Refactoring of some code

pkg/obitax/sequence_predicate.go

@@ -0,0 +1,71 @@
+package obitax
+
+import (
+	log "github.com/sirupsen/logrus"
+
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/goutils"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
+)
+
+func (taxonomy *Taxonomy) IsAValidTaxon(withAutoCorrection ...bool) obiseq.SequencePredicate {
+	deprecatedTaxidsWarning := make(map[int]bool)
+
+	autocorrection := false
+	if len(withAutoCorrection) > 0 {
+		autocorrection = withAutoCorrection[0]
+	}
+
+	f := func(sequence *obiseq.BioSequence) bool {
+		taxid := sequence.Taxid()
+		taxon, err := taxonomy.Taxon(taxid)
+
+		if err == nil && taxon.taxid != taxid {
+			if autocorrection {
+				sequence.SetTaxid(taxon.taxid)
+				log.Printf("Sequence %s : Taxid %d updated with %d", taxid, taxon.taxid)
+			} else {
+				if _, ok := deprecatedTaxidsWarning[taxid]; !ok {
+					deprecatedTaxidsWarning[taxid] = true
+					log.Printf("Taxid %d is deprecated and must be replaced by %d", taxid, taxon.taxid)
+				}
+			}
+		}
+
+		return err == nil
+	}
+
+	return f
+}
+
+// A function that takes a taxonomy and a taxid as arguments and returns a function that takes a
+// pointer to a BioSequence as an argument and returns a boolean.
+func (taxonomy *Taxonomy) IsSubCladeOf(taxid int) obiseq.SequencePredicate {
+	parent, err := taxonomy.Taxon(taxid)
+
+	if err != nil {
+		log.Fatalf("Cannot find taxon : %d (%v)", taxid, err)
+	}
+
+	f := func(sequence *obiseq.BioSequence) bool {
+		taxon, err := taxonomy.Taxon(sequence.Taxid())
+		return err == nil && taxon.IsSubCladeOf(parent)
+	}
+
+	return f
+}
+
+func (taxonomy *Taxonomy) HasRequiredRank(rank string) obiseq.SequencePredicate {
+
+	if !goutils.Contains(taxonomy.RankList(), rank) {
+		log.Fatalf("%s is not a valid rank (allowed ranks are %v)",
+			rank,
+			taxonomy.RankList())
+	}
+
+	f := func(sequence *obiseq.BioSequence) bool {
+		taxon, err := taxonomy.Taxon(sequence.Taxid())
+		return err == nil && taxon.HasRankDefined(rank)
+	}
+
+	return f
+}