X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fdatamodel%2FSequenceNode.java;h=943751e622628c4a81ba8af980a53fb170e5e202;hb=1698842ec6755d1995dae7c1a590efbfc8f6e4d5;hp=ac2e9e25eb6bd7865c0e3a58a2a592a9f85b588e;hpb=efc31b4a8d5cee63555586804a2b79c06bdb5a14;p=jalview.git

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index ac2e9e2..943751e 100755
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
@@ -20,130 +20,130 @@ package jalview.datamodel;
 
 import java.awt.*;
 
-
 /**
  * DOCUMENT ME!
  *
  * @author $author$
  * @version $Revision$
  */
-public class SequenceNode extends BinaryNode
+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;
-
-    /**
-     * Creates a new SequenceNode object.
-     */
-    public SequenceNode()
-    {
-        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)
-    {
-        super(val, parent, name);
-        this.dist = dist;
-    }
-
-    /**
-     * 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()
-    {
-        return dummy;
-    }
-
-    /* @param placeholder is true if the sequence refered to in the
-     *  element node is not actually present in the associated alignment
-     */
-    public boolean isPlaceholder()
+  /** 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;
+
+  /**
+   * Creates a new SequenceNode object.
+   */
+  public SequenceNode()
+  {
+    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)
+  {
+    super(val, parent, name);
+    this.dist = dist;
+  }
+
+  /**
+   * 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()
+  {
+    return dummy;
+  }
+
+  /* @param placeholder is true if the sequence refered to in the
+   *  element node is not actually present in the associated alignment
+   */
+  public boolean isPlaceholder()
+  {
+    return placeholder;
+  }
+
+  /**
+   * 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;
+  }
+
+  /**
+   * 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
     {
-        return placeholder;
-    }
-
-    /**
-     * DOCUMENT ME!
-     *
-     * @param newstate DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public boolean setDummy(boolean newstate)
-    {
-        boolean oldstate = dummy;
-        dummy = newstate;
-
-        return oldstate;
+      c = (SequenceNode) c.parent();
     }
+    while ( (c != null) && c.dummy);
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param Placeholder DOCUMENT ME!
-     */
-    public void setPlaceholder(boolean Placeholder)
-    {
-        this.placeholder = Placeholder;
-    }
-
-    /**
-     * 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;
-    }
+    return c;
+  }
 }