JAL-3806 more lax allowance (3 positions) for stop codon

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

diff --git a/src/jalview/datamodel/BinaryNode.java b/src/jalview/datamodel/BinaryNode.java
index 0a22419..c0ff0e4 100755 (executable)
--- a/src/jalview/datamodel/BinaryNode.java
+++ b/src/jalview/datamodel/BinaryNode.java
@@ -1,20 +1,22 @@
 /*
- * 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;
 
@@ -52,11 +54,11 @@ public class BinaryNode
    * Creates a new BinaryNode object.
    * 
    * @param element
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param parent
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * @param name
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    */
   public BinaryNode(Object element, BinaryNode parent, String name)
   {
@@ -81,7 +83,7 @@ public class BinaryNode
    * DOCUMENT ME!
    * 
    * @param v
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -104,7 +106,7 @@ public class BinaryNode
    * DOCUMENT ME!
    * 
    * @param n
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -127,7 +129,7 @@ public class BinaryNode
    * DOCUMENT ME!
    * 
    * @param n
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -150,7 +152,7 @@ public class BinaryNode
    * DOCUMENT ME!
    * 
    * @param n
-   *                DOCUMENT ME!
+   *          DOCUMENT ME!
    * 
    * @return DOCUMENT ME!
    */
@@ -260,7 +262,9 @@ public class BinaryNode
   /**
    * 
    * set the display name
-   * @param new name
+   * 
+   * @param new
+   *          name
    */
   public void setName(String name)
   {
@@ -288,7 +292,8 @@ public class BinaryNode
   }
 
   /**
-   * get bootstrap 
+   * get bootstrap
+   * 
    * @return integer value
    */
   public int getBootstrap()