X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=78c4e600bc8d580e6a8df4a5854ebe8227217376;hb=ae83cc59079dc5374a41402889b6f4192f66e9e2;hp=b1141c5ff2e80ca7b862ca2eb22608e67fb6577a;hpb=abbfeb71cd52eb9f5ce500c3dd5c0d3b32d4ecb1;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index b1141c5..78c4e60 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -284,12 +284,21 @@ public class NJTree
 
                 if (nam != null)
                 {
+                    if (!leaf.isPlaceholder()) {
+                      // remapping the node to a new sequenceI - should remove any refs to old one.
+                      // TODO - make many sequenceI to one leaf mappings possible! (JBPNote)
+                    }
                     leaf.setPlaceholder(false);
                     leaf.setElement(nam);
                 }
                 else
                 {
+                    if (!leaf.isPlaceholder()) {
+                        // Construct a new placeholder sequence object for this leaf
+                        leaf.setElement(new Sequence(leaf.getName(), "THISISAPLACEHLDER"));
+                    }
                     leaf.setPlaceholder(true);
+                    
                 }
             }
         }