Clear node depths when merging knuckle nodes

Updates #814
shawnlaffan · Nov 25, 2022 · 4529b4d · 4529b4d
1 parent c597809
commit 4529b4d
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Showing 3 changed files with 27 additions and 1 deletion.
diff --git a/lib/Biodiverse/Tree.pm b/lib/Biodiverse/Tree.pm
@@ -2796,7 +2796,15 @@ sub merge_knuckle_nodes {
         }
 
     }
-    $self->delete_all_cached_values;
+
+    if (keys %deleted) {
+        $self->delete_all_cached_values;
+
+        #  brute force
+        foreach my $node ($self->get_node_refs) {
+            $node->set_depth_aa (undef);
+        }
+    }
 
     return scalar keys %deleted;
 }

diff --git a/lib/Biodiverse/TreeNode.pm b/lib/Biodiverse/TreeNode.pm
@@ -457,6 +457,10 @@ sub set_depth {
     $self->{NODE_VALUES}{DEPTH} = $args{depth};
 }
 
+sub set_depth_aa {
+    $_[0]->{NODE_VALUES}{DEPTH} = $_[1];
+}
+
 sub get_depth {
     my $self = shift;
 

diff --git a/t/13-Tree.t b/t/13-Tree.t
@@ -1334,6 +1334,20 @@ sub test_knuckle_nodes {
 
     my $comp = $tree_with_knuckles->trees_are_same(comparison => $tree_no_knuckles);
     ok $comp, 'got expected tree topology after clearing knuckles';
+
+    my $tree = get_tree_object_from_sample_data();
+    foreach my $name_num (qw /18 21 25/) {
+        $tree->delete_node(node => "Genus:sp$name_num");
+    }
+    foreach my $node ($tree->get_node_refs) {
+        $node->get_depth;  #  trigger depth storage
+    }
+    $tree->merge_knuckle_nodes;
+    foreach my $node ($tree->get_node_refs) {
+        next if $node->is_root_node;
+        my $parent = $node->get_parent;
+        is ($node->get_depth, $parent->get_depth + 1, "correct depth for " . $node->get_name);
+    }
 }