Formatting changes

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

diff --git a/src/jalview/datamodel/SequenceNode.java b/src/jalview/datamodel/SequenceNode.java
index f86c63e..ac2e9e2 100755 (executable)
--- a/src/jalview/datamodel/SequenceNode.java
+++ b/src/jalview/datamodel/SequenceNode.java
@@ -1,46 +1,88 @@
 /*\r
-* Jalview - A Sequence Alignment Editor and Viewer\r
-* Copyright (C) 2005 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
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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.*;\r
 \r
 \r
-public class SequenceNode extends BinaryNode {\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class SequenceNode 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
     private boolean placeholder = false;\r
 \r
-    public SequenceNode() {\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
+    /**\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
 \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
+        float dist, int bootstrap, boolean dummy)\r
+    {\r
         super(val, parent, name);\r
         this.dist = dist;\r
         this.bootstrap = bootstrap;\r
@@ -50,25 +92,41 @@ public class SequenceNode extends BinaryNode {
     /**\r
      * @param dummy true if node is created for the representation of polytomous trees\r
      */\r
-    public boolean isDummy() {\r
+    public boolean isDummy()\r
+    {\r
         return dummy;\r
     }\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
+    public boolean isPlaceholder()\r
+    {\r
         return placeholder;\r
     }\r
 \r
-    public boolean setDummy(boolean newstate) {\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
-    public void setPlaceholder(boolean Placeholder) {\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
@@ -76,12 +134,15 @@ public class SequenceNode extends BinaryNode {
      * 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
-    public SequenceNode AscendTree() {\r
+    public SequenceNode AscendTree()\r
+    {\r
         SequenceNode c = this;\r
 \r
-        do {\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