X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fdatamodel%2FBinaryNode.java;h=5b55594c75a541b6d8623727564ac4be71504941;hb=4b7d3640209c4434d569c746672cf9eed4250ace;hp=bfe8c04d3e1decdafc42fbcd55ab0288c05e74a0;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index bfe8c04..5b55594 100755
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,23 +1,27 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1)
- * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.datamodel;
 
+import java.awt.Color;
+
 /**
  * DOCUMENT ME!
  * 
@@ -36,9 +40,27 @@ public class BinaryNode
 
   BinaryNode parent;
 
-  /** DOCUMENT ME!! */
+  /** Bootstrap value */
   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.
    */
@@ -46,25 +68,41 @@ public class BinaryNode
   {
     left = right = parent = null;
     bootstrap = 0;
+    dist = 0;
   }
 
   /**
    * Creates a new BinaryNode object.
    * 
    * @param element
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param parent
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
-  public BinaryNode(Object element, BinaryNode parent, String name)
+  public BinaryNode(Object element, BinaryNode parent, String name,
+          double dist)
   {
+    this();
     this.element = element;
     this.parent = parent;
     this.name = name;
+    this.dist = dist;
+  }
 
-    left = right = null;
+  public BinaryNode(Object element, BinaryNode parent, String name,
+          double dist, int bootstrap)
+  {
+    this(element, parent, name, dist);
+    this.bootstrap = bootstrap;
+  }
+
+  public BinaryNode(Object val, BinaryNode parent, String name, double dist,
+          int bootstrap, boolean dummy)
+  {
+    this(val, parent, name, dist, bootstrap);
+    this.dummy = dummy;
   }
 
   /**
@@ -81,7 +119,7 @@ public class BinaryNode
    * DOCUMENT ME!
    * 
    * @param v
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -104,7 +142,7 @@ public class BinaryNode
    * DOCUMENT ME!
    * 
    * @param n
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -127,7 +165,7 @@ public class BinaryNode
    * DOCUMENT ME!
    * 
    * @param n
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -150,7 +188,7 @@ public class BinaryNode
    * DOCUMENT ME!
    * 
    * @param n
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -260,7 +298,9 @@ public class BinaryNode
   /**
    * 
    * set the display name
-   * @param new name
+   * 
+   * @param new
+   *          name
    */
   public void setName(String name)
   {
@@ -288,11 +328,53 @@ public class BinaryNode
   }
 
   /**
-   * get bootstrap 
+   * get bootstrap
+   * 
    * @return integer value
    */
   public int getBootstrap()
   {
     return bootstrap;
   }
+
+  /**
+   * @param dummy
+   *          true if node is created for the representation of polytomous trees
+   */
+  public boolean isDummy()
+  {
+    return dummy;
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param newstate
+   *          DOCUMENT ME!
+   * 
+   * @return DOCUMENT ME!
+   */
+  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.
+   * 
+   */
+  public BinaryNode AscendTree()
+  {
+    BinaryNode c = this;
+
+    do
+    {
+      c = c.parent();
+    } while ((c != null) && c.dummy);
+
+    return c;
+  }
 }