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[jalview.git] / src / jalview / analysis / NJTree.java

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 3f5f442..78c4e60 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -133,7 +133,7 @@ public class NJTree
         SequenceI nam;
         String realnam;
         Vector one2many=new Vector();
-
+        int countOne2Many=0;
         while (i < leaves.size())
         {
             j = (SequenceNode) leaves.elementAt(i++);
@@ -149,8 +149,9 @@ public class NJTree
             {
                 j.setElement(nam);
                 if (one2many.contains(nam)) {
-                  if (jalview.bin.Cache.log.isDebugEnabled())
-                    jalview.bin.Cache.log.debug("One 2 many relationship for "+nam.getName());
+                  countOne2Many++;
+                //  if (jalview.bin.Cache.log.isDebugEnabled())
+                //    jalview.bin.Cache.log.debug("One 2 many relationship for "+nam.getName());
                 } else {
                   one2many.addElement(nam);
                   namesleft--;
@@ -162,10 +163,10 @@ public class NJTree
                 j.setPlaceholder(true);
             }
         }
-        if (jalview.bin.Cache.log.isDebugEnabled()) {
-          jalview.bin.Cache.log.debug("There were "+one2many.size()+" alignment sequences linked to two or more leaves.");
-        }
-        one2many.clear();
+      //  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();
     }
 
     /**
@@ -283,12 +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);
+                    
                 }
             }
         }