Fisrt functional version

pkg/obiseq/taxonomy_classifier.go

@@ -0,0 +1,79 @@
+package obiseq
+
+import (
+	"git.metabarcoding.org/obitools/obitools4/obitools4/pkg/obitax"
+	log "github.com/sirupsen/logrus"
+)
+
+// TaxonomyClassifier is a function that creates a new instance of the BioSequenceClassifier
+// for taxonomic classification based on a given taxonomic rank, taxonomy, and abort flag.
+//
+// Parameters:
+// - taxonomicRank: the taxonomic rank to classify the sequences at.
+// - taxonomy: the taxonomy object used for classification.
+// - abortOnMissing: a flag indicating whether to abort if a taxon is missing in the taxonomy.
+//
+// Return:
+// - *obiseq.BioSequenceClassifier: the new instance of the BioSequenceClassifier.
+func TaxonomyClassifier(taxonomicRank string,
+	taxonomy *obitax.Taxonomy,
+	abortOnMissing bool) *BioSequenceClassifier {
+
+	keys := make(map[*obitax.TaxNode]int)
+	codes := make([]*obitax.TaxNode, 1)
+	codes[0] = nil
+	keys[nil] = 0
+
+	code := func(sequence *BioSequence) int {
+		taxon := sequence.Taxon(taxonomy)
+		if taxon != nil {
+			ttaxon := taxon.TaxonAtRank(taxonomicRank)
+			if abortOnMissing && ttaxon == nil {
+				log.Fatalf("Taxon at rank %s not found in taxonomy for taxid %d", taxonomicRank, taxon.String())
+			}
+		} else {
+			if abortOnMissing {
+				log.Fatalf("Sequence %s: Taxid %s not found in taxonomy",
+					sequence.Id(),
+					sequence.Taxid())
+			}
+			taxon = nil
+		}
+
+		k, ok := keys[taxon.Node]
+
+		if ok {
+			return k
+		}
+
+		k = len(codes)
+		keys[taxon.Node] = k
+		codes = append(codes, taxon.Node)
+
+		return k
+	}
+
+	value := func(k int) string {
+		taxon := codes[k]
+		return taxon.ScientificName()
+	}
+
+	reset := func() {
+		keys = make(map[*obitax.TaxNode]int)
+		codes = make([]*obitax.TaxNode, 1)
+		codes[0] = nil
+		keys[nil] = 0
+	}
+
+	clone := func() *BioSequenceClassifier {
+		return TaxonomyClassifier(taxonomicRank, taxonomy, abortOnMissing)
+	}
+
+	c := BioSequenceClassifier{
+		Code:  code,
+		Value: value,
+		Reset: reset,
+		Clone: clone,
+		Type:  "TaxonomyClassifier"}
+	return &c
+}