X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2Fdescriptors%2FJSeqDescriptor.java;h=ba1c904e05f7604ac118db7290309f76fc377cbc;hb=b2f9a8d7bce642ff4011bc6d49e02bb0569fbb11;hp=5283afeccbc692c616051e0fb6f53482fc2e81e5;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
index 5283afe..ba1c904 100644
--- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
@@ -1,614 +1,622 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
- * 
- * This file is part of Jalview.
- * 
- * Jalview is free software: you can redistribute it and/or
- * modify it under the terms of the GNU General Public License 
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- * 
- * Jalview is distributed in the hope that it will be useful, but 
- * WITHOUT ANY WARRANTY; without even the implied warranty 
- * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
- * PURPOSE.  See the GNU General Public License for more details.
- * 
- * You should have received a copy of the GNU General Public License along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
- */
-package jalview.schemabinding.version2.descriptors;
-
-//---------------------------------/
-//- Imported classes and packages -/
-//---------------------------------/
-
-import jalview.schemabinding.version2.JSeq;
-
-/**
- * Class JSeqDescriptor.
- * 
- * @version $Revision$ $Date$
- */
-public class JSeqDescriptor 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 JSeqDescriptor()
-  {
-    super();
-    _nsURI = "www.jalview.org";
-    _xmlName = "JSeq";
-    _elementDefinition = true;
-
-    // -- 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
-
-    // -- _colour
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_colour", "colour",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasColour())
-        {
-          return null;
-        }
-        return new java.lang.Integer(target.getColour());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteColour();
-            return;
-          }
-          target.setColour(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _colour
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _start
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_start", "start",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasStart())
-        {
-          return null;
-        }
-        return new java.lang.Integer(target.getStart());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // ignore null values for non optional primitives
-          if (value == null)
-          {
-            return;
-          }
-
-          target.setStart(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _start
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _end
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_end", "end",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasEnd())
-        {
-          return null;
-        }
-        return new java.lang.Integer(target.getEnd());
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // ignore null values for non optional primitives
-          if (value == null)
-          {
-            return;
-          }
-
-          target.setEnd(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _end
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-    // -- _id
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.String.class, "_id", "id",
-            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
-      {
-        JSeq target = (JSeq) object;
-        return target.getId();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) 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 null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setRequired(true);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _id
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(1);
-    { // -- local scope
-      org.exolab.castor.xml.validators.StringValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setWhiteSpace("preserve");
-    }
-    desc.setValidator(fieldValidator);
-    // -- _hidden
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Boolean.TYPE, "_hidden", "hidden",
-            org.exolab.castor.xml.NodeType.Attribute);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        if (!target.hasHidden())
-        {
-          return null;
-        }
-        return (target.getHidden() ? java.lang.Boolean.TRUE
-                : java.lang.Boolean.FALSE);
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // if null, use delete method for optional primitives
-          if (value == null)
-          {
-            target.deleteHidden();
-            return;
-          }
-          target.setHidden(((java.lang.Boolean) value).booleanValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setMultivalued(false);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _hidden
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    { // -- local scope
-      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
-      fieldValidator.setValidator(typeValidator);
-    }
-    desc.setValidator(fieldValidator);
-    // -- initialize element descriptors
-
-    // -- _featuresList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.Features.class, "_featuresList",
-            "features", org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getFeatures();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target
-                  .addFeatures((jalview.schemabinding.version2.Features) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllFeatures();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return new jalview.schemabinding.version2.Features();
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _featuresList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
-    }
-    desc.setValidator(fieldValidator);
-    // -- _pdbidsList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            jalview.schemabinding.version2.Pdbids.class, "_pdbidsList",
-            "pdbids", org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getPdbids();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.addPdbids((jalview.schemabinding.version2.Pdbids) value);
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllPdbids();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return new jalview.schemabinding.version2.Pdbids();
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _pdbidsList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
-    }
-    desc.setValidator(fieldValidator);
-    // -- _hiddenSequencesList
-    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
-            java.lang.Integer.TYPE, "_hiddenSequencesList",
-            "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
-    handler = new org.exolab.castor.xml.XMLFieldHandler()
-    {
-      public java.lang.Object getValue(java.lang.Object object)
-              throws IllegalStateException
-      {
-        JSeq target = (JSeq) object;
-        return target.getHiddenSequences();
-      }
-
-      public void setValue(java.lang.Object object, java.lang.Object value)
-              throws IllegalStateException, IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          // ignore null values for non optional primitives
-          if (value == null)
-          {
-            return;
-          }
-
-          target.addHiddenSequences(((java.lang.Integer) value).intValue());
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public void resetValue(Object object) throws IllegalStateException,
-              IllegalArgumentException
-      {
-        try
-        {
-          JSeq target = (JSeq) object;
-          target.removeAllHiddenSequences();
-        } catch (java.lang.Exception ex)
-        {
-          throw new IllegalStateException(ex.toString());
-        }
-      }
-
-      public java.lang.Object newInstance(java.lang.Object parent)
-      {
-        return null;
-      }
-    };
-    desc.setHandler(handler);
-    desc.setNameSpaceURI("www.jalview.org");
-    desc.setMultivalued(true);
-    addFieldDescriptor(desc);
-
-    // -- validation code for: _hiddenSequencesList
-    fieldValidator = new org.exolab.castor.xml.FieldValidator();
-    fieldValidator.setMinOccurs(0);
-    { // -- local scope
-      org.exolab.castor.xml.validators.IntValidator typeValidator;
-      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
-      fieldValidator.setValidator(typeValidator);
-      typeValidator.setMinInclusive(-2147483648);
-      typeValidator.setMaxInclusive(2147483647);
-    }
-    desc.setValidator(fieldValidator);
-  }
-
-  // -----------/
-  // - 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.JSeq.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;
-  }
-
-}
+/*******************************************************************************
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.1)
+ * Copyright (C) 2014 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License along with Jalview.  
+ * If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ ******************************************************************************/
+/*
+ * This class was automatically generated with 
+ * <a href="http://www.castor.org">Castor 1.1</a>, using an XML
+ * Schema.
+ * $Id$
+ */
+
+package jalview.schemabinding.version2.descriptors;
+
+//---------------------------------/
+//- Imported classes and packages -/
+//---------------------------------/
+
+import jalview.schemabinding.version2.JSeq;
+
+/**
+ * Class JSeqDescriptor.
+ * 
+ * @version $Revision$ $Date$
+ */
+public class JSeqDescriptor 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 JSeqDescriptor()
+  {
+    super();
+    _nsURI = "www.jalview.org";
+    _xmlName = "JSeq";
+    _elementDefinition = true;
+
+    // -- 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
+
+    // -- _colour
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_colour", "colour",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasColour())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getColour());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteColour();
+            return;
+          }
+          target.setColour(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _colour
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _start
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_start", "start",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasStart())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getStart());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setStart(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _start
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _end
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_end", "end",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasEnd())
+        {
+          return null;
+        }
+        return new java.lang.Integer(target.getEnd());
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.setEnd(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _end
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+    // -- _id
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.String.class, "_id", "id",
+            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
+      {
+        JSeq target = (JSeq) object;
+        return target.getId();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) 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 null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setRequired(true);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _id
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(1);
+    { // -- local scope
+      org.exolab.castor.xml.validators.StringValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.StringValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setWhiteSpace("preserve");
+    }
+    desc.setValidator(fieldValidator);
+    // -- _hidden
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_hidden", "hidden",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasHidden())
+        {
+          return null;
+        }
+        return (target.getHidden() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteHidden();
+            return;
+          }
+          target.setHidden(((java.lang.Boolean) value).booleanValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _hidden
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
+    // -- initialize element descriptors
+
+    // -- _featuresList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Features.class, "_featuresList",
+            "features", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getFeatures();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.addFeatures((jalview.schemabinding.version2.Features) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.removeAllFeatures();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Features();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _featuresList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _pdbidsList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            jalview.schemabinding.version2.Pdbids.class, "_pdbidsList",
+            "pdbids", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getPdbids();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.addPdbids((jalview.schemabinding.version2.Pdbids) value);
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.removeAllPdbids();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return new jalview.schemabinding.version2.Pdbids();
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _pdbidsList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+    }
+    desc.setValidator(fieldValidator);
+    // -- _hiddenSequencesList
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Integer.TYPE, "_hiddenSequencesList",
+            "hiddenSequences", org.exolab.castor.xml.NodeType.Element);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        return target.getHiddenSequences();
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // ignore null values for non optional primitives
+          if (value == null)
+          {
+            return;
+          }
+
+          target.addHiddenSequences(((java.lang.Integer) value).intValue());
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public void resetValue(Object object) throws IllegalStateException,
+              IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          target.removeAllHiddenSequences();
+        } catch (java.lang.Exception ex)
+        {
+          throw new IllegalStateException(ex.toString());
+        }
+      }
+
+      public java.lang.Object newInstance(java.lang.Object parent)
+      {
+        return null;
+      }
+    };
+    desc.setHandler(handler);
+    desc.setNameSpaceURI("www.jalview.org");
+    desc.setMultivalued(true);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _hiddenSequencesList
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    fieldValidator.setMinOccurs(0);
+    { // -- local scope
+      org.exolab.castor.xml.validators.IntValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.IntValidator();
+      fieldValidator.setValidator(typeValidator);
+      typeValidator.setMinInclusive(-2147483648);
+      typeValidator.setMaxInclusive(2147483647);
+    }
+    desc.setValidator(fieldValidator);
+  }
+
+  // -----------/
+  // - 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.JSeq.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;
+  }
+
+}