New schema, new objects

[jalview.git] / src / org / vamsas / objects / core / Alignment.java

diff --git a/src/org/vamsas/objects/core/Alignment.java b/src/org/vamsas/objects/core/Alignment.java
index 8143217..e3aa240 100755 (executable)
--- a/src/org/vamsas/objects/core/Alignment.java
+++ b/src/org/vamsas/objects/core/Alignment.java
@@ -1,6 +1,6 @@
 /*\r
  * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML\r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
  * Schema.\r
  * $Id$\r
  */\r
@@ -80,8 +80,7 @@ public class Alignment implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public Alignment() \r
-     {\r
+    public Alignment() {\r
         super();\r
         _alignmentAnnotationsList = new Vector();\r
         _treeList = new Vector();\r
@@ -243,7 +242,7 @@ public class Alignment implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _alignmentAnnotationsList.size())) {\r
-            throw new IndexOutOfBoundsException("getAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.AlignmentAnnotations) _alignmentAnnotationsList.elementAt(index);\r
@@ -291,7 +290,7 @@ public class Alignment implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _alignmentSequenceList.size())) {\r
-            throw new IndexOutOfBoundsException("getAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.AlignmentSequence) _alignmentSequenceList.elementAt(index);\r
@@ -372,7 +371,7 @@ public class Alignment implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _treeList.size())) {\r
-            throw new IndexOutOfBoundsException("getTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.Tree) _treeList.elementAt(index);\r
@@ -561,7 +560,7 @@ public class Alignment implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _alignmentAnnotationsList.size())) {\r
-            throw new IndexOutOfBoundsException("setAlignmentAnnotations: Index value '"+index+"' not in range [0.."+_alignmentAnnotationsList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _alignmentAnnotationsList.setElementAt(vAlignmentAnnotations, index);\r
     } //-- void setAlignmentAnnotations(int, org.vamsas.objects.core.AlignmentAnnotations) \r
@@ -595,7 +594,7 @@ public class Alignment implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _alignmentSequenceList.size())) {\r
-            throw new IndexOutOfBoundsException("setAlignmentSequence: Index value '"+index+"' not in range [0.."+_alignmentSequenceList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _alignmentSequenceList.setElementAt(vAlignmentSequence, index);\r
     } //-- void setAlignmentSequence(int, org.vamsas.objects.core.AlignmentSequence) \r
@@ -659,7 +658,7 @@ public class Alignment implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _treeList.size())) {\r
-            throw new IndexOutOfBoundsException("setTree: Index value '"+index+"' not in range [0.."+_treeList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _treeList.setElementAt(vTree, index);\r
     } //-- void setTree(int, org.vamsas.objects.core.Tree) \r
@@ -686,13 +685,13 @@ public class Alignment implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return Alignment\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.Alignment unmarshal(java.io.Reader reader)\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
         throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
     {\r
         return (org.vamsas.objects.core.Alignment) Unmarshaller.unmarshal(org.vamsas.objects.core.Alignment.class, reader);\r
-    } //-- org.vamsas.objects.core.Alignment unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r