New schema, new objects

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

diff --git a/src/org/vamsas/objects/core/AlignmentAnnotations.java b/src/org/vamsas/objects/core/AlignmentAnnotations.java
index 5b62ccd..fd5fece 100755 (executable)
--- a/src/org/vamsas/objects/core/AlignmentAnnotations.java
+++ b/src/org/vamsas/objects/core/AlignmentAnnotations.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
@@ -75,8 +75,7 @@ public class AlignmentAnnotations implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public AlignmentAnnotations() \r
-     {\r
+    public AlignmentAnnotations() {\r
         super();\r
         _annotationElementList = new Vector();\r
     } //-- org.vamsas.objects.core.AlignmentAnnotations()\r
@@ -147,7 +146,7 @@ public class AlignmentAnnotations implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _annotationElementList.size())) {\r
-            throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
@@ -332,7 +331,7 @@ public class AlignmentAnnotations implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _annotationElementList.size())) {\r
-            throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _annotationElementList.setElementAt(vAnnotationElement, index);\r
     } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) \r
@@ -410,13 +409,13 @@ public class AlignmentAnnotations implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return AlignmentAnnotations\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.AlignmentAnnotations 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.AlignmentAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentAnnotations.class, reader);\r
-    } //-- org.vamsas.objects.core.AlignmentAnnotations unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java b/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java
index fe187b6..1d95f72 100755 (executable)
--- a/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java
+++ b/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.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
@@ -53,8 +53,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
      //- Constructors -/\r
     //----------------/\r
 \r
-    public AlignmentAnnotationsDescriptor() \r
-     {\r
+    public AlignmentAnnotationsDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "AlignmentAnnotations";\r
@@ -62,13 +61,13 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _graph\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -94,10 +93,9 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _graph\r
@@ -111,7 +109,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -132,9 +130,8 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r
@@ -146,7 +143,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
         \r
         //-- _annotationElementList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -167,7 +164,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.AnnotationElement();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r
@@ -183,7 +180,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
         //-- _label\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -204,7 +201,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r
@@ -223,7 +220,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
         //-- _description\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -244,7 +241,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r
@@ -262,7 +259,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
         desc.setValidator(fieldValidator);\r
         //-- _provenance\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -283,7 +280,7 @@ public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.X
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Provenance();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r

diff --git a/src/org/vamsas/objects/core/AlignmentDescriptor.java b/src/org/vamsas/objects/core/AlignmentDescriptor.java
index 46c8c21..c02d0e7 100755 (executable)
--- a/src/org/vamsas/objects/core/AlignmentDescriptor.java
+++ b/src/org/vamsas/objects/core/AlignmentDescriptor.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
@@ -53,8 +53,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
      //- Constructors -/\r
     //----------------/\r
 \r
-    public AlignmentDescriptor() \r
-     {\r
+    public AlignmentDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "Alignment";\r
@@ -62,14 +61,14 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _gapChar\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -90,10 +89,9 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _gapChar\r
@@ -107,7 +105,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
         desc.setValidator(fieldValidator);\r
         //-- _aligned\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -135,9 +133,8 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _aligned\r
@@ -150,7 +147,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -171,9 +168,8 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r
@@ -185,7 +181,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
         \r
         //-- _alignmentAnnotationsList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentAnnotations.class, "_alignmentAnnotationsList", "AlignmentAnnotations", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -206,7 +202,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.AlignmentAnnotations();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(true);\r
@@ -220,7 +216,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
         desc.setValidator(fieldValidator);\r
         //-- _treeList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -241,7 +237,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Tree();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(true);\r
@@ -255,7 +251,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
         desc.setValidator(fieldValidator);\r
         //-- _alignmentSequenceList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentSequence.class, "_alignmentSequenceList", "alignmentSequence", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -276,7 +272,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.AlignmentSequence();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r
@@ -291,7 +287,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
         desc.setValidator(fieldValidator);\r
         //-- _provenance\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -312,7 +308,7 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Provenance();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r

diff --git a/src/org/vamsas/objects/core/AlignmentSequence.java b/src/org/vamsas/objects/core/AlignmentSequence.java
index 52ceee2..dcde8c4 100755 (executable)
--- a/src/org/vamsas/objects/core/AlignmentSequence.java
+++ b/src/org/vamsas/objects/core/AlignmentSequence.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
@@ -50,8 +50,7 @@ implements java.io.Serializable
      //- Constructors -/\r
     //----------------/\r
 \r
-    public AlignmentSequence() \r
-     {\r
+    public AlignmentSequence() {\r
         super();\r
     } //-- org.vamsas.objects.core.AlignmentSequence()\r
 \r
@@ -154,13 +153,13 @@ implements java.io.Serializable
      * \r
      * \r
      * @param reader\r
-     * @return SequenceType\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.SequenceType 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.AlignmentSequence) Unmarshaller.unmarshal(org.vamsas.objects.core.AlignmentSequence.class, reader);\r
-    } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java
index 4a722b8..c50f916 100755 (executable)
--- a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java
+++ b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.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
@@ -53,21 +53,20 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc
      //- Constructors -/\r
     //----------------/\r
 \r
-    public AlignmentSequenceDescriptor() \r
-     {\r
+    public AlignmentSequenceDescriptor() {\r
         super();\r
         setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor());\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "alignmentSequence";\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -88,9 +87,8 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r
@@ -101,7 +99,7 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc
         //-- _refid\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_refid", "refid", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setReference(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -122,10 +120,9 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.Object();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _refid\r

diff --git a/src/org/vamsas/objects/core/AnnotationElement.java b/src/org/vamsas/objects/core/AnnotationElement.java
index b0d2682..f9c0e8c 100755 (executable)
--- a/src/org/vamsas/objects/core/AnnotationElement.java
+++ b/src/org/vamsas/objects/core/AnnotationElement.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
@@ -78,8 +78,7 @@ public class AnnotationElement implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public AnnotationElement() \r
-     {\r
+    public AnnotationElement() {\r
         super();\r
     } //-- org.vamsas.objects.core.AnnotationElement()\r
 \r
@@ -311,13 +310,13 @@ public class AnnotationElement implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return AnnotationElement\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.AnnotationElement 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.AnnotationElement) Unmarshaller.unmarshal(org.vamsas.objects.core.AnnotationElement.class, reader);\r
-    } //-- org.vamsas.objects.core.AnnotationElement unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java b/src/org/vamsas/objects/core/AnnotationElementDescriptor.java
index d02838b..24c55e6 100755 (executable)
--- a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java
+++ b/src/org/vamsas/objects/core/AnnotationElementDescriptor.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
@@ -53,8 +53,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
      //- Constructors -/\r
     //----------------/\r
 \r
-    public AnnotationElementDescriptor() \r
-     {\r
+    public AnnotationElementDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "annotationElement";\r
@@ -62,13 +61,13 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _position\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -94,24 +93,23 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _position\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         fieldValidator.setMinOccurs(1);\r
         { //-- local scope\r
-            IntegerValidator typeValidator= new IntegerValidator();\r
+            IntegerValidator typeValidator = new IntegerValidator();\r
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -132,9 +130,8 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r
@@ -147,7 +144,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
         //-- _displayCharacter\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -168,7 +165,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(false);\r
@@ -185,7 +182,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
         //-- _description\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -206,7 +203,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(false);\r
@@ -223,7 +220,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
         //-- _secondaryStructure\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -244,7 +241,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(false);\r
@@ -261,7 +258,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
         desc.setValidator(fieldValidator);\r
         //-- _value\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_value", "value", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -289,7 +286,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(false);\r

diff --git a/src/org/vamsas/objects/core/Application.java b/src/org/vamsas/objects/core/Application.java
index 94b8e84..5283c35 100755 (executable)
--- a/src/org/vamsas/objects/core/Application.java
+++ b/src/org/vamsas/objects/core/Application.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
@@ -65,8 +65,7 @@ public class Application implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public Application() \r
-     {\r
+    public Application() {\r
         super();\r
         _userList = new Vector();\r
     } //-- org.vamsas.objects.core.Application()\r
@@ -161,7 +160,7 @@ public class Application implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _userList.size())) {\r
-            throw new IndexOutOfBoundsException("getUser: Index value '"+index+"' not in range [0.."+_userList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.User) _userList.elementAt(index);\r
@@ -320,7 +319,7 @@ public class Application implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _userList.size())) {\r
-            throw new IndexOutOfBoundsException("setUser: Index value '"+index+"' not in range [0.."+_userList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _userList.setElementAt(vUser, index);\r
     } //-- void setUser(int, org.vamsas.objects.core.User) \r
@@ -357,13 +356,13 @@ public class Application implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return Application\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.Application 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.Application) Unmarshaller.unmarshal(org.vamsas.objects.core.Application.class, reader);\r
-    } //-- org.vamsas.objects.core.Application unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/ApplicationData.java b/src/org/vamsas/objects/core/ApplicationData.java
index d775ea5..bf61e7b 100755 (executable)
--- a/src/org/vamsas/objects/core/ApplicationData.java
+++ b/src/org/vamsas/objects/core/ApplicationData.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
@@ -45,8 +45,7 @@ public class ApplicationData implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public ApplicationData() \r
-     {\r
+    public ApplicationData() {\r
         super();\r
         _applicationList = new Vector();\r
     } //-- org.vamsas.objects.core.ApplicationData()\r
@@ -108,7 +107,7 @@ public class ApplicationData implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _applicationList.size())) {\r
-            throw new IndexOutOfBoundsException("getApplication: Index value '"+index+"' not in range [0.."+_applicationList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.Application) _applicationList.elementAt(index);\r
@@ -226,7 +225,7 @@ public class ApplicationData implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _applicationList.size())) {\r
-            throw new IndexOutOfBoundsException("setApplication: Index value '"+index+"' not in range [0.."+_applicationList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _applicationList.setElementAt(vApplication, index);\r
     } //-- void setApplication(int, org.vamsas.objects.core.Application) \r
@@ -253,13 +252,13 @@ public class ApplicationData implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return ApplicationData\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.ApplicationData 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.ApplicationData) Unmarshaller.unmarshal(org.vamsas.objects.core.ApplicationData.class, reader);\r
-    } //-- org.vamsas.objects.core.ApplicationData unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/ApplicationDataDescriptor.java b/src/org/vamsas/objects/core/ApplicationDataDescriptor.java
index b7ef5b5..ac7225f 100755 (executable)
--- a/src/org/vamsas/objects/core/ApplicationDataDescriptor.java
+++ b/src/org/vamsas/objects/core/ApplicationDataDescriptor.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
@@ -53,8 +53,7 @@ public class ApplicationDataDescriptor extends org.exolab.castor.xml.util.XMLCla
      //- Constructors -/\r
     //----------------/\r
 \r
-    public ApplicationDataDescriptor() \r
-     {\r
+    public ApplicationDataDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "ApplicationData";\r
@@ -62,7 +61,7 @@ public class ApplicationDataDescriptor extends org.exolab.castor.xml.util.XMLCla
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
@@ -70,7 +69,7 @@ public class ApplicationDataDescriptor extends org.exolab.castor.xml.util.XMLCla
         \r
         //-- _applicationList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Application.class, "_applicationList", "Application", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -91,7 +90,7 @@ public class ApplicationDataDescriptor extends org.exolab.castor.xml.util.XMLCla
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Application();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(true);\r

diff --git a/src/org/vamsas/objects/core/ApplicationDescriptor.java b/src/org/vamsas/objects/core/ApplicationDescriptor.java
index e6be012..ef61bd7 100755 (executable)
--- a/src/org/vamsas/objects/core/ApplicationDescriptor.java
+++ b/src/org/vamsas/objects/core/ApplicationDescriptor.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
@@ -53,8 +53,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
      //- Constructors -/\r
     //----------------/\r
 \r
-    public ApplicationDescriptor() \r
-     {\r
+    public ApplicationDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "Application";\r
@@ -62,14 +61,14 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _version\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -90,10 +89,9 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _version\r
@@ -108,7 +106,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         //-- _name\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -129,10 +127,9 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _name\r
@@ -147,7 +144,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         //-- _urn\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -168,10 +165,9 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _urn\r
@@ -186,7 +182,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         //-- _data\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_data", "data", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -207,10 +203,9 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _data\r
@@ -226,7 +221,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         \r
         //-- _userList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.User.class, "_userList", "User", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -247,7 +242,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.User();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r

diff --git a/src/org/vamsas/objects/core/DataSet.java b/src/org/vamsas/objects/core/DataSet.java
index b3d6671..4de0939 100755 (executable)
--- a/src/org/vamsas/objects/core/DataSet.java
+++ b/src/org/vamsas/objects/core/DataSet.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
@@ -70,8 +70,7 @@ public class DataSet implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public DataSet() \r
-     {\r
+    public DataSet() {\r
         super();\r
         _sequenceList = new Vector();\r
         _dataSetAnnotationsList = new Vector();\r
@@ -253,7 +252,7 @@ public class DataSet implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _alignmentList.size())) {\r
-            throw new IndexOutOfBoundsException("getAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.Alignment) _alignmentList.elementAt(index);\r
@@ -301,7 +300,7 @@ public class DataSet implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _dataSetAnnotationsList.size())) {\r
-            throw new IndexOutOfBoundsException("getDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.DataSetAnnotations) _dataSetAnnotationsList.elementAt(index);\r
@@ -371,7 +370,7 @@ public class DataSet implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _sequenceList.size())) {\r
-            throw new IndexOutOfBoundsException("getSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.Sequence) _sequenceList.elementAt(index);\r
@@ -419,7 +418,7 @@ public class DataSet 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
@@ -609,7 +608,7 @@ public class DataSet implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _alignmentList.size())) {\r
-            throw new IndexOutOfBoundsException("setAlignment: Index value '"+index+"' not in range [0.."+_alignmentList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _alignmentList.setElementAt(vAlignment, index);\r
     } //-- void setAlignment(int, org.vamsas.objects.core.Alignment) \r
@@ -643,7 +642,7 @@ public class DataSet implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _dataSetAnnotationsList.size())) {\r
-            throw new IndexOutOfBoundsException("setDataSetAnnotations: Index value '"+index+"' not in range [0.."+_dataSetAnnotationsList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _dataSetAnnotationsList.setElementAt(vDataSetAnnotations, index);\r
     } //-- void setDataSetAnnotations(int, org.vamsas.objects.core.DataSetAnnotations) \r
@@ -697,7 +696,7 @@ public class DataSet implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _sequenceList.size())) {\r
-            throw new IndexOutOfBoundsException("setSequence: Index value '"+index+"' not in range [0.."+_sequenceList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _sequenceList.setElementAt(vSequence, index);\r
     } //-- void setSequence(int, org.vamsas.objects.core.Sequence) \r
@@ -731,7 +730,7 @@ public class DataSet 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
@@ -758,13 +757,13 @@ public class DataSet implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return DataSet\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.DataSet 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.DataSet) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSet.class, reader);\r
-    } //-- org.vamsas.objects.core.DataSet unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/DataSetAnnotations.java b/src/org/vamsas/objects/core/DataSetAnnotations.java
index 42d684a..c8c6a4e 100755 (executable)
--- a/src/org/vamsas/objects/core/DataSetAnnotations.java
+++ b/src/org/vamsas/objects/core/DataSetAnnotations.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
@@ -43,12 +43,22 @@ public class DataSetAnnotations implements java.io.Serializable {
     /**\r
      * Field _end\r
      */\r
-    private java.lang.String _end;\r
+    private int _end;\r
+\r
+    /**\r
+     * keeps track of state for field: _end\r
+     */\r
+    private boolean _has_end;\r
 \r
     /**\r
      * Field _begin\r
      */\r
-    private java.lang.String _begin;\r
+    private int _begin;\r
+\r
+    /**\r
+     * keeps track of state for field: _begin\r
+     */\r
+    private boolean _has_begin;\r
 \r
     /**\r
      * Field _seqRef\r
@@ -85,8 +95,7 @@ public class DataSetAnnotations implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public DataSetAnnotations() \r
-     {\r
+    public DataSetAnnotations() {\r
         super();\r
         _annotationElementList = new Vector();\r
         _provenanceList = new Vector();\r
@@ -152,6 +161,24 @@ public class DataSetAnnotations implements java.io.Serializable {
     } //-- void addProvenance(int, org.vamsas.objects.core.Provenance) \r
 \r
     /**\r
+     * Method deleteBegin\r
+     * \r
+     */\r
+    public void deleteBegin()\r
+    {\r
+        this._has_begin= false;\r
+    } //-- void deleteBegin() \r
+\r
+    /**\r
+     * Method deleteEnd\r
+     * \r
+     */\r
+    public void deleteEnd()\r
+    {\r
+        this._has_end= false;\r
+    } //-- void deleteEnd() \r
+\r
+    /**\r
      * Method enumerateAnnotationElement\r
      * \r
      * \r
@@ -188,7 +215,7 @@ public class DataSetAnnotations implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _annotationElementList.size())) {\r
-            throw new IndexOutOfBoundsException("getAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.AnnotationElement) _annotationElementList.elementAt(index);\r
@@ -226,13 +253,13 @@ public class DataSetAnnotations implements java.io.Serializable {
     /**\r
      * Returns the value of field 'begin'.\r
      * \r
-     * @return String\r
+     * @return int\r
      * @return the value of field 'begin'.\r
      */\r
-    public java.lang.String getBegin()\r
+    public int getBegin()\r
     {\r
         return this._begin;\r
-    } //-- java.lang.String getBegin() \r
+    } //-- int getBegin() \r
 \r
     /**\r
      * Returns the value of field 'description'.\r
@@ -248,13 +275,13 @@ public class DataSetAnnotations implements java.io.Serializable {
     /**\r
      * Returns the value of field 'end'.\r
      * \r
-     * @return String\r
+     * @return int\r
      * @return the value of field 'end'.\r
      */\r
-    public java.lang.String getEnd()\r
+    public int getEnd()\r
     {\r
         return this._end;\r
-    } //-- java.lang.String getEnd() \r
+    } //-- int getEnd() \r
 \r
     /**\r
      * Returns the value of field 'id'.\r
@@ -280,7 +307,7 @@ public class DataSetAnnotations implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _provenanceList.size())) {\r
-            throw new IndexOutOfBoundsException("getProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index);\r
@@ -349,6 +376,30 @@ public class DataSetAnnotations implements java.io.Serializable {
     } //-- java.lang.String getType() \r
 \r
     /**\r
+     * Method hasBegin\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasBegin()\r
+    {\r
+        return this._has_begin;\r
+    } //-- boolean hasBegin() \r
+\r
+    /**\r
+     * Method hasEnd\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasEnd()\r
+    {\r
+        return this._has_end;\r
+    } //-- boolean hasEnd() \r
+\r
+    /**\r
      * Method isValid\r
      * \r
      * \r
@@ -455,7 +506,7 @@ public class DataSetAnnotations implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _annotationElementList.size())) {\r
-            throw new IndexOutOfBoundsException("setAnnotationElement: Index value '"+index+"' not in range [0.."+_annotationElementList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _annotationElementList.setElementAt(vAnnotationElement, index);\r
     } //-- void setAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) \r
@@ -481,10 +532,11 @@ public class DataSetAnnotations implements java.io.Serializable {
      * \r
      * @param begin the value of field 'begin'.\r
      */\r
-    public void setBegin(java.lang.String begin)\r
+    public void setBegin(int begin)\r
     {\r
         this._begin = begin;\r
-    } //-- void setBegin(java.lang.String) \r
+        this._has_begin = true;\r
+    } //-- void setBegin(int) \r
 \r
     /**\r
      * Sets the value of field 'description'.\r
@@ -501,10 +553,11 @@ public class DataSetAnnotations implements java.io.Serializable {
      * \r
      * @param end the value of field 'end'.\r
      */\r
-    public void setEnd(java.lang.String end)\r
+    public void setEnd(int end)\r
     {\r
         this._end = end;\r
-    } //-- void setEnd(java.lang.String) \r
+        this._has_end = true;\r
+    } //-- void setEnd(int) \r
 \r
     /**\r
      * Sets the value of field 'id'.\r
@@ -529,7 +582,7 @@ public class DataSetAnnotations implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _provenanceList.size())) {\r
-            throw new IndexOutOfBoundsException("setProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _provenanceList.setElementAt(vProvenance, index);\r
     } //-- void setProvenance(int, org.vamsas.objects.core.Provenance) \r
@@ -586,13 +639,13 @@ public class DataSetAnnotations implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return DataSetAnnotations\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.DataSetAnnotations 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.DataSetAnnotations) Unmarshaller.unmarshal(org.vamsas.objects.core.DataSetAnnotations.class, reader);\r
-    } //-- org.vamsas.objects.core.DataSetAnnotations unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java b/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java
index fdebfc2..9dcbb86 100755 (executable)
--- a/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java
+++ b/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.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
@@ -53,8 +53,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
      //- Constructors -/\r
     //----------------/\r
 \r
-    public DataSetAnnotationsDescriptor() \r
-     {\r
+    public DataSetAnnotationsDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "DataSetAnnotations";\r
@@ -62,14 +61,14 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _type\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -90,10 +89,9 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _type\r
@@ -106,21 +104,25 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
         }\r
         desc.setValidator(fieldValidator);\r
         //-- _end\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
-        desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
                 DataSetAnnotations target = (DataSetAnnotations) object;\r
-                return target.getEnd();\r
+                if(!target.hasEnd())\r
+                    return null;\r
+                return new java.lang.Integer(target.getEnd());\r
             }\r
             public void setValue( java.lang.Object object, java.lang.Object value) \r
                 throws IllegalStateException, IllegalArgumentException\r
             {\r
                 try {\r
                     DataSetAnnotations target = (DataSetAnnotations) object;\r
-                    target.setEnd( (java.lang.String) value);\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setEnd( ((java.lang.Integer)value).intValue());\r
                 }\r
                 catch (java.lang.Exception ex) {\r
                     throw new IllegalStateException(ex.toString());\r
@@ -129,37 +131,39 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _end\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         fieldValidator.setMinOccurs(1);\r
         { //-- local scope\r
-            StringValidator typeValidator = new StringValidator();\r
-            typeValidator.setWhiteSpace("preserve");\r
+            IntegerValidator typeValidator = new IntegerValidator();\r
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
         //-- _begin\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);\r
-        desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
                 DataSetAnnotations target = (DataSetAnnotations) object;\r
-                return target.getBegin();\r
+                if(!target.hasBegin())\r
+                    return null;\r
+                return new java.lang.Integer(target.getBegin());\r
             }\r
             public void setValue( java.lang.Object object, java.lang.Object value) \r
                 throws IllegalStateException, IllegalArgumentException\r
             {\r
                 try {\r
                     DataSetAnnotations target = (DataSetAnnotations) object;\r
-                    target.setBegin( (java.lang.String) value);\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.setBegin( ((java.lang.Integer)value).intValue());\r
                 }\r
                 catch (java.lang.Exception ex) {\r
                     throw new IllegalStateException(ex.toString());\r
@@ -168,25 +172,23 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _begin\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         fieldValidator.setMinOccurs(1);\r
         { //-- local scope\r
-            StringValidator typeValidator = new StringValidator();\r
-            typeValidator.setWhiteSpace("preserve");\r
+            IntegerValidator typeValidator = new IntegerValidator();\r
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
         //-- _seqRef\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_seqRef", "seqRef", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setReference(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -207,10 +209,9 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.Object();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _seqRef\r
@@ -222,7 +223,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -243,9 +244,8 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r
@@ -258,7 +258,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
         //-- _description\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -279,7 +279,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(false);\r
@@ -296,7 +296,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
         //-- _status\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -317,7 +317,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(false);\r
@@ -333,7 +333,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
         desc.setValidator(fieldValidator);\r
         //-- _annotationElementList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -354,7 +354,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.AnnotationElement();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(true);\r
@@ -368,7 +368,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
         desc.setValidator(fieldValidator);\r
         //-- _provenanceList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenanceList", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -389,7 +389,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Provenance();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r

diff --git a/src/org/vamsas/objects/core/DataSetDescriptor.java b/src/org/vamsas/objects/core/DataSetDescriptor.java
index d938f51..6651358 100755 (executable)
--- a/src/org/vamsas/objects/core/DataSetDescriptor.java
+++ b/src/org/vamsas/objects/core/DataSetDescriptor.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
@@ -53,8 +53,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
      //- Constructors -/\r
     //----------------/\r
 \r
-    public DataSetDescriptor() \r
-     {\r
+    public DataSetDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "DataSet";\r
@@ -62,14 +61,14 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -90,9 +89,8 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r
@@ -104,7 +102,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
         \r
         //-- _sequenceList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -125,7 +123,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Sequence();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r
@@ -140,7 +138,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
         desc.setValidator(fieldValidator);\r
         //-- _dataSetAnnotationsList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSetAnnotations.class, "_dataSetAnnotationsList", "DataSetAnnotations", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -161,7 +159,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.DataSetAnnotations();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(true);\r
@@ -175,7 +173,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
         desc.setValidator(fieldValidator);\r
         //-- _alignmentList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Alignment.class, "_alignmentList", "Alignment", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -196,7 +194,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Alignment();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(true);\r
@@ -210,7 +208,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
         desc.setValidator(fieldValidator);\r
         //-- _treeList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -231,7 +229,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Tree();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(true);\r
@@ -245,7 +243,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
         desc.setValidator(fieldValidator);\r
         //-- _provenance\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -266,7 +264,7 @@ public class DataSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Provenance();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r

diff --git a/src/org/vamsas/objects/core/DbRef.java b/src/org/vamsas/objects/core/DbRef.java
index 47d57f2..10109b2 100755 (executable)
--- a/src/org/vamsas/objects/core/DbRef.java
+++ b/src/org/vamsas/objects/core/DbRef.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
@@ -36,17 +36,17 @@ public class DbRef implements java.io.Serializable {
     /**\r
      * Field _source\r
      */\r
-    private java.lang.Object _source;\r
+    private java.lang.String _source;\r
 \r
     /**\r
      * Field _version\r
      */\r
-    private java.lang.Object _version;\r
+    private java.lang.String _version;\r
 \r
     /**\r
      * Field _accessionId\r
      */\r
-    private java.lang.Object _accessionId;\r
+    private java.lang.String _accessionId;\r
 \r
     /**\r
      * Field _id\r
@@ -58,8 +58,7 @@ public class DbRef implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public DbRef() \r
-     {\r
+    public DbRef() {\r
         super();\r
     } //-- org.vamsas.objects.core.DbRef()\r
 \r
@@ -71,13 +70,13 @@ public class DbRef implements java.io.Serializable {
     /**\r
      * Returns the value of field 'accessionId'.\r
      * \r
-     * @return Object\r
+     * @return String\r
      * @return the value of field 'accessionId'.\r
      */\r
-    public java.lang.Object getAccessionId()\r
+    public java.lang.String getAccessionId()\r
     {\r
         return this._accessionId;\r
-    } //-- java.lang.Object getAccessionId() \r
+    } //-- java.lang.String getAccessionId() \r
 \r
     /**\r
      * Returns the value of field 'id'.\r
@@ -93,24 +92,24 @@ public class DbRef implements java.io.Serializable {
     /**\r
      * Returns the value of field 'source'.\r
      * \r
-     * @return Object\r
+     * @return String\r
      * @return the value of field 'source'.\r
      */\r
-    public java.lang.Object getSource()\r
+    public java.lang.String getSource()\r
     {\r
         return this._source;\r
-    } //-- java.lang.Object getSource() \r
+    } //-- java.lang.String getSource() \r
 \r
     /**\r
      * Returns the value of field 'version'.\r
      * \r
-     * @return Object\r
+     * @return String\r
      * @return the value of field 'version'.\r
      */\r
-    public java.lang.Object getVersion()\r
+    public java.lang.String getVersion()\r
     {\r
         return this._version;\r
-    } //-- java.lang.Object getVersion() \r
+    } //-- java.lang.String getVersion() \r
 \r
     /**\r
      * Method isValid\r
@@ -163,10 +162,10 @@ public class DbRef implements java.io.Serializable {
      * \r
      * @param accessionId the value of field 'accessionId'.\r
      */\r
-    public void setAccessionId(java.lang.Object accessionId)\r
+    public void setAccessionId(java.lang.String accessionId)\r
     {\r
         this._accessionId = accessionId;\r
-    } //-- void setAccessionId(java.lang.Object) \r
+    } //-- void setAccessionId(java.lang.String) \r
 \r
     /**\r
      * Sets the value of field 'id'.\r
@@ -183,20 +182,20 @@ public class DbRef implements java.io.Serializable {
      * \r
      * @param source the value of field 'source'.\r
      */\r
-    public void setSource(java.lang.Object source)\r
+    public void setSource(java.lang.String source)\r
     {\r
         this._source = source;\r
-    } //-- void setSource(java.lang.Object) \r
+    } //-- void setSource(java.lang.String) \r
 \r
     /**\r
      * Sets the value of field 'version'.\r
      * \r
      * @param version the value of field 'version'.\r
      */\r
-    public void setVersion(java.lang.Object version)\r
+    public void setVersion(java.lang.String version)\r
     {\r
         this._version = version;\r
-    } //-- void setVersion(java.lang.Object) \r
+    } //-- void setVersion(java.lang.String) \r
 \r
     /**\r
      * Method unmarshal\r
@@ -204,13 +203,13 @@ public class DbRef implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return DbRef\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.DbRef 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.DbRef) Unmarshaller.unmarshal(org.vamsas.objects.core.DbRef.class, reader);\r
-    } //-- org.vamsas.objects.core.DbRef unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/DbRefDescriptor.java b/src/org/vamsas/objects/core/DbRefDescriptor.java
index 726c0cb..e679843 100755 (executable)
--- a/src/org/vamsas/objects/core/DbRefDescriptor.java
+++ b/src/org/vamsas/objects/core/DbRefDescriptor.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
@@ -53,19 +53,19 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
      //- Constructors -/\r
     //----------------/\r
 \r
-    public DbRefDescriptor() \r
-     {\r
+    public DbRefDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "dbRef";\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _source\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -77,28 +77,31 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
             {\r
                 try {\r
                     DbRef target = (DbRef) object;\r
-                    target.setSource( (java.lang.Object) value);\r
+                    target.setSource( (java.lang.String) value);\r
                 }\r
                 catch (java.lang.Exception ex) {\r
                     throw new IllegalStateException(ex.toString());\r
                 }\r
             }\r
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
-                return new java.lang.Object();\r
+                return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _source\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
         //-- _version\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -110,28 +113,31 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
             {\r
                 try {\r
                     DbRef target = (DbRef) object;\r
-                    target.setVersion( (java.lang.Object) value);\r
+                    target.setVersion( (java.lang.String) value);\r
                 }\r
                 catch (java.lang.Exception ex) {\r
                     throw new IllegalStateException(ex.toString());\r
                 }\r
             }\r
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
-                return new java.lang.Object();\r
+                return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _version\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
         //-- _accessionId\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -143,29 +149,31 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
             {\r
                 try {\r
                     DbRef target = (DbRef) object;\r
-                    target.setAccessionId( (java.lang.Object) value);\r
+                    target.setAccessionId( (java.lang.String) value);\r
                 }\r
                 catch (java.lang.Exception ex) {\r
                     throw new IllegalStateException(ex.toString());\r
                 }\r
             }\r
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
-                return new java.lang.Object();\r
+                return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _accessionId\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -186,9 +194,8 @@ public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r

diff --git a/src/org/vamsas/objects/core/Entry.java b/src/org/vamsas/objects/core/Entry.java
index 8232a43..9e41a3c 100755 (executable)
--- a/src/org/vamsas/objects/core/Entry.java
+++ b/src/org/vamsas/objects/core/Entry.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
@@ -58,8 +58,7 @@ public class Entry implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public Entry() \r
-     {\r
+    public Entry() {\r
         super();\r
     } //-- org.vamsas.objects.core.Entry()\r
 \r
@@ -204,13 +203,13 @@ public class Entry implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return Entry\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.Entry 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.Entry) Unmarshaller.unmarshal(org.vamsas.objects.core.Entry.class, reader);\r
-    } //-- org.vamsas.objects.core.Entry unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/EntryDescriptor.java b/src/org/vamsas/objects/core/EntryDescriptor.java
index 981ee47..b404b3a 100755 (executable)
--- a/src/org/vamsas/objects/core/EntryDescriptor.java
+++ b/src/org/vamsas/objects/core/EntryDescriptor.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
@@ -53,8 +53,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
      //- Constructors -/\r
     //----------------/\r
 \r
-    public EntryDescriptor() \r
-     {\r
+    public EntryDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "entry";\r
@@ -62,14 +61,14 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -90,9 +89,8 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r
@@ -105,7 +103,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
         //-- _user\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_user", "User", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -126,7 +124,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r
@@ -145,7 +143,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
         //-- _action\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_action", "Action", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -166,7 +164,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r
@@ -184,7 +182,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
         desc.setValidator(fieldValidator);\r
         //-- _date\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.exolab.castor.types.Date.class, "_date", "Date", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -205,7 +203,7 @@ public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.exolab.castor.types.Date();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r

diff --git a/src/org/vamsas/objects/core/Newick.java b/src/org/vamsas/objects/core/Newick.java
index c0988ec..3c59ad7 100755 (executable)
--- a/src/org/vamsas/objects/core/Newick.java
+++ b/src/org/vamsas/objects/core/Newick.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
@@ -53,8 +53,7 @@ public class Newick implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public Newick() \r
-     {\r
+    public Newick() {\r
         super();\r
         setContent("");\r
     } //-- org.vamsas.objects.core.Newick()\r
@@ -181,13 +180,13 @@ public class Newick implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return Newick\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.Newick 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.Newick) Unmarshaller.unmarshal(org.vamsas.objects.core.Newick.class, reader);\r
-    } //-- org.vamsas.objects.core.Newick unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/NewickDescriptor.java b/src/org/vamsas/objects/core/NewickDescriptor.java
index 97ea4ff..474da72 100755 (executable)
--- a/src/org/vamsas/objects/core/NewickDescriptor.java
+++ b/src/org/vamsas/objects/core/NewickDescriptor.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
@@ -53,18 +53,17 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
      //- Constructors -/\r
     //----------------/\r
 \r
-    public NewickDescriptor() \r
-     {\r
+    public NewickDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "newick";\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- _content\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -85,7 +84,7 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         addFieldDescriptor(desc);\r
         \r
@@ -102,7 +101,7 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
         //-- _title\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -123,9 +122,8 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _title\r
@@ -139,7 +137,7 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -160,9 +158,8 @@ public class NewickDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r

diff --git a/src/org/vamsas/objects/core/Provenance.java b/src/org/vamsas/objects/core/Provenance.java
index 360f035..0011b05 100755 (executable)
--- a/src/org/vamsas/objects/core/Provenance.java
+++ b/src/org/vamsas/objects/core/Provenance.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
@@ -45,8 +45,7 @@ public class Provenance implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public Provenance() \r
-     {\r
+    public Provenance() {\r
         super();\r
         _entryList = new Vector();\r
     } //-- org.vamsas.objects.core.Provenance()\r
@@ -108,7 +107,7 @@ public class Provenance implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _entryList.size())) {\r
-            throw new IndexOutOfBoundsException("getEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.Entry) _entryList.elementAt(index);\r
@@ -226,7 +225,7 @@ public class Provenance implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _entryList.size())) {\r
-            throw new IndexOutOfBoundsException("setEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _entryList.setElementAt(vEntry, index);\r
     } //-- void setEntry(int, org.vamsas.objects.core.Entry) \r
@@ -253,13 +252,13 @@ public class Provenance implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return Provenance\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.Provenance 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.Provenance) Unmarshaller.unmarshal(org.vamsas.objects.core.Provenance.class, reader);\r
-    } //-- org.vamsas.objects.core.Provenance unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/ProvenanceDescriptor.java b/src/org/vamsas/objects/core/ProvenanceDescriptor.java
index 480ee5f..17b283c 100755 (executable)
--- a/src/org/vamsas/objects/core/ProvenanceDescriptor.java
+++ b/src/org/vamsas/objects/core/ProvenanceDescriptor.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
@@ -53,8 +53,7 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes
      //- Constructors -/\r
     //----------------/\r
 \r
-    public ProvenanceDescriptor() \r
-     {\r
+    public ProvenanceDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "Provenance";\r
@@ -62,7 +61,7 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
@@ -70,7 +69,7 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes
         \r
         //-- _entryList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Entry.class, "_entryList", "entry", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -91,7 +90,7 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Entry();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r

diff --git a/src/org/vamsas/objects/core/Sequence.java b/src/org/vamsas/objects/core/Sequence.java
index daf6657..2a7e0ec 100755 (executable)
--- a/src/org/vamsas/objects/core/Sequence.java
+++ b/src/org/vamsas/objects/core/Sequence.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
@@ -57,8 +57,7 @@ implements java.io.Serializable
      //- Constructors -/\r
     //----------------/\r
 \r
-    public Sequence() \r
-     {\r
+    public Sequence() {\r
         super();\r
         _dbRefList = new Vector();\r
     } //-- org.vamsas.objects.core.Sequence()\r
@@ -120,7 +119,7 @@ implements java.io.Serializable
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _dbRefList.size())) {\r
-            throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);\r
@@ -260,7 +259,7 @@ implements java.io.Serializable
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _dbRefList.size())) {\r
-            throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _dbRefList.setElementAt(vDbRef, index);\r
     } //-- void setDbRef(int, org.vamsas.objects.core.DbRef) \r
@@ -307,13 +306,13 @@ implements java.io.Serializable
      * \r
      * \r
      * @param reader\r
-     * @return SequenceType\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.SequenceType 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.Sequence) Unmarshaller.unmarshal(org.vamsas.objects.core.Sequence.class, reader);\r
-    } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/SequenceDescriptor.java b/src/org/vamsas/objects/core/SequenceDescriptor.java
index 6f25ae1..e17ff8f 100755 (executable)
--- a/src/org/vamsas/objects/core/SequenceDescriptor.java
+++ b/src/org/vamsas/objects/core/SequenceDescriptor.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
@@ -53,8 +53,7 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc
      //- Constructors -/\r
     //----------------/\r
 \r
-    public SequenceDescriptor() \r
-     {\r
+    public SequenceDescriptor() {\r
         super();\r
         setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor());\r
         nsURI = "http://www.vamsas.org";\r
@@ -63,14 +62,14 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -91,10 +90,9 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r
@@ -106,7 +104,7 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc
         //-- _dictionary\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -127,9 +125,8 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _dictionary\r
@@ -144,7 +141,7 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc
         \r
         //-- _dbRefList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -165,7 +162,7 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.DbRef();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(true);\r

diff --git a/src/org/vamsas/objects/core/SequenceType.java b/src/org/vamsas/objects/core/SequenceType.java
index 7ecd190..957edb5 100755 (executable)
--- a/src/org/vamsas/objects/core/SequenceType.java
+++ b/src/org/vamsas/objects/core/SequenceType.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
@@ -68,8 +68,7 @@ public class SequenceType implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public SequenceType() \r
-     {\r
+    public SequenceType() {\r
         super();\r
     } //-- org.vamsas.objects.core.SequenceType()\r
 \r
@@ -258,13 +257,13 @@ public class SequenceType implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return SequenceType\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.SequenceType 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.SequenceType) Unmarshaller.unmarshal(org.vamsas.objects.core.SequenceType.class, reader);\r
-    } //-- org.vamsas.objects.core.SequenceType unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java
index eda209f..6090776 100755 (executable)
--- a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java
+++ b/src/org/vamsas/objects/core/SequenceTypeDescriptor.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
@@ -53,8 +53,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
      //- Constructors -/\r
     //----------------/\r
 \r
-    public SequenceTypeDescriptor() \r
-     {\r
+    public SequenceTypeDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "SequenceType";\r
@@ -62,13 +61,13 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _start\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -94,23 +93,22 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _start\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         fieldValidator.setMinOccurs(1);\r
         { //-- local scope\r
-            IntegerValidator typeValidator= new IntegerValidator();\r
+            IntegerValidator typeValidator = new IntegerValidator();\r
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
         //-- _end\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -136,17 +134,16 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _end\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         fieldValidator.setMinOccurs(1);\r
         { //-- local scope\r
-            IntegerValidator typeValidator= new IntegerValidator();\r
+            IntegerValidator typeValidator = new IntegerValidator();\r
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
@@ -155,7 +152,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
         //-- _sequence\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -176,7 +173,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r
@@ -195,7 +192,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
         //-- _name\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -216,7 +213,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r

diff --git a/src/org/vamsas/objects/core/Tree.java b/src/org/vamsas/objects/core/Tree.java
index f18cd05..1e37459 100755 (executable)
--- a/src/org/vamsas/objects/core/Tree.java
+++ b/src/org/vamsas/objects/core/Tree.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
@@ -60,8 +60,7 @@ public class Tree implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public Tree() \r
-     {\r
+    public Tree() {\r
         super();\r
         _newickList = new Vector();\r
     } //-- org.vamsas.objects.core.Tree()\r
@@ -134,7 +133,7 @@ public class Tree implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _newickList.size())) {\r
-            throw new IndexOutOfBoundsException("getNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.Newick) _newickList.elementAt(index);\r
@@ -284,7 +283,7 @@ public class Tree implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _newickList.size())) {\r
-            throw new IndexOutOfBoundsException("setNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _newickList.setElementAt(vNewick, index);\r
     } //-- void setNewick(int, org.vamsas.objects.core.Newick) \r
@@ -331,13 +330,13 @@ public class Tree implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return Tree\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.Tree 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.Tree) Unmarshaller.unmarshal(org.vamsas.objects.core.Tree.class, reader);\r
-    } //-- org.vamsas.objects.core.Tree unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/TreeDescriptor.java b/src/org/vamsas/objects/core/TreeDescriptor.java
index bd1ecb0..17c7ff6 100755 (executable)
--- a/src/org/vamsas/objects/core/TreeDescriptor.java
+++ b/src/org/vamsas/objects/core/TreeDescriptor.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
@@ -53,8 +53,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
      //- Constructors -/\r
     //----------------/\r
 \r
-    public TreeDescriptor() \r
-     {\r
+    public TreeDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "Tree";\r
@@ -62,14 +61,14 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -90,9 +89,8 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r
@@ -105,7 +103,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
         //-- _title\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -126,7 +124,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(false);\r
@@ -142,7 +140,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
         desc.setValidator(fieldValidator);\r
         //-- _newickList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Newick.class, "_newickList", "newick", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -163,7 +161,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Newick();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r
@@ -178,7 +176,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
         desc.setValidator(fieldValidator);\r
         //-- _provenance\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -199,7 +197,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Provenance();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setRequired(true);\r

diff --git a/src/org/vamsas/objects/core/User.java b/src/org/vamsas/objects/core/User.java
index 598bceb..16455e9 100755 (executable)
--- a/src/org/vamsas/objects/core/User.java
+++ b/src/org/vamsas/objects/core/User.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
@@ -53,8 +53,7 @@ public class User implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public User() \r
-     {\r
+    public User() {\r
         super();\r
     } //-- org.vamsas.objects.core.User()\r
 \r
@@ -178,13 +177,13 @@ public class User implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return User\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.User 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.User) Unmarshaller.unmarshal(org.vamsas.objects.core.User.class, reader);\r
-    } //-- org.vamsas.objects.core.User unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/UserDescriptor.java b/src/org/vamsas/objects/core/UserDescriptor.java
index f318dde..7e50932 100755 (executable)
--- a/src/org/vamsas/objects/core/UserDescriptor.java
+++ b/src/org/vamsas/objects/core/UserDescriptor.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
@@ -53,20 +53,19 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
      //- Constructors -/\r
     //----------------/\r
 \r
-    public UserDescriptor() \r
-     {\r
+    public UserDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "User";\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _fullname\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fullname", "fullname", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -87,9 +86,8 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _fullname\r
@@ -103,7 +101,7 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
         //-- _organization\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_organization", "organization", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -124,9 +122,8 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _organization\r
@@ -140,7 +137,7 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
         //-- _data\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_data", "data", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setImmutable(true);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -161,9 +158,8 @@ public class UserDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return null;\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _data\r

diff --git a/src/org/vamsas/objects/core/VAMSAS.java b/src/org/vamsas/objects/core/VAMSAS.java
index 8d9b765..e419b5c 100755 (executable)
--- a/src/org/vamsas/objects/core/VAMSAS.java
+++ b/src/org/vamsas/objects/core/VAMSAS.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
@@ -55,8 +55,7 @@ public class VAMSAS implements java.io.Serializable {
      //- Constructors -/\r
     //----------------/\r
 \r
-    public VAMSAS() \r
-     {\r
+    public VAMSAS() {\r
         super();\r
         _treeList = new Vector();\r
         _dataSetList = new Vector();\r
@@ -158,7 +157,7 @@ public class VAMSAS implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _dataSetList.size())) {\r
-            throw new IndexOutOfBoundsException("getDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         \r
         return (org.vamsas.objects.core.DataSet) _dataSetList.elementAt(index);\r
@@ -217,7 +216,7 @@ public class VAMSAS 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
@@ -359,7 +358,7 @@ public class VAMSAS implements java.io.Serializable {
     {\r
         //-- check bounds for index\r
         if ((index < 0) || (index > _dataSetList.size())) {\r
-            throw new IndexOutOfBoundsException("setDataSet: Index value '"+index+"' not in range [0.."+_dataSetList.size()+ "]");\r
+            throw new IndexOutOfBoundsException();\r
         }\r
         _dataSetList.setElementAt(vDataSet, index);\r
     } //-- void setDataSet(int, org.vamsas.objects.core.DataSet) \r
@@ -403,7 +402,7 @@ public class VAMSAS 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
@@ -430,13 +429,13 @@ public class VAMSAS implements java.io.Serializable {
      * \r
      * \r
      * @param reader\r
-     * @return VAMSAS\r
+     * @return Object\r
      */\r
-    public static org.vamsas.objects.core.VAMSAS 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.VAMSAS) Unmarshaller.unmarshal(org.vamsas.objects.core.VAMSAS.class, reader);\r
-    } //-- org.vamsas.objects.core.VAMSAS unmarshal(java.io.Reader) \r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
 \r
     /**\r
      * Method validate\r

diff --git a/src/org/vamsas/objects/core/VAMSASDescriptor.java b/src/org/vamsas/objects/core/VAMSASDescriptor.java
index 053b0e1..40c8f6a 100755 (executable)
--- a/src/org/vamsas/objects/core/VAMSASDescriptor.java
+++ b/src/org/vamsas/objects/core/VAMSASDescriptor.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
@@ -53,8 +53,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
      //- Constructors -/\r
     //----------------/\r
 \r
-    public VAMSASDescriptor() \r
-     {\r
+    public VAMSASDescriptor() {\r
         super();\r
         nsURI = "http://www.vamsas.org";\r
         xmlName = "VAMSAS";\r
@@ -62,14 +61,14 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
         //-- set grouping compositor\r
         setCompositorAsSequence();\r
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.mapping.FieldHandler             handler        = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
         this.identity = desc;\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -90,9 +89,8 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new java.lang.String();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
-        desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _id\r
@@ -104,7 +102,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
         \r
         //-- _treeList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -125,7 +123,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.Tree();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(true);\r
@@ -139,7 +137,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
         desc.setValidator(fieldValidator);\r
         //-- _dataSetList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DataSet.class, "_dataSetList", "DataSet", org.exolab.castor.xml.NodeType.Element);\r
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
@@ -160,7 +158,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
             public java.lang.Object newInstance( java.lang.Object parent ) {\r
                 return new org.vamsas.objects.core.DataSet();\r
             }\r
-        };\r
+        } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("http://www.vamsas.org");\r
         desc.setMultivalued(true);\r