X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FNJTree.java;h=b1141c5ff2e80ca7b862ca2eb22608e67fb6577a;hb=bb9b4018d314ed5858504faf2bc848178bc9f6a9;hp=1ab9c02592fb9e4a69cae039fa3d8ae860311d2c;hpb=e61219eaa31557203fa518aa03cba2cc651e1b84;p=jalview.git

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 1ab9c02..b1141c5 100755
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -132,7 +132,8 @@ public class NJTree
         SequenceNode j;
         SequenceI nam;
         String realnam;
-
+        Vector one2many=new Vector();
+        int countOne2Many=0;
         while (i < leaves.size())
         {
             j = (SequenceNode) leaves.elementAt(i++);
@@ -147,7 +148,14 @@ public class NJTree
             if (nam != null)
             {
                 j.setElement(nam);
-                namesleft--;
+                if (one2many.contains(nam)) {
+                  countOne2Many++;
+                //  if (jalview.bin.Cache.log.isDebugEnabled())
+                //    jalview.bin.Cache.log.debug("One 2 many relationship for "+nam.getName());
+                } else {
+                  one2many.addElement(nam);
+                  namesleft--;
+                }
             }
             else
             {
@@ -155,6 +163,10 @@ public class NJTree
                 j.setPlaceholder(true);
             }
         }
+      //  if (jalview.bin.Cache.log.isDebugEnabled() && countOne2Many>0) {
+      //    jalview.bin.Cache.log.debug("There were "+countOne2Many+" alignment sequence ids (out of "+one2many.size()+" unique ids) linked to two or more leaves.");
+      //  }
+      //  one2many.clear();
     }
 
     /**