Simplified schema

diff --git a/src/jalview/schemabinding/version2/Alignment.java b/src/jalview/schemabinding/version2/Alignment.java
deleted file mode 100755 (executable)
index 3b9d53b..0000000
--- a/src/jalview/schemabinding/version2/Alignment.java
+++ /dev/null
@@ -1,173 +0,0 @@
-/*\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 Alignment.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class Alignment implements java.io.Serializable {\r
-\r
-\r
-      //--------------------------/\r
-     //- Class/Member Variables -/\r
-    //--------------------------/\r
-\r
-    /**\r
-     * Field _annotation\r
-     */\r
-    private jalview.schemabinding.version2.Annotation _annotation;\r
-\r
-    /**\r
-     * Field _sequenceSet\r
-     */\r
-    private jalview.schemabinding.version2.SequenceSet _sequenceSet;\r
-\r
-\r
-      //----------------/\r
-     //- Constructors -/\r
-    //----------------/\r
-\r
-    public Alignment() {\r
-        super();\r
-    } //-- jalview.schemabinding.version2.Alignment()\r
-\r
-\r
-      //-----------/\r
-     //- Methods -/\r
-    //-----------/\r
-\r
-    /**\r
-     * Returns the value of field 'annotation'.\r
-     * \r
-     * @return Annotation\r
-     * @return the value of field 'annotation'.\r
-     */\r
-    public jalview.schemabinding.version2.Annotation getAnnotation()\r
-    {\r
-        return this._annotation;\r
-    } //-- jalview.schemabinding.version2.Annotation getAnnotation() \r
-\r
-    /**\r
-     * Returns the value of field 'sequenceSet'.\r
-     * \r
-     * @return SequenceSet\r
-     * @return the value of field 'sequenceSet'.\r
-     */\r
-    public jalview.schemabinding.version2.SequenceSet getSequenceSet()\r
-    {\r
-        return this._sequenceSet;\r
-    } //-- jalview.schemabinding.version2.SequenceSet getSequenceSet() \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 'annotation'.\r
-     * \r
-     * @param annotation the value of field 'annotation'.\r
-     */\r
-    public void setAnnotation(jalview.schemabinding.version2.Annotation annotation)\r
-    {\r
-        this._annotation = annotation;\r
-    } //-- void setAnnotation(jalview.schemabinding.version2.Annotation) \r
-\r
-    /**\r
-     * Sets the value of field 'sequenceSet'.\r
-     * \r
-     * @param sequenceSet the value of field 'sequenceSet'.\r
-     */\r
-    public void setSequenceSet(jalview.schemabinding.version2.SequenceSet sequenceSet)\r
-    {\r
-        this._sequenceSet = sequenceSet;\r
-    } //-- void setSequenceSet(jalview.schemabinding.version2.SequenceSet) \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.Alignment) Unmarshaller.unmarshal(jalview.schemabinding.version2.Alignment.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/AlignmentDescriptor.java b/src/jalview/schemabinding/version2/AlignmentDescriptor.java
deleted file mode 100755 (executable)
index b285229..0000000
--- a/src/jalview/schemabinding/version2/AlignmentDescriptor.java
+++ /dev/null
@@ -1,243 +0,0 @@
-/*\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 AlignmentDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class AlignmentDescriptor 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 AlignmentDescriptor() {\r
-        super();\r
-        nsURI = "www.vamsas.ac.uk/jalview/version2";\r
-        xmlName = "Alignment";\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
-        //-- _annotation\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotation", "Annotation", 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
-                Alignment target = (Alignment) object;\r
-                return target.getAnnotation();\r
-            }\r
-            public void setValue( java.lang.Object object, java.lang.Object value) \r
-                throws IllegalStateException, IllegalArgumentException\r
-            {\r
-                try {\r
-                    Alignment target = (Alignment) object;\r
-                    target.setAnnotation( (jalview.schemabinding.version2.Annotation) 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.Annotation();\r
-            }\r
-        } );\r
-        desc.setHandler(handler);\r
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-        desc.setMultivalued(false);\r
-        addFieldDescriptor(desc);\r
-        \r
-        //-- validation code for: _annotation\r
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-        { //-- local scope\r
-        }\r
-        desc.setValidator(fieldValidator);\r
-        //-- _sequenceSet\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSet.class, "_sequenceSet", "SequenceSet", 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
-                Alignment target = (Alignment) object;\r
-                return target.getSequenceSet();\r
-            }\r
-            public void setValue( java.lang.Object object, java.lang.Object value) \r
-                throws IllegalStateException, IllegalArgumentException\r
-            {\r
-                try {\r
-                    Alignment target = (Alignment) object;\r
-                    target.setSequenceSet( (jalview.schemabinding.version2.SequenceSet) 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.SequenceSet();\r
-            }\r
-        } );\r
-        desc.setHandler(handler);\r
-        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-        desc.setRequired(true);\r
-        desc.setMultivalued(false);\r
-        addFieldDescriptor(desc);\r
-        \r
-        //-- validation code for: _sequenceSet\r
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-        fieldValidator.setMinOccurs(1);\r
-        { //-- local scope\r
-        }\r
-        desc.setValidator(fieldValidator);\r
-    } //-- jalview.schemabinding.version2.AlignmentDescriptor()\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.Alignment.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/VAMSAS.java b/src/jalview/schemabinding/version2/VAMSAS.java
index 9550690..03633d6 100755 (executable)
--- a/src/jalview/schemabinding/version2/VAMSAS.java
+++ b/src/jalview/schemabinding/version2/VAMSAS.java
@@ -36,11 +36,6 @@ public class VAMSAS implements java.io.Serializable {
     //--------------------------/\r
 \r
     /**\r
-     * Field _alignmentList\r
-     */\r
-    private java.util.Vector _alignmentList;\r
-\r
-    /**\r
      * Field _treeList\r
      */\r
     private java.util.Vector _treeList;\r
@@ -57,7 +52,6 @@ public class VAMSAS implements java.io.Serializable {
 \r
     public VAMSAS() {\r
         super();\r
-        _alignmentList = new Vector();\r
         _treeList = new Vector();\r
         _sequenceSetList = new Vector();\r
     } //-- jalview.schemabinding.version2.VAMSAS()\r
@@ -68,33 +62,6 @@ public class VAMSAS implements java.io.Serializable {
     //-----------/\r
 \r
     /**\r
-     * Method addAlignment\r
-     * \r
-     * \r
-     * \r
-     * @param vAlignment\r
-     */\r
-    public void addAlignment(jalview.schemabinding.version2.Alignment vAlignment)\r
-        throws java.lang.IndexOutOfBoundsException\r
-    {\r
-        _alignmentList.addElement(vAlignment);\r
-    } //-- void addAlignment(jalview.schemabinding.version2.Alignment) \r
-\r
-    /**\r
-     * Method addAlignment\r
-     * \r
-     * \r
-     * \r
-     * @param index\r
-     * @param vAlignment\r
-     */\r
-    public void addAlignment(int index, jalview.schemabinding.version2.Alignment vAlignment)\r
-        throws java.lang.IndexOutOfBoundsException\r
-    {\r
-        _alignmentList.insertElementAt(vAlignment, index);\r
-    } //-- void addAlignment(int, jalview.schemabinding.version2.Alignment) \r
-\r
-    /**\r
      * Method addSequenceSet\r
      * \r
      * \r
@@ -149,18 +116,6 @@ public class VAMSAS implements java.io.Serializable {
     } //-- void addTree(int, java.lang.String) \r
 \r
     /**\r
-     * Method enumerateAlignment\r
-     * \r
-     * \r
-     * \r
-     * @return Enumeration\r
-     */\r
-    public java.util.Enumeration enumerateAlignment()\r
-    {\r
-        return _alignmentList.elements();\r
-    } //-- java.util.Enumeration enumerateAlignment() \r
-\r
-    /**\r
      * Method enumerateSequenceSet\r
      * \r
      * \r
@@ -185,54 +140,6 @@ public class VAMSAS implements java.io.Serializable {
     } //-- java.util.Enumeration enumerateTree() \r
 \r
     /**\r
-     * Method getAlignment\r
-     * \r
-     * \r
-     * \r
-     * @param index\r
-     * @return Alignment\r
-     */\r
-    public jalview.schemabinding.version2.Alignment getAlignment(int index)\r
-        throws java.lang.IndexOutOfBoundsException\r
-    {\r
-        //-- check bounds for index\r
-        if ((index < 0) || (index > _alignmentList.size())) {\r
-            throw new IndexOutOfBoundsException();\r
-        }\r
-        \r
-        return (jalview.schemabinding.version2.Alignment) _alignmentList.elementAt(index);\r
-    } //-- jalview.schemabinding.version2.Alignment getAlignment(int) \r
-\r
-    /**\r
-     * Method getAlignment\r
-     * \r
-     * \r
-     * \r
-     * @return Alignment\r
-     */\r
-    public jalview.schemabinding.version2.Alignment[] getAlignment()\r
-    {\r
-        int size = _alignmentList.size();\r
-        jalview.schemabinding.version2.Alignment[] mArray = new jalview.schemabinding.version2.Alignment[size];\r
-        for (int index = 0; index < size; index++) {\r
-            mArray[index] = (jalview.schemabinding.version2.Alignment) _alignmentList.elementAt(index);\r
-        }\r
-        return mArray;\r
-    } //-- jalview.schemabinding.version2.Alignment[] getAlignment() \r
-\r
-    /**\r
-     * Method getAlignmentCount\r
-     * \r
-     * \r
-     * \r
-     * @return int\r
-     */\r
-    public int getAlignmentCount()\r
-    {\r
-        return _alignmentList.size();\r
-    } //-- int getAlignmentCount() \r
-\r
-    /**\r
      * Method getSequenceSet\r
      * \r
      * \r
@@ -375,30 +282,6 @@ public class VAMSAS implements java.io.Serializable {
     } //-- void marshal(org.xml.sax.ContentHandler) \r
 \r
     /**\r
-     * Method removeAlignment\r
-     * \r
-     * \r
-     * \r
-     * @param index\r
-     * @return Alignment\r
-     */\r
-    public jalview.schemabinding.version2.Alignment removeAlignment(int index)\r
-    {\r
-        java.lang.Object obj = _alignmentList.elementAt(index);\r
-        _alignmentList.removeElementAt(index);\r
-        return (jalview.schemabinding.version2.Alignment) obj;\r
-    } //-- jalview.schemabinding.version2.Alignment removeAlignment(int) \r
-\r
-    /**\r
-     * Method removeAllAlignment\r
-     * \r
-     */\r
-    public void removeAllAlignment()\r
-    {\r
-        _alignmentList.removeAllElements();\r
-    } //-- void removeAllAlignment() \r
-\r
-    /**\r
      * Method removeAllSequenceSet\r
      * \r
      */\r
@@ -447,40 +330,6 @@ public class VAMSAS implements java.io.Serializable {
     } //-- java.lang.String removeTree(int) \r
 \r
     /**\r
-     * Method setAlignment\r
-     * \r
-     * \r
-     * \r
-     * @param index\r
-     * @param vAlignment\r
-     */\r
-    public void setAlignment(int index, jalview.schemabinding.version2.Alignment vAlignment)\r
-        throws java.lang.IndexOutOfBoundsException\r
-    {\r
-        //-- check bounds for index\r
-        if ((index < 0) || (index > _alignmentList.size())) {\r
-            throw new IndexOutOfBoundsException();\r
-        }\r
-        _alignmentList.setElementAt(vAlignment, index);\r
-    } //-- void setAlignment(int, jalview.schemabinding.version2.Alignment) \r
-\r
-    /**\r
-     * Method setAlignment\r
-     * \r
-     * \r
-     * \r
-     * @param alignmentArray\r
-     */\r
-    public void setAlignment(jalview.schemabinding.version2.Alignment[] alignmentArray)\r
-    {\r
-        //-- copy array\r
-        _alignmentList.removeAllElements();\r
-        for (int i = 0; i < alignmentArray.length; i++) {\r
-            _alignmentList.addElement(alignmentArray[i]);\r
-        }\r
-    } //-- void setAlignment(jalview.schemabinding.version2.Alignment) \r
-\r
-    /**\r
      * Method setSequenceSet\r
      * \r
      * \r

diff --git a/src/jalview/schemabinding/version2/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/VAMSASDescriptor.java
index 02140e0..fad185b 100755 (executable)
--- a/src/jalview/schemabinding/version2/VAMSASDescriptor.java
+++ b/src/jalview/schemabinding/version2/VAMSASDescriptor.java
@@ -67,41 +67,6 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
         \r
         //-- initialize element descriptors\r
         \r
-        //-- _alignmentList\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Alignment.class, "_alignmentList", "Alignment", 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
-                VAMSAS target = (VAMSAS) object;\r
-                return target.getAlignment();\r
-            }\r
-            public void setValue( java.lang.Object object, java.lang.Object value) \r
-                throws IllegalStateException, IllegalArgumentException\r
-            {\r
-                try {\r
-                    VAMSAS target = (VAMSAS) object;\r
-                    target.addAlignment( (jalview.schemabinding.version2.Alignment) 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.Alignment();\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: _alignmentList\r
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-        fieldValidator.setMinOccurs(0);\r
-        { //-- local scope\r
-        }\r
-        desc.setValidator(fieldValidator);\r
         //-- _treeList\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);\r
         desc.setImmutable(true);\r