JAL-4134 - refactor tree calculation code to work with binaryNode base type.

diff --git a/src/jalview/analysis/AverageDistanceTree.java b/src/jalview/analysis/AverageDistanceTree.java
index c726627..760962e 100644 (file)
--- a/src/jalview/analysis/AverageDistanceTree.java
+++ b/src/jalview/analysis/AverageDistanceTree.java
@@ -22,7 +22,7 @@ package jalview.analysis;
 
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.datamodel.SequenceNode;
+import jalview.datamodel.BinaryNode;
 import jalview.viewmodel.AlignmentViewport;
 
 /**
@@ -113,25 +113,25 @@ public class AverageDistanceTree extends TreeBuilder
    * {@inheritDoc}
    */
   @Override
-  protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
+  protected void findNewDistances(BinaryNode nodei, BinaryNode nodej,
           double dist)
   {
     double ih = 0;
     double jh = 0;
 
-    SequenceNode sni = nodei;
-    SequenceNode snj = nodej;
+    BinaryNode sni = nodei;
+    BinaryNode snj = nodej;
 
     while (sni != null)
     {
       ih = ih + sni.dist;
-      sni = (SequenceNode) sni.left();
+      sni = (BinaryNode) sni.left();
     }
 
     while (snj != null)
     {
       jh = jh + snj.dist;
-      snj = (SequenceNode) snj.left();
+      snj = (BinaryNode) snj.left();
     }
 
     nodei.dist = ((dist / 2) - ih);

diff --git a/src/jalview/analysis/NJTree.java b/src/jalview/analysis/NJTree.java
index 522c2b1..9a39ac0 100644 (file)
--- a/src/jalview/analysis/NJTree.java
+++ b/src/jalview/analysis/NJTree.java
@@ -22,7 +22,7 @@ package jalview.analysis;
 
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
-import jalview.datamodel.SequenceNode;
+import jalview.datamodel.BinaryNode;
 import jalview.viewmodel.AlignmentViewport;
 
 /**
@@ -81,7 +81,7 @@ public class NJTree extends TreeBuilder
    * {@inheritDoc}
    */
   @Override
-  protected void findNewDistances(SequenceNode nodei, SequenceNode nodej,
+  protected void findNewDistances(BinaryNode nodei, BinaryNode nodej,
           double dist)
   {
     nodei.dist = ((dist + ri) - rj) / 2;

diff --git a/src/jalview/analysis/TreeBuilder.java b/src/jalview/analysis/TreeBuilder.java
index 0601dd9..78dc37f 100644 (file)
--- a/src/jalview/analysis/TreeBuilder.java
+++ b/src/jalview/analysis/TreeBuilder.java
@@ -23,6 +23,7 @@ package jalview.analysis;
 import jalview.api.analysis.ScoreModelI;
 import jalview.api.analysis.SimilarityParamsI;
 import jalview.datamodel.AlignmentView;
+import jalview.datamodel.BinaryNode;
 import jalview.datamodel.CigarArray;
 import jalview.datamodel.SeqCigar;
 import jalview.datamodel.SequenceI;
@@ -61,9 +62,9 @@ public abstract class TreeBuilder
 
   protected double rj;
 
-  SequenceNode maxdist;
+  BinaryNode maxdist;
 
-  SequenceNode top;
+  BinaryNode top;
 
   double maxDistValue;
 
@@ -121,7 +122,7 @@ public abstract class TreeBuilder
    * 
    * @return DOCUMENT ME!
    */
-  double findHeight(SequenceNode nd)
+  double findHeight(BinaryNode nd)
   {
     if (nd == null)
     {
@@ -130,7 +131,7 @@ public abstract class TreeBuilder
 
     if ((nd.left() == null) && (nd.right() == null))
     {
-      nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+      nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
 
       if (nd.height > maxheight)
       {
@@ -145,7 +146,7 @@ public abstract class TreeBuilder
     {
       if (nd.parent() != null)
       {
-        nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+        nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
       }
       else
       {
@@ -153,8 +154,8 @@ public abstract class TreeBuilder
         nd.height = (float) 0.0;
       }
 
-      maxheight = findHeight((SequenceNode) (nd.left()));
-      maxheight = findHeight((SequenceNode) (nd.right()));
+      maxheight = findHeight((BinaryNode) (nd.left()));
+      maxheight = findHeight((BinaryNode) (nd.right()));
     }
 
     return maxheight;
@@ -166,7 +167,7 @@ public abstract class TreeBuilder
    * @param nd
    *          DOCUMENT ME!
    */
-  void reCount(SequenceNode nd)
+  void reCount(BinaryNode nd)
   {
     ycount = 0;
     // _lycount = 0;
@@ -180,7 +181,7 @@ public abstract class TreeBuilder
    * @param nd
    *          DOCUMENT ME!
    */
-  void _reCount(SequenceNode nd)
+  void _reCount(BinaryNode nd)
   {
     // if (_lycount<_lylimit)
     // {
@@ -196,11 +197,11 @@ public abstract class TreeBuilder
     if ((nd.left() != null) && (nd.right() != null))
     {
 
-      _reCount((SequenceNode) nd.left());
-      _reCount((SequenceNode) nd.right());
+      _reCount(nd.left());
+      _reCount((BinaryNode) nd.right());
 
-      SequenceNode l = (SequenceNode) nd.left();
-      SequenceNode r = (SequenceNode) nd.right();
+      BinaryNode l = nd.left();
+      BinaryNode r = nd.right();
 
       nd.count = l.count + r.count;
       nd.ycount = (l.ycount + r.ycount) / 2;
@@ -218,7 +219,7 @@ public abstract class TreeBuilder
    * 
    * @return DOCUMENT ME!
    */
-  public SequenceNode getTopNode()
+  public BinaryNode getTopNode()
   {
     return top;
   }
@@ -310,7 +311,7 @@ public abstract class TreeBuilder
    * 
    * @param nd
    */
-  void findMaxDist(SequenceNode nd)
+  void findMaxDist(BinaryNode nd)
   {
     if (nd == null)
     {
@@ -329,8 +330,8 @@ public abstract class TreeBuilder
     }
     else
     {
-      findMaxDist((SequenceNode) nd.left());
-      findMaxDist((SequenceNode) nd.right());
+      findMaxDist((BinaryNode) nd.left());
+      findMaxDist((BinaryNode) nd.right());
     }
   }
 
@@ -417,8 +418,8 @@ public abstract class TreeBuilder
     sn.setLeft((node.elementAt(i)));
     sn.setRight((node.elementAt(j)));
 
-    SequenceNode tmpi = (node.elementAt(i));
-    SequenceNode tmpj = (node.elementAt(j));
+    BinaryNode tmpi = (node.elementAt(i));
+    BinaryNode tmpj = (node.elementAt(j));
 
     findNewDistances(tmpi, tmpj, dist);
 
@@ -440,8 +441,8 @@ public abstract class TreeBuilder
    * Computes and stores new distances for nodei and nodej, given the previous
    * distance between them
    */
-  protected abstract void findNewDistances(SequenceNode nodei,
-          SequenceNode nodej, double previousDistance);
+  protected abstract void findNewDistances(BinaryNode nodei,
+          BinaryNode nodej, double previousDistance);
 
   /**
    * Calculates and saves the distance between the combination of cluster(i) and

diff --git a/src/jalview/analysis/TreeModel.java b/src/jalview/analysis/TreeModel.java
index 4d5e4b2..703702a 100644 (file)
--- a/src/jalview/analysis/TreeModel.java
+++ b/src/jalview/analysis/TreeModel.java
@@ -95,7 +95,7 @@ public class TreeModel
    */
   public TreeModel(TreeBuilder tree)
   {
-    this(tree.getSequences(), tree.getTopNode(), tree.hasDistances(),
+    this(tree.getSequences(), (SequenceNode) tree.getTopNode(), tree.hasDistances(),
             tree.hasBootstrap(), tree.hasRootDistance());
     seqData = tree.getOriginalData();
   }
@@ -345,7 +345,7 @@ public class TreeModel
    * @param nd
    *          SequenceNode
    */
-  void printNode(SequenceNode nd)
+  void printNode(BinaryNode nd)
   {
     if (nd == null)
     {
@@ -361,8 +361,8 @@ public class TreeModel
     else
     {
       System.out.println("Dist " + nd.dist);
-      printNode((SequenceNode) nd.left());
-      printNode((SequenceNode) nd.right());
+      printNode((BinaryNode) nd.left());
+      printNode((BinaryNode) nd.right());
     }
   }
 
@@ -422,7 +422,7 @@ public class TreeModel
    * 
    * @return DOCUMENT ME!
    */
-  public double findHeight(SequenceNode nd)
+  public double findHeight(BinaryNode nd)
   {
     if (nd == null)
     {
@@ -431,7 +431,7 @@ public class TreeModel
 
     if ((nd.left() == null) && (nd.right() == null))
     {
-      nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+      nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
 
       if (nd.height > maxheight)
       {
@@ -446,7 +446,7 @@ public class TreeModel
     {
       if (nd.parent() != null)
       {
-        nd.height = ((SequenceNode) nd.parent()).height + nd.dist;
+        nd.height = ((BinaryNode) nd.parent()).height + nd.dist;
       }
       else
       {
@@ -454,8 +454,8 @@ public class TreeModel
         nd.height = (float) 0.0;
       }
 
-      maxheight = findHeight((SequenceNode) (nd.left()));
-      maxheight = findHeight((SequenceNode) (nd.right()));
+      maxheight = findHeight((BinaryNode) (nd.left()));
+      maxheight = findHeight((BinaryNode) (nd.right()));
     }
 
     return maxheight;
@@ -467,7 +467,7 @@ public class TreeModel
    * @param nd
    *          DOCUMENT ME!
    */
-  void printN(SequenceNode nd)
+  void printN(BinaryNode nd)
   {
     if (nd == null)
     {
@@ -476,8 +476,8 @@ public class TreeModel
 
     if ((nd.left() != null) && (nd.right() != null))
     {
-      printN((SequenceNode) nd.left());
-      printN((SequenceNode) nd.right());
+      printN((BinaryNode) nd.left());
+      printN((BinaryNode) nd.right());
     }
     else
     {
@@ -494,7 +494,7 @@ public class TreeModel
    * @param nd
    *          DOCUMENT ME!
    */
-  public void reCount(SequenceNode nd)
+  public void reCount(BinaryNode nd)
   {
     ycount = 0;
     // _lycount = 0;
@@ -510,7 +510,7 @@ public class TreeModel
    * @param nd
    *          DOCUMENT ME!
    */
-  void _reCount(SequenceNode nd)
+  void _reCount(BinaryNode nd)
   {
     // if (_lycount<_lylimit)
     // {
@@ -526,11 +526,11 @@ public class TreeModel
     if ((nd.left() != null) && (nd.right() != null))
     {
 
-      _reCount((SequenceNode) nd.left());
-      _reCount((SequenceNode) nd.right());
+      _reCount((BinaryNode) nd.left());
+      _reCount((BinaryNode) nd.right());
 
-      SequenceNode l = (SequenceNode) nd.left();
-      SequenceNode r = (SequenceNode) nd.right();
+      BinaryNode l = (BinaryNode) nd.left();
+      BinaryNode r = (BinaryNode) nd.right();
 
       nd.count = l.count + r.count;
       nd.ycount = (l.ycount + r.ycount) / 2;
@@ -549,14 +549,14 @@ public class TreeModel
    * @param nd
    *          DOCUMENT ME!
    */
-  public void swapNodes(SequenceNode nd)
+  public void swapNodes(BinaryNode nd)
   {
     if (nd == null)
     {
       return;
     }
 
-    SequenceNode tmp = (SequenceNode) nd.left();
+    BinaryNode tmp = (BinaryNode) nd.left();
 
     nd.setLeft(nd.right());
     nd.setRight(tmp);
@@ -570,7 +570,7 @@ public class TreeModel
    * @param dir
    *          DOCUMENT ME!
    */
-  void changeDirection(SequenceNode nd, SequenceNode dir)
+  void changeDirection(BinaryNode nd, BinaryNode dir)
   {
     if (nd == null)
     {
@@ -579,9 +579,9 @@ public class TreeModel
 
     if (nd.parent() != top)
     {
-      changeDirection((SequenceNode) nd.parent(), nd);
+      changeDirection((BinaryNode) nd.parent(), nd);
 
-      SequenceNode tmp = (SequenceNode) nd.parent();
+      BinaryNode tmp = (BinaryNode) nd.parent();
 
       if (dir == nd.left())
       {

diff --git a/src/jalview/appletgui/TreeCanvas.java b/src/jalview/appletgui/TreeCanvas.java
index 2e5f938..1355916 100755 (executable)
--- a/src/jalview/appletgui/TreeCanvas.java
+++ b/src/jalview/appletgui/TreeCanvas.java
@@ -23,6 +23,7 @@ package jalview.appletgui;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
+import jalview.datamodel.BinaryNode;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -263,9 +264,9 @@ public class TreeCanvas extends Panel
       }
 
       int ystart = (int) (node.left() == null ? 0
-              : (((SequenceNode) node.left()).ycount * chunk)) + offy;
+              : (((BinaryNode) node.left()).ycount * chunk)) + offy;
       int yend = (int) (node.right() == null ? 0
-              : (((SequenceNode) node.right()).ycount * chunk)) + offy;
+              : (((BinaryNode) node.right()).ycount * chunk)) + offy;
 
       Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
       nodeHash.put(node, pos);
@@ -338,20 +339,20 @@ public class TreeCanvas extends Panel
     int width = getSize().width;
     int height = getSize().height;
 
-    SequenceNode top = tree.getTopNode();
+    BinaryNode top = tree.getTopNode();
 
     double wscale = (float) (width * .8 - offx * 2) / tree.getMaxHeight();
     if (top.count == 0)
     {
-      top.count = ((SequenceNode) top.left()).count
-              + ((SequenceNode) top.right()).count;
+      top.count = ((BinaryNode) top.left()).count
+              + ((BinaryNode) top.right()).count;
     }
     float chunk = (float) (height - offy) / top.count;
 
     pickNode(pickBox, top, chunk, wscale, width, offx, offy);
   }
 
-  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
+  public void pickNode(Rectangle pickBox, BinaryNode node, float chunk,
           double scale, int width, int offx, int offy)
   {
     if (node == null)
@@ -384,14 +385,14 @@ public class TreeCanvas extends Panel
     }
     else
     {
-      pickNode(pickBox, (SequenceNode) node.left(), chunk, scale, width,
+      pickNode(pickBox, (BinaryNode) node.left(), chunk, scale, width,
               offx, offy);
-      pickNode(pickBox, (SequenceNode) node.right(), chunk, scale, width,
+      pickNode(pickBox, (BinaryNode) node.right(), chunk, scale, width,
               offx, offy);
     }
   }
 
-  public void setColor(SequenceNode node, Color c)
+  public void setColor(BinaryNode node, Color c)
   {
     if (node == null)
     {
@@ -410,8 +411,8 @@ public class TreeCanvas extends Panel
     else
     {
       node.color = c;
-      setColor((SequenceNode) node.left(), c);
-      setColor((SequenceNode) node.right(), c);
+      setColor((BinaryNode) node.left(), c);
+      setColor((BinaryNode) node.right(), c);
     }
   }
 
@@ -469,12 +470,12 @@ public class TreeCanvas extends Panel
 
     double wscale = (width - labelLength - offx * 2) / tree.getMaxHeight();
 
-    SequenceNode top = tree.getTopNode();
+    BinaryNode top = tree.getTopNode();
 
     if (top.count == 0)
     {
-      top.count = ((SequenceNode) top.left()).count
-              + ((SequenceNode) top.right()).count;
+      top.count = ((BinaryNode) top.left()).count
+              + ((BinaryNode) top.right()).count;
     }
     float chunk = (float) (height - offy) / top.count;
 

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index c0ff0e4..6d392d4 100755 (executable)
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -20,6 +20,8 @@
  */
 package jalview.datamodel;
 
+import java.awt.Color;
+
 /**
  * DOCUMENT ME!
  * 
@@ -41,6 +43,24 @@ public class BinaryNode
   /** DOCUMENT ME!! */
   public int bootstrap;
 
+  /** DOCUMENT ME!! */
+  public double dist;
+
+  /** DOCUMENT ME!! */
+  public int count;
+
+  /** DOCUMENT ME!! */
+  public double height;
+
+  /** DOCUMENT ME!! */
+  public float ycount;
+
+  /** DOCUMENT ME!! */
+  public Color color = Color.black;
+
+  /** DOCUMENT ME!! */
+  public boolean dummy = false;
+
   /**
    * Creates a new BinaryNode object.
    */
@@ -300,4 +320,20 @@ public class BinaryNode
   {
     return bootstrap;
   }
+
+  /**
+   * ascends the tree but doesn't stop until a non-dummy node is discovered.
+   * 
+   */
+  public BinaryNode AscendTree()
+  {
+    BinaryNode c = this;
+  
+    do
+    {
+      c = c.parent();
+    } while ((c != null) && c.dummy);
+  
+    return c;
+  }
 }

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 0a694c2..30179f5 100755 (executable)
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -20,8 +20,6 @@
  */
 package jalview.datamodel;
 
-import java.awt.Color;
-
 /**
  * DOCUMENT ME!
  * 
@@ -30,24 +28,6 @@ import java.awt.Color;
  */
 public class SequenceNode extends BinaryNode
 {
-  /** DOCUMENT ME!! */
-  public double dist;
-
-  /** DOCUMENT ME!! */
-  public int count;
-
-  /** DOCUMENT ME!! */
-  public double height;
-
-  /** DOCUMENT ME!! */
-  public float ycount;
-
-  /** DOCUMENT ME!! */
-  public Color color = Color.black;
-
-  /** DOCUMENT ME!! */
-  public boolean dummy = false;
-
   private boolean placeholder = false;
 
   /**
@@ -70,7 +50,7 @@ public class SequenceNode extends BinaryNode
    * @param name
    *          DOCUMENT ME!
    */
-  public SequenceNode(Object val, SequenceNode parent, double dist,
+  public SequenceNode(Object val, BinaryNode parent, double dist,
           String name)
   {
     super(val, parent, name);
@@ -93,7 +73,7 @@ public class SequenceNode extends BinaryNode
    * @param dummy
    *          DOCUMENT ME!
    */
-  public SequenceNode(Object val, SequenceNode parent, String name,
+  public SequenceNode(Object val, BinaryNode parent, String name,
           double dist, int bootstrap, boolean dummy)
   {
     super(val, parent, name);
@@ -148,23 +128,6 @@ public class SequenceNode extends BinaryNode
   }
 
   /**
-   * 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;
-  }
-
-  /**
    * test if this node has a name that might be a label rather than a bootstrap
    * value
    * 

diff --git a/src/jalview/gui/TreeCanvas.java b/src/jalview/gui/TreeCanvas.java
index 6f143db..a5f1ab9 100755 (executable)
--- a/src/jalview/gui/TreeCanvas.java
+++ b/src/jalview/gui/TreeCanvas.java
@@ -50,6 +50,7 @@ import javax.swing.ToolTipManager;
 import jalview.analysis.Conservation;
 import jalview.analysis.TreeModel;
 import jalview.api.AlignViewportI;
+import jalview.datamodel.BinaryNode;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
@@ -332,9 +333,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
       }
 
       int ystart = (node.left() == null ? 0
-              : (int) (((SequenceNode) node.left()).ycount * chunk)) + offy;
+              : (int) (((BinaryNode) node.left()).ycount * chunk)) + offy;
       int yend = (node.right() == null ? 0
-              : (int) (((SequenceNode) node.right()).ycount * chunk))
+              : (int) (((BinaryNode) node.right()).ycount * chunk))
               + offy;
 
       Rectangle pos = new Rectangle(xend - 2, ypos - 2, 5, 5);
@@ -415,14 +416,14 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     int width = getWidth();
     int height = getHeight();
 
-    SequenceNode top = tree.getTopNode();
+    BinaryNode top = tree.getTopNode();
 
     double wscale = ((width * .8) - (offx * 2)) / tree.getMaxHeight();
 
     if (top.count == 0)
     {
-      top.count = ((SequenceNode) top.left()).count
-              + ((SequenceNode) top.right()).count;
+      top.count = ((BinaryNode) top.left()).count
+              + ((BinaryNode) top.right()).count;
     }
 
     float chunk = (float) (height - (offy)) / top.count;
@@ -448,7 +449,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * @param offy
    *          DOCUMENT ME!
    */
-  public void pickNode(Rectangle pickBox, SequenceNode node, float chunk,
+  public void pickNode(Rectangle pickBox, BinaryNode node, float chunk,
           double wscale, int width, int offx, int offy)
   {
     if (node == null)
@@ -481,9 +482,9 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     }
     else
     {
-      pickNode(pickBox, (SequenceNode) node.left(), chunk, wscale, width,
+      pickNode(pickBox, (BinaryNode) node.left(), chunk, wscale, width,
               offx, offy);
-      pickNode(pickBox, (SequenceNode) node.right(), chunk, wscale, width,
+      pickNode(pickBox, (BinaryNode) node.right(), chunk, wscale, width,
               offx, offy);
     }
   }
@@ -496,7 +497,7 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
    * @param c
    *          DOCUMENT ME!
    */
-  public void setColor(SequenceNode node, Color c)
+  public void setColor(BinaryNode node, Color c)
   {
     if (node == null)
     {
@@ -516,8 +517,8 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
         }
       }
     }
-    setColor((SequenceNode) node.left(), c);
-    setColor((SequenceNode) node.right(), c);
+    setColor((BinaryNode) node.left(), c);
+    setColor((BinaryNode) node.right(), c);
   }
 
   /**
@@ -713,12 +714,12 @@ public class TreeCanvas extends JPanel implements MouseListener, Runnable,
     double wscale = (width - labelLength - (offx * 2))
             / tree.getMaxHeight();
 
-    SequenceNode top = tree.getTopNode();
+    BinaryNode top = tree.getTopNode();
 
     if (top.count == 0)
     {
-      top.count = ((SequenceNode) top.left()).count
-              + ((SequenceNode) top.right()).count;
+      top.count = ((BinaryNode) top.left()).count
+              + ((BinaryNode) top.right()).count;
     }
 
     float chunk = (float) (height - (offy)) / top.count;

diff --git a/src/jalview/gui/TreePanel.java b/src/jalview/gui/TreePanel.java
index 76e1884..9a4f2c4 100755 (executable)
--- a/src/jalview/gui/TreePanel.java
+++ b/src/jalview/gui/TreePanel.java
@@ -721,7 +721,7 @@ public class TreePanel extends GTreePanel
                 && !((SequenceNode) node).isDummy())
         {
           String newname = null;
-          SequenceI sq = (SequenceI) ((SequenceNode) node).element();
+          SequenceI sq = (SequenceI) ((BinaryNode) node).element();
           if (sq != null)
           {
             // search dbrefs, features and annotation
@@ -763,7 +763,7 @@ public class TreePanel extends GTreePanel
           {
             // String oldname = ((SequenceNode) node).getName();
             // TODO : save oldname in the undo object for this modification.
-            ((SequenceNode) node).setName(newname);
+            ((BinaryNode) node).setName(newname);
           }
         }
       }

diff --git a/src/jalview/io/NewickFile.java b/src/jalview/io/NewickFile.java
index 027390a..879b7d4 100755 (executable)
--- a/src/jalview/io/NewickFile.java
+++ b/src/jalview/io/NewickFile.java
@@ -28,6 +28,7 @@ package jalview.io;
 
 import java.util.Locale;
 
+import jalview.datamodel.BinaryNode;
 import jalview.datamodel.SequenceNode;
 import jalview.util.MessageManager;
 
@@ -275,8 +276,8 @@ public class NewickFile extends FileParse
 
     root = new SequenceNode();
 
-    SequenceNode realroot = null;
-    SequenceNode c = root;
+    BinaryNode realroot = null;
+    BinaryNode c = root;
 
     int d = -1;
     int cp = 0;
@@ -323,21 +324,21 @@ public class NewickFile extends FileParse
         {
           c.setRight(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (SequenceNode) c.right();
+          c = (BinaryNode) c.right();
         }
         else
         {
           if (c.left() != null)
           {
             // Dummy node for polytomy - keeps c.left free for new node
-            SequenceNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
+            BinaryNode tmpn = new SequenceNode(null, c, null, 0, 0, true);
             tmpn.SetChildren(c.left(), c.right());
             c.setRight(tmpn);
           }
 
           c.setLeft(new SequenceNode(null, c, null, DefDistance,
                   DefBootstrap, false));
-          c = (SequenceNode) c.left();
+          c = (BinaryNode) c.left();
         }
 
         if (realroot == null)
@@ -518,7 +519,7 @@ public class NewickFile extends FileParse
         else
         {
           // Find a place to put the leaf
-          SequenceNode newnode = new SequenceNode(null, c, nodename,
+          BinaryNode newnode = new SequenceNode(null, c, nodename,
                   (HasDistances) ? distance : DefDistance,
                   (HasBootstrap) ? bootstrap : DefBootstrap, false);
           parseNHXNodeProps(c, commentString2);
@@ -538,7 +539,7 @@ public class NewickFile extends FileParse
             {
               // Insert a dummy node for polytomy
               // dummy nodes have distances
-              SequenceNode newdummy = new SequenceNode(null, c, null,
+              BinaryNode newdummy = new SequenceNode(null, c, null,
                       (HasDistances ? 0 : DefDistance), 0, true);
               newdummy.SetChildren(c.left(), newnode);
               c.setLeft(newdummy);
@@ -577,7 +578,7 @@ public class NewickFile extends FileParse
               // Just advance focus, if we need to
               if ((c.left() != null) && (!c.left().isLeaf()))
               {
-                c = (SequenceNode) c.left();
+                c = (BinaryNode) c.left();
               }
             }
           }
@@ -631,7 +632,7 @@ public class NewickFile extends FileParse
    * @param commentString
    * @param commentString2
    */
-  private void parseNHXNodeProps(SequenceNode c, String commentString)
+  private void parseNHXNodeProps(BinaryNode c, String commentString)
   {
     // TODO: store raw comment on the sequenceNode so it can be recovered when
     // tree is output
@@ -832,7 +833,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  private String printNodeField(SequenceNode c)
+  private String printNodeField(BinaryNode c)
   {
     return ((c.getName() == null) ? "" : nodeName(c.getName()))
             + ((HasBootstrap) ? ((c.getBootstrap() > -1)
@@ -849,7 +850,7 @@ public class NewickFile extends FileParse
    * 
    * @return DOCUMENT ME!
    */
-  private String printRootField(SequenceNode root)
+  private String printRootField(BinaryNode root)
   {
     return (printRootInfo)
             ? (((root.getName() == null) ? "" : nodeName(root.getName()))

diff --git a/src/jalview/io/vamsas/Tree.java b/src/jalview/io/vamsas/Tree.java
index e8f6f6b..260894d 100644 (file)
--- a/src/jalview/io/vamsas/Tree.java
+++ b/src/jalview/io/vamsas/Tree.java
@@ -394,7 +394,7 @@ public class Tree extends DatastoreItem
       {
         if (!((jalview.datamodel.SequenceNode) tnode).isPlaceholder())
         {
-          Object assocseq = ((jalview.datamodel.SequenceNode) tnode)
+          Object assocseq = ((BinaryNode) tnode)
                   .element();
           if (assocseq instanceof SequenceI)
           {

diff --git a/test/jalview/io/NewickFileTests.java b/test/jalview/io/NewickFileTests.java
index beedb11..02c5ccd 100644 (file)
--- a/test/jalview/io/NewickFileTests.java
+++ b/test/jalview/io/NewickFileTests.java
@@ -24,6 +24,7 @@ import static org.testng.ConversionUtils.wrapDataProvider;
 
 import jalview.analysis.SequenceIdMatcher;
 import jalview.analysis.TreeModel;
+import jalview.datamodel.BinaryNode;
 import jalview.datamodel.SequenceI;
 import jalview.datamodel.SequenceNode;
 import jalview.gui.JvOptionPane;
@@ -119,7 +120,7 @@ public class NewickFileTests
               stage + "Newick file is invalid ('"
                       + nf_regen.getWarningMessage() + "')",
               nf_regen.isValid());
-      SequenceNode tree_regen = nf.getTree();
+      BinaryNode tree_regen = nf.getTree();
       AssertJUnit.assertTrue(stage + "Null Tree", tree_regen != null);
       stage = "Compare original and generated tree" + treename;