg/obitax/lca.go
	new file:   pkg/obitax/taxid.go
	modified:   pkg/obitax/taxon.go
	modified:   pkg/obitax/taxonomy.go
	modified:   pkg/obitax/taxonslice.go
	modified:   pkg/obitools/obicleandb/obicleandb.go
	modified:   pkg/obitools/obigrep/options.go
	modified:   pkg/obitools/obilandmark/obilandmark.go
	modified:   pkg/obitools/obilandmark/options.go
	modified:   pkg/obitools/obirefidx/famlilyindexing.go
	modified:   pkg/obitools/obirefidx/geomindexing.go
	modified:   pkg/obitools/obirefidx/obirefidx.go
	modified:   pkg/obitools/obirefidx/options.go
	modified:   pkg/obitools/obitag/obigeomtag.go
	modified:   pkg/obitools/obitag/obitag.go
	modified:   pkg/obitools/obitag/options.go
	modified:   pkg/obiutils/strings.go

pkg/obitax/taxid.go

@@ -0,0 +1,60 @@
+package obitax
+
+import (
+	"fmt"
+	"strconv"
+
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obiutils"
+)
+
+// Taxid represents a taxonomic identifier as a pointer to a string.
+type Taxid *string
+
+// TaxidFactory is a factory for creating Taxid instances from strings and integers.
+type TaxidFactory struct {
+	inner    *InnerString
+	code     string
+	alphabet obiutils.AsciiSet
+}
+
+// NewTaxidFactory creates and returns a new instance of TaxidFactory.
+func NewTaxidFactory(code string, alphabet obiutils.AsciiSet) *TaxidFactory {
+	return &TaxidFactory{
+		inner:    NewInnerString(),
+		code:     code + ":",
+		alphabet: alphabet,
+	}
+	// Initialize and return a new TaxidFactory.
+}
+
+// FromString converts a string representation of a taxonomic identifier into a Taxid.
+// It extracts the relevant part of the string after the first colon (':') if present.
+func (f *TaxidFactory) FromString(taxid string) (Taxid, error) {
+	taxid = obiutils.AsciiSpaceSet.TrimLeft(taxid)
+	part1, part2 := obiutils.SplitInTwo(taxid, ':')
+	if len(part2) == 0 {
+		taxid = part1
+	} else {
+		if part1 != f.code {
+			return nil, fmt.Errorf("taxid %s string does not start with taxonomy code %s", taxid, f.code)
+		}
+		taxid = part2
+	}
+
+	taxid, err := f.alphabet.FirstWord(taxid) // Get the first word from the input string.
+
+	if err != nil {
+		return nil, err
+	}
+
+	// Return a new Taxid by innerizing the extracted taxid string.
+	rep := Taxid(f.inner.Innerize(taxid))
+	return rep, nil
+}
+
+// FromInt converts an integer taxonomic identifier into a Taxid.
+// It first converts the integer to a string and then innerizes it.
+func (f *TaxidFactory) FromInt(taxid int) (Taxid, error) {
+	s := strconv.Itoa(taxid)        // Convert the integer to a string.
+	return f.inner.Innerize(s), nil // Return a new Taxid by innerizing the string.
+}