gotree ltt takes node dates from the tree if present, otherwise in mu…

…tations

test.sh

@@ -2166,3 +2166,17 @@ EOF
 echo "(((A:1,B:1):1,C:2):3,(D:4,(E:3,((F:1.5,G:1.5):0.5,H:2):1):1):1);" | $GOTREE ltt > result
 diff -q -b expected result
 rm -f expected result
+
+echo "->gotree ltt with dates"
+cat > expected <<EOF
+0	2019.000000	2
+0	2020.000000	3
+0	2021.000000	4
+0	2022.000000	6
+0	2022.500000	7
+0	2023.000000	8
+0	2024.000000	0
+EOF
+echo '(((A[&date="2024"]:1,B[&date="2024"]:1)[&date="2023"]:1,C[&date="2024"]:2)[&date="2022"]:3,(D[&date="2024"]:4,(E[&date="2024"]:3,((F[&date="2024"]:1.5,G[&date="2024"]:1.5)[&date="2022.5"]:0.5,H[&date="2024"]:2)[&date="2022"]:1)[&date="2021"]:1)[&date="2020"]:1)[&date="2019"];' | $GOTREE ltt > result
+diff -q -b expected result
+rm -f expected result

tree/algo.go

@@ -972,7 +972,8 @@ func (t *Tree) LTT() (lttdata []LTTData) {
 	// 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)
+		io.LogWarning(err)
+		io.LogWarning(fmt.Errorf("using mutations instead of dates"))
 		dists = t.NodeRootDistance()
 	}
 

tree/tree.go

@@ -966,26 +966,30 @@ func (t *Tree) NodeDates() (ndates []float64, err error) {
 	pattern = regexp.MustCompile(`(?i)&date="(.+)"`)
 	nnodes := 0
 	t.PreOrder(func(cur *Node, prev *Node, e *Edge) (keep bool) {
-		stop := false
+		keep = true
 		if cur.Id() != nnodes {
 			err = fmt.Errorf("node id does not correspond to postorder traversal: %d vs %d", cur.Id(), nnodes)
-			stop = true
-		} else {
+			keep = false
+		} else if len(cur.Comments()) > 0 {
+			keep = false
 			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 {
+				} else if date, err = strconv.ParseFloat(matches[1], 64); err != nil {
 					err = fmt.Errorf("one of the node date is malformed: %s", c)
-					stop = true
+				} else {
+					ndates = append(ndates, date)
+					err = nil
+					keep = true
 				}
-				ndates = append(ndates, date)
 			}
+		} else {
+			err = fmt.Errorf("a node with no date found")
+			keep = false
 		}
 		nnodes += 1
-		return !stop
+		return
 	})
 	return
 }