Merge branch 'releases/Release_2_11_3_Branch'

[jalview.git] / src / jalview / datamodel / SequenceNode.java

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index ea3e515..9d00fa5 100755 (executable)
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,51 +1,33 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 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.*;
-
 /**
  * DOCUMENT ME!
  * 
  * @author $author$
  * @version $Revision$
  */
-public class SequenceNode extends BinaryNode
+public class SequenceNode extends BinaryNode<SequenceI>
 {
-  /** DOCUMENT ME!! */
-  public float dist;
-
-  /** DOCUMENT ME!! */
-  public int count;
-
-  /** DOCUMENT ME!! */
-  public float height;
-
-  /** DOCUMENT ME!! */
-  public float ycount;
-
-  /** DOCUMENT ME!! */
-  public Color color = Color.black;
-
-  /** DOCUMENT ME!! */
-  public boolean dummy = false;
-
   private boolean placeholder = false;
 
   /**
@@ -56,58 +38,22 @@ public class SequenceNode extends BinaryNode
     super();
   }
 
-  /**
-   * Creates a new SequenceNode object.
-   * 
-   * @param val
-   *                DOCUMENT ME!
-   * @param parent
-   *                DOCUMENT ME!
-   * @param dist
-   *                DOCUMENT ME!
-   * @param name
-   *                DOCUMENT ME!
-   */
-  public SequenceNode(Object val, SequenceNode parent, float dist,
-          String name)
+  public SequenceNode(SequenceI val, BinaryNode<SequenceI> parent,
+          String name, double dist, int bootstrap, boolean dummy)
   {
-    super(val, parent, name);
-    this.dist = dist;
+    super(val, parent, name, dist, bootstrap, dummy);
   }
 
-  /**
-   * Creates a new SequenceNode object.
-   * 
-   * @param val
-   *                DOCUMENT ME!
-   * @param parent
-   *                DOCUMENT ME!
-   * @param name
-   *                DOCUMENT ME!
-   * @param dist
-   *                DOCUMENT ME!
-   * @param bootstrap
-   *                DOCUMENT ME!
-   * @param dummy
-   *                DOCUMENT ME!
-   */
-  public SequenceNode(Object val, SequenceNode parent, String name,
-          float dist, int bootstrap, boolean dummy)
+  public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent,
+          String name, double dist, int bootstrap)
   {
-    super(val, parent, name);
-    this.dist = dist;
-    this.bootstrap = bootstrap;
-    this.dummy = dummy;
+    super(element, parent, name, dist, bootstrap);
   }
 
-  /**
-   * @param dummy
-   *                true if node is created for the representation of polytomous
-   *                trees
-   */
-  public boolean isDummy()
+  public SequenceNode(SequenceI element, BinaryNode<SequenceI> parent,
+          String name, double dist)
   {
-    return dummy;
+    super(element, parent, name, dist);
   }
 
   /*
@@ -122,24 +68,8 @@ public class SequenceNode extends BinaryNode
   /**
    * DOCUMENT ME!
    * 
-   * @param newstate
-   *                DOCUMENT ME!
-   * 
-   * @return DOCUMENT ME!
-   */
-  public boolean setDummy(boolean newstate)
-  {
-    boolean oldstate = dummy;
-    dummy = newstate;
-
-    return oldstate;
-  }
-
-  /**
-   * DOCUMENT ME!
-   * 
    * @param Placeholder
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public void setPlaceholder(boolean Placeholder)
   {
@@ -147,23 +77,6 @@ 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
    * 
@@ -177,7 +90,9 @@ public class SequenceNode extends BinaryNode
       {
         char q = name.charAt(c);
         if ('0' <= q && q <= '9')
+        {
           continue;
+        }
         return true;
       }
     }