X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FVAMSAS.java;h=dc4837c2d297e9c9a90732cfcadeaf650fa0ec14;hb=8dbf6e85ebb3dbcd84635f194457cd4dc65010cf;hp=c06de295e68d9d8763e8bba6b772c15013ee9c94;hpb=4d7f98a6dd54d9863ba449ec79dcd95d25ed863d;p=jalview.git

diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
index c06de29..dc4837c 100644
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,3 +1,23 @@
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $(date) The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *  
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ *******************************************************************************/
 /*
  * This class was automatically generated with 
  * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
@@ -105,7 +125,8 @@ public class VAMSAS implements java.io.Serializable
    * @throws java.lang.IndexOutOfBoundsException
    *           if the index given is outside the bounds of the collection
    */
-  public void addSequenceSet(final int index, final SequenceSet vSequenceSet)
+  public void addSequenceSet(final int index,
+          final SequenceSet vSequenceSet)
           throws java.lang.IndexOutOfBoundsException
   {
     this._sequenceSetList.add(index, vSequenceSet);
@@ -182,9 +203,9 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._alignmentList.size())
     {
-      throw new IndexOutOfBoundsException("getAlignment: Index value '"
-              + index + "' not in range [0.."
-              + (this._alignmentList.size() - 1) + "]");
+      throw new IndexOutOfBoundsException(
+              "getAlignment: Index value '" + index + "' not in range [0.."
+                      + (this._alignmentList.size() - 1) + "]");
     }
 
     return (Alignment) _alignmentList.get(index);
@@ -469,9 +490,9 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._alignmentList.size())
     {
-      throw new IndexOutOfBoundsException("setAlignment: Index value '"
-              + index + "' not in range [0.."
-              + (this._alignmentList.size() - 1) + "]");
+      throw new IndexOutOfBoundsException(
+              "setAlignment: Index value '" + index + "' not in range [0.."
+                      + (this._alignmentList.size() - 1) + "]");
     }
 
     this._alignmentList.set(index, vAlignment);
@@ -501,7 +522,8 @@ public class VAMSAS implements java.io.Serializable
    * @throws java.lang.IndexOutOfBoundsException
    *           if the index given is outside the bounds of the collection
    */
-  public void setSequenceSet(final int index, final SequenceSet vSequenceSet)
+  public void setSequenceSet(final int index,
+          final SequenceSet vSequenceSet)
           throws java.lang.IndexOutOfBoundsException
   {
     // check bounds for index
@@ -579,12 +601,13 @@ public class VAMSAS implements java.io.Serializable
    *           if this object is an invalid instance according to the schema
    * @return the unmarshaled jalview.binding.VAMSAS
    */
-  public static jalview.binding.VAMSAS unmarshal(final java.io.Reader reader)
+  public static jalview.binding.VAMSAS unmarshal(
+          final java.io.Reader reader)
           throws org.exolab.castor.xml.MarshalException,
           org.exolab.castor.xml.ValidationException
   {
-    return (jalview.binding.VAMSAS) Unmarshaller.unmarshal(
-            jalview.binding.VAMSAS.class, reader);
+    return (jalview.binding.VAMSAS) Unmarshaller
+            .unmarshal(jalview.binding.VAMSAS.class, reader);
   }
 
   /**