Formatting

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

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index 905bd15..943751e 100755 (executable)
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,54 +1,149 @@
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ *\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA\r
+ */\r
 package jalview.datamodel;\r
 \r
-import java.awt.Color;\r
-\r
-public class SequenceNode extends BinaryNode {\r
+import java.awt.*;\r
 \r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SequenceNode\r
+    extends BinaryNode\r
+{\r
+  /** DOCUMENT ME!! */\r
   public float dist;\r
+\r
+  /** DOCUMENT ME!! */\r
   public int count;\r
+\r
+  /** DOCUMENT ME!! */\r
   public float height;\r
+\r
+  /** DOCUMENT ME!! */\r
   public float ycount;\r
+\r
+  /** DOCUMENT ME!! */\r
   public Color color = Color.black;\r
+\r
+  /** DOCUMENT ME!! */\r
   public boolean dummy = false;\r
-  public SequenceNode() {\r
+  private boolean placeholder = false;\r
+\r
+  /**\r
+   * Creates a new SequenceNode object.\r
+   */\r
+  public SequenceNode()\r
+  {\r
     super();\r
   }\r
 \r
-  public SequenceNode(Object val, SequenceNode parent, float dist,String name) {\r
-    super(val,parent,name);\r
+  /**\r
+   * Creates a new SequenceNode object.\r
+   *\r
+   * @param val DOCUMENT ME!\r
+   * @param parent DOCUMENT ME!\r
+   * @param dist DOCUMENT ME!\r
+   * @param name DOCUMENT ME!\r
+   */\r
+  public SequenceNode(Object val, SequenceNode parent, float dist, String name)\r
+  {\r
+    super(val, parent, name);\r
     this.dist = dist;\r
   }\r
-  public SequenceNode(Object val, SequenceNode parent, String name, float dist, int bootstrap, boolean dummy) {\r
-    super(val,parent,name);\r
+\r
+  /**\r
+   * Creates a new SequenceNode object.\r
+   *\r
+   * @param val DOCUMENT ME!\r
+   * @param parent DOCUMENT ME!\r
+   * @param name DOCUMENT ME!\r
+   * @param dist DOCUMENT ME!\r
+   * @param bootstrap DOCUMENT ME!\r
+   * @param dummy DOCUMENT ME!\r
+   */\r
+  public SequenceNode(Object val, SequenceNode parent, String name,\r
+                      float dist, int bootstrap, boolean dummy)\r
+  {\r
+    super(val, parent, name);\r
     this.dist = dist;\r
     this.bootstrap = bootstrap;\r
     this.dummy = dummy;\r
   }\r
 \r
-\r
   /**\r
    * @param dummy true if node is created for the representation of polytomous trees\r
    */\r
-\r
-  public boolean isDummy() {\r
+  public boolean isDummy()\r
+  {\r
     return dummy;\r
   }\r
-  public boolean setDummy(boolean newstate) {\r
+\r
+  /* @param placeholder is true if the sequence refered to in the\r
+   *  element node is not actually present in the associated alignment\r
+   */\r
+  public boolean isPlaceholder()\r
+  {\r
+    return placeholder;\r
+  }\r
+\r
+  /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param newstate DOCUMENT ME!\r
+   *\r
+   * @return DOCUMENT ME!\r
+   */\r
+  public boolean setDummy(boolean newstate)\r
+  {\r
     boolean oldstate = dummy;\r
     dummy = newstate;\r
+\r
     return oldstate;\r
   }\r
 \r
   /**\r
+   * DOCUMENT ME!\r
+   *\r
+   * @param Placeholder DOCUMENT ME!\r
+   */\r
+  public void setPlaceholder(boolean Placeholder)\r
+  {\r
+    this.placeholder = Placeholder;\r
+  }\r
+\r
+  /**\r
    * ascends the tree but doesn't stop until a non-dummy node is discovered.\r
    * This will probably break if the tree is a mixture of BinaryNodes and SequenceNodes.\r
    */\r
-\r
-  public SequenceNode AscendTree() {\r
+  public SequenceNode AscendTree()\r
+  {\r
     SequenceNode c = this;\r
-    do {\r
+\r
+    do\r
+    {\r
       c = (SequenceNode) c.parent();\r
-    } while (c!=null && c.dummy);\r
+    }\r
+    while ( (c != null) && c.dummy);\r
+\r
     return c;\r
   }\r
 }\r