JAL-1620 version bump and release notes

[jalview.git] / src / jalview / schemabinding / version2 / SequenceSet.java

diff --git a/src/jalview/schemabinding/version2/SequenceSet.java b/src/jalview/schemabinding/version2/SequenceSet.java
index 8be8022..347df4a 100644 (file)
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.java
@@ -1,16 +1,31 @@
 /*
- * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
- * Schema.
- * $Id$
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
+ * Copyright (C) 2014 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.
  */
-
 package jalview.schemabinding.version2;
 
 //---------------------------------/
 //- Imported classes and packages -/
 //---------------------------------/
 
+import jalview.util.MessageManager;
+
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 
@@ -251,9 +266,11 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._alcodonFrameList.size())
     {
-      throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '"
-              + index + "' not in range [0.."
-              + (this._alcodonFrameList.size() - 1) + "]");
+        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+                         "getAlcodonFrame",
+                         Integer.valueOf(index).toString(),
+                         Integer.valueOf((this._alcodonFrameList.size() - 1)).toString()
+          })); 
     }
 
     return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList
@@ -301,9 +318,11 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._annotationList.size())
     {
-      throw new IndexOutOfBoundsException("getAnnotation: Index value '"
-              + index + "' not in range [0.."
-              + (this._annotationList.size() - 1) + "]");
+        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+                 "getAnnotation",
+                 Integer.valueOf(index).toString(),
+                 Integer.valueOf((this._alcodonFrameList.size() - 1)).toString()
+        })); 
     }
 
     return (jalview.schemabinding.version2.Annotation) _annotationList
@@ -374,9 +393,11 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceList.size())
     {
-      throw new IndexOutOfBoundsException("getSequence: Index value '"
-              + index + "' not in range [0.."
-              + (this._sequenceList.size() - 1) + "]");
+        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+                         "getSequence",
+                         Integer.valueOf(index).toString(),
+                         Integer.valueOf((this._sequenceList.size() - 1)).toString()
+          })); 
     }
 
     return (jalview.schemabinding.version2.Sequence) _sequenceList
@@ -425,10 +446,11 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceSetPropertiesList.size())
     {
-      throw new IndexOutOfBoundsException(
-              "getSequenceSetProperties: Index value '" + index
-                      + "' not in range [0.."
-                      + (this._sequenceSetPropertiesList.size() - 1) + "]");
+        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+                 "getSequenceSetProperties",
+                 Integer.valueOf(index).toString(),
+                 Integer.valueOf((this._sequenceSetPropertiesList.size() - 1)).toString()
+        })); 
     }
 
     return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList
@@ -664,9 +686,11 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._alcodonFrameList.size())
     {
-      throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '"
-              + index + "' not in range [0.."
-              + (this._alcodonFrameList.size() - 1) + "]");
+        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+                         "setAlcodonFrame",
+                         Integer.valueOf(index).toString(),
+                         Integer.valueOf((this._alcodonFrameList.size() - 1)).toString()
+          })); 
     }
 
     this._alcodonFrameList.set(index, vAlcodonFrame);
@@ -704,9 +728,11 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._annotationList.size())
     {
-      throw new IndexOutOfBoundsException("setAnnotation: Index value '"
-              + index + "' not in range [0.."
-              + (this._annotationList.size() - 1) + "]");
+        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+                 "setAnnotation",
+                 Integer.valueOf(index).toString(),
+                 Integer.valueOf((this._annotationList.size() - 1)).toString()
+        })); 
     }
 
     this._annotationList.set(index, vAnnotation);
@@ -769,9 +795,11 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceList.size())
     {
-      throw new IndexOutOfBoundsException("setSequence: Index value '"
-              + index + "' not in range [0.."
-              + (this._sequenceList.size() - 1) + "]");
+        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+                         "setSequence",
+                         Integer.valueOf(index).toString(),
+                         Integer.valueOf((this._sequenceList.size() - 1)).toString()
+          })); 
     }
 
     this._sequenceList.set(index, vSequence);
@@ -810,10 +838,11 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceSetPropertiesList.size())
     {
-      throw new IndexOutOfBoundsException(
-              "setSequenceSetProperties: Index value '" + index
-                      + "' not in range [0.."
-                      + (this._sequenceSetPropertiesList.size() - 1) + "]");
+        throw new IndexOutOfBoundsException(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+                 "setSequenceSetProperties",
+                 Integer.valueOf(index).toString(),
+                 Integer.valueOf((this._sequenceSetPropertiesList.size() - 1)).toString()
+        })); 
     }
 
     this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);