X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FVAMSAS.java;h=b5a32da99851eb7d9a7b909dc3cdb9f22cd8211c;hb=f063821ed0be9c1581af74643a1aa5798731af65;hp=d7f98ceba006ce78cce718768116ad424781325a;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git

diff --git a/src/jalview/binding/VAMSAS.java b/src/jalview/binding/VAMSAS.java
index d7f98ce..b5a32da 100644
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,31 +1,16 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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
+ * Schema.
+ * $Id$
  */
+
 package jalview.binding;
 
 //---------------------------------/
 //- Imported classes and packages -/
 //---------------------------------/
 
-import jalview.util.MessageManager;
-
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 
@@ -120,7 +105,8 @@ 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);
@@ -197,11 +183,9 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._alignmentList.size())
     {
-        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-      		  "getAlignment",
-      		  Integer.valueOf(index).toString(),
-      		  Integer.valueOf((this._alignmentList.size() - 1)).toString()
-        })); 
+      throw new IndexOutOfBoundsException(
+              "getAlignment: Index value '" + index + "' not in range [0.."
+                      + (this._alignmentList.size() - 1) + "]");
     }
 
     return (Alignment) _alignmentList.get(index);
@@ -246,11 +230,9 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceSetList.size())
     {
-        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-        		  "getSequenceSet",
-        		  Integer.valueOf(index).toString(),
-        		  Integer.valueOf((this._sequenceSetList.size() - 1)).toString()
-          })); 
+      throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceSetList.size() - 1) + "]");
     }
 
     return (SequenceSet) _sequenceSetList.get(index);
@@ -295,11 +277,8 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._treeList.size())
     {
-        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-      		  "getTree",
-      		  Integer.valueOf(index).toString(),
-      		  Integer.valueOf((this._treeList.size() - 1)).toString()
-        })); 
+      throw new IndexOutOfBoundsException("getTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
     }
 
     return (java.lang.String) _treeList.get(index);
@@ -491,11 +470,9 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._alignmentList.size())
     {
-        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-        		  "setAlignment",
-        		  Integer.valueOf(index).toString(),
-        		  Integer.valueOf((this._alignmentList.size() - 1)).toString()
-          })); 
+      throw new IndexOutOfBoundsException(
+              "setAlignment: Index value '" + index + "' not in range [0.."
+                      + (this._alignmentList.size() - 1) + "]");
     }
 
     this._alignmentList.set(index, vAlignment);
@@ -525,17 +502,16 @@ 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
     if (index < 0 || index >= this._sequenceSetList.size())
     {
-        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-      		  "setSequenceSet",
-      		  Integer.valueOf(index).toString(),
-      		  Integer.valueOf((this._sequenceSetList.size() - 1)).toString()
-        })); 
+      throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceSetList.size() - 1) + "]");
     }
 
     this._sequenceSetList.set(index, vSequenceSet);
@@ -571,11 +547,8 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._treeList.size())
     {
-        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
-        		  "setTree",
-        		  Integer.valueOf(index).toString(),
-        		  Integer.valueOf((this._treeList.size() - 1)).toString()
-          })); 
+      throw new IndexOutOfBoundsException("setTree: Index value '" + index
+              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
     }
 
     this._treeList.set(index, vTree);
@@ -608,12 +581,13 @@ 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);
   }
 
   /**