added PropertyChangeListeners for alignviewport.alignment.sequences

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

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 8708f1d..cf15d78 100755 (executable)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -86,6 +86,26 @@ public class NJTree {
     }\r
   }\r
 \r
+  /**\r
+   *\r
+   * used when the alignment associated to a tree has changed.\r
+   *\r
+   * @param alignment Vector\r
+   */\r
+  public void UpdatePlaceHolders(Vector alignment) {\r
+    Vector leaves = new Vector();\r
+    findLeaves(top, leaves);\r
+    int sz = leaves.size();\r
+    int i=0;\r
+    while (i<sz) {\r
+      SequenceNode leaf = (SequenceNode) leaves.elementAt(i++);\r
+      if (alignment.contains(leaf.element()))\r
+        leaf.setPlaceholder(false);\r
+      else\r
+        leaf.setPlaceholder(true);\r
+    }\r
+  }\r
+\r
   public NJTree(SequenceI[] sequence,int start, int end) {\r
     this(sequence,"NJ","BL",start,end);\r
   }\r