JAL-2879 save/restore feature sub-attributes in Jalview project
authorgmungoc <g.m.carstairs@dundee.ac.uk>
Thu, 14 Dec 2017 15:02:04 +0000 (15:02 +0000)
committergmungoc <g.m.carstairs@dundee.ac.uk>
Thu, 14 Dec 2017 15:02:04 +0000 (15:02 +0000)
schemas/jalview.xsd
src/jalview/gui/Jalview2XML.java
src/jalview/schemabinding/version2/OtherData.java
src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java

index f0bd638..d0bdf42 100755 (executable)
                        <xs:element name="otherData" minOccurs="0" maxOccurs="unbounded">
                                <xs:complexType>
                                        <xs:attribute name="key" type="xs:string" use="required" />
+                                       <xs:attribute name="key2" type="xs:string" use="optional">
+                                               <xs:annotation>
+                                                       <xs:documentation>key2 may be used for a sub-attribute of key</xs:documentation>
+                                               </xs:annotation>
+                                       </xs:attribute>
                                        <xs:attribute name="value" type="xs:string" use="required" />
                                </xs:complexType>
                        </xs:element>
index 4a15024..7a06d08 100644 (file)
@@ -879,15 +879,33 @@ public class Jalview2XML
         }
         if (sf.otherDetails != null)
         {
-          String key;
-          Iterator<String> keys = sf.otherDetails.keySet().iterator();
-          while (keys.hasNext())
+          /*
+           * save feature attributes, which may be simple strings or
+           * map valued (have sub-attributes)
+           */
+          for (Entry<String, Object> entry : sf.otherDetails.entrySet())
           {
-            key = keys.next();
-            OtherData keyValue = new OtherData();
-            keyValue.setKey(key);
-            keyValue.setValue(sf.otherDetails.get(key).toString());
-            features.addOtherData(keyValue);
+            String key = entry.getKey();
+            Object value = entry.getValue();
+            if (value instanceof Map<?, ?>)
+            {
+              for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
+                      .entrySet())
+              {
+                OtherData otherData = new OtherData();
+                otherData.setKey(key);
+                otherData.setKey2(subAttribute.getKey());
+                otherData.setValue(subAttribute.getValue().toString());
+                features.addOtherData(otherData);
+              }
+            }
+            else
+            {
+              OtherData otherData = new OtherData();
+              otherData.setKey(key);
+              otherData.setValue(value.toString());
+              features.addOtherData(otherData);
+            }
           }
         }
 
@@ -2962,19 +2980,46 @@ public class Jalview2XML
                     features[f].getEnd(), features[f].getScore(),
                     features[f].getFeatureGroup());
             sf.setStatus(features[f].getStatus());
+
+            /*
+             * load any feature attributes - include map-valued attributes
+             */
+            Map<String, Map<String, String>> mapAttributes = new HashMap<>();
             for (int od = 0; od < features[f].getOtherDataCount(); od++)
             {
               OtherData keyValue = features[f].getOtherData(od);
-              if (keyValue.getKey().startsWith("LINK"))
+              String attributeName = keyValue.getKey();
+              String attributeValue = keyValue.getValue();
+              if (attributeName.startsWith("LINK"))
               {
-                sf.addLink(keyValue.getValue());
+                sf.addLink(attributeValue);
               }
               else
               {
-                sf.setValue(keyValue.getKey(), keyValue.getValue());
+                String subAttribute = keyValue.getKey2();
+                if (subAttribute == null)
+                {
+                  // simple string-valued attribute
+                  sf.setValue(attributeName, attributeValue);
+                }
+                else
+                {
+                  // attribute 'key' has sub-attribute 'key2'
+                  if (!mapAttributes.containsKey(attributeName))
+                  {
+                    mapAttributes.put(attributeName, new HashMap<>());
+                  }
+                  mapAttributes.get(attributeName).put(subAttribute,
+                          attributeValue);
+                }
               }
-
             }
+            for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
+                    .entrySet())
+            {
+              sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
+            }
+
             // adds feature to datasequence's feature set (since Jalview 2.10)
             al.getSequenceAt(i).addSequenceFeature(sf);
           }
@@ -5333,7 +5378,7 @@ public class Jalview2XML
 
     if (this.frefedSequence == null)
     {
-      frefedSequence = new Vector<SeqFref>();
+      frefedSequence = new Vector<>();
     }
 
     viewportsAdded.clear();
index fb6b276..31797fe 100644 (file)
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2;
 
-//---------------------------------/
-//- Imported classes and packages -/
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
 
 import org.exolab.castor.xml.Marshaller;
@@ -19,163 +19,181 @@ import org.exolab.castor.xml.Unmarshaller;
  * 
  * @version $Revision$ $Date$
  */
-public class OtherData implements java.io.Serializable
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _key.
-   */
-  private java.lang.String _key;
-
-  /**
-   * Field _value.
-   */
-  private java.lang.String _value;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public OtherData()
-  {
-    super();
-  }
-
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * Returns the value of field 'key'.
-   * 
-   * @return the value of field 'Key'.
-   */
-  public java.lang.String getKey()
-  {
-    return this._key;
-  }
-
-  /**
-   * Returns the value of field 'value'.
-   * 
-   * @return the value of field 'Value'.
-   */
-  public java.lang.String getValue()
-  {
-    return this._value;
-  }
-
-  /**
-   * Method isValid.
-   * 
-   * @return true if this object is valid according to the schema
-   */
-  public boolean isValid()
-  {
-    try
-    {
-      validate();
-    } catch (org.exolab.castor.xml.ValidationException vex)
-    {
-      return false;
+public class OtherData implements java.io.Serializable {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _key.
+     */
+    private java.lang.String _key;
+
+    /**
+     * key2 may be used for a sub-attribute of key
+     */
+    private java.lang.String _key2;
+
+    /**
+     * Field _value.
+     */
+    private java.lang.String _value;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public OtherData() {
+        super();
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
+
+    /**
+     * Returns the value of field 'key'.
+     * 
+     * @return the value of field 'Key'.
+     */
+    public java.lang.String getKey(
+    ) {
+        return this._key;
+    }
+
+    /**
+     * Returns the value of field 'key2'. The field 'key2' has the
+     * following description: key2 may be used for a sub-attribute
+     * of key
+     * 
+     * @return the value of field 'Key2'.
+     */
+    public java.lang.String getKey2(
+    ) {
+        return this._key2;
+    }
+
+    /**
+     * Returns the value of field 'value'.
+     * 
+     * @return the value of field 'Value'.
+     */
+    public java.lang.String getValue(
+    ) {
+        return this._value;
+    }
+
+    /**
+     * Method isValid.
+     * 
+     * @return true if this object is valid according to the schema
+     */
+    public boolean isValid(
+    ) {
+        try {
+            validate();
+        } catch (org.exolab.castor.xml.ValidationException vex) {
+            return false;
+        }
+        return true;
+    }
+
+    /**
+     * 
+     * 
+     * @param out
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void marshal(
+            final java.io.Writer out)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        Marshaller.marshal(this, out);
+    }
+
+    /**
+     * 
+     * 
+     * @param handler
+     * @throws java.io.IOException if an IOException occurs during
+     * marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     */
+    public void marshal(
+            final org.xml.sax.ContentHandler handler)
+    throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        Marshaller.marshal(this, handler);
+    }
+
+    /**
+     * Sets the value of field 'key'.
+     * 
+     * @param key the value of field 'key'.
+     */
+    public void setKey(
+            final java.lang.String key) {
+        this._key = key;
+    }
+
+    /**
+     * Sets the value of field 'key2'. The field 'key2' has the
+     * following description: key2 may be used for a sub-attribute
+     * of key
+     * 
+     * @param key2 the value of field 'key2'.
+     */
+    public void setKey2(
+            final java.lang.String key2) {
+        this._key2 = key2;
+    }
+
+    /**
+     * Sets the value of field 'value'.
+     * 
+     * @param value the value of field 'value'.
+     */
+    public void setValue(
+            final java.lang.String value) {
+        this._value = value;
+    }
+
+    /**
+     * Method unmarshal.
+     * 
+     * @param reader
+     * @throws org.exolab.castor.xml.MarshalException if object is
+     * null or if any SAXException is thrown during marshaling
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     * @return the unmarshaled
+     * jalview.schemabinding.version2.OtherData
+     */
+    public static jalview.schemabinding.version2.OtherData unmarshal(
+            final java.io.Reader reader)
+    throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException {
+        return (jalview.schemabinding.version2.OtherData) Unmarshaller.unmarshal(jalview.schemabinding.version2.OtherData.class, reader);
+    }
+
+    /**
+     * 
+     * 
+     * @throws org.exolab.castor.xml.ValidationException if this
+     * object is an invalid instance according to the schema
+     */
+    public void validate(
+    )
+    throws org.exolab.castor.xml.ValidationException {
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
+        validator.validate(this);
     }
-    return true;
-  }
-
-  /**
-   * 
-   * 
-   * @param out
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   */
-  public void marshal(final java.io.Writer out)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    Marshaller.marshal(this, out);
-  }
-
-  /**
-   * 
-   * 
-   * @param handler
-   * @throws java.io.IOException
-   *           if an IOException occurs during marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   */
-  public void marshal(final org.xml.sax.ContentHandler handler)
-          throws java.io.IOException,
-          org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    Marshaller.marshal(this, handler);
-  }
-
-  /**
-   * Sets the value of field 'key'.
-   * 
-   * @param key
-   *          the value of field 'key'.
-   */
-  public void setKey(final java.lang.String key)
-  {
-    this._key = key;
-  }
-
-  /**
-   * Sets the value of field 'value'.
-   * 
-   * @param value
-   *          the value of field 'value'.
-   */
-  public void setValue(final java.lang.String value)
-  {
-    this._value = value;
-  }
-
-  /**
-   * Method unmarshal.
-   * 
-   * @param reader
-   * @throws org.exolab.castor.xml.MarshalException
-   *           if object is null or if any SAXException is thrown during
-   *           marshaling
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   * @return the unmarshaled jalview.schemabinding.version2.OtherData
-   */
-  public static jalview.schemabinding.version2.OtherData unmarshal(
-          final java.io.Reader reader)
-          throws org.exolab.castor.xml.MarshalException,
-          org.exolab.castor.xml.ValidationException
-  {
-    return (jalview.schemabinding.version2.OtherData) Unmarshaller
-            .unmarshal(jalview.schemabinding.version2.OtherData.class,
-                    reader);
-  }
-
-  /**
-   * 
-   * 
-   * @throws org.exolab.castor.xml.ValidationException
-   *           if this object is an invalid instance according to the schema
-   */
-  public void validate() throws org.exolab.castor.xml.ValidationException
-  {
-    org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();
-    validator.validate(this);
-  }
 
 }
index f582311..ab7a626 100644 (file)
@@ -7,8 +7,8 @@
 
 package jalview.schemabinding.version2.descriptors;
 
-//---------------------------------/
-//- Imported classes and packages -/
+  //---------------------------------/
+ //- Imported classes and packages -/
 //---------------------------------/
 
 import jalview.schemabinding.version2.OtherData;
@@ -18,231 +18,255 @@ import jalview.schemabinding.version2.OtherData;
  * 
  * @version $Revision$ $Date$
  */
-public class OtherDataDescriptor extends
-        org.exolab.castor.xml.util.XMLClassDescriptorImpl
-{
-
-  // --------------------------/
-  // - Class/Member Variables -/
-  // --------------------------/
-
-  /**
-   * Field _elementDefinition.
-   */
-  private boolean _elementDefinition;
-
-  /**
-   * Field _nsPrefix.
-   */
-  private java.lang.String _nsPrefix;
-
-  /**
-   * Field _nsURI.
-   */
-  private java.lang.String _nsURI;
-
-  /**
-   * Field _xmlName.
-   */
-  private java.lang.String _xmlName;
-
-  // ----------------/
-  // - Constructors -/
-  // ----------------/
-
-  public OtherDataDescriptor()
-  {
-    super();
-    _nsURI = "www.jalview.org";
-    _xmlName = "otherData";
-    _elementDefinition = true;
-    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
-
-    // -- _key
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_key", "key",
-            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
-      {
-        OtherData target = (OtherData) object;
-        return target.getKey();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          OtherData target = (OtherData) object;
-          target.setKey((java.lang.String) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
+public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {
+
+
+      //--------------------------/
+     //- Class/Member Variables -/
+    //--------------------------/
+
+    /**
+     * Field _elementDefinition.
+     */
+    private boolean _elementDefinition;
+
+    /**
+     * Field _nsPrefix.
+     */
+    private java.lang.String _nsPrefix;
+
+    /**
+     * Field _nsURI.
+     */
+    private java.lang.String _nsURI;
+
+    /**
+     * Field _xmlName.
+     */
+    private java.lang.String _xmlName;
+
+
+      //----------------/
+     //- Constructors -/
+    //----------------/
+
+    public OtherDataDescriptor() {
+        super();
+        _nsURI = "www.jalview.org";
+        _xmlName = "otherData";
+        _elementDefinition = true;
+        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
+        
+        //-- _key
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key", "key", 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
+            {
+                OtherData target = (OtherData) object;
+                return target.getKey();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    OtherData target = (OtherData) object;
+                    target.setKey( (java.lang.String) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _key
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            org.exolab.castor.xml.validators.StringValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setWhiteSpace("preserve");
+        }
+        desc.setValidator(fieldValidator);
+        //-- _key2
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_key2", "key2", 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
+            {
+                OtherData target = (OtherData) object;
+                return target.getKey2();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    OtherData target = (OtherData) object;
+                    target.setKey2( (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: _key2
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            org.exolab.castor.xml.validators.StringValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setWhiteSpace("preserve");
+        }
+        desc.setValidator(fieldValidator);
+        //-- _value
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_value", "value", 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
+            {
+                OtherData target = (OtherData) object;
+                return target.getValue();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    OtherData target = (OtherData) object;
+                    target.setValue( (java.lang.String) value);
+                } catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance(java.lang.Object parent) {
+                return null;
+            }
+        };
+        desc.setHandler(handler);
+        desc.setRequired(true);
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _value
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(1);
+        { //-- local scope
+            org.exolab.castor.xml.validators.StringValidator typeValidator;
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+            fieldValidator.setValidator(typeValidator);
+            typeValidator.setWhiteSpace("preserve");
         }
-      }
+        desc.setValidator(fieldValidator);
+        //-- initialize element descriptors
+        
+    }
+
+
+      //-----------/
+     //- Methods -/
+    //-----------/
 
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
+    /**
+     * Method getAccessMode.
+     * 
+     * @return the access mode specified for this class.
+     */
+    public org.exolab.castor.mapping.AccessMode getAccessMode(
+    ) {
         return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _key
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
     }
-    desc.setValidator(fieldValidator);
-    // -- _value
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_value", "value",
-            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
-      {
-        OtherData target = (OtherData) object;
-        return target.getValue();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          OtherData target = (OtherData) object;
-          target.setValue((java.lang.String) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
 
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _value
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
+    /**
+     * Method getIdentity.
+     * 
+     * @return the identity field, null if this class has no
+     * identity.
+     */
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity(
+    ) {
+        return super.getIdentity();
+    }
+
+    /**
+     * Method getJavaClass.
+     * 
+     * @return the Java class represented by this descriptor.
+     */
+    public java.lang.Class getJavaClass(
+    ) {
+        return jalview.schemabinding.version2.OtherData.class;
+    }
+
+    /**
+     * Method getNameSpacePrefix.
+     * 
+     * @return the namespace prefix to use when marshaling as XML.
+     */
+    public java.lang.String getNameSpacePrefix(
+    ) {
+        return _nsPrefix;
+    }
+
+    /**
+     * Method getNameSpaceURI.
+     * 
+     * @return the namespace URI used when marshaling and
+     * unmarshaling as XML.
+     */
+    public java.lang.String getNameSpaceURI(
+    ) {
+        return _nsURI;
+    }
+
+    /**
+     * Method getValidator.
+     * 
+     * @return a specific validator for the class described by this
+     * ClassDescriptor.
+     */
+    public org.exolab.castor.xml.TypeValidator getValidator(
+    ) {
+        return this;
+    }
+
+    /**
+     * Method getXMLName.
+     * 
+     * @return the XML Name for the Class being described.
+     */
+    public java.lang.String getXMLName(
+    ) {
+        return _xmlName;
+    }
+
+    /**
+     * Method isElementDefinition.
+     * 
+     * @return true if XML schema definition of this Class is that
+     * of a global
+     * element or element with anonymous type definition.
+     */
+    public boolean isElementDefinition(
+    ) {
+        return _elementDefinition;
     }
-    desc.setValidator(fieldValidator);
-    // -- initialize element descriptors
-
-  }
-
-  // -----------/
-  // - Methods -/
-  // -----------/
-
-  /**
-   * Method getAccessMode.
-   * 
-   * @return the access mode specified for this class.
-   */
-  public org.exolab.castor.mapping.AccessMode getAccessMode()
-  {
-    return null;
-  }
-
-  /**
-   * Method getIdentity.
-   * 
-   * @return the identity field, null if this class has no identity.
-   */
-  public org.exolab.castor.mapping.FieldDescriptor getIdentity()
-  {
-    return super.getIdentity();
-  }
-
-  /**
-   * Method getJavaClass.
-   * 
-   * @return the Java class represented by this descriptor.
-   */
-  public java.lang.Class getJavaClass()
-  {
-    return jalview.schemabinding.version2.OtherData.class;
-  }
-
-  /**
-   * Method getNameSpacePrefix.
-   * 
-   * @return the namespace prefix to use when marshaling as XML.
-   */
-  public java.lang.String getNameSpacePrefix()
-  {
-    return _nsPrefix;
-  }
-
-  /**
-   * Method getNameSpaceURI.
-   * 
-   * @return the namespace URI used when marshaling and unmarshaling as XML.
-   */
-  public java.lang.String getNameSpaceURI()
-  {
-    return _nsURI;
-  }
-
-  /**
-   * Method getValidator.
-   * 
-   * @return a specific validator for the class described by this
-   *         ClassDescriptor.
-   */
-  public org.exolab.castor.xml.TypeValidator getValidator()
-  {
-    return this;
-  }
-
-  /**
-   * Method getXMLName.
-   * 
-   * @return the XML Name for the Class being described.
-   */
-  public java.lang.String getXMLName()
-  {
-    return _xmlName;
-  }
-
-  /**
-   * Method isElementDefinition.
-   * 
-   * @return true if XML schema definition of this Class is that of a global
-   *         element or element with anonymous type definition.
-   */
-  public boolean isElementDefinition()
-  {
-    return _elementDefinition;
-  }
 
 }