X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceNode.java;h=905bd15dda65009149dc327e96a2e899ffb24c6b;hb=116786d279dcb83f05afd625ad6e39627a37e1e8;hp=6e35ee34363044087b4a05b3b32b94cc40999e77;hpb=1ecf6419aba86993b3c223bf5ec0fa79427baf85;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 6e35ee3..905bd15 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -9,13 +9,46 @@ public class SequenceNode extends BinaryNode {
   public float height;
   public float ycount;
   public Color color = Color.black;
-
+  public boolean dummy = false;
   public SequenceNode() {
     super();
   }
-  
+
   public SequenceNode(Object val, SequenceNode parent, float dist,String name) {
     super(val,parent,name);
     this.dist = dist;
   }
+  public SequenceNode(Object val, SequenceNode parent, String name, float dist, int bootstrap, boolean dummy) {
+    super(val,parent,name);
+    this.dist = dist;
+    this.bootstrap = bootstrap;
+    this.dummy = dummy;
+  }
+
+
+  /**
+   * @param dummy true if node is created for the representation of polytomous trees
+   */
+
+  public boolean isDummy() {
+    return dummy;
+  }
+  public boolean setDummy(boolean newstate) {
+    boolean oldstate = dummy;
+    dummy = newstate;
+    return oldstate;
+  }
+
+  /**
+   * ascends the tree but doesn't stop until a non-dummy node is discovered.
+   * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.
+   */
+
+  public SequenceNode AscendTree() {
+    SequenceNode c = this;
+    do {
+      c = (SequenceNode) c.parent();
+    } while (c!=null && c.dummy);
+    return c;
+  }
 }