Remove debug

cmd/ltt.go

@@ -93,8 +93,6 @@ Image width and height can be specified (in inch) with --image-width and --image
 
 		if lttoutimagefile != "none" {
 			// Save the plot to a PNG file.
-			fmt.Println(font.Length(float64(lttoutimagewidth)) * vg.Inch)
-			fmt.Println(font.Length(float64(lttoutimageheight)) * vg.Inch)
 			if err = p.Save(font.Length(lttoutimagewidth)*vg.Inch, font.Length(lttoutimageheight)*vg.Inch, lttoutimagefile); err != nil {
 				io.LogError(err)
 				return

tree/algo.go

@@ -965,9 +965,17 @@ type LTTData struct {
 // LTTData describes a Lineage to Time data point
 func (t *Tree) LTT() (lttdata []LTTData) {
 	var lttdatadup []LTTData
+	var dists []float64
+	var err error
 
 	// We compute distance from root to all nodes
-	dists := t.NodeRootDistance()
+	// If the field [&date=] exists, then takes it
+	// Otherwise, computes the distance to the root
+	if dists, err = t.NodeDates(); err != nil {
+		io.LogError(err)
+		dists = t.NodeRootDistance()
+	}
+
 	// This initializes
 	lttdatadup = make([]LTTData, len(dists))
 	// Version with one point per x, already summed up

tree/tree.go

@@ -953,6 +953,43 @@ func (t *Tree) computeDepthUnRooted() {
 	}
 }
 
+// Get Node dates
+// Returns a slice of float correspsponding to all node dates (internal and external)
+// Node IDs are their index in the slice.
+// If one node does not have date or a malformed date, returns an error
+func (t *Tree) NodeDates() (ndates []float64, err error) {
+	var date float64
+	var pattern *regexp.Regexp
+	var matches []string
+
+	ndates = make([]float64, 0)
+	pattern = regexp.MustCompile(`(?i)&date="(.+)"`)
+	nnodes := 0
+	t.PreOrder(func(cur *Node, prev *Node, e *Edge) (keep bool) {
+		stop := false
+		if cur.Id() != nnodes {
+			err = fmt.Errorf("node id does not correspond to postorder traversal: %d vs %d", cur.Id(), nnodes)
+			stop = true
+		} else {
+			for _, c := range cur.Comments() {
+				matches = pattern.FindStringSubmatch(c)
+				if len(matches) < 2 {
+					err = fmt.Errorf("no date found: %s", c)
+					stop = true
+				}
+				if date, err = strconv.ParseFloat(matches[1], 64); err != nil {
+					err = fmt.Errorf("one of the node date is malformed: %s", c)
+					stop = true
+				}
+				ndates = append(ndates, date)
+			}
+		}
+		nnodes += 1
+		return !stop
+	})
+	return
+}
+
 // Computes distance of all nodes to root / pseudo root.
 // Indices of the nodes in the rdists slice correspond to node ids
 func (t *Tree) NodeRootDistance() (rdists []float64) {