X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fbinding%2FVAMSAS.java;h=0bb696abc03a82b5a16820f45266590d6ae8bde0;hb=ab43013b7e357b84b4abade0dba949668dfb2a0e;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..0bb696a
--- a/src/jalview/binding/VAMSAS.java
+++ b/src/jalview/binding/VAMSAS.java
@@ -1,19 +1,22 @@
 /*
- * 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 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.
- * 
+ * 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.
  */
 package jalview.binding;
 
@@ -21,6 +24,8 @@ package jalview.binding;
 //- Imported classes and packages -/
 //---------------------------------/
 
+import jalview.util.MessageManager;
+
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 
@@ -192,9 +197,11 @@ 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+      		  "getAlignment",
+      		  Integer.valueOf(index).toString(),
+      		  Integer.valueOf((this._alignmentList.size() - 1)).toString()
+        })); 
     }
 
     return (Alignment) _alignmentList.get(index);
@@ -239,9 +246,11 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceSetList.size())
     {
-      throw new IndexOutOfBoundsException("getSequenceSet: Index value '"
-              + index + "' not in range [0.."
-              + (this._sequenceSetList.size() - 1) + "]");
+        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()
+          })); 
     }
 
     return (SequenceSet) _sequenceSetList.get(index);
@@ -286,8 +295,11 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._treeList.size())
     {
-      throw new IndexOutOfBoundsException("getTree: Index value '" + index
-              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+        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()
+        })); 
     }
 
     return (java.lang.String) _treeList.get(index);
@@ -479,9 +491,11 @@ 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(MessageManager.formatMessage("exception.index_value_not_in_range", new String[]{
+        		  "setAlignment",
+        		  Integer.valueOf(index).toString(),
+        		  Integer.valueOf((this._alignmentList.size() - 1)).toString()
+          })); 
     }
 
     this._alignmentList.set(index, vAlignment);
@@ -517,9 +531,11 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceSetList.size())
     {
-      throw new IndexOutOfBoundsException("setSequenceSet: Index value '"
-              + index + "' not in range [0.."
-              + (this._sequenceSetList.size() - 1) + "]");
+        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()
+        })); 
     }
 
     this._sequenceSetList.set(index, vSequenceSet);
@@ -555,8 +571,11 @@ public class VAMSAS implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._treeList.size())
     {
-      throw new IndexOutOfBoundsException("setTree: Index value '" + index
-              + "' not in range [0.." + (this._treeList.size() - 1) + "]");
+        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()
+          })); 
     }
 
     this._treeList.set(index, vTree);