Merge pull request #879 from shawnlaffan/issue_877_part2

treenode to R phylo: handle root length properly
shawnlaffan · Sep 19, 2023 · f1b4962 · f1b4962
2 parents 9216d7f + 1e856b9
commit f1b4962
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Showing 2 changed files with 11 additions and 3 deletions.
diff --git a/lib/Biodiverse/TreeNode.pm b/lib/Biodiverse/TreeNode.pm
@@ -2355,7 +2355,6 @@ sub to_R_phylo {
 
         my $length = $node->get_length;
         $length =~ s/,/./; #  hack for issue #775 (another comma radix char)
-        push @length_arr, $length;
 
         if ($node->is_terminal_node) {
             push @tip_labels, $name;
@@ -2367,6 +2366,8 @@ sub to_R_phylo {
 
         next NODE if $node->is_root_node;
 
+        push @length_arr, $length;
+
         my $parent_id;
         my $parent = $node->get_parent;
 
@@ -2389,7 +2390,7 @@ sub to_R_phylo {
         'Nnode'       => (scalar @internal_labels + 1),
         'node.label'  => \@internal_labels,
         'tip.label'   => \@tip_labels,
-        'root.edge'   => 0,
+        'root.edge'   => $self->get_length,
     );
 
     return wantarray ? %str :   \%str;

diff --git a/t/13-Tree.t b/t/13-Tree.t
@@ -947,8 +947,15 @@ sub test_export_Rphylo {
     my @trees = $rn->get_tree_array;
     my $tree1 = shift @trees;
 
+    #  another one
+    $nwk = '(A:1, B:1):5.8';
+    $rn  = Biodiverse::ReadNexus->new;
+    $success = $rn->import_newick (data => $nwk);
+    @trees = $rn->get_tree_array;
+    my $tree3 = shift @trees;
+
     my $i;
-    foreach my $tree ($tree1, $tree2) {
+    foreach my $tree ($tree1, $tree2, $tree3) {
         $i++;
         my $result = $tree->to_R_phylo;
         #  round trip it