A first prototype for the space of sequences

Former-commit-id: 07dc6ef044b5b6a6fb45dc2acb01dffe71a96195

pkg/obitools/obilandmark/obilandmark.go

@@ -10,6 +10,9 @@ import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obioptions"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiseq"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obistats"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitax"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obirefidx"
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obiutils"
 	"github.com/schollz/progressbar/v3"
 	log "github.com/sirupsen/logrus"
@@ -103,14 +106,14 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
 	library := iterator.Load()
 
 	library_size := len(library)
-	n_landmark := NCenter()
+	n_landmark := CLINCenter()
 
 	landmark_idx := obistats.SampleIntWithoutReplacement(n_landmark, library_size)
 	log.Infof("Library contains %d sequence", len(library))
 
 	var seqworld obiutils.Matrix[float64]
 
-	for loop := 0; loop < 5; loop++ {
+	for loop := 0; loop < 2; loop++ {
 		sort.IntSlice(landmark_idx).Sort()
 		log.Debugf("Selected indices : %v", landmark_idx)
 
@@ -154,14 +157,52 @@ func CLISelectLandmarkSequences(iterator obiiter.IBioSequence) obiiter.IBioSeque
 	}
 
 	classes := obistats.AssignToClass(&seqworld, &initialCenters)
+
 	for i, seq := range library {
-		seq.SetAttribute("landmark_coord", seqworld[i])
+		ic, _ := obiutils.InterfaceToIntSlice(seqworld[i])
+		seq.SetCoordinate(ic)
 		seq.SetAttribute("landmark_class", classes[i])
 		if i, ok := seq_landmark[i]; ok {
 			seq.SetAttribute("landmark_id", i)
 		}
 	}
 
+	if obifind.CLIHasSelectedTaxonomy() {
+		taxo, err := obifind.CLILoadSelectedTaxonomy()
+		if err != nil {
+			log.Fatal(err)
+		}
+
+		taxa := make(obitax.TaxonSet, len(library))
+
+		for i, seq := range library {
+			taxa[i], err = taxo.Taxon(seq.Taxid())
+			if err != nil {
+				log.Fatal(err)
+			}
+		}
+
+		pbopt := make([]progressbar.Option, 0, 5)
+		pbopt = append(pbopt,
+			progressbar.OptionSetWriter(os.Stderr),
+			progressbar.OptionSetWidth(15),
+			progressbar.OptionShowCount(),
+			progressbar.OptionShowIts(),
+			progressbar.OptionSetDescription("[Sequence Indexing]"),
+		)
+
+		bar := progressbar.NewOptions(len(library), pbopt...)
+
+		for i, seq := range library {
+			idx := obirefidx.GeomIndexSesquence(i, library, &taxa, taxo)
+			seq.SetOBITagGeomRefIndex(idx)
+
+			if i%10 == 0 {
+				bar.Add(10)
+			}
+		}
+	}
+
 	return obiiter.IBatchOver(library, obioptions.CLIBatchSize())
 
 }

pkg/obitools/obilandmark/options.go

@@ -2,28 +2,37 @@ package obilandmark
 
 import (
 	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obiconvert"
+	"git.metabarcoding.org/lecasofts/go/obitools/pkg/obitools/obifind"
 	"github.com/DavidGamba/go-getoptions"
 )
 
 var _nCenter = 200
 
-// ObilandmarkOptionSet sets the options for Obilandmark.
+// LandmarkOptionSet sets the options for Obilandmark.
 //
 // options: a pointer to the getoptions.GetOpt struct.
 // Return type: none.
-func ObilandmarkOptionSet(options *getoptions.GetOpt) {
+func LandmarkOptionSet(options *getoptions.GetOpt) {
 
 	options.IntVar(&_nCenter, "center", _nCenter,
 		options.Alias("n"),
-		options.Description("Maximum numbers of differences between two variant sequences (default: %d)."))
+		options.Description("Number of landmark sequences to be selected."))
 }
 
+// OptionSet is a function that sets the options for the GetOpt struct.
+//
+// It takes a pointer to a GetOpt struct as its parameter and does not return anything.
 func OptionSet(options *getoptions.GetOpt) {
 	obiconvert.InputOptionSet(options)
 	obiconvert.OutputOptionSet(options)
-	ObilandmarkOptionSet(options)
+	obifind.LoadTaxonomyOptionSet(options, false, false)
+	LandmarkOptionSet(options)
 }
 
-func NCenter() int {
+// CLINCenter returns desired number of centers as specified by user.
+//
+// No parameters.
+// Returns an integer value.
+func CLINCenter() int {
 	return _nCenter
 }