JAL-3120 preserve feature colour/mincolour/maxcolour while modifying,

[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 e20bd57..8be8022 100644 (file)
--- a/src/jalview/schemabinding/version2/SequenceSet.java
+++ b/src/jalview/schemabinding/version2/SequenceSet.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.schemabinding.version2;
 
 //---------------------------------/
 //- Imported classes and packages -/
 //---------------------------------/
 
-import jalview.util.MessageManager;
-
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
 
@@ -266,11 +251,9 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._alcodonFrameList.size())
     {
-        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()
-          })); 
+      throw new IndexOutOfBoundsException("getAlcodonFrame: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodonFrameList.size() - 1) + "]");
     }
 
     return (jalview.schemabinding.version2.AlcodonFrame) _alcodonFrameList
@@ -318,11 +301,9 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._annotationList.size())
     {
-        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()
-        })); 
+      throw new IndexOutOfBoundsException("getAnnotation: Index value '"
+              + index + "' not in range [0.."
+              + (this._annotationList.size() - 1) + "]");
     }
 
     return (jalview.schemabinding.version2.Annotation) _annotationList
@@ -393,11 +374,9 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceList.size())
     {
-        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()
-          })); 
+      throw new IndexOutOfBoundsException("getSequence: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceList.size() - 1) + "]");
     }
 
     return (jalview.schemabinding.version2.Sequence) _sequenceList
@@ -446,11 +425,10 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceSetPropertiesList.size())
     {
-        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()
-        })); 
+      throw new IndexOutOfBoundsException(
+              "getSequenceSetProperties: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._sequenceSetPropertiesList.size() - 1) + "]");
     }
 
     return (jalview.schemabinding.version2.SequenceSetProperties) _sequenceSetPropertiesList
@@ -686,11 +664,9 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._alcodonFrameList.size())
     {
-        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()
-          })); 
+      throw new IndexOutOfBoundsException("setAlcodonFrame: Index value '"
+              + index + "' not in range [0.."
+              + (this._alcodonFrameList.size() - 1) + "]");
     }
 
     this._alcodonFrameList.set(index, vAlcodonFrame);
@@ -728,11 +704,9 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._annotationList.size())
     {
-        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()
-        })); 
+      throw new IndexOutOfBoundsException("setAnnotation: Index value '"
+              + index + "' not in range [0.."
+              + (this._annotationList.size() - 1) + "]");
     }
 
     this._annotationList.set(index, vAnnotation);
@@ -795,11 +769,9 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceList.size())
     {
-        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()
-          })); 
+      throw new IndexOutOfBoundsException("setSequence: Index value '"
+              + index + "' not in range [0.."
+              + (this._sequenceList.size() - 1) + "]");
     }
 
     this._sequenceList.set(index, vSequence);
@@ -838,11 +810,10 @@ public class SequenceSet implements java.io.Serializable
     // check bounds for index
     if (index < 0 || index >= this._sequenceSetPropertiesList.size())
     {
-        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()
-        })); 
+      throw new IndexOutOfBoundsException(
+              "setSequenceSetProperties: Index value '" + index
+                      + "' not in range [0.."
+                      + (this._sequenceSetPropertiesList.size() - 1) + "]");
     }
 
     this._sequenceSetPropertiesList.set(index, vSequenceSetProperties);