DBRefs and HiddenRegions saved

diff --git a/src/jalview/schemabinding/version2/DBRef.java b/src/jalview/schemabinding/version2/DBRef.java
new file mode 100644 (file)
index 0000000..576a4ad
--- /dev/null
+++ b/src/jalview/schemabinding/version2/DBRef.java
@@ -0,0 +1,199 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class DBRef.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class DBRef implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _source\r
+     */\r
+    private java.lang.String _source;\r
+\r
+    /**\r
+     * Field _version\r
+     */\r
+    private java.lang.String _version;\r
+\r
+    /**\r
+     * Field _accessionId\r
+     */\r
+    private java.lang.String _accessionId;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public DBRef() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.DBRef()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Returns the value of field 'accessionId'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'accessionId'.\r
+     */\r
+    public java.lang.String getAccessionId()\r
+    {\r
+        return this._accessionId;\r
+    } //-- java.lang.String getAccessionId() \r
+\r
+    /**\r
+     * Returns the value of field 'source'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'source'.\r
+     */\r
+    public java.lang.String getSource()\r
+    {\r
+        return this._source;\r
+    } //-- java.lang.String getSource() \r
+\r
+    /**\r
+     * Returns the value of field 'version'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'version'.\r
+     */\r
+    public java.lang.String getVersion()\r
+    {\r
+        return this._version;\r
+    } //-- java.lang.String getVersion() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'accessionId'.\r
+     * \r
+     * @param accessionId the value of field 'accessionId'.\r
+     */\r
+    public void setAccessionId(java.lang.String accessionId)\r
+    {\r
+        this._accessionId = accessionId;\r
+    } //-- void setAccessionId(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'source'.\r
+     * \r
+     * @param source the value of field 'source'.\r
+     */\r
+    public void setSource(java.lang.String source)\r
+    {\r
+        this._source = source;\r
+    } //-- void setSource(java.lang.String) \r
+\r
+    /**\r
+     * Sets the value of field 'version'.\r
+     * \r
+     * @param version the value of field 'version'.\r
+     */\r
+    public void setVersion(java.lang.String version)\r
+    {\r
+        this._version = version;\r
+    } //-- void setVersion(java.lang.String) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.DBRef) Unmarshaller.unmarshal(jalview.schemabinding.version2.DBRef.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
+\r
+}\r

diff --git a/src/jalview/schemabinding/version2/DBRefDescriptor.java b/src/jalview/schemabinding/version2/DBRefDescriptor.java
new file mode 100644 (file)
index 0000000..939d5b1
--- /dev/null
+++ b/src/jalview/schemabinding/version2/DBRefDescriptor.java
@@ -0,0 +1,278 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
+\r
+/**\r
+ * Class DBRefDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public DBRefDescriptor() {\r
+        super();\r
+        nsURI = "www.vamsas.ac.uk/jalview/version2";\r
+        xmlName = "DBRef";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _source\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_source", "source", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                DBRef target = (DBRef) object;\r
+                return target.getSource();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    DBRef target = (DBRef) object;\r
+                    target.setSource( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _source\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _version\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_version", "version", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                DBRef target = (DBRef) object;\r
+                return target.getVersion();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    DBRef target = (DBRef) object;\r
+                    target.setVersion( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _version\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _accessionId\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_accessionId", "accessionId", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                DBRef target = (DBRef) object;\r
+                return target.getAccessionId();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    DBRef target = (DBRef) object;\r
+                    target.setAccessionId( (java.lang.String) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _accessionId\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.DBRefDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.DBRef.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
+\r
+}\r

diff --git a/src/jalview/schemabinding/version2/HiddenColumns.java b/src/jalview/schemabinding/version2/HiddenColumns.java
new file mode 100644 (file)
index 0000000..5b83e64
--- /dev/null
+++ b/src/jalview/schemabinding/version2/HiddenColumns.java
@@ -0,0 +1,227 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import java.io.IOException;\r
+import java.io.Reader;\r
+import java.io.Serializable;\r
+import java.io.Writer;\r
+import org.exolab.castor.xml.MarshalException;\r
+import org.exolab.castor.xml.Marshaller;\r
+import org.exolab.castor.xml.Unmarshaller;\r
+import org.exolab.castor.xml.ValidationException;\r
+import org.xml.sax.ContentHandler;\r
+\r
+/**\r
+ * Class HiddenColumns.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class HiddenColumns implements java.io.Serializable {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _start\r
+     */\r
+    private int _start;\r
+\r
+    /**\r
+     * keeps track of state for field: _start\r
+     */\r
+    private boolean _has_start;\r
+\r
+    /**\r
+     * Field _end\r
+     */\r
+    private int _end;\r
+\r
+    /**\r
+     * keeps track of state for field: _end\r
+     */\r
+    private boolean _has_end;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public HiddenColumns() {\r
+        super();\r
+    } //-- jalview.schemabinding.version2.HiddenColumns()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method deleteEnd\r
+     * \r
+     */\r
+    public void deleteEnd()\r
+    {\r
+        this._has_end= false;\r
+    } //-- void deleteEnd() \r
+\r
+    /**\r
+     * Method deleteStart\r
+     * \r
+     */\r
+    public void deleteStart()\r
+    {\r
+        this._has_start= false;\r
+    } //-- void deleteStart() \r
+\r
+    /**\r
+     * Returns the value of field 'end'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'end'.\r
+     */\r
+    public int getEnd()\r
+    {\r
+        return this._end;\r
+    } //-- int getEnd() \r
+\r
+    /**\r
+     * Returns the value of field 'start'.\r
+     * \r
+     * @return int\r
+     * @return the value of field 'start'.\r
+     */\r
+    public int getStart()\r
+    {\r
+        return this._start;\r
+    } //-- int getStart() \r
+\r
+    /**\r
+     * Method hasEnd\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasEnd()\r
+    {\r
+        return this._has_end;\r
+    } //-- boolean hasEnd() \r
+\r
+    /**\r
+     * Method hasStart\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasStart()\r
+    {\r
+        return this._has_start;\r
+    } //-- boolean hasStart() \r
+\r
+    /**\r
+     * Method isValid\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean isValid()\r
+    {\r
+        try {\r
+            validate();\r
+        }\r
+        catch (org.exolab.castor.xml.ValidationException vex) {\r
+            return false;\r
+        }\r
+        return true;\r
+    } //-- boolean isValid() \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param out\r
+     */\r
+    public void marshal(java.io.Writer out)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, out);\r
+    } //-- void marshal(java.io.Writer) \r
+\r
+    /**\r
+     * Method marshal\r
+     * \r
+     * \r
+     * \r
+     * @param handler\r
+     */\r
+    public void marshal(org.xml.sax.ContentHandler handler)\r
+        throws java.io.IOException, org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        \r
+        Marshaller.marshal(this, handler);\r
+    } //-- void marshal(org.xml.sax.ContentHandler) \r
+\r
+    /**\r
+     * Sets the value of field 'end'.\r
+     * \r
+     * @param end the value of field 'end'.\r
+     */\r
+    public void setEnd(int end)\r
+    {\r
+        this._end = end;\r
+        this._has_end = true;\r
+    } //-- void setEnd(int) \r
+\r
+    /**\r
+     * Sets the value of field 'start'.\r
+     * \r
+     * @param start the value of field 'start'.\r
+     */\r
+    public void setStart(int start)\r
+    {\r
+        this._start = start;\r
+        this._has_start = true;\r
+    } //-- void setStart(int) \r
+\r
+    /**\r
+     * Method unmarshal\r
+     * \r
+     * \r
+     * \r
+     * @param reader\r
+     * @return Object\r
+     */\r
+    public static java.lang.Object unmarshal(java.io.Reader reader)\r
+        throws org.exolab.castor.xml.MarshalException, org.exolab.castor.xml.ValidationException\r
+    {\r
+        return (jalview.schemabinding.version2.HiddenColumns) Unmarshaller.unmarshal(jalview.schemabinding.version2.HiddenColumns.class, reader);\r
+    } //-- java.lang.Object unmarshal(java.io.Reader) \r
+\r
+    /**\r
+     * Method validate\r
+     * \r
+     */\r
+    public void validate()\r
+        throws org.exolab.castor.xml.ValidationException\r
+    {\r
+        org.exolab.castor.xml.Validator validator = new org.exolab.castor.xml.Validator();\r
+        validator.validate(this);\r
+    } //-- void validate() \r
+\r
+}\r

diff --git a/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
new file mode 100644 (file)
index 0000000..df99628
--- /dev/null
+++ b/src/jalview/schemabinding/version2/HiddenColumnsDescriptor.java
@@ -0,0 +1,252 @@
+/*\r
+ * This class was automatically generated with \r
+ * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
+ * Schema.\r
+ * $Id$\r
+ */\r
+\r
+package jalview.schemabinding.version2;\r
+\r
+  //---------------------------------/\r
+ //- Imported classes and packages -/\r
+//---------------------------------/\r
+\r
+import org.exolab.castor.mapping.AccessMode;\r
+import org.exolab.castor.xml.TypeValidator;\r
+import org.exolab.castor.xml.XMLFieldDescriptor;\r
+import org.exolab.castor.xml.validators.*;\r
+\r
+/**\r
+ * Class HiddenColumnsDescriptor.\r
+ * \r
+ * @version $Revision$ $Date$\r
+ */\r
+public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+\r
+\r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field nsPrefix\r
+     */\r
+    private java.lang.String nsPrefix;\r
+\r
+    /**\r
+     * Field nsURI\r
+     */\r
+    private java.lang.String nsURI;\r
+\r
+    /**\r
+     * Field xmlName\r
+     */\r
+    private java.lang.String xmlName;\r
+\r
+    /**\r
+     * Field identity\r
+     */\r
+    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
+\r
+\r
+      //----------------/\r
+     //- Constructors -/\r
+    //----------------/\r
+\r
+    public HiddenColumnsDescriptor() {\r
+        super();\r
+        nsURI = "www.jalview.org";\r
+        xmlName = "hiddenColumns";\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- _start\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_start", "start", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                HiddenColumns target = (HiddenColumns) object;\r
+                if(!target.hasStart())\r
+                    return null;\r
+                return new java.lang.Integer(target.getStart());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    HiddenColumns target = (HiddenColumns) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteStart();\r
+                        return;\r
+                    }\r
+                    target.setStart( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _start\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _end\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                HiddenColumns target = (HiddenColumns) object;\r
+                if(!target.hasEnd())\r
+                    return null;\r
+                return new java.lang.Integer(target.getEnd());\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    HiddenColumns target = (HiddenColumns) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteEnd();\r
+                        return;\r
+                    }\r
+                    target.setEnd( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _end\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- initialize element descriptors\r
+        \r
+    } //-- jalview.schemabinding.version2.HiddenColumnsDescriptor()\r
+\r
+\r
+      //-----------/\r
+     //- Methods -/\r
+    //-----------/\r
+\r
+    /**\r
+     * Method getAccessMode\r
+     * \r
+     * \r
+     * \r
+     * @return AccessMode\r
+     */\r
+    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
+\r
+    /**\r
+     * Method getExtends\r
+     * \r
+     * \r
+     * \r
+     * @return ClassDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
+    {\r
+        return null;\r
+    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
+\r
+    /**\r
+     * Method getIdentity\r
+     * \r
+     * \r
+     * \r
+     * @return FieldDescriptor\r
+     */\r
+    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
+    {\r
+        return identity;\r
+    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
+\r
+    /**\r
+     * Method getJavaClass\r
+     * \r
+     * \r
+     * \r
+     * @return Class\r
+     */\r
+    public java.lang.Class getJavaClass()\r
+    {\r
+        return jalview.schemabinding.version2.HiddenColumns.class;\r
+    } //-- java.lang.Class getJavaClass() \r
+\r
+    /**\r
+     * Method getNameSpacePrefix\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpacePrefix()\r
+    {\r
+        return nsPrefix;\r
+    } //-- java.lang.String getNameSpacePrefix() \r
+\r
+    /**\r
+     * Method getNameSpaceURI\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getNameSpaceURI()\r
+    {\r
+        return nsURI;\r
+    } //-- java.lang.String getNameSpaceURI() \r
+\r
+    /**\r
+     * Method getValidator\r
+     * \r
+     * \r
+     * \r
+     * @return TypeValidator\r
+     */\r
+    public org.exolab.castor.xml.TypeValidator getValidator()\r
+    {\r
+        return this;\r
+    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
+\r
+    /**\r
+     * Method getXMLName\r
+     * \r
+     * \r
+     * \r
+     * @return String\r
+     */\r
+    public java.lang.String getXMLName()\r
+    {\r
+        return xmlName;\r
+    } //-- java.lang.String getXMLName() \r
+\r
+}\r

diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 0d8dc08..19e2e6d 100755 (executable)
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -76,6 +76,16 @@ public class JSeq implements java.io.Serializable {
     private boolean _has_id;\r
 \r
     /**\r
+     * Field _hidden\r
+     */\r
+    private boolean _hidden;\r
+\r
+    /**\r
+     * keeps track of state for field: _hidden\r
+     */\r
+    private boolean _has_hidden;\r
+\r
+    /**\r
      * Field _featuresList\r
      */\r
     private java.util.Vector _featuresList;\r
@@ -85,6 +95,11 @@ public class JSeq implements java.io.Serializable {
      */\r
     private java.util.Vector _pdbidsList;\r
 \r
+    /**\r
+     * Field _hiddenSequencesList\r
+     */\r
+    private java.util.Vector _hiddenSequencesList;\r
+\r
 \r
       //----------------/\r
      //- Constructors -/\r
@@ -94,6 +109,7 @@ public class JSeq implements java.io.Serializable {
         super();\r
         _featuresList = new Vector();\r
         _pdbidsList = new Vector();\r
+        _hiddenSequencesList = new Vector();\r
     } //-- jalview.schemabinding.version2.JSeq()\r
 \r
 \r
@@ -129,6 +145,33 @@ public class JSeq implements java.io.Serializable {
     } //-- void addFeatures(int, jalview.schemabinding.version2.Features) \r
 \r
     /**\r
+     * Method addHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param vHiddenSequences\r
+     */\r
+    public void addHiddenSequences(int vHiddenSequences)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _hiddenSequencesList.addElement(new java.lang.Integer(vHiddenSequences));\r
+    } //-- void addHiddenSequences(int) \r
+\r
+    /**\r
+     * Method addHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vHiddenSequences\r
+     */\r
+    public void addHiddenSequences(int index, int vHiddenSequences)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _hiddenSequencesList.insertElementAt(new java.lang.Integer(vHiddenSequences), index);\r
+    } //-- void addHiddenSequences(int, int) \r
+\r
+    /**\r
      * Method addPdbids\r
      * \r
      * \r
@@ -174,6 +217,15 @@ public class JSeq implements java.io.Serializable {
     } //-- void deleteEnd() \r
 \r
     /**\r
+     * Method deleteHidden\r
+     * \r
+     */\r
+    public void deleteHidden()\r
+    {\r
+        this._has_hidden= false;\r
+    } //-- void deleteHidden() \r
+\r
+    /**\r
      * Method deleteId\r
      * \r
      */\r
@@ -204,6 +256,18 @@ public class JSeq implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateFeatures() \r
 \r
     /**\r
+     * Method enumerateHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateHiddenSequences()\r
+    {\r
+        return _hiddenSequencesList.elements();\r
+    } //-- java.util.Enumeration enumerateHiddenSequences() \r
+\r
+    /**\r
      * Method enumeratePdbids\r
      * \r
      * \r
@@ -286,6 +350,65 @@ public class JSeq implements java.io.Serializable {
     } //-- int getFeaturesCount() \r
 \r
     /**\r
+     * Returns the value of field 'hidden'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'hidden'.\r
+     */\r
+    public boolean getHidden()\r
+    {\r
+        return this._hidden;\r
+    } //-- boolean getHidden() \r
+\r
+    /**\r
+     * Method getHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return int\r
+     */\r
+    public int getHiddenSequences(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _hiddenSequencesList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();\r
+    } //-- int getHiddenSequences(int) \r
+\r
+    /**\r
+     * Method getHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int[] getHiddenSequences()\r
+    {\r
+        int size = _hiddenSequencesList.size();\r
+        int[] mArray = new int[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = ((java.lang.Integer)_hiddenSequencesList.elementAt(index)).intValue();\r
+        }\r
+        return mArray;\r
+    } //-- int[] getHiddenSequences() \r
+\r
+    /**\r
+     * Method getHiddenSequencesCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getHiddenSequencesCount()\r
+    {\r
+        return _hiddenSequencesList.size();\r
+    } //-- int getHiddenSequencesCount() \r
+\r
+    /**\r
      * Returns the value of field 'id'.\r
      * \r
      * @return int\r
@@ -380,6 +503,18 @@ public class JSeq implements java.io.Serializable {
     } //-- boolean hasEnd() \r
 \r
     /**\r
+     * Method hasHidden\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasHidden()\r
+    {\r
+        return this._has_hidden;\r
+    } //-- boolean hasHidden() \r
+\r
+    /**\r
      * Method hasId\r
      * \r
      * \r
@@ -459,6 +594,15 @@ public class JSeq implements java.io.Serializable {
     } //-- void removeAllFeatures() \r
 \r
     /**\r
+     * Method removeAllHiddenSequences\r
+     * \r
+     */\r
+    public void removeAllHiddenSequences()\r
+    {\r
+        _hiddenSequencesList.removeAllElements();\r
+    } //-- void removeAllHiddenSequences() \r
+\r
+    /**\r
      * Method removeAllPdbids\r
      * \r
      */\r
@@ -483,6 +627,21 @@ public class JSeq implements java.io.Serializable {
     } //-- jalview.schemabinding.version2.Features removeFeatures(int) \r
 \r
     /**\r
+     * Method removeHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return int\r
+     */\r
+    public int removeHiddenSequences(int index)\r
+    {\r
+        java.lang.Object obj = _hiddenSequencesList.elementAt(index);\r
+        _hiddenSequencesList.removeElementAt(index);\r
+        return ((java.lang.Integer)obj).intValue();\r
+    } //-- int removeHiddenSequences(int) \r
+\r
+    /**\r
      * Method removePdbids\r
      * \r
      * \r
@@ -554,6 +713,51 @@ public class JSeq implements java.io.Serializable {
     } //-- void setFeatures(jalview.schemabinding.version2.Features) \r
 \r
     /**\r
+     * Sets the value of field 'hidden'.\r
+     * \r
+     * @param hidden the value of field 'hidden'.\r
+     */\r
+    public void setHidden(boolean hidden)\r
+    {\r
+        this._hidden = hidden;\r
+        this._has_hidden = true;\r
+    } //-- void setHidden(boolean) \r
+\r
+    /**\r
+     * Method setHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vHiddenSequences\r
+     */\r
+    public void setHiddenSequences(int index, int vHiddenSequences)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _hiddenSequencesList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _hiddenSequencesList.setElementAt(new java.lang.Integer(vHiddenSequences), index);\r
+    } //-- void setHiddenSequences(int, int) \r
+\r
+    /**\r
+     * Method setHiddenSequences\r
+     * \r
+     * \r
+     * \r
+     * @param hiddenSequencesArray\r
+     */\r
+    public void setHiddenSequences(int[] hiddenSequencesArray)\r
+    {\r
+        //-- copy array\r
+        _hiddenSequencesList.removeAllElements();\r
+        for (int i = 0; i < hiddenSequencesArray.length; i++) {\r
+            _hiddenSequencesList.addElement(new java.lang.Integer(hiddenSequencesArray[i]));\r
+        }\r
+    } //-- void setHiddenSequences(int) \r
+\r
+    /**\r
      * Sets the value of field 'id'.\r
      * \r
      * @param id the value of field 'id'.\r

diff --git a/src/jalview/schemabinding/version2/JSeqDescriptor.java b/src/jalview/schemabinding/version2/JSeqDescriptor.java
index f19b91c..eef74d2 100755 (executable)
--- a/src/jalview/schemabinding/version2/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/JSeqDescriptor.java
@@ -229,6 +229,47 @@ public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
+        //-- _hidden\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_hidden", "hidden", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JSeq target = (JSeq) object;\r
+                if(!target.hasHidden())\r
+                    return null;\r
+                return (target.getHidden() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JSeq target = (JSeq) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteHidden();\r
+                        return;\r
+                    }\r
+                    target.setHidden( ((java.lang.Boolean)value).booleanValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _hidden\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
         //-- initialize element descriptors\r
         \r
         //-- _featuresList\r
@@ -301,6 +342,46 @@ public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
         { //-- local scope\r
         }\r
         desc.setValidator(fieldValidator);\r
+        //-- _hiddenSequencesList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_hiddenSequencesList", "hiddenSequences", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                JSeq target = (JSeq) object;\r
+                return target.getHiddenSequences();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    JSeq target = (JSeq) object;\r
+                    // ignore null values for non optional primitives\r
+                    if (value == null) return;\r
+                    \r
+                    target.addHiddenSequences( ((java.lang.Integer)value).intValue());\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return null;\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _hiddenSequencesList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
+            IntegerValidator typeValidator= new IntegerValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
     } //-- jalview.schemabinding.version2.JSeqDescriptor()\r
 \r
 \r

diff --git a/src/jalview/schemabinding/version2/Sequence.java b/src/jalview/schemabinding/version2/Sequence.java
index 7a15332..993ad23 100755 (executable)
--- a/src/jalview/schemabinding/version2/Sequence.java
+++ b/src/jalview/schemabinding/version2/Sequence.java
@@ -15,6 +15,8 @@ import java.io.IOException;
 import java.io.Reader;\r
 import java.io.Serializable;\r
 import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
 import org.exolab.castor.xml.MarshalException;\r
 import org.exolab.castor.xml.Marshaller;\r
 import org.exolab.castor.xml.Unmarshaller;\r
@@ -26,17 +28,28 @@ import org.xml.sax.ContentHandler;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class Sequence extends SequenceType \r
+public class Sequence extends jalview.schemabinding.version2.SequenceType \r
 implements java.io.Serializable\r
 {\r
 \r
 \r
+      //--------------------------/\r
+     //- Class/Member Variables -/\r
+    //--------------------------/\r
+\r
+    /**\r
+     * Field _DBRefList\r
+     */\r
+    private java.util.Vector _DBRefList;\r
+\r
+\r
       //----------------/\r
      //- Constructors -/\r
     //----------------/\r
 \r
     public Sequence() {\r
         super();\r
+        _DBRefList = new Vector();\r
     } //-- jalview.schemabinding.version2.Sequence()\r
 \r
 \r
@@ -45,6 +58,93 @@ implements java.io.Serializable
     //-----------/\r
 \r
     /**\r
+     * Method addDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param vDBRef\r
+     */\r
+    public void addDBRef(jalview.schemabinding.version2.DBRef vDBRef)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _DBRefList.addElement(vDBRef);\r
+    } //-- void addDBRef(jalview.schemabinding.version2.DBRef) \r
+\r
+    /**\r
+     * Method addDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vDBRef\r
+     */\r
+    public void addDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _DBRefList.insertElementAt(vDBRef, index);\r
+    } //-- void addDBRef(int, jalview.schemabinding.version2.DBRef) \r
+\r
+    /**\r
+     * Method enumerateDBRef\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateDBRef()\r
+    {\r
+        return _DBRefList.elements();\r
+    } //-- java.util.Enumeration enumerateDBRef() \r
+\r
+    /**\r
+     * Method getDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return DBRef\r
+     */\r
+    public jalview.schemabinding.version2.DBRef getDBRef(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _DBRefList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.DBRef getDBRef(int) \r
+\r
+    /**\r
+     * Method getDBRef\r
+     * \r
+     * \r
+     * \r
+     * @return DBRef\r
+     */\r
+    public jalview.schemabinding.version2.DBRef[] getDBRef()\r
+    {\r
+        int size = _DBRefList.size();\r
+        jalview.schemabinding.version2.DBRef[] mArray = new jalview.schemabinding.version2.DBRef[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.DBRef) _DBRefList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.DBRef[] getDBRef() \r
+\r
+    /**\r
+     * Method getDBRefCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getDBRefCount()\r
+    {\r
+        return _DBRefList.size();\r
+    } //-- int getDBRefCount() \r
+\r
+    /**\r
      * Method isValid\r
      * \r
      * \r
@@ -91,6 +191,64 @@ implements java.io.Serializable
     } //-- void marshal(org.xml.sax.ContentHandler) \r
 \r
     /**\r
+     * Method removeAllDBRef\r
+     * \r
+     */\r
+    public void removeAllDBRef()\r
+    {\r
+        _DBRefList.removeAllElements();\r
+    } //-- void removeAllDBRef() \r
+\r
+    /**\r
+     * Method removeDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return DBRef\r
+     */\r
+    public jalview.schemabinding.version2.DBRef removeDBRef(int index)\r
+    {\r
+        java.lang.Object obj = _DBRefList.elementAt(index);\r
+        _DBRefList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.DBRef) obj;\r
+    } //-- jalview.schemabinding.version2.DBRef removeDBRef(int) \r
+\r
+    /**\r
+     * Method setDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vDBRef\r
+     */\r
+    public void setDBRef(int index, jalview.schemabinding.version2.DBRef vDBRef)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _DBRefList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _DBRefList.setElementAt(vDBRef, index);\r
+    } //-- void setDBRef(int, jalview.schemabinding.version2.DBRef) \r
+\r
+    /**\r
+     * Method setDBRef\r
+     * \r
+     * \r
+     * \r
+     * @param DBRefArray\r
+     */\r
+    public void setDBRef(jalview.schemabinding.version2.DBRef[] DBRefArray)\r
+    {\r
+        //-- copy array\r
+        _DBRefList.removeAllElements();\r
+        for (int i = 0; i < DBRefArray.length; i++) {\r
+            _DBRefList.addElement(DBRefArray[i]);\r
+        }\r
+    } //-- void setDBRef(jalview.schemabinding.version2.DBRef) \r
+\r
+    /**\r
      * Method unmarshal\r
      * \r
      * \r

diff --git a/src/jalview/schemabinding/version2/SequenceDescriptor.java b/src/jalview/schemabinding/version2/SequenceDescriptor.java
index 9e1a7f3..555284a 100755 (executable)
--- a/src/jalview/schemabinding/version2/SequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceDescriptor.java
@@ -21,7 +21,7 @@ import org.exolab.castor.xml.validators.*;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class SequenceDescriptor extends SequenceTypeDescriptor {\r
+public class SequenceDescriptor extends jalview.schemabinding.version2.SequenceTypeDescriptor {\r
 \r
 \r
       //--------------------------/\r
@@ -55,9 +55,54 @@ public class SequenceDescriptor extends SequenceTypeDescriptor {
 \r
     public SequenceDescriptor() {\r
         super();\r
-        setExtendsWithoutFlatten(new SequenceTypeDescriptor());\r
+        setExtendsWithoutFlatten(new jalview.schemabinding.version2.SequenceTypeDescriptor());\r
         nsURI = "www.vamsas.ac.uk/jalview/version2";\r
         xmlName = "Sequence";\r
+        \r
+        //-- set grouping compositor\r
+        setCompositorAsSequence();\r
+        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
+        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
+        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
+        //-- initialize attribute descriptors\r
+        \r
+        //-- initialize element descriptors\r
+        \r
+        //-- _DBRefList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.DBRef.class, "_DBRefList", "DBRef", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Sequence target = (Sequence) object;\r
+                return target.getDBRef();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Sequence target = (Sequence) object;\r
+                    target.addDBRef( (jalview.schemabinding.version2.DBRef) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.DBRef();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _DBRefList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
+        }\r
+        desc.setValidator(fieldValidator);\r
     } //-- jalview.schemabinding.version2.SequenceDescriptor()\r
 \r
 \r

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 543c110..557e454 100755 (executable)
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -15,6 +15,8 @@ import java.io.IOException;
 import java.io.Reader;\r
 import java.io.Serializable;\r
 import java.io.Writer;\r
+import java.util.Enumeration;\r
+import java.util.Vector;\r
 import org.exolab.castor.xml.MarshalException;\r
 import org.exolab.castor.xml.Marshaller;\r
 import org.exolab.castor.xml.Unmarshaller;\r
@@ -283,6 +285,11 @@ public class Viewport implements java.io.Serializable {
      */\r
     private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
 \r
+    /**\r
+     * Field _hiddenColumnsList\r
+     */\r
+    private java.util.Vector _hiddenColumnsList;\r
+\r
 \r
       //----------------/\r
      //- Constructors -/\r
@@ -290,6 +297,7 @@ public class Viewport implements java.io.Serializable {
 \r
     public Viewport() {\r
         super();\r
+        _hiddenColumnsList = new Vector();\r
     } //-- jalview.schemabinding.version2.Viewport()\r
 \r
 \r
@@ -298,6 +306,33 @@ public class Viewport implements java.io.Serializable {
     //-----------/\r
 \r
     /**\r
+     * Method addHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param vHiddenColumns\r
+     */\r
+    public void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _hiddenColumnsList.addElement(vHiddenColumns);\r
+    } //-- void addHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+\r
+    /**\r
+     * Method addHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vHiddenColumns\r
+     */\r
+    public void addHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        _hiddenColumnsList.insertElementAt(vHiddenColumns, index);\r
+    } //-- void addHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+\r
+    /**\r
      * Method deleteConsThreshold\r
      * \r
      */\r
@@ -505,6 +540,18 @@ public class Viewport implements java.io.Serializable {
     } //-- void deleteYpos() \r
 \r
     /**\r
+     * Method enumerateHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @return Enumeration\r
+     */\r
+    public java.util.Enumeration enumerateHiddenColumns()\r
+    {\r
+        return _hiddenColumnsList.elements();\r
+    } //-- java.util.Enumeration enumerateHiddenColumns() \r
+\r
+    /**\r
      * Returns the value of field 'annotationColours'.\r
      * \r
      * @return AnnotationColours\r
@@ -593,6 +640,54 @@ public class Viewport implements java.io.Serializable {
     } //-- int getHeight() \r
 \r
     /**\r
+     * Method getHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return HiddenColumns\r
+     */\r
+    public jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int index)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        \r
+        return (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
+    } //-- jalview.schemabinding.version2.HiddenColumns getHiddenColumns(int) \r
+\r
+    /**\r
+     * Method getHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @return HiddenColumns\r
+     */\r
+    public jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns()\r
+    {\r
+        int size = _hiddenColumnsList.size();\r
+        jalview.schemabinding.version2.HiddenColumns[] mArray = new jalview.schemabinding.version2.HiddenColumns[size];\r
+        for (int index = 0; index < size; index++) {\r
+            mArray[index] = (jalview.schemabinding.version2.HiddenColumns) _hiddenColumnsList.elementAt(index);\r
+        }\r
+        return mArray;\r
+    } //-- jalview.schemabinding.version2.HiddenColumns[] getHiddenColumns() \r
+\r
+    /**\r
+     * Method getHiddenColumnsCount\r
+     * \r
+     * \r
+     * \r
+     * @return int\r
+     */\r
+    public int getHiddenColumnsCount()\r
+    {\r
+        return _hiddenColumnsList.size();\r
+    } //-- int getHiddenColumnsCount() \r
+\r
+    /**\r
      * Returns the value of field 'pidSelected'.\r
      * \r
      * @return boolean\r
@@ -1124,6 +1219,30 @@ public class Viewport implements java.io.Serializable {
     } //-- void marshal(org.xml.sax.ContentHandler) \r
 \r
     /**\r
+     * Method removeAllHiddenColumns\r
+     * \r
+     */\r
+    public void removeAllHiddenColumns()\r
+    {\r
+        _hiddenColumnsList.removeAllElements();\r
+    } //-- void removeAllHiddenColumns() \r
+\r
+    /**\r
+     * Method removeHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @return HiddenColumns\r
+     */\r
+    public jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int index)\r
+    {\r
+        java.lang.Object obj = _hiddenColumnsList.elementAt(index);\r
+        _hiddenColumnsList.removeElementAt(index);\r
+        return (jalview.schemabinding.version2.HiddenColumns) obj;\r
+    } //-- jalview.schemabinding.version2.HiddenColumns removeHiddenColumns(int) \r
+\r
+    /**\r
      * Sets the value of field 'annotationColours'.\r
      * \r
      * @param annotationColours the value of field\r
@@ -1211,6 +1330,40 @@ public class Viewport implements java.io.Serializable {
     } //-- void setHeight(int) \r
 \r
     /**\r
+     * Method setHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param index\r
+     * @param vHiddenColumns\r
+     */\r
+    public void setHiddenColumns(int index, jalview.schemabinding.version2.HiddenColumns vHiddenColumns)\r
+        throws java.lang.IndexOutOfBoundsException\r
+    {\r
+        //-- check bounds for index\r
+        if ((index < 0) || (index > _hiddenColumnsList.size())) {\r
+            throw new IndexOutOfBoundsException();\r
+        }\r
+        _hiddenColumnsList.setElementAt(vHiddenColumns, index);\r
+    } //-- void setHiddenColumns(int, jalview.schemabinding.version2.HiddenColumns) \r
+\r
+    /**\r
+     * Method setHiddenColumns\r
+     * \r
+     * \r
+     * \r
+     * @param hiddenColumnsArray\r
+     */\r
+    public void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns[] hiddenColumnsArray)\r
+    {\r
+        //-- copy array\r
+        _hiddenColumnsList.removeAllElements();\r
+        for (int i = 0; i < hiddenColumnsArray.length; i++) {\r
+            _hiddenColumnsList.addElement(hiddenColumnsArray[i]);\r
+        }\r
+    } //-- void setHiddenColumns(jalview.schemabinding.version2.HiddenColumns) \r
+\r
+    /**\r
      * Sets the value of field 'pidSelected'.\r
      * \r
      * @param pidSelected the value of field 'pidSelected'.\r

diff --git a/src/jalview/schemabinding/version2/ViewportDescriptor.java b/src/jalview/schemabinding/version2/ViewportDescriptor.java
index 02e9be9..b98f97b 100755 (executable)
--- a/src/jalview/schemabinding/version2/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/ViewportDescriptor.java
@@ -1152,6 +1152,41 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         { //-- local scope\r
         }\r
         desc.setValidator(fieldValidator);\r
+        //-- _hiddenColumnsList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element);\r
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Viewport target = (Viewport) object;\r
+                return target.getHiddenColumns();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value);\r
+                }\r
+                catch (java.lang.Exception ex) {\r
+                    throw new IllegalStateException(ex.toString());\r
+                }\r
+            }\r
+            public java.lang.Object newInstance( java.lang.Object parent ) {\r
+                return new jalview.schemabinding.version2.HiddenColumns();\r
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        desc.setNameSpaceURI("www.jalview.org");\r
+        desc.setMultivalued(true);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _hiddenColumnsList\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
+        { //-- local scope\r
+        }\r
+        desc.setValidator(fieldValidator);\r
     } //-- jalview.schemabinding.version2.ViewportDescriptor()\r
 \r
 \r