X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FVAMSAS.java;h=dc4837c2d297e9c9a90732cfcadeaf650fa0ec14;hb=8dbf6e85ebb3dbcd84635f194457cd4dc65010cf;hp=d7610d41fb6d0b1a450cbe308b3d4dc7a1e29ee1;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
old mode 100755
new mode 100644
index d7610d4..dc4837c
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,20 +1,30 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
+/*******************************************************************************
+ * 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.
- * 
+ * 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/>.
+ *
+ * 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
+ * Schema.
+ * $Id$
  */
+
 package jalview.binding;
 
 //---------------------------------/
@@ -115,7 +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);
@@ -192,9 +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);
@@ -479,9 +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);
@@ -511,7 +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
@@ -589,12 +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);
   }
 
   /**