applied LGPLv3 and source code formatting.

[vamsas.git] / src / uk / ac / vamsas / objects / utils / trees / BinaryNode.java

diff --git a/src/uk/ac/vamsas/objects/utils/trees/BinaryNode.java b/src/uk/ac/vamsas/objects/utils/trees/BinaryNode.java
index bc41783..5cf8664 100644 (file)
--- a/src/uk/ac/vamsas/objects/utils/trees/BinaryNode.java
+++ b/src/uk/ac/vamsas/objects/utils/trees/BinaryNode.java
@@ -1,5 +1,23 @@
-/**\r
+/*\r
+ * This file is part of the Vamsas Client version 0.1. \r
+ * Copyright 2009 by Jim Procter, Iain Milne, Pierre Marguerite, \r
+ *  Andrew Waterhouse and Dominik Lindner.\r
  * \r
+ * Earlier versions have also been incorporated into Jalview version 2.4 \r
+ * since 2008, and TOPALi version 2 since 2007.\r
+ * \r
+ * The Vamsas Client is free software: you can redistribute it and/or modify\r
+ * it under the terms of the GNU Lesser General Public License as published by\r
+ * the Free Software Foundation, either version 3 of the License, or\r
+ * (at your option) any later version.\r
+ *  \r
+ * The Vamsas Client 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 Lesser General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU Lesser General Public License\r
+ * along with the Vamsas Client.  If not, see <http://www.gnu.org/licenses/>.\r
  */\r
 package uk.ac.vamsas.objects.utils.trees;\r
 \r
@@ -18,7 +36,7 @@ public class BinaryNode {
   BinaryNode parent;\r
 \r
   /** bootstrap is non-negative integer */\r
-  public int bootstrap=-1;\r
+  public int bootstrap = -1;\r
 \r
   /**\r
    * Creates a new BinaryNode object.\r
@@ -140,10 +158,10 @@ public class BinaryNode {
   }\r
 \r
   /**\r
-   * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children\r
-   * of this node (removing any old references) a null parameter DOES NOT mean\r
-   * that the pointer to the corresponding child node is set to NULL - you\r
-   * should use setChild(null), or detach() for this.\r
+   * attaches FIRST and SECOND node arguments as the LEFT and RIGHT children of\r
+   * this node (removing any old references) a null parameter DOES NOT mean that\r
+   * the pointer to the corresponding child node is set to NULL - you should use\r
+   * setChild(null), or detach() for this.\r
    * \r
    */\r
   public void SetChildren(BinaryNode leftchild, BinaryNode rightchild) {\r
@@ -253,26 +271,20 @@ public class BinaryNode {
   }\r
   /**\r
    * \r
-   * @return unquoted string of form VorbaId|v|node name string\r
-  public String getNewickNodeName() {\r
-    if (element!=null || name!=null)\r
-      {\r
-      return ((element!=null) ? element.getVorbaId().getId()+"|v|" : "")\r
-        + ((name == null) ? "" : name);\r
-      }\r
-    return "";\r
-  }\r
-  \r
-   * note we probably don't need this now\r
-\r
-   * public boolean parseNodeNameString(uk.ac.vamsas.client.ClientDocument binder)\r
-  {\r
-    \r
-    if (element==null && name!=null && name.indexOf("|v|")>-1)\r
-    {\r
-      element = binder.getObject(null).getVorbaId(); // TODO: fix THIS ! name.substring(0, name.indexOf("|v")));\r
-      \r
-    }\r
-    return false;\r
-  }*/\r
-}
\ No newline at end of file
+   * @return unquoted string of form VorbaId|v|node name string public String\r
+   *         getNewickNodeName() { if (element!=null || name!=null) { return\r
+   *         ((element!=null) ? element.getVorbaId().getId()+"|v|" : "") +\r
+   *         ((name == null) ? "" : name); } return ""; }\r
+   * \r
+   *         note we probably don't need this now\r
+   * \r
+   *         public boolean\r
+   *         parseNodeNameString(uk.ac.vamsas.client.ClientDocument binder) {\r
+   * \r
+   *         if (element==null && name!=null && name.indexOf("|v|")>-1) {\r
+   *         element = binder.getObject(null).getVorbaId(); // TODO: fix THIS !\r
+   *         name.substring(0, name.indexOf("|v")));\r
+   * \r
+   *         } return false; }\r
+   */\r
+}\r