latest schema.
authorjprocter <jprocter@compbio.dundee.ac.uk>
Tue, 20 Sep 2005 16:33:50 +0000 (16:33 +0000)
committerjprocter <jprocter@compbio.dundee.ac.uk>
Tue, 20 Sep 2005 16:33:50 +0000 (16:33 +0000)
git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@38 be28352e-c001-0410-b1a7-c7978e42abec

24 files changed:
schemas/vamsas15_9.xsd
src/org/vamsas/client/SimpleClientFactory.java
src/org/vamsas/client/object.java
src/org/vamsas/objects/core/.castor.cdr
src/org/vamsas/objects/core/Alignment.java
src/org/vamsas/objects/core/AlignmentDescriptor.java
src/org/vamsas/objects/core/AlignmentSequence.java
src/org/vamsas/objects/core/AlignmentSequenceDescriptor.java
src/org/vamsas/objects/core/Application.java
src/org/vamsas/objects/core/ApplicationDescriptor.java
src/org/vamsas/objects/core/Newick.java [new file with mode: 0644]
src/org/vamsas/objects/core/NewickDescriptor.java [new file with mode: 0644]
src/org/vamsas/objects/core/Provenance.java
src/org/vamsas/objects/core/ProvenanceDescriptor.java
src/org/vamsas/objects/core/Sequence.java
src/org/vamsas/objects/core/SequenceDescriptor.java
src/org/vamsas/objects/core/SequenceSetAnnotations.java
src/org/vamsas/objects/core/SequenceSetAnnotationsDescriptor.java
src/org/vamsas/objects/core/SequenceType.java
src/org/vamsas/objects/core/SequenceTypeDescriptor.java
src/org/vamsas/objects/core/Tree.java
src/org/vamsas/objects/core/TreeDescriptor.java
src/org/vamsas/objects/core/User.java [new file with mode: 0644]
src/org/vamsas/objects/core/UserDescriptor.java [new file with mode: 0644]

index 1a5ba63..dd12108 100644 (file)
                        <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
                        <xs:element ref="vamsas:SequenceSet" minOccurs="0" maxOccurs="unbounded"/>
                </xs:sequence>
-               <xs:attribute name="id" type="xs:ID"/>
+               <xs:attribute name="id" type="xs:ID"  minOccurs="0" maxOccurs="1"/>
     </xs:complexType>
     <xs:element name="Tree">
                <xs:complexType>
                <xs:sequence>
-                       <xs:element name="newickFormat" type="xs:string" minOccurs="1" maxOccurs="unbounded"/>
+                       <xs:element name="title" type="xs:string" minOccurs="0" maxOccurs="1"/>
+                       <xs:element name="newick" minOccurs="1" maxOccurs="unbounded">
+                         <xs:complexType>
+                         <xs:simpleContent>
+                         <xs:extension base="xs:string">
+                         <xs:attribute name="title" type="xs:string" minOccurs="0" maxOccurs="1"/>
+                         <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+                         </xs:extension>
+                         </xs:simpleContent>
+                         </xs:complexType>
+                       </xs:element>
                        <xs:element ref="vamsas:Provenance" minOccurs="1" maxOccurs="1"/>
                    </xs:sequence>
-               <xs:attribute name="id" type="xs:ID"/>
+               <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
        </xs:complexType>
        </xs:element>
        <xs:element name="Provenance">
                <xs:complexType>
-                       <xs:sequence maxOccurs="unbounded">
-                               <xs:element name="entry">
+                       <xs:sequence>
+                               <xs:element name="entry" minOccurs="0" maxOccurs="unbounded">
                                        <xs:complexType>
                                                <xs:sequence>
                                                        <xs:element name="User" type="xs:string"/>
                                                        <xs:element name="Action" type="xs:string"/>
                                                        <xs:element name="Date" type="xs:date"/>
                                                </xs:sequence>
-                                       <xs:attribute name="id" type="xs:ID"/>
+                                               <xs:attribute name="id" type="xs:ID"  minOccurs="0" maxOccurs="1"/>
                                        </xs:complexType>
                                </xs:element>
                        </xs:sequence>
                </xs:complexType>
        </xs:element>
+
        <xs:element name="SequenceSet">
                <xs:complexType>
                        <xs:sequence>
                                        <xs:complexType>
                                                <xs:complexContent>
                                                        <xs:extension base="vamsas:SequenceType">
+                                                               <xs:sequence>
+                                                                   <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
+                                                                       <xs:complexType>
+                                                                               <xs:attribute name="source"/>
+                                                                               <xs:attribute name="version"/>
+                                                                               <xs:attribute name="accessionId"/>
+                                                                               <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
+                                                                       </xs:complexType>
+                                                                       </xs:element>
+                                                               </xs:sequence>
+                                                               <xs:attribute name="id" type="xs:ID" minOccurs="1" maxOccurs="1"/>
                                                                <xs:attribute name="dictionary" type="xs:string"/>
                                                        </xs:extension>
                                                </xs:complexContent>
                                                        <xs:element name="description" type="xs:string" minOccurs="0"/>
                                                        <xs:element name="status" type="xs:string" minOccurs="0"/>
                                                        <xs:element ref="vamsas:annotationElement" minOccurs="0" maxOccurs="unbounded"/>
-                                                       <xs:element ref="vamsas:Provenance"/>
+                                                       <xs:element ref="vamsas:Provenance" minOccurs="0" maxOccurs="unbounded"/>
                                                </xs:sequence>
                                                <xs:attribute name="type" type="xs:string" use="required"/>
                                                <xs:attribute name="end" type="xs:string" use="required"/>
                                                <xs:attribute name="begin" type="xs:string" use="required"/>
                                                <xs:attribute name="seqRef" type="xs:IDREF" use="required"/>
-                                               <xs:attribute name="id" type="xs:ID"/>
+                                               <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
                                        </xs:complexType>
                                </xs:element>
                                <xs:element name="Alignment" minOccurs="0" maxOccurs="unbounded">
                                                                                <xs:element ref="vamsas:Provenance"/>
                                                                        </xs:sequence>
                                                                        <xs:attribute name="graph" type="xs:boolean" use="required"/>
-                                                                       <xs:attribute name="id" type="xs:ID"/>
+                                                                       <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
                                                                </xs:complexType>
                                                        </xs:element>
                                                        <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
                                                                <xs:complexType>
                                                                        <xs:complexContent>
                                                                                <xs:extension base="vamsas:SequenceType">
+                                                                                       <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
                                                                                        <xs:attribute name="refid" type="xs:IDREF" use="required"/>
                                                                                </xs:extension>
                                                                        </xs:complexContent>
                                                        </xs:element>
                                                        <xs:element ref="vamsas:Provenance"/>
                                                </xs:sequence>
+                                               <xs:attribute name="id" type="xs:ID" minOccurs="0" maxOccurs="1"/>
                                        </xs:complexType>
                                </xs:element>
                                <xs:element ref="vamsas:Tree" minOccurs="0" maxOccurs="unbounded"/>
                        </xs:sequence>
                        <xs:attribute name="gapChar" type="xs:string" use="required"/>
                        <xs:attribute name="aligned" type="xs:boolean" use="optional"/>
-                       <xs:attribute name="id" type="xs:ID"/>
+                       <xs:attribute name="id" type="xs:ID"  minOccurs="0" maxOccurs="1"/>
                </xs:complexType>
        </xs:element>
        <xs:element name="annotationElement">
                                <xs:element name="value" type="xs:float"/>
                        </xs:sequence>
                        <xs:attribute name="position" type="xs:int" use="required"/>
-                       <xs:attribute name="id" type="xs:ID"/>
+                       <xs:attribute name="id" type="xs:ID"  minOccurs="0" maxOccurs="1"/>
                </xs:complexType>
        </xs:element>
     <xs:complexType name="SequenceType">
                <xs:sequence>
                        <xs:element name="sequence" type="xs:string"/>
                        <xs:element name="name" type="xs:string"/>
-                       <xs:element name="dbRef" minOccurs="0" maxOccurs="unbounded">
-                               <xs:complexType>
-                                       <xs:attribute name="source"/>
-                                       <xs:attribute name="version"/>
-                                       <xs:attribute name="accessionId"/>
-                                       <xs:attribute name="id" type="xs:ID"/>
-                               </xs:complexType>
-                       </xs:element>
                </xs:sequence>
                <xs:attribute name="start" type="xs:int" use="required"/>
                <xs:attribute name="end" type="xs:int" use="required"/>
-               <xs:attribute name="id" type="xs:ID"/>
        </xs:complexType>
        
     <xs:complexType name="ApplicationData">
                <xs:sequence>
                        <xs:element name="Application">
                                <xs:complexType>
+                                       <xs:sequence>
+                                         <xs:element name="User">
+                                         <xs:complexType>
+                                               <xs:attribute name="fullname" type="xs:string"/>
+                                               <xs:attribute name="organization" type="xs:string"/>
+                                               <xs:attribute name="data" type="xs:string"/>
+                                         </xs:complexType>
+                                         </xs:element>
+                                       </xs:sequence>
                                        <xs:attribute name="version" type="xs:string"/>
                                        <xs:attribute name="name" type="xs:string"/>
-                                       <xs:attribute name="session" type="xs:string"/>
+                                       <xs:attribute name="urn" type="xs:string"/>
                                        <xs:attribute name="data" type="xs:string"/>
                                </xs:complexType>
                        </xs:element>
index 5a53bd2..5b9346f 100644 (file)
@@ -1,28 +1,38 @@
 package org.vamsas.client;
+
+import java.io.File;
+import java.io.IOException;
+
 /**
  * TODO document type SimpleClientFactory
  * @author jimp
  *
  */
 public class SimpleClientFactory implements IClientFactory {
-  static SimpleClientFactory singleton = null;
-
-  static private void CreateClientFactory() {
-    if (singleton != null) {
-
-    } else {
-      // Create singleton class.
-
-    }
+  File sessionArena;
+  
+  /**
+   * default constructor - called by CreateClientFactory only.
+   *
+   */
+  public SimpleClientFactory() {
+    sessionArena = null;
   }
   /**
    * Create a client factory that works with sessions at the given
    * path.
    * @param path
    */
-  public SimpleClientFactory(String path) {
+  public SimpleClientFactory(String path) throws IOException {
     // Check path is valid and read/writeable.
-    // make housekeeping files...
+    File newarena = new File(path);
+    if (newarena.isDirectory() && newarena.canRead() && newarena.canWrite()) {
+      sessionArena = newarena;
+    } else {
+      sessionArena = null;
+      throw(new IOException("Cannot read and write to a directory called "+path));
+    }
   }
   /* (non-Javadoc)
    * @see org.vamsas.client.IClientFactory#getIClient(org.vamsas.client.ClientHandle)
index 4f19c26..e1384a4 100644 (file)
@@ -18,6 +18,7 @@ public abstract class object {
      * to any object in the vamsas document
      */
        protected boolean __stored_in_document=false;
+    protected long __last_hash=0;
     protected VorbaId vorbaId=null;
     protected IVorbaIdFactory __vorba=null;
     /**
@@ -68,4 +69,14 @@ public abstract class object {
     protected void set__stored_in_document(boolean __stored_in_document) {
       this.__stored_in_document = __stored_in_document;
     }
+    /**
+     * __last_hash is the hash value computed 
+     * when the object was last checked against 
+     * a IClientDocument generated by the 
+     * object's parent IClient instance.
+     * @return Returns the __last_hash.
+     */
+    public long get__last_hash() {
+      return __last_hash;
+    }
 }
index ce4c376..ffd7903 100644 (file)
@@ -1,18 +1,19 @@
 -- 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.Provenance=org.vamsas.objects.core.ProvenanceDes...
+org.vamsas.objects.core.SequenceType=org.vamsas.objects.core.SequenceTypeD...
+org.vamsas.objects.core.Newick=org.vamsas.objects.core.NewickDescriptor
 org.vamsas.objects.core.AnnotationElement=org.vamsas.objects.core.AnnotationEle...
+org.vamsas.objects.core.AlignmentSequence=org.vamsas.objects.core.AlignmentSequ...
+org.vamsas.objects.core.Alignment=org.vamsas.objects.core.AlignmentDesc...
+org.vamsas.objects.core.DbRef=org.vamsas.objects.core.DbRefDescriptor
+org.vamsas.objects.core.User=org.vamsas.objects.core.UserDescriptor
+org.vamsas.objects.core.SequenceSetAnnotations=org.vamsas.objects.core.SequenceSetAn...
+org.vamsas.objects.core.Application=org.vamsas.objects.core.ApplicationDe...
+org.vamsas.objects.core.VAMSAS=org.vamsas.objects.core.VAMSASDescriptor
+org.vamsas.objects.core.Sequence=org.vamsas.objects.core.SequenceDescr...
 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...
+org.vamsas.objects.core.AlignmentAnnotations=org.vamsas.objects.core.AlignmentAnno...
index b9fa81c..9a6d432 100644 (file)
@@ -38,6 +38,11 @@ implements java.io.Serializable
     //--------------------------/
 
     /**
+     * Field _id
+     */
+    private java.lang.String _id;
+
+    /**
      * Field _alignmentAnnotations
      */
     private org.vamsas.objects.core.AlignmentAnnotations _alignmentAnnotations;
@@ -169,6 +174,13 @@ implements java.io.Serializable
         if (obj instanceof Alignment) {
         
             Alignment temp = (Alignment)obj;
+            if (this._id != null) {
+                if (temp._id == null) return false;
+                else if (!(this._id.equals(temp._id))) 
+                    return false;
+            }
+            else if (temp._id != null)
+                return false;
             if (this._alignmentAnnotations != null) {
                 if (temp._alignmentAnnotations == null) return false;
                 else if (!(this._alignmentAnnotations.equals(temp._alignmentAnnotations))) 
@@ -262,6 +274,17 @@ implements java.io.Serializable
     } //-- int getAlignmentSequenceCount() 
 
     /**
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
+
+    /**
      * Returns the value of field 'provenance'.
      * 
      * @return Provenance
@@ -460,6 +483,16 @@ implements java.io.Serializable
     } //-- void setAlignmentSequence(org.vamsas.objects.core.AlignmentSequence) 
 
     /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(java.lang.String id)
+    {
+        this._id = id;
+    } //-- void setId(java.lang.String) 
+
+    /**
      * Sets the value of field 'provenance'.
      * 
      * @param provenance the value of field 'provenance'.
index 684f619..4d65fe1 100644 (file)
@@ -66,6 +66,40 @@ public class AlignmentDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;
         //-- initialize attribute descriptors
         
+        //-- _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
+            {
+                Alignment target = (Alignment) object;
+                return target.getId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Alignment target = (Alignment) 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.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
         //-- initialize element descriptors
         
         //-- _alignmentAnnotations
index 91fd691..6761934 100644 (file)
@@ -36,6 +36,11 @@ implements java.io.Serializable
     //--------------------------/
 
     /**
+     * Field _id
+     */
+    private java.lang.String _id;
+
+    /**
      * Field _refid
      */
     private java.lang.Object _refid;
@@ -72,6 +77,13 @@ implements java.io.Serializable
         if (obj instanceof AlignmentSequence) {
         
             AlignmentSequence temp = (AlignmentSequence)obj;
+            if (this._id != null) {
+                if (temp._id == null) return false;
+                else if (!(this._id.equals(temp._id))) 
+                    return false;
+            }
+            else if (temp._id != null)
+                return false;
             if (this._refid != null) {
                 if (temp._refid == null) return false;
                 else if (!(this._refid.equals(temp._refid))) 
@@ -85,6 +97,17 @@ implements java.io.Serializable
     } //-- boolean equals(java.lang.Object) 
 
     /**
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
+
+    /**
      * Returns the value of field 'refid'.
      * 
      * @return Object
@@ -142,6 +165,16 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(java.lang.String id)
+    {
+        this._id = id;
+    } //-- void setId(java.lang.String) 
+
+    /**
      * Sets the value of field 'refid'.
      * 
      * @param refid the value of field 'refid'.
index b49e045..e219b2b 100644 (file)
@@ -64,6 +64,40 @@ public class AlignmentSequenceDescriptor extends org.vamsas.objects.core.Sequenc
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;
         //-- initialize attribute descriptors
         
+        //-- _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
+            {
+                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.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.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
         //-- _refid
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_refid", "refid", org.exolab.castor.xml.NodeType.Attribute);
         desc.setReference(true);
index 1b2659c..0567205 100644 (file)
@@ -46,15 +46,20 @@ implements java.io.Serializable
     private java.lang.String _name;
 
     /**
-     * Field _session
+     * Field _urn
      */
-    private java.lang.String _session;
+    private java.lang.String _urn;
 
     /**
      * Field _data
      */
     private java.lang.String _data;
 
+    /**
+     * Field _user
+     */
+    private org.vamsas.objects.core.User _user;
+
 
       //----------------/
      //- Constructors -/
@@ -101,12 +106,12 @@ implements java.io.Serializable
             }
             else if (temp._name != null)
                 return false;
-            if (this._session != null) {
-                if (temp._session == null) return false;
-                else if (!(this._session.equals(temp._session))) 
+            if (this._urn != null) {
+                if (temp._urn == null) return false;
+                else if (!(this._urn.equals(temp._urn))) 
                     return false;
             }
-            else if (temp._session != null)
+            else if (temp._urn != null)
                 return false;
             if (this._data != null) {
                 if (temp._data == null) return false;
@@ -115,6 +120,13 @@ implements java.io.Serializable
             }
             else if (temp._data != null)
                 return false;
+            if (this._user != null) {
+                if (temp._user == null) return false;
+                else if (!(this._user.equals(temp._user))) 
+                    return false;
+            }
+            else if (temp._user != null)
+                return false;
             return true;
         }
         return false;
@@ -143,15 +155,26 @@ implements java.io.Serializable
     } //-- java.lang.String getName() 
 
     /**
-     * Returns the value of field 'session'.
+     * Returns the value of field 'urn'.
      * 
      * @return String
-     * @return the value of field 'session'.
+     * @return the value of field 'urn'.
+     */
+    public java.lang.String getUrn()
+    {
+        return this._urn;
+    } //-- java.lang.String getUrn() 
+
+    /**
+     * Returns the value of field 'user'.
+     * 
+     * @return User
+     * @return the value of field 'user'.
      */
-    public java.lang.String getSession()
+    public org.vamsas.objects.core.User getUser()
     {
-        return this._session;
-    } //-- java.lang.String getSession() 
+        return this._user;
+    } //-- org.vamsas.objects.core.User getUser() 
 
     /**
      * Returns the value of field 'version'.
@@ -231,14 +254,24 @@ implements java.io.Serializable
     } //-- void setName(java.lang.String) 
 
     /**
-     * Sets the value of field 'session'.
+     * Sets the value of field 'urn'.
+     * 
+     * @param urn the value of field 'urn'.
+     */
+    public void setUrn(java.lang.String urn)
+    {
+        this._urn = urn;
+    } //-- void setUrn(java.lang.String) 
+
+    /**
+     * Sets the value of field 'user'.
      * 
-     * @param session the value of field 'session'.
+     * @param user the value of field 'user'.
      */
-    public void setSession(java.lang.String session)
+    public void setUser(org.vamsas.objects.core.User user)
     {
-        this._session = session;
-    } //-- void setSession(java.lang.String) 
+        this._user = user;
+    } //-- void setUser(org.vamsas.objects.core.User) 
 
     /**
      * Sets the value of field 'version'.
index 7b3a6a6..0f956fa 100644 (file)
@@ -58,6 +58,9 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         super();
         nsURI = "http://www.vamsas.org";
         xmlName = "Application";
+        
+        //-- 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;
@@ -137,22 +140,22 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _session
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_session", "session", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _urn
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_urn", "urn", 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
             {
                 Application target = (Application) object;
-                return target.getSession();
+                return target.getUrn();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
                     Application target = (Application) object;
-                    target.setSession( (java.lang.String) value);
+                    target.setUrn( (java.lang.String) value);
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -166,7 +169,7 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         desc.setMultivalued(false);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _session
+        //-- validation code for: _urn
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
             StringValidator typeValidator = new StringValidator();
@@ -213,6 +216,42 @@ public class ApplicationDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         desc.setValidator(fieldValidator);
         //-- initialize element descriptors
         
+        //-- _user
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.User.class, "_user", "User", org.exolab.castor.xml.NodeType.Element);
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Application target = (Application) object;
+                return target.getUser();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Application target = (Application) object;
+                    target.setUser( (org.vamsas.objects.core.User) 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.User();
+            }
+        };
+        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
+        }
+        desc.setValidator(fieldValidator);
     } //-- org.vamsas.objects.core.ApplicationDescriptor()
 
 
diff --git a/src/org/vamsas/objects/core/Newick.java b/src/org/vamsas/objects/core/Newick.java
new file mode 100644 (file)
index 0000000..3d2bd2a
--- /dev/null
@@ -0,0 +1,248 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class Newick.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class Newick extends org.vamsas.client.object 
+implements java.io.Serializable
+{
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * internal content storage
+     */
+    private java.lang.String _content = "";
+
+    /**
+     * Field _title
+     */
+    private java.lang.String _title;
+
+    /**
+     * Field _id
+     */
+    private java.lang.String _id;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public Newick() 
+     {
+        super();
+        setContent("");
+    } //-- org.vamsas.objects.core.Newick()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Note: hashCode() has not been overriden
+     * 
+     * @param obj
+     * @return boolean
+     */
+    public boolean equals(java.lang.Object obj)
+    {
+        if ( this == obj )
+            return true;
+        
+        if (super.equals(obj)==false)
+            return false;
+        
+        if (obj instanceof Newick) {
+        
+            Newick temp = (Newick)obj;
+            if (this._content != null) {
+                if (temp._content == null) return false;
+                else if (!(this._content.equals(temp._content))) 
+                    return false;
+            }
+            else if (temp._content != null)
+                return false;
+            if (this._title != null) {
+                if (temp._title == null) return false;
+                else if (!(this._title.equals(temp._title))) 
+                    return false;
+            }
+            else if (temp._title != null)
+                return false;
+            if (this._id != null) {
+                if (temp._id == null) return false;
+                else if (!(this._id.equals(temp._id))) 
+                    return false;
+            }
+            else if (temp._id != null)
+                return false;
+            return true;
+        }
+        return false;
+    } //-- boolean equals(java.lang.Object) 
+
+    /**
+     * Returns the value of field 'content'. The field 'content'
+     * has the following description: internal content storage
+     * 
+     * @return String
+     * @return the value of field 'content'.
+     */
+    public java.lang.String getContent()
+    {
+        return this._content;
+    } //-- java.lang.String getContent() 
+
+    /**
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
+
+    /**
+     * Returns the value of field 'title'.
+     * 
+     * @return String
+     * @return the value of field 'title'.
+     */
+    public java.lang.String getTitle()
+    {
+        return this._title;
+    } //-- java.lang.String getTitle() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'content'. The field 'content' has
+     * the following description: internal content storage
+     * 
+     * @param content the value of field 'content'.
+     */
+    public void setContent(java.lang.String content)
+    {
+        this._content = content;
+    } //-- void setContent(java.lang.String) 
+
+    /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(java.lang.String id)
+    {
+        this._id = id;
+    } //-- void setId(java.lang.String) 
+
+    /**
+     * Sets the value of field 'title'.
+     * 
+     * @param title the value of field 'title'.
+     */
+    public void setTitle(java.lang.String title)
+    {
+        this._title = title;
+    } //-- void setTitle(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return Newick
+     */
+    public static org.vamsas.objects.core.Newick unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (org.vamsas.objects.core.Newick) Unmarshaller.unmarshal(org.vamsas.objects.core.Newick.class, reader);
+    } //-- org.vamsas.objects.core.Newick unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/org/vamsas/objects/core/NewickDescriptor.java b/src/org/vamsas/objects/core/NewickDescriptor.java
new file mode 100644 (file)
index 0000000..ee208f6
--- /dev/null
@@ -0,0 +1,278 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M2</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 NewickDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class NewickDescriptor 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 NewickDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "newick";
+        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
+            {
+                Newick target = (Newick) object;
+                return target.getContent();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Newick target = (Newick) 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
+        
+        //-- _title
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", 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
+            {
+                Newick target = (Newick) object;
+                return target.getTitle();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Newick target = (Newick) object;
+                    target.setTitle( (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: _title
+        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
+            {
+                Newick target = (Newick) object;
+                return target.getId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Newick target = (Newick) 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.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- org.vamsas.objects.core.NewickDescriptor()
+
+
+      //-----------/
+     //- 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.Newick.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() 
+
+}
index 9f0adc5..3c3eb8d 100644 (file)
@@ -38,9 +38,9 @@ implements java.io.Serializable
     //--------------------------/
 
     /**
-     * Field _items
+     * Field _entryList
      */
-    private java.util.Vector _items;
+    private java.util.Vector _entryList;
 
 
       //----------------/
@@ -50,7 +50,7 @@ implements java.io.Serializable
     public Provenance() 
      {
         super();
-        _items = new Vector();
+        _entryList = new Vector();
     } //-- org.vamsas.objects.core.Provenance()
 
 
@@ -59,43 +59,43 @@ implements java.io.Serializable
     //-----------/
 
     /**
-     * Method addProvenanceItem
+     * Method addEntry
      * 
      * 
      * 
-     * @param vProvenanceItem
+     * @param vEntry
      */
-    public void addProvenanceItem(org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+    public void addEntry(org.vamsas.objects.core.Entry vEntry)
         throws java.lang.IndexOutOfBoundsException
     {
-        _items.addElement(vProvenanceItem);
-    } //-- void addProvenanceItem(org.vamsas.objects.core.ProvenanceItem) 
+        _entryList.addElement(vEntry);
+    } //-- void addEntry(org.vamsas.objects.core.Entry) 
 
     /**
-     * Method addProvenanceItem
+     * Method addEntry
      * 
      * 
      * 
      * @param index
-     * @param vProvenanceItem
+     * @param vEntry
      */
-    public void addProvenanceItem(int index, org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+    public void addEntry(int index, org.vamsas.objects.core.Entry vEntry)
         throws java.lang.IndexOutOfBoundsException
     {
-        _items.insertElementAt(vProvenanceItem, index);
-    } //-- void addProvenanceItem(int, org.vamsas.objects.core.ProvenanceItem) 
+        _entryList.insertElementAt(vEntry, index);
+    } //-- void addEntry(int, org.vamsas.objects.core.Entry) 
 
     /**
-     * Method enumerateProvenanceItem
+     * Method enumerateEntry
      * 
      * 
      * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateProvenanceItem()
+    public java.util.Enumeration enumerateEntry()
     {
-        return _items.elements();
-    } //-- java.util.Enumeration enumerateProvenanceItem() 
+        return _entryList.elements();
+    } //-- java.util.Enumeration enumerateEntry() 
 
     /**
      * Note: hashCode() has not been overriden
@@ -114,12 +114,12 @@ implements java.io.Serializable
         if (obj instanceof Provenance) {
         
             Provenance temp = (Provenance)obj;
-            if (this._items != null) {
-                if (temp._items == null) return false;
-                else if (!(this._items.equals(temp._items))) 
+            if (this._entryList != null) {
+                if (temp._entryList == null) return false;
+                else if (!(this._entryList.equals(temp._entryList))) 
                     return false;
             }
-            else if (temp._items != null)
+            else if (temp._entryList != null)
                 return false;
             return true;
         }
@@ -127,52 +127,52 @@ implements java.io.Serializable
     } //-- boolean equals(java.lang.Object) 
 
     /**
-     * Method getProvenanceItem
+     * Method getEntry
      * 
      * 
      * 
      * @param index
-     * @return ProvenanceItem
+     * @return Entry
      */
-    public org.vamsas.objects.core.ProvenanceItem getProvenanceItem(int index)
+    public org.vamsas.objects.core.Entry getEntry(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _items.size())) {
-            throw new IndexOutOfBoundsException("getProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]");
+        if ((index < 0) || (index > _entryList.size())) {
+            throw new IndexOutOfBoundsException("getEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");
         }
         
-        return (org.vamsas.objects.core.ProvenanceItem) _items.elementAt(index);
-    } //-- org.vamsas.objects.core.ProvenanceItem getProvenanceItem(int) 
+        return (org.vamsas.objects.core.Entry) _entryList.elementAt(index);
+    } //-- org.vamsas.objects.core.Entry getEntry(int) 
 
     /**
-     * Method getProvenanceItem
+     * Method getEntry
      * 
      * 
      * 
-     * @return ProvenanceItem
+     * @return Entry
      */
-    public org.vamsas.objects.core.ProvenanceItem[] getProvenanceItem()
+    public org.vamsas.objects.core.Entry[] getEntry()
     {
-        int size = _items.size();
-        org.vamsas.objects.core.ProvenanceItem[] mArray = new org.vamsas.objects.core.ProvenanceItem[size];
+        int size = _entryList.size();
+        org.vamsas.objects.core.Entry[] mArray = new org.vamsas.objects.core.Entry[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.ProvenanceItem) _items.elementAt(index);
+            mArray[index] = (org.vamsas.objects.core.Entry) _entryList.elementAt(index);
         }
         return mArray;
-    } //-- org.vamsas.objects.core.ProvenanceItem[] getProvenanceItem() 
+    } //-- org.vamsas.objects.core.Entry[] getEntry() 
 
     /**
-     * Method getProvenanceItemCount
+     * Method getEntryCount
      * 
      * 
      * 
      * @return int
      */
-    public int getProvenanceItemCount()
+    public int getEntryCount()
     {
-        return _items.size();
-    } //-- int getProvenanceItemCount() 
+        return _entryList.size();
+    } //-- int getEntryCount() 
 
     /**
      * Method isValid
@@ -221,62 +221,62 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAllProvenanceItem
+     * Method removeAllEntry
      * 
      */
-    public void removeAllProvenanceItem()
+    public void removeAllEntry()
     {
-        _items.removeAllElements();
-    } //-- void removeAllProvenanceItem() 
+        _entryList.removeAllElements();
+    } //-- void removeAllEntry() 
 
     /**
-     * Method removeProvenanceItem
+     * Method removeEntry
      * 
      * 
      * 
      * @param index
-     * @return ProvenanceItem
+     * @return Entry
      */
-    public org.vamsas.objects.core.ProvenanceItem removeProvenanceItem(int index)
+    public org.vamsas.objects.core.Entry removeEntry(int index)
     {
-        java.lang.Object obj = _items.elementAt(index);
-        _items.removeElementAt(index);
-        return (org.vamsas.objects.core.ProvenanceItem) obj;
-    } //-- org.vamsas.objects.core.ProvenanceItem removeProvenanceItem(int) 
+        java.lang.Object obj = _entryList.elementAt(index);
+        _entryList.removeElementAt(index);
+        return (org.vamsas.objects.core.Entry) obj;
+    } //-- org.vamsas.objects.core.Entry removeEntry(int) 
 
     /**
-     * Method setProvenanceItem
+     * Method setEntry
      * 
      * 
      * 
      * @param index
-     * @param vProvenanceItem
+     * @param vEntry
      */
-    public void setProvenanceItem(int index, org.vamsas.objects.core.ProvenanceItem vProvenanceItem)
+    public void setEntry(int index, org.vamsas.objects.core.Entry vEntry)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _items.size())) {
-            throw new IndexOutOfBoundsException("setProvenanceItem: Index value '"+index+"' not in range [0.."+_items.size()+ "]");
+        if ((index < 0) || (index > _entryList.size())) {
+            throw new IndexOutOfBoundsException("setEntry: Index value '"+index+"' not in range [0.."+_entryList.size()+ "]");
         }
-        _items.setElementAt(vProvenanceItem, index);
-    } //-- void setProvenanceItem(int, org.vamsas.objects.core.ProvenanceItem) 
+        _entryList.setElementAt(vEntry, index);
+    } //-- void setEntry(int, org.vamsas.objects.core.Entry) 
 
     /**
-     * Method setProvenanceItem
+     * Method setEntry
      * 
      * 
      * 
-     * @param provenanceItemArray
+     * @param entryArray
      */
-    public void setProvenanceItem(org.vamsas.objects.core.ProvenanceItem[] provenanceItemArray)
+    public void setEntry(org.vamsas.objects.core.Entry[] entryArray)
     {
         //-- copy array
-        _items.removeAllElements();
-        for (int i = 0; i < provenanceItemArray.length; i++) {
-            _items.addElement(provenanceItemArray[i]);
+        _entryList.removeAllElements();
+        for (int i = 0; i < entryArray.length; i++) {
+            _entryList.addElement(entryArray[i]);
         }
-    } //-- void setProvenanceItem(org.vamsas.objects.core.ProvenanceItem) 
+    } //-- void setEntry(org.vamsas.objects.core.Entry) 
 
     /**
      * Method unmarshal
index 71db58f..23b355d 100644 (file)
@@ -56,7 +56,11 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes
     public ProvenanceDescriptor() 
      {
         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;
@@ -64,37 +68,36 @@ public class ProvenanceDescriptor extends org.exolab.castor.xml.util.XMLClassDes
         
         //-- 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);
+        //-- _entryList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Entry.class, "_entryList", "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
             {
                 Provenance target = (Provenance) object;
-                return target.getProvenanceItem();
+                return target.getEntry();
             }
             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);
+                    target.addEntry( (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.ProvenanceItem();
+                return new org.vamsas.objects.core.Entry();
             }
         };
         desc.setHandler(handler);
-        desc.setContainer(true);
-        desc.setClassDescriptor(new org.vamsas.objects.core.ProvenanceItemDescriptor());
+        desc.setNameSpaceURI("http://www.vamsas.org");
         desc.setMultivalued(true);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _items
+        //-- validation code for: _entryList
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         fieldValidator.setMinOccurs(0);
         { //-- local scope
index 5988d65..27a1d8d 100644 (file)
@@ -15,6 +15,8 @@ import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
+import java.util.Enumeration;
+import java.util.Vector;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -36,10 +38,20 @@ implements java.io.Serializable
     //--------------------------/
 
     /**
+     * Field _id
+     */
+    private java.lang.String _id;
+
+    /**
      * Field _dictionary
      */
     private java.lang.String _dictionary;
 
+    /**
+     * Field _dbRefList
+     */
+    private java.util.Vector _dbRefList;
+
 
       //----------------/
      //- Constructors -/
@@ -48,6 +60,7 @@ implements java.io.Serializable
     public Sequence() 
      {
         super();
+        _dbRefList = new Vector();
     } //-- org.vamsas.objects.core.Sequence()
 
 
@@ -56,6 +69,45 @@ implements java.io.Serializable
     //-----------/
 
     /**
+     * Method addDbRef
+     * 
+     * 
+     * 
+     * @param vDbRef
+     */
+    public void addDbRef(org.vamsas.objects.core.DbRef vDbRef)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _dbRefList.addElement(vDbRef);
+    } //-- void addDbRef(org.vamsas.objects.core.DbRef) 
+
+    /**
+     * Method addDbRef
+     * 
+     * 
+     * 
+     * @param index
+     * @param vDbRef
+     */
+    public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _dbRefList.insertElementAt(vDbRef, index);
+    } //-- void addDbRef(int, org.vamsas.objects.core.DbRef) 
+
+    /**
+     * Method enumerateDbRef
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateDbRef()
+    {
+        return _dbRefList.elements();
+    } //-- java.util.Enumeration enumerateDbRef() 
+
+    /**
      * Note: hashCode() has not been overriden
      * 
      * @param obj
@@ -72,6 +124,13 @@ implements java.io.Serializable
         if (obj instanceof Sequence) {
         
             Sequence temp = (Sequence)obj;
+            if (this._id != null) {
+                if (temp._id == null) return false;
+                else if (!(this._id.equals(temp._id))) 
+                    return false;
+            }
+            else if (temp._id != null)
+                return false;
             if (this._dictionary != null) {
                 if (temp._dictionary == null) return false;
                 else if (!(this._dictionary.equals(temp._dictionary))) 
@@ -79,12 +138,67 @@ implements java.io.Serializable
             }
             else if (temp._dictionary != null)
                 return false;
+            if (this._dbRefList != null) {
+                if (temp._dbRefList == null) return false;
+                else if (!(this._dbRefList.equals(temp._dbRefList))) 
+                    return false;
+            }
+            else if (temp._dbRefList != null)
+                return false;
             return true;
         }
         return false;
     } //-- boolean equals(java.lang.Object) 
 
     /**
+     * Method getDbRef
+     * 
+     * 
+     * 
+     * @param index
+     * @return DbRef
+     */
+    public org.vamsas.objects.core.DbRef getDbRef(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _dbRefList.size())) {
+            throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
+        }
+        
+        return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
+    } //-- org.vamsas.objects.core.DbRef getDbRef(int) 
+
+    /**
+     * Method getDbRef
+     * 
+     * 
+     * 
+     * @return DbRef
+     */
+    public org.vamsas.objects.core.DbRef[] getDbRef()
+    {
+        int size = _dbRefList.size();
+        org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
+        }
+        return mArray;
+    } //-- org.vamsas.objects.core.DbRef[] getDbRef() 
+
+    /**
+     * Method getDbRefCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getDbRefCount()
+    {
+        return _dbRefList.size();
+    } //-- int getDbRefCount() 
+
+    /**
      * Returns the value of field 'dictionary'.
      * 
      * @return String
@@ -96,6 +210,17 @@ implements java.io.Serializable
     } //-- java.lang.String getDictionary() 
 
     /**
+     * Returns the value of field 'id'.
+     * 
+     * @return String
+     * @return the value of field 'id'.
+     */
+    public java.lang.String getId()
+    {
+        return this._id;
+    } //-- java.lang.String getId() 
+
+    /**
      * Method isValid
      * 
      * 
@@ -142,6 +267,64 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
+     * Method removeAllDbRef
+     * 
+     */
+    public void removeAllDbRef()
+    {
+        _dbRefList.removeAllElements();
+    } //-- void removeAllDbRef() 
+
+    /**
+     * Method removeDbRef
+     * 
+     * 
+     * 
+     * @param index
+     * @return DbRef
+     */
+    public org.vamsas.objects.core.DbRef removeDbRef(int index)
+    {
+        java.lang.Object obj = _dbRefList.elementAt(index);
+        _dbRefList.removeElementAt(index);
+        return (org.vamsas.objects.core.DbRef) obj;
+    } //-- org.vamsas.objects.core.DbRef removeDbRef(int) 
+
+    /**
+     * Method setDbRef
+     * 
+     * 
+     * 
+     * @param index
+     * @param vDbRef
+     */
+    public void setDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _dbRefList.size())) {
+            throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
+        }
+        _dbRefList.setElementAt(vDbRef, index);
+    } //-- void setDbRef(int, org.vamsas.objects.core.DbRef) 
+
+    /**
+     * Method setDbRef
+     * 
+     * 
+     * 
+     * @param dbRefArray
+     */
+    public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray)
+    {
+        //-- copy array
+        _dbRefList.removeAllElements();
+        for (int i = 0; i < dbRefArray.length; i++) {
+            _dbRefList.addElement(dbRefArray[i]);
+        }
+    } //-- void setDbRef(org.vamsas.objects.core.DbRef) 
+
+    /**
      * Sets the value of field 'dictionary'.
      * 
      * @param dictionary the value of field 'dictionary'.
@@ -152,6 +335,16 @@ implements java.io.Serializable
     } //-- void setDictionary(java.lang.String) 
 
     /**
+     * Sets the value of field 'id'.
+     * 
+     * @param id the value of field 'id'.
+     */
+    public void setId(java.lang.String id)
+    {
+        this._id = id;
+    } //-- void setId(java.lang.String) 
+
+    /**
      * Method unmarshal
      * 
      * 
index 202b67f..7486c01 100644 (file)
@@ -59,11 +59,48 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc
         setExtendsWithoutFlatten(new org.vamsas.objects.core.SequenceTypeDescriptor());
         nsURI = "http://www.vamsas.org";
         xmlName = "Sequence";
+        
+        //-- 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
         
+        //-- _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.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _id
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
         //-- _dictionary
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_dictionary", "dictionary", org.exolab.castor.xml.NodeType.Attribute);
         desc.setImmutable(true);
@@ -103,6 +140,41 @@ public class SequenceDescriptor extends org.vamsas.objects.core.SequenceTypeDesc
         desc.setValidator(fieldValidator);
         //-- initialize element descriptors
         
+        //-- _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
+            {
+                Sequence target = (Sequence) object;
+                return target.getDbRef();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Sequence target = (Sequence) 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.SequenceDescriptor()
 
 
index 347636c..04e249d 100644 (file)
@@ -78,9 +78,9 @@ implements java.io.Serializable
     private java.util.Vector _annotationElementList;
 
     /**
-     * Field _provenance
+     * Field _provenanceList
      */
-    private org.vamsas.objects.core.Provenance _provenance;
+    private java.util.Vector _provenanceList;
 
 
       //----------------/
@@ -91,6 +91,7 @@ implements java.io.Serializable
      {
         super();
         _annotationElementList = new Vector();
+        _provenanceList = new Vector();
     } //-- org.vamsas.objects.core.SequenceSetAnnotations()
 
 
@@ -126,6 +127,33 @@ implements java.io.Serializable
     } //-- void addAnnotationElement(int, org.vamsas.objects.core.AnnotationElement) 
 
     /**
+     * Method addProvenance
+     * 
+     * 
+     * 
+     * @param vProvenance
+     */
+    public void addProvenance(org.vamsas.objects.core.Provenance vProvenance)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _provenanceList.addElement(vProvenance);
+    } //-- void addProvenance(org.vamsas.objects.core.Provenance) 
+
+    /**
+     * Method addProvenance
+     * 
+     * 
+     * 
+     * @param index
+     * @param vProvenance
+     */
+    public void addProvenance(int index, org.vamsas.objects.core.Provenance vProvenance)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        _provenanceList.insertElementAt(vProvenance, index);
+    } //-- void addProvenance(int, org.vamsas.objects.core.Provenance) 
+
+    /**
      * Method enumerateAnnotationElement
      * 
      * 
@@ -138,6 +166,18 @@ implements java.io.Serializable
     } //-- java.util.Enumeration enumerateAnnotationElement() 
 
     /**
+     * Method enumerateProvenance
+     * 
+     * 
+     * 
+     * @return Enumeration
+     */
+    public java.util.Enumeration enumerateProvenance()
+    {
+        return _provenanceList.elements();
+    } //-- java.util.Enumeration enumerateProvenance() 
+
+    /**
      * Note: hashCode() has not been overriden
      * 
      * @param obj
@@ -210,12 +250,12 @@ implements java.io.Serializable
             }
             else if (temp._annotationElementList != null)
                 return false;
-            if (this._provenance != null) {
-                if (temp._provenance == null) return false;
-                else if (!(this._provenance.equals(temp._provenance))) 
+            if (this._provenanceList != null) {
+                if (temp._provenanceList == null) return false;
+                else if (!(this._provenanceList.equals(temp._provenanceList))) 
                     return false;
             }
-            else if (temp._provenance != null)
+            else if (temp._provenanceList != null)
                 return false;
             return true;
         }
@@ -315,15 +355,52 @@ implements java.io.Serializable
     } //-- java.lang.String getId() 
 
     /**
-     * Returns the value of field 'provenance'.
+     * Method getProvenance
+     * 
+     * 
+     * 
+     * @param index
+     * @return Provenance
+     */
+    public org.vamsas.objects.core.Provenance getProvenance(int index)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _provenanceList.size())) {
+            throw new IndexOutOfBoundsException("getProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]");
+        }
+        
+        return (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index);
+    } //-- org.vamsas.objects.core.Provenance getProvenance(int) 
+
+    /**
+     * Method getProvenance
+     * 
+     * 
      * 
      * @return Provenance
-     * @return the value of field 'provenance'.
      */
-    public org.vamsas.objects.core.Provenance getProvenance()
+    public org.vamsas.objects.core.Provenance[] getProvenance()
     {
-        return this._provenance;
-    } //-- org.vamsas.objects.core.Provenance getProvenance() 
+        int size = _provenanceList.size();
+        org.vamsas.objects.core.Provenance[] mArray = new org.vamsas.objects.core.Provenance[size];
+        for (int index = 0; index < size; index++) {
+            mArray[index] = (org.vamsas.objects.core.Provenance) _provenanceList.elementAt(index);
+        }
+        return mArray;
+    } //-- org.vamsas.objects.core.Provenance[] getProvenance() 
+
+    /**
+     * Method getProvenanceCount
+     * 
+     * 
+     * 
+     * @return int
+     */
+    public int getProvenanceCount()
+    {
+        return _provenanceList.size();
+    } //-- int getProvenanceCount() 
 
     /**
      * Returns the value of field 'seqRef'.
@@ -414,6 +491,15 @@ implements java.io.Serializable
     } //-- void removeAllAnnotationElement() 
 
     /**
+     * Method removeAllProvenance
+     * 
+     */
+    public void removeAllProvenance()
+    {
+        _provenanceList.removeAllElements();
+    } //-- void removeAllProvenance() 
+
+    /**
      * Method removeAnnotationElement
      * 
      * 
@@ -429,6 +515,21 @@ implements java.io.Serializable
     } //-- org.vamsas.objects.core.AnnotationElement removeAnnotationElement(int) 
 
     /**
+     * Method removeProvenance
+     * 
+     * 
+     * 
+     * @param index
+     * @return Provenance
+     */
+    public org.vamsas.objects.core.Provenance removeProvenance(int index)
+    {
+        java.lang.Object obj = _provenanceList.elementAt(index);
+        _provenanceList.removeElementAt(index);
+        return (org.vamsas.objects.core.Provenance) obj;
+    } //-- org.vamsas.objects.core.Provenance removeProvenance(int) 
+
+    /**
      * Method setAnnotationElement
      * 
      * 
@@ -503,13 +604,37 @@ implements java.io.Serializable
     } //-- void setId(java.lang.String) 
 
     /**
-     * Sets the value of field 'provenance'.
+     * Method setProvenance
+     * 
+     * 
+     * 
+     * @param index
+     * @param vProvenance
+     */
+    public void setProvenance(int index, org.vamsas.objects.core.Provenance vProvenance)
+        throws java.lang.IndexOutOfBoundsException
+    {
+        //-- check bounds for index
+        if ((index < 0) || (index > _provenanceList.size())) {
+            throw new IndexOutOfBoundsException("setProvenance: Index value '"+index+"' not in range [0.."+_provenanceList.size()+ "]");
+        }
+        _provenanceList.setElementAt(vProvenance, index);
+    } //-- void setProvenance(int, org.vamsas.objects.core.Provenance) 
+
+    /**
+     * Method setProvenance
+     * 
+     * 
      * 
-     * @param provenance the value of field 'provenance'.
+     * @param provenanceArray
      */
-    public void setProvenance(org.vamsas.objects.core.Provenance provenance)
+    public void setProvenance(org.vamsas.objects.core.Provenance[] provenanceArray)
     {
-        this._provenance = provenance;
+        //-- copy array
+        _provenanceList.removeAllElements();
+        for (int i = 0; i < provenanceArray.length; i++) {
+            _provenanceList.addElement(provenanceArray[i]);
+        }
     } //-- void setProvenance(org.vamsas.objects.core.Provenance) 
 
     /**
index c270df7..6fc4a18 100644 (file)
@@ -366,8 +366,8 @@ public class SequenceSetAnnotationsDescriptor extends org.exolab.castor.xml.util
         { //-- 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);
+        //-- _provenanceList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Provenance.class, "_provenanceList", "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
@@ -380,7 +380,7 @@ public class SequenceSetAnnotationsDescriptor extends org.exolab.castor.xml.util
             {
                 try {
                     SequenceSetAnnotations target = (SequenceSetAnnotations) object;
-                    target.setProvenance( (org.vamsas.objects.core.Provenance) value);
+                    target.addProvenance( (org.vamsas.objects.core.Provenance) value);
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -392,13 +392,12 @@ public class SequenceSetAnnotationsDescriptor extends org.exolab.castor.xml.util
         };
         desc.setHandler(handler);
         desc.setNameSpaceURI("http://www.vamsas.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
+        desc.setMultivalued(true);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _provenance
+        //-- validation code for: _provenanceList
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
+        fieldValidator.setMinOccurs(0);
         { //-- local scope
         }
         desc.setValidator(fieldValidator);
index e6204d6..1adc80a 100644 (file)
@@ -15,8 +15,6 @@ import java.io.IOException;
 import java.io.Reader;
 import java.io.Serializable;
 import java.io.Writer;
-import java.util.Enumeration;
-import java.util.Vector;
 import org.exolab.castor.xml.MarshalException;
 import org.exolab.castor.xml.Marshaller;
 import org.exolab.castor.xml.Unmarshaller;
@@ -58,11 +56,6 @@ implements java.io.Serializable
     private boolean _has_end;
 
     /**
-     * Field _id
-     */
-    private java.lang.String _id;
-
-    /**
      * Field _sequence
      */
     private java.lang.String _sequence;
@@ -72,11 +65,6 @@ implements java.io.Serializable
      */
     private java.lang.String _name;
 
-    /**
-     * Field _dbRefList
-     */
-    private java.util.Vector _dbRefList;
-
 
       //----------------/
      //- Constructors -/
@@ -85,7 +73,6 @@ implements java.io.Serializable
     public SequenceType() 
      {
         super();
-        _dbRefList = new Vector();
     } //-- org.vamsas.objects.core.SequenceType()
 
 
@@ -94,33 +81,6 @@ implements java.io.Serializable
     //-----------/
 
     /**
-     * Method addDbRef
-     * 
-     * 
-     * 
-     * @param vDbRef
-     */
-    public void addDbRef(org.vamsas.objects.core.DbRef vDbRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _dbRefList.addElement(vDbRef);
-    } //-- void addDbRef(org.vamsas.objects.core.DbRef) 
-
-    /**
-     * Method addDbRef
-     * 
-     * 
-     * 
-     * @param index
-     * @param vDbRef
-     */
-    public void addDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        _dbRefList.insertElementAt(vDbRef, index);
-    } //-- void addDbRef(int, org.vamsas.objects.core.DbRef) 
-
-    /**
      * Method deleteEnd
      * 
      */
@@ -139,18 +99,6 @@ implements java.io.Serializable
     } //-- void deleteStart() 
 
     /**
-     * Method enumerateDbRef
-     * 
-     * 
-     * 
-     * @return Enumeration
-     */
-    public java.util.Enumeration enumerateDbRef()
-    {
-        return _dbRefList.elements();
-    } //-- java.util.Enumeration enumerateDbRef() 
-
-    /**
      * Note: hashCode() has not been overriden
      * 
      * @param obj
@@ -175,13 +123,6 @@ implements java.io.Serializable
                 return false;
             if (this._has_end != temp._has_end)
                 return false;
-            if (this._id != null) {
-                if (temp._id == null) return false;
-                else if (!(this._id.equals(temp._id))) 
-                    return false;
-            }
-            else if (temp._id != null)
-                return false;
             if (this._sequence != null) {
                 if (temp._sequence == null) return false;
                 else if (!(this._sequence.equals(temp._sequence))) 
@@ -196,67 +137,12 @@ implements java.io.Serializable
             }
             else if (temp._name != null)
                 return false;
-            if (this._dbRefList != null) {
-                if (temp._dbRefList == null) return false;
-                else if (!(this._dbRefList.equals(temp._dbRefList))) 
-                    return false;
-            }
-            else if (temp._dbRefList != null)
-                return false;
             return true;
         }
         return false;
     } //-- boolean equals(java.lang.Object) 
 
     /**
-     * Method getDbRef
-     * 
-     * 
-     * 
-     * @param index
-     * @return DbRef
-     */
-    public org.vamsas.objects.core.DbRef getDbRef(int index)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _dbRefList.size())) {
-            throw new IndexOutOfBoundsException("getDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
-        }
-        
-        return (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
-    } //-- org.vamsas.objects.core.DbRef getDbRef(int) 
-
-    /**
-     * Method getDbRef
-     * 
-     * 
-     * 
-     * @return DbRef
-     */
-    public org.vamsas.objects.core.DbRef[] getDbRef()
-    {
-        int size = _dbRefList.size();
-        org.vamsas.objects.core.DbRef[] mArray = new org.vamsas.objects.core.DbRef[size];
-        for (int index = 0; index < size; index++) {
-            mArray[index] = (org.vamsas.objects.core.DbRef) _dbRefList.elementAt(index);
-        }
-        return mArray;
-    } //-- org.vamsas.objects.core.DbRef[] getDbRef() 
-
-    /**
-     * Method getDbRefCount
-     * 
-     * 
-     * 
-     * @return int
-     */
-    public int getDbRefCount()
-    {
-        return _dbRefList.size();
-    } //-- int getDbRefCount() 
-
-    /**
      * Returns the value of field 'end'.
      * 
      * @return int
@@ -268,17 +154,6 @@ implements java.io.Serializable
     } //-- int getEnd() 
 
     /**
-     * Returns the value of field 'id'.
-     * 
-     * @return String
-     * @return the value of field 'id'.
-     */
-    public java.lang.String getId()
-    {
-        return this._id;
-    } //-- java.lang.String getId() 
-
-    /**
      * Returns the value of field 'name'.
      * 
      * @return String
@@ -382,64 +257,6 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAllDbRef
-     * 
-     */
-    public void removeAllDbRef()
-    {
-        _dbRefList.removeAllElements();
-    } //-- void removeAllDbRef() 
-
-    /**
-     * Method removeDbRef
-     * 
-     * 
-     * 
-     * @param index
-     * @return DbRef
-     */
-    public org.vamsas.objects.core.DbRef removeDbRef(int index)
-    {
-        java.lang.Object obj = _dbRefList.elementAt(index);
-        _dbRefList.removeElementAt(index);
-        return (org.vamsas.objects.core.DbRef) obj;
-    } //-- org.vamsas.objects.core.DbRef removeDbRef(int) 
-
-    /**
-     * Method setDbRef
-     * 
-     * 
-     * 
-     * @param index
-     * @param vDbRef
-     */
-    public void setDbRef(int index, org.vamsas.objects.core.DbRef vDbRef)
-        throws java.lang.IndexOutOfBoundsException
-    {
-        //-- check bounds for index
-        if ((index < 0) || (index > _dbRefList.size())) {
-            throw new IndexOutOfBoundsException("setDbRef: Index value '"+index+"' not in range [0.."+_dbRefList.size()+ "]");
-        }
-        _dbRefList.setElementAt(vDbRef, index);
-    } //-- void setDbRef(int, org.vamsas.objects.core.DbRef) 
-
-    /**
-     * Method setDbRef
-     * 
-     * 
-     * 
-     * @param dbRefArray
-     */
-    public void setDbRef(org.vamsas.objects.core.DbRef[] dbRefArray)
-    {
-        //-- copy array
-        _dbRefList.removeAllElements();
-        for (int i = 0; i < dbRefArray.length; i++) {
-            _dbRefList.addElement(dbRefArray[i]);
-        }
-    } //-- void setDbRef(org.vamsas.objects.core.DbRef) 
-
-    /**
      * Sets the value of field 'end'.
      * 
      * @param end the value of field 'end'.
@@ -451,16 +268,6 @@ implements java.io.Serializable
     } //-- void setEnd(int) 
 
     /**
-     * Sets the value of field 'id'.
-     * 
-     * @param id the value of field 'id'.
-     */
-    public void setId(java.lang.String id)
-    {
-        this._id = id;
-    } //-- void setId(java.lang.String) 
-
-    /**
      * Sets the value of field 'name'.
      * 
      * @param name the value of field 'name'.
index 3740da3..0c4ded0 100644 (file)
@@ -150,40 +150,6 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
             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
-            {
-                SequenceType target = (SequenceType) object;
-                return target.getId();
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceType target = (SequenceType) 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.setMultivalued(false);
-        addFieldDescriptor(desc);
-        
-        //-- validation code for: _id
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        { //-- local scope
-        }
-        desc.setValidator(fieldValidator);
         //-- initialize element descriptors
         
         //-- _sequence
@@ -266,41 +232,6 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
             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()
 
 
index ddb22b8..a6cbad3 100644 (file)
@@ -43,9 +43,14 @@ implements java.io.Serializable
     private java.lang.String _id;
 
     /**
-     * Field _newickFormatList
+     * Field _title
      */
-    private java.util.Vector _newickFormatList;
+    private java.lang.String _title;
+
+    /**
+     * Field _newickList
+     */
+    private java.util.Vector _newickList;
 
     /**
      * Field _provenance
@@ -60,7 +65,7 @@ implements java.io.Serializable
     public Tree() 
      {
         super();
-        _newickFormatList = new Vector();
+        _newickList = new Vector();
     } //-- org.vamsas.objects.core.Tree()
 
 
@@ -69,43 +74,43 @@ implements java.io.Serializable
     //-----------/
 
     /**
-     * Method addNewickFormat
+     * Method addNewick
      * 
      * 
      * 
-     * @param vNewickFormat
+     * @param vNewick
      */
-    public void addNewickFormat(java.lang.String vNewickFormat)
+    public void addNewick(org.vamsas.objects.core.Newick vNewick)
         throws java.lang.IndexOutOfBoundsException
     {
-        _newickFormatList.addElement(vNewickFormat);
-    } //-- void addNewickFormat(java.lang.String) 
+        _newickList.addElement(vNewick);
+    } //-- void addNewick(org.vamsas.objects.core.Newick) 
 
     /**
-     * Method addNewickFormat
+     * Method addNewick
      * 
      * 
      * 
      * @param index
-     * @param vNewickFormat
+     * @param vNewick
      */
-    public void addNewickFormat(int index, java.lang.String vNewickFormat)
+    public void addNewick(int index, org.vamsas.objects.core.Newick vNewick)
         throws java.lang.IndexOutOfBoundsException
     {
-        _newickFormatList.insertElementAt(vNewickFormat, index);
-    } //-- void addNewickFormat(int, java.lang.String) 
+        _newickList.insertElementAt(vNewick, index);
+    } //-- void addNewick(int, org.vamsas.objects.core.Newick) 
 
     /**
-     * Method enumerateNewickFormat
+     * Method enumerateNewick
      * 
      * 
      * 
      * @return Enumeration
      */
-    public java.util.Enumeration enumerateNewickFormat()
+    public java.util.Enumeration enumerateNewick()
     {
-        return _newickFormatList.elements();
-    } //-- java.util.Enumeration enumerateNewickFormat() 
+        return _newickList.elements();
+    } //-- java.util.Enumeration enumerateNewick() 
 
     /**
      * Note: hashCode() has not been overriden
@@ -131,12 +136,19 @@ implements java.io.Serializable
             }
             else if (temp._id != null)
                 return false;
-            if (this._newickFormatList != null) {
-                if (temp._newickFormatList == null) return false;
-                else if (!(this._newickFormatList.equals(temp._newickFormatList))) 
+            if (this._title != null) {
+                if (temp._title == null) return false;
+                else if (!(this._title.equals(temp._title))) 
+                    return false;
+            }
+            else if (temp._title != null)
+                return false;
+            if (this._newickList != null) {
+                if (temp._newickList == null) return false;
+                else if (!(this._newickList.equals(temp._newickList))) 
                     return false;
             }
-            else if (temp._newickFormatList != null)
+            else if (temp._newickList != null)
                 return false;
             if (this._provenance != null) {
                 if (temp._provenance == null) return false;
@@ -162,52 +174,52 @@ implements java.io.Serializable
     } //-- java.lang.String getId() 
 
     /**
-     * Method getNewickFormat
+     * Method getNewick
      * 
      * 
      * 
      * @param index
-     * @return String
+     * @return Newick
      */
-    public java.lang.String getNewickFormat(int index)
+    public org.vamsas.objects.core.Newick getNewick(int index)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _newickFormatList.size())) {
-            throw new IndexOutOfBoundsException("getNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]");
+        if ((index < 0) || (index > _newickList.size())) {
+            throw new IndexOutOfBoundsException("getNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]");
         }
         
-        return (String)_newickFormatList.elementAt(index);
-    } //-- java.lang.String getNewickFormat(int) 
+        return (org.vamsas.objects.core.Newick) _newickList.elementAt(index);
+    } //-- org.vamsas.objects.core.Newick getNewick(int) 
 
     /**
-     * Method getNewickFormat
+     * Method getNewick
      * 
      * 
      * 
-     * @return String
+     * @return Newick
      */
-    public java.lang.String[] getNewickFormat()
+    public org.vamsas.objects.core.Newick[] getNewick()
     {
-        int size = _newickFormatList.size();
-        java.lang.String[] mArray = new java.lang.String[size];
+        int size = _newickList.size();
+        org.vamsas.objects.core.Newick[] mArray = new org.vamsas.objects.core.Newick[size];
         for (int index = 0; index < size; index++) {
-            mArray[index] = (String)_newickFormatList.elementAt(index);
+            mArray[index] = (org.vamsas.objects.core.Newick) _newickList.elementAt(index);
         }
         return mArray;
-    } //-- java.lang.String[] getNewickFormat() 
+    } //-- org.vamsas.objects.core.Newick[] getNewick() 
 
     /**
-     * Method getNewickFormatCount
+     * Method getNewickCount
      * 
      * 
      * 
      * @return int
      */
-    public int getNewickFormatCount()
+    public int getNewickCount()
     {
-        return _newickFormatList.size();
-    } //-- int getNewickFormatCount() 
+        return _newickList.size();
+    } //-- int getNewickCount() 
 
     /**
      * Returns the value of field 'provenance'.
@@ -221,6 +233,17 @@ implements java.io.Serializable
     } //-- org.vamsas.objects.core.Provenance getProvenance() 
 
     /**
+     * Returns the value of field 'title'.
+     * 
+     * @return String
+     * @return the value of field 'title'.
+     */
+    public java.lang.String getTitle()
+    {
+        return this._title;
+    } //-- java.lang.String getTitle() 
+
+    /**
      * Method isValid
      * 
      * 
@@ -267,28 +290,28 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) 
 
     /**
-     * Method removeAllNewickFormat
+     * Method removeAllNewick
      * 
      */
-    public void removeAllNewickFormat()
+    public void removeAllNewick()
     {
-        _newickFormatList.removeAllElements();
-    } //-- void removeAllNewickFormat() 
+        _newickList.removeAllElements();
+    } //-- void removeAllNewick() 
 
     /**
-     * Method removeNewickFormat
+     * Method removeNewick
      * 
      * 
      * 
      * @param index
-     * @return String
+     * @return Newick
      */
-    public java.lang.String removeNewickFormat(int index)
+    public org.vamsas.objects.core.Newick removeNewick(int index)
     {
-        java.lang.Object obj = _newickFormatList.elementAt(index);
-        _newickFormatList.removeElementAt(index);
-        return (String)obj;
-    } //-- java.lang.String removeNewickFormat(int) 
+        java.lang.Object obj = _newickList.elementAt(index);
+        _newickList.removeElementAt(index);
+        return (org.vamsas.objects.core.Newick) obj;
+    } //-- org.vamsas.objects.core.Newick removeNewick(int) 
 
     /**
      * Sets the value of field 'id'.
@@ -301,38 +324,38 @@ implements java.io.Serializable
     } //-- void setId(java.lang.String) 
 
     /**
-     * Method setNewickFormat
+     * Method setNewick
      * 
      * 
      * 
      * @param index
-     * @param vNewickFormat
+     * @param vNewick
      */
-    public void setNewickFormat(int index, java.lang.String vNewickFormat)
+    public void setNewick(int index, org.vamsas.objects.core.Newick vNewick)
         throws java.lang.IndexOutOfBoundsException
     {
         //-- check bounds for index
-        if ((index < 0) || (index > _newickFormatList.size())) {
-            throw new IndexOutOfBoundsException("setNewickFormat: Index value '"+index+"' not in range [0.."+_newickFormatList.size()+ "]");
+        if ((index < 0) || (index > _newickList.size())) {
+            throw new IndexOutOfBoundsException("setNewick: Index value '"+index+"' not in range [0.."+_newickList.size()+ "]");
         }
-        _newickFormatList.setElementAt(vNewickFormat, index);
-    } //-- void setNewickFormat(int, java.lang.String) 
+        _newickList.setElementAt(vNewick, index);
+    } //-- void setNewick(int, org.vamsas.objects.core.Newick) 
 
     /**
-     * Method setNewickFormat
+     * Method setNewick
      * 
      * 
      * 
-     * @param newickFormatArray
+     * @param newickArray
      */
-    public void setNewickFormat(java.lang.String[] newickFormatArray)
+    public void setNewick(org.vamsas.objects.core.Newick[] newickArray)
     {
         //-- copy array
-        _newickFormatList.removeAllElements();
-        for (int i = 0; i < newickFormatArray.length; i++) {
-            _newickFormatList.addElement(newickFormatArray[i]);
+        _newickList.removeAllElements();
+        for (int i = 0; i < newickArray.length; i++) {
+            _newickList.addElement(newickArray[i]);
         }
-    } //-- void setNewickFormat(java.lang.String) 
+    } //-- void setNewick(org.vamsas.objects.core.Newick) 
 
     /**
      * Sets the value of field 'provenance'.
@@ -345,6 +368,16 @@ implements java.io.Serializable
     } //-- void setProvenance(org.vamsas.objects.core.Provenance) 
 
     /**
+     * Sets the value of field 'title'.
+     * 
+     * @param title the value of field 'title'.
+     */
+    public void setTitle(java.lang.String title)
+    {
+        this._title = title;
+    } //-- void setTitle(java.lang.String) 
+
+    /**
      * Method unmarshal
      * 
      * 
index af3b115..a4c7d8d 100644 (file)
@@ -102,22 +102,22 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
         desc.setValidator(fieldValidator);
         //-- initialize element descriptors
         
-        //-- _newickFormatList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_newickFormatList", "newickFormat", org.exolab.castor.xml.NodeType.Element);
+        //-- _title
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_title", "title", 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();
+                return target.getTitle();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
                     Tree target = (Tree) object;
-                    target.addNewickFormat( (java.lang.String) value);
+                    target.setTitle( (java.lang.String) value);
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -129,19 +129,53 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
         };
         desc.setHandler(handler);
         desc.setNameSpaceURI("http://www.vamsas.org");
-        desc.setRequired(true);
-        desc.setMultivalued(true);
+        desc.setMultivalued(false);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _newickFormatList
+        //-- validation code for: _title
         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);
+        //-- _newickList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Newick.class, "_newickList", "newick", 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.getNewick();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Tree target = (Tree) object;
+                    target.addNewick( (org.vamsas.objects.core.Newick) 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.Newick();
+            }
+        };
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("http://www.vamsas.org");
+        desc.setRequired(true);
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _newickList
+        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() {
diff --git a/src/org/vamsas/objects/core/User.java b/src/org/vamsas/objects/core/User.java
new file mode 100644 (file)
index 0000000..037d544
--- /dev/null
@@ -0,0 +1,245 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package org.vamsas.objects.core;
+
+  //---------------------------------/
+ //- Imported classes and packages -/
+//---------------------------------/
+
+import java.io.IOException;
+import java.io.Reader;
+import java.io.Serializable;
+import java.io.Writer;
+import org.exolab.castor.xml.MarshalException;
+import org.exolab.castor.xml.Marshaller;
+import org.exolab.castor.xml.Unmarshaller;
+import org.exolab.castor.xml.ValidationException;
+import org.xml.sax.ContentHandler;
+
+/**
+ * Class User.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class User extends org.vamsas.client.object 
+implements java.io.Serializable
+{
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _fullname
+     */
+    private java.lang.String _fullname;
+
+    /**
+     * Field _organization
+     */
+    private java.lang.String _organization;
+
+    /**
+     * Field _data
+     */
+    private java.lang.String _data;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public User() 
+     {
+        super();
+    } //-- org.vamsas.objects.core.User()
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Note: hashCode() has not been overriden
+     * 
+     * @param obj
+     * @return boolean
+     */
+    public boolean equals(java.lang.Object obj)
+    {
+        if ( this == obj )
+            return true;
+        
+        if (super.equals(obj)==false)
+            return false;
+        
+        if (obj instanceof User) {
+        
+            User temp = (User)obj;
+            if (this._fullname != null) {
+                if (temp._fullname == null) return false;
+                else if (!(this._fullname.equals(temp._fullname))) 
+                    return false;
+            }
+            else if (temp._fullname != null)
+                return false;
+            if (this._organization != null) {
+                if (temp._organization == null) return false;
+                else if (!(this._organization.equals(temp._organization))) 
+                    return false;
+            }
+            else if (temp._organization != null)
+                return false;
+            if (this._data != null) {
+                if (temp._data == null) return false;
+                else if (!(this._data.equals(temp._data))) 
+                    return false;
+            }
+            else if (temp._data != null)
+                return false;
+            return true;
+        }
+        return false;
+    } //-- boolean equals(java.lang.Object) 
+
+    /**
+     * Returns the value of field 'data'.
+     * 
+     * @return String
+     * @return the value of field 'data'.
+     */
+    public java.lang.String getData()
+    {
+        return this._data;
+    } //-- java.lang.String getData() 
+
+    /**
+     * Returns the value of field 'fullname'.
+     * 
+     * @return String
+     * @return the value of field 'fullname'.
+     */
+    public java.lang.String getFullname()
+    {
+        return this._fullname;
+    } //-- java.lang.String getFullname() 
+
+    /**
+     * Returns the value of field 'organization'.
+     * 
+     * @return String
+     * @return the value of field 'organization'.
+     */
+    public java.lang.String getOrganization()
+    {
+        return this._organization;
+    } //-- java.lang.String getOrganization() 
+
+    /**
+     * Method isValid
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean isValid()
+    {
+        try {
+            validate();
+        }
+        catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    } //-- boolean isValid() 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param out
+     */
+    public void marshal(java.io.Writer out)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, out);
+    } //-- void marshal(java.io.Writer) 
+
+    /**
+     * Method marshal
+     * 
+     * 
+     * 
+     * @param handler
+     */
+    public void marshal(org.xml.sax.ContentHandler handler)
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        
+        Marshaller.marshal(this, handler);
+    } //-- void marshal(org.xml.sax.ContentHandler) 
+
+    /**
+     * Sets the value of field 'data'.
+     * 
+     * @param data the value of field 'data'.
+     */
+    public void setData(java.lang.String data)
+    {
+        this._data = data;
+    } //-- void setData(java.lang.String) 
+
+    /**
+     * Sets the value of field 'fullname'.
+     * 
+     * @param fullname the value of field 'fullname'.
+     */
+    public void setFullname(java.lang.String fullname)
+    {
+        this._fullname = fullname;
+    } //-- void setFullname(java.lang.String) 
+
+    /**
+     * Sets the value of field 'organization'.
+     * 
+     * @param organization the value of field 'organization'.
+     */
+    public void setOrganization(java.lang.String organization)
+    {
+        this._organization = organization;
+    } //-- void setOrganization(java.lang.String) 
+
+    /**
+     * Method unmarshal
+     * 
+     * 
+     * 
+     * @param reader
+     * @return User
+     */
+    public static org.vamsas.objects.core.User unmarshal(java.io.Reader reader)
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException
+    {
+        return (org.vamsas.objects.core.User) Unmarshaller.unmarshal(org.vamsas.objects.core.User.class, reader);
+    } //-- org.vamsas.objects.core.User unmarshal(java.io.Reader) 
+
+    /**
+     * Method validate
+     * 
+     */
+    public void validate()
+        throws org.exolab.castor.xml.ValidationException
+    {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
+    } //-- void validate() 
+
+}
diff --git a/src/org/vamsas/objects/core/UserDescriptor.java b/src/org/vamsas/objects/core/UserDescriptor.java
new file mode 100644 (file)
index 0000000..c38181a
--- /dev/null
@@ -0,0 +1,282 @@
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 0.9.9M2</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 UserDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class UserDescriptor 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 UserDescriptor() 
+     {
+        super();
+        nsURI = "http://www.vamsas.org";
+        xmlName = "User";
+        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
+        
+        //-- _fullname
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fullname", "fullname", 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
+            {
+                User target = (User) object;
+                return target.getFullname();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    User target = (User) object;
+                    target.setFullname( (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: _fullname
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _organization
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_organization", "organization", 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
+            {
+                User target = (User) object;
+                return target.getOrganization();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    User target = (User) object;
+                    target.setOrganization( (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: _organization
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _data
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_data", "data", 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
+            {
+                User target = (User) object;
+                return target.getData();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    User target = (User) object;
+                    target.setData( (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: _data
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    } //-- org.vamsas.objects.core.UserDescriptor()
+
+
+      //-----------/
+     //- 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.User.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() 
+
+}