X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceNode.java;h=943751e622628c4a81ba8af980a53fb170e5e202;hb=1698842ec6755d1995dae7c1a590efbfc8f6e4d5;hp=5e16c57e7473dce69b334c573776ddadcd9bad3e;hpb=c3db82330376f20423dc617cfa92d131dc40e515;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 5e16c57..943751e 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,40 +1,102 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * 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 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.
+ *
+ * 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
+ */
 package jalview.datamodel;
 
 import java.awt.*;
 
-public class SequenceNode extends BinaryNode {
-
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SequenceNode
+    extends BinaryNode
+{
+  /** 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;
 
-  public SequenceNode() {
+  /**
+   * Creates a new SequenceNode object.
+   */
+  public SequenceNode()
+  {
     super();
   }
 
-  public SequenceNode(Object val, SequenceNode parent, float dist,String name) {
-    super(val,parent,name);
+  /**
+   * 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)
+  {
+    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);
+
+  /**
+   * 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)
+  {
+    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() {
+  public boolean isDummy()
+  {
     return dummy;
   }
+
   /* @param placeholder is true if the sequence refered to in the
    *  element node is not actually present in the associated alignment
    */
@@ -43,12 +105,26 @@ public class SequenceNode extends BinaryNode {
     return placeholder;
   }
 
-  public boolean setDummy(boolean newstate) {
+  /**
+   * 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!
+   */
   public void setPlaceholder(boolean Placeholder)
   {
     this.placeholder = Placeholder;
@@ -58,12 +134,16 @@ 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() {
+  public SequenceNode AscendTree()
+  {
     SequenceNode c = this;
-    do {
+
+    do
+    {
       c = (SequenceNode) c.parent();
-    } while (c!=null && c.dummy);
+    }
+    while ( (c != null) && c.dummy);
+
     return c;
   }
 }