refactored core objects and regenerated.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@24 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/org/vamsas/objects/core/.castor.cdr b/src/org/vamsas/objects/core/.castor.cdr
new file mode 100644 (file)
index 0000000..ce4c376
--- /dev/null
+++ b/src/org/vamsas/objects/core/.castor.cdr
@@ -0,0 +1,18 @@
+-- listing properties --
+org.vamsas.objects.core.ProvenanceItem=org.vamsas.objects.core.ProvenanceIte...
+org.vamsas.objects.core.AlignmentAnnotations=org.vamsas.objects.core.AlignmentAnno...
+org.vamsas.objects.core.Tree=org.vamsas.objects.core.TreeDescriptor
+org.vamsas.objects.core.Sequence=org.vamsas.objects.core.SequenceDescr...
+org.vamsas.objects.core.AnnotationElement=org.vamsas.objects.core.AnnotationEle...
+org.vamsas.objects.core.LockFile=org.vamsas.objects.core.LockFileDescr...
+org.vamsas.objects.core.Entry=org.vamsas.objects.core.EntryDescriptor
+org.vamsas.objects.core.SequenceType=org.vamsas.objects.core.SequenceTypeD...
+org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor
+org.vamsas.objects.core.SequenceSet=org.vamsas.objects.core.SequenceSetDe...
+org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor
+org.vamsas.objects.core.ApplicationData=org.vamsas.objects.core.ApplicationDa...
+org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe...
+org.vamsas.objects.core.Provenance=org.vamsas.objects.core.ProvenanceDes...
+org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ...
+org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc...
+org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn...

diff --git a/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java b/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java
new file mode 100644 (file)
index 0000000..d680cd8
--- /dev/null
+++ b/src/org/vamsas/objects/core/AlignmentAnnotationsDescriptor.java
@@ -0,0 +1,368 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AlignmentAnnotationsDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AlignmentAnnotationsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AlignmentAnnotationsDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "AlignmentAnnotations";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _graph
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_graph", "graph", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AlignmentAnnotations target = (AlignmentAnnotations) object;
+                if(!target.hasGraph())
+                    return null;
+                return (target.getGraph() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AlignmentAnnotations target = (AlignmentAnnotations) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setGraph( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _graph
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _annotationElementList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AlignmentAnnotations target = (AlignmentAnnotations) object;
+                return target.getAnnotationElement();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AlignmentAnnotations target = (AlignmentAnnotations) object;
+                    target.addAnnotationElement( (org.vamsas.objects.core.AnnotationElement) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.AnnotationElement();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _annotationElementList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _label
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_label", "label", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AlignmentAnnotations target = (AlignmentAnnotations) object;
+                return target.getLabel();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AlignmentAnnotations target = (AlignmentAnnotations) object;
+                    target.setLabel( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _label
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _description
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AlignmentAnnotations target = (AlignmentAnnotations) object;
+                return target.getDescription();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AlignmentAnnotations target = (AlignmentAnnotations) object;
+                    target.setDescription( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _description
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _provenance
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AlignmentAnnotations target = (AlignmentAnnotations) object;
+                return target.getProvenance();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AlignmentAnnotations target = (AlignmentAnnotations) object;
+                    target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Provenance();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _provenance
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.AlignmentAnnotationsDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.AlignmentAnnotations.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/AlignmentDescriptor.java b/src/org/vamsas/objects/core/AlignmentDescriptor.java
new file mode 100644 (file)
index 0000000..497eb37
--- /dev/null
+++ b/src/org/vamsas/objects/core/AlignmentDescriptor.java
@@ -0,0 +1,315 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AlignmentDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AlignmentDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "Alignment";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _alignmentAnnotations
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentAnnotations.class, "_alignmentAnnotations", "AlignmentAnnotations", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Alignment target = (Alignment) object;
+                return target.getAlignmentAnnotations();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Alignment target = (Alignment) object;
+                    target.setAlignmentAnnotations( (org.vamsas.objects.core.AlignmentAnnotations) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.AlignmentAnnotations();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _alignmentAnnotations
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _treeList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "tree", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Alignment target = (Alignment) object;
+                return target.getTree();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Alignment target = (Alignment) object;
+                    target.addTree( (org.vamsas.objects.core.Tree) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Tree();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _treeList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _alignmentSequenceList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AlignmentSequence.class, "_alignmentSequenceList", "alignmentSequence", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Alignment target = (Alignment) object;
+                return target.getAlignmentSequence();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Alignment target = (Alignment) object;
+                    target.addAlignmentSequence( (org.vamsas.objects.core.AlignmentSequence) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.AlignmentSequence();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _alignmentSequenceList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(2);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _provenance
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Alignment target = (Alignment) object;
+                return target.getProvenance();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Alignment target = (Alignment) object;
+                    target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Provenance();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _provenance
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.AlignmentDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.Alignment.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java
new file mode 100644 (file)
index 0000000..dd1680a
--- /dev/null
+++ b/src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java
@@ -0,0 +1,210 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AlignmentSequenceDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDescriptor {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AlignmentSequenceDescriptor() 
+     {
+        super();
+        setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor());
+        nsURI = "http://www.vamsas.org";
+        xmlName = "alignmentSequence";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _id
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setReference(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AlignmentSequence target = (AlignmentSequence) object;
+                return target.getId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AlignmentSequence target = (AlignmentSequence) object;
+                    target.setId( (java.lang.Object) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new java.lang.Object();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- org.vamsas.objects.core.AlignmentSequenceDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return super.getExtends();
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        if (identity == null)
+            return super.getIdentity();
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.AlignmentSequence.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java b/src/org/vamsas/objects/core/AnnotationElementDescriptor.java
new file mode 100644 (file)
index 0000000..419388a
--- /dev/null
+++ b/src/org/vamsas/objects/core/AnnotationElementDescriptor.java
@@ -0,0 +1,380 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class AnnotationElementDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public AnnotationElementDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "annotationElement";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _position
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_position", "position", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                if(!target.hasPosition())
+                    return null;
+                return new java.lang.Integer(target.getPosition());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setPosition( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _position
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _displayCharacter
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_displayCharacter", "displayCharacter", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                return target.getDisplayCharacter();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    target.setDisplayCharacter( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _displayCharacter
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _description
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                return target.getDescription();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    target.setDescription( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _description
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _secondaryStructure
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_secondaryStructure", "secondaryStructure", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                return target.getSecondaryStructure();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    target.setSecondaryStructure( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _secondaryStructure
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setLength(1);
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _value
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_value", "value", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                AnnotationElement target = (AnnotationElement) object;
+                if(!target.hasValue())
+                    return null;
+                return new java.lang.Float(target.getValue());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    AnnotationElement target = (AnnotationElement) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setValue( ((java.lang.Float)value).floatValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _value
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            FloatValidator typeValidator = new FloatValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.AnnotationElementDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.AnnotationElement.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/ApplicationDataDescriptor.java b/src/org/vamsas/objects/core/ApplicationDataDescriptor.java
new file mode 100644 (file)
index 0000000..6386e8d
--- /dev/null
+++ b/src/org/vamsas/objects/core/ApplicationDataDescriptor.java
@@ -0,0 +1,210 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class ApplicationDataDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ApplicationDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public ApplicationDataDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "ApplicationData";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _application
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Application.class, "_application", "Application", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                ApplicationData target = (ApplicationData) object;
+                return target.getApplication();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    ApplicationData target = (ApplicationData) object;
+                    target.setApplication( (org.vamsas.objects.core.Application) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Application();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _application
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.ApplicationDataDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.ApplicationData.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/ApplicationDescriptor.java b/src/org/vamsas/objects/core/ApplicationDescriptor.java
new file mode 100644 (file)
index 0000000..1b5b429
--- /dev/null
+++ b/src/org/vamsas/objects/core/ApplicationDescriptor.java
@@ -0,0 +1,237 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class ApplicationDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public ApplicationDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "Application";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _version
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Application target = (Application) object;
+                return target.getVersion();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Application target = (Application) object;
+                    target.setVersion( (java.lang.Object) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new java.lang.Object();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _version
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _name
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_name", "name", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Application target = (Application) object;
+                return target.getName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Application target = (Application) object;
+                    target.setName( (java.lang.Object) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new java.lang.Object();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _name
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- org.vamsas.objects.core.ApplicationDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.Application.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/DbRefDescriptor.java b/src/org/vamsas/objects/core/DbRefDescriptor.java
new file mode 100644 (file)
index 0000000..25833ad
--- /dev/null
+++ b/src/org/vamsas/objects/core/DbRefDescriptor.java
@@ -0,0 +1,270 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class DbRefDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class DbRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public DbRefDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "dbRef";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _source
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                DbRef target = (DbRef) object;
+                return target.getSource();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    DbRef target = (DbRef) object;
+                    target.setSource( (java.lang.Object) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new java.lang.Object();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _source
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _version
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                DbRef target = (DbRef) object;
+                return target.getVersion();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    DbRef target = (DbRef) object;
+                    target.setVersion( (java.lang.Object) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new java.lang.Object();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _version
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _accessionId
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                DbRef target = (DbRef) object;
+                return target.getAccessionId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    DbRef target = (DbRef) object;
+                    target.setAccessionId( (java.lang.Object) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new java.lang.Object();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _accessionId
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- org.vamsas.objects.core.DbRefDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.DbRef.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/EntryDescriptor.java b/src/org/vamsas/objects/core/EntryDescriptor.java
new file mode 100644 (file)
index 0000000..e9651fb
--- /dev/null
+++ b/src/org/vamsas/objects/core/EntryDescriptor.java
@@ -0,0 +1,292 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class EntryDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class EntryDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public EntryDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "entry";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _user
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_user", "User", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Entry target = (Entry) object;
+                return target.getUser();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Entry target = (Entry) object;
+                    target.setUser( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _user
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _action
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_action", "Action", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Entry target = (Entry) object;
+                return target.getAction();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Entry target = (Entry) object;
+                    target.setAction( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _action
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _date
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.exolab.castor.types.Date.class, "_date", "Date", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Entry target = (Entry) object;
+                return target.getDate();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Entry target = (Entry) object;
+                    target.setDate( (org.exolab.castor.types.Date) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.exolab.castor.types.Date();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _date
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            DateTimeValidator typeValidator = new DateTimeValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.EntryDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.Entry.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/LockFileDescriptor.java b/src/org/vamsas/objects/core/LockFileDescriptor.java
new file mode 100644 (file)
index 0000000..804521f
--- /dev/null
+++ b/src/org/vamsas/objects/core/LockFileDescriptor.java
@@ -0,0 +1,207 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class LockFileDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class LockFileDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public LockFileDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "LockFile";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- _content
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_content", "PCDATA", org.exolab.castor.xml.NodeType.Text);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                LockFile target = (LockFile) object;
+                return target.getContent();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    LockFile target = (LockFile) object;
+                    target.setContent( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _content
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+    } //-- org.vamsas.objects.core.LockFileDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.LockFile.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/ProvenanceDescriptor.java b/src/org/vamsas/objects/core/ProvenanceDescriptor.java
new file mode 100644 (file)
index 0000000..50225b3
--- /dev/null
+++ b/src/org/vamsas/objects/core/ProvenanceDescriptor.java
@@ -0,0 +1,206 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class ProvenanceDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public ProvenanceDescriptor() 
+     {
+        super();
+        xmlName = "Provenance";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _items
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.ProvenanceItem.class, "_items", (String)null, org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Provenance target = (Provenance) object;
+                return target.getProvenanceItem();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Provenance target = (Provenance) object;
+                    target.addProvenanceItem( (org.vamsas.objects.core.ProvenanceItem) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.ProvenanceItem();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setContainer(true);
+        desc.setClassDescriptor(new org.vamsas.objects.core.ProvenanceItemDescriptor());
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _items
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.ProvenanceDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.Provenance.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/ProvenanceItemDescriptor.java b/src/org/vamsas/objects/core/ProvenanceItemDescriptor.java
new file mode 100644 (file)
index 0000000..5dbca13
--- /dev/null
+++ b/src/org/vamsas/objects/core/ProvenanceItemDescriptor.java
@@ -0,0 +1,210 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class ProvenanceItemDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class ProvenanceItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public ProvenanceItemDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "Provenance";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _entry
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Entry.class, "_entry", "entry", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                ProvenanceItem target = (ProvenanceItem) object;
+                return target.getEntry();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    ProvenanceItem target = (ProvenanceItem) object;
+                    target.setEntry( (org.vamsas.objects.core.Entry) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Entry();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _entry
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.ProvenanceItemDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.ProvenanceItem.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/SequenceDescriptor.java b/src/org/vamsas/objects/core/SequenceDescriptor.java
new file mode 100644 (file)
index 0000000..c515dce
--- /dev/null
+++ b/src/org/vamsas/objects/core/SequenceDescriptor.java
@@ -0,0 +1,247 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class SequenceDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDescriptor {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public SequenceDescriptor() 
+     {
+        super();
+        setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor());
+        nsURI = "http://www.vamsas.org";
+        xmlName = "Sequence";
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _dictionary
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Sequence target = (Sequence) object;
+                return target.getDictionary();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Sequence target = (Sequence) object;
+                    target.setDictionary( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _dictionary
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _id
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+        this.identity = desc;
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Sequence target = (Sequence) object;
+                return target.getId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Sequence target = (Sequence) object;
+                    target.setId( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new java.lang.String();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- org.vamsas.objects.core.SequenceDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return super.getExtends();
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        if (identity == null)
+            return super.getIdentity();
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.Sequence.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java b/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java
new file mode 100644 (file)
index 0000000..f648ed4
--- /dev/null
+++ b/src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java
@@ -0,0 +1,474 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class SequenceSetAnnotationsDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class SequenceSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public SequenceSetAnnotationsDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "SequenceSetAnnotations";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _type
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_type", "type", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                return target.getType();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                    target.setType( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _type
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _end
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                return target.getEnd();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                    target.setEnd( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _end
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _begin
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                return target.getBegin();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                    target.setBegin( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _begin
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _seqRef
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_seqRef", "seqRef", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setReference(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                return target.getSeqRef();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                    target.setSeqRef( (java.lang.Object) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new java.lang.Object();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _seqRef
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _description
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_description", "description", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                return target.getDescription();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                    target.setDescription( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _description
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _status
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_status", "status", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                return target.getStatus();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                    target.setStatus( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _status
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _annotationElementList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.AnnotationElement.class, "_annotationElementList", "annotationElement", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                return target.getAnnotationElement();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                    target.addAnnotationElement( (org.vamsas.objects.core.AnnotationElement) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.AnnotationElement();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _annotationElementList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _provenance
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                return target.getProvenance();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSetAnnotations target = (SequenceSetAnnotations) object;
+                    target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Provenance();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _provenance
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.SequenceSetAnnotationsDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.SequenceSetAnnotations.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/SequenceSetDescriptor.java b/src/org/vamsas/objects/core/SequenceSetDescriptor.java
new file mode 100644 (file)
index 0000000..f6d090e
--- /dev/null
+++ b/src/org/vamsas/objects/core/SequenceSetDescriptor.java
@@ -0,0 +1,433 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class SequenceSetDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public SequenceSetDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "SequenceSet";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _gapChar
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                return target.getGapChar();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    target.setGapChar( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _gapChar
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _aligned
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                if(!target.hasAligned())
+                    return null;
+                return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteAligned();
+                        return;
+                    }
+                    target.setAligned( ((java.lang.Boolean)value).booleanValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _aligned
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _sequenceList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                return target.getSequence();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    target.addSequence( (org.vamsas.objects.core.Sequence) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Sequence();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _sequenceList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _sequenceSetAnnotationsList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.SequenceSetAnnotations.class, "_sequenceSetAnnotationsList", "SequenceSetAnnotations", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                return target.getSequenceSetAnnotations();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    target.addSequenceSetAnnotations( (org.vamsas.objects.core.SequenceSetAnnotations) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.SequenceSetAnnotations();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _sequenceSetAnnotationsList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _alignmentList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Alignment.class, "_alignmentList", "Alignment", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                return target.getAlignment();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    target.addAlignment( (org.vamsas.objects.core.Alignment) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Alignment();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _alignmentList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _tree
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_tree", "tree", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                return target.getTree();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    target.setTree( (org.vamsas.objects.core.Tree) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Tree();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _tree
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _provenance
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceSet target = (SequenceSet) object;
+                return target.getProvenance();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceSet target = (SequenceSet) object;
+                    target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Provenance();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _provenance
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.SequenceSetDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.SequenceSet.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java
new file mode 100644 (file)
index 0000000..be52f24
--- /dev/null
+++ b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java
@@ -0,0 +1,373 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class SequenceTypeDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public SequenceTypeDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "SequenceType";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- _start
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceType target = (SequenceType) object;
+                if(!target.hasStart())
+                    return null;
+                return new java.lang.Integer(target.getStart());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceType target = (SequenceType) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setStart( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _start
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _end
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceType target = (SequenceType) object;
+                if(!target.hasEnd())
+                    return null;
+                return new java.lang.Integer(target.getEnd());
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceType target = (SequenceType) object;
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setEnd( ((java.lang.Integer)value).intValue());
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _end
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            IntegerValidator typeValidator= new IntegerValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+        //-- _sequence
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequence", "sequence", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceType target = (SequenceType) object;
+                return target.getSequence();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceType target = (SequenceType) object;
+                    target.setSequence( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _sequence
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _name
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_name", "name", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceType target = (SequenceType) object;
+                return target.getName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceType target = (SequenceType) object;
+                    target.setName( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _name
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _dbRefList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.DbRef.class, "_dbRefList", "dbRef", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                SequenceType target = (SequenceType) object;
+                return target.getDbRef();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    SequenceType target = (SequenceType) object;
+                    target.addDbRef( (org.vamsas.objects.core.DbRef) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.DbRef();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _dbRefList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.SequenceTypeDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.SequenceType.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/TreeDescriptor.java b/src/org/vamsas/objects/core/TreeDescriptor.java
new file mode 100644 (file)
index 0000000..0918e4e
--- /dev/null
+++ b/src/org/vamsas/objects/core/TreeDescriptor.java
@@ -0,0 +1,250 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class TreeDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public TreeDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "tree";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _provenance
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                return target.getProvenance();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.Provenance();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _provenance
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _newickFormat
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newickFormat", "newickFormat", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Tree target = (Tree) object;
+                return target.getNewickFormat();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    target.setNewickFormat( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _newickFormat
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.TreeDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.Tree.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}

diff --git a/src/org/vamsas/objects/core/VAMSASDescriptor.java b/src/org/vamsas/objects/core/VAMSASDescriptor.java
new file mode 100644 (file)
index 0000000..a01bd55
--- /dev/null
+++ b/src/org/vamsas/objects/core/VAMSASDescriptor.java
@@ -0,0 +1,248 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import org.exolab.castor.mapping.AccessMode;
+import org.exolab.castor.xml.TypeValidator;
+import org.exolab.castor.xml.XMLFieldDescriptor;
+import org.exolab.castor.xml.validators.*;
+
+/**
+ * Class VAMSASDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field nsPrefix
+     */
+    private java.lang.String nsPrefix;
+
+    /**
+     * Field nsURI
+     */
+    private java.lang.String nsURI;
+
+    /**
+     * Field xmlName
+     */
+    private java.lang.String xmlName;
+
+    /**
+     * Field identity
+     */
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public VAMSASDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "VAMSAS";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
+        org.exolab.castor.mapping.FieldHandler             handler        = null;
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;
+        //-- initialize attribute descriptors
+        
+        //-- initialize element descriptors
+        
+        //-- _treeList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
+        desc.setImmutable(true);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                VAMSAS target = (VAMSAS) object;
+                return target.getTree();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    VAMSAS target = (VAMSAS) object;
+                    target.addTree( (java.lang.String) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _treeList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _sequenceSetList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.SequenceSet.class, "_sequenceSetList", "SequenceSet", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                VAMSAS target = (VAMSAS) object;
+                return target.getSequenceSet();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    VAMSAS target = (VAMSAS) object;
+                    target.addSequenceSet( (org.vamsas.objects.core.SequenceSet) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new org.vamsas.objects.core.SequenceSet();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _sequenceSetList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+    } //-- org.vamsas.objects.core.VAMSASDescriptor()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Method getAccessMode
+     * 
+     * 
+     * 
+     * @return AccessMode
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() 
+
+    /**
+     * Method getExtends
+     * 
+     * 
+     * 
+     * @return ClassDescriptor
+     */
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()
+    {
+        return null;
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() 
+
+    /**
+     * Method getIdentity
+     * 
+     * 
+     * 
+     * @return FieldDescriptor
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()
+    {
+        return identity;
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() 
+
+    /**
+     * Method getJavaClass
+     * 
+     * 
+     * 
+     * @return Class
+     */
+    public java.lang.Class getJavaClass()
+    {
+        return org.vamsas.objects.core.VAMSAS.class;
+    } //-- java.lang.Class getJavaClass() 
+
+    /**
+     * Method getNameSpacePrefix
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpacePrefix()
+    {
+        return nsPrefix;
+    } //-- java.lang.String getNameSpacePrefix() 
+
+    /**
+     * Method getNameSpaceURI
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getNameSpaceURI()
+    {
+        return nsURI;
+    } //-- java.lang.String getNameSpaceURI() 
+
+    /**
+     * Method getValidator
+     * 
+     * 
+     * 
+     * @return TypeValidator
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator()
+    {
+        return this;
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() 
+
+    /**
+     * Method getXMLName
+     * 
+     * 
+     * 
+     * @return String
+     */
+    public java.lang.String getXMLName()
+    {
+        return xmlName;
+    } //-- java.lang.String getXMLName() 
+
+}