sequence mappings and DbRef mapping objects unified and source binding for castor...

[vamsas.git] / src / uk / ac / vamsas / objects / core / descriptors / SequenceMappingDescriptor.java

diff --git a/src/uk/ac/vamsas/objects/core/descriptors/SequenceMappingDescriptor.java b/src/uk/ac/vamsas/objects/core/descriptors/SequenceMappingDescriptor.java
index 69ae934..396515e 100644 (file)
--- a/src/uk/ac/vamsas/objects/core/descriptors/SequenceMappingDescriptor.java
+++ b/src/uk/ac/vamsas/objects/core/descriptors/SequenceMappingDescriptor.java
@@ -18,7 +18,7 @@ import uk.ac.vamsas.objects.core.SequenceMapping;
  * \r
  * @version $Revision$ $Date$\r
  */\r
-public class SequenceMappingDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
+public class SequenceMappingDescriptor extends uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor {\r
 \r
 \r
       //--------------------------/\r
@@ -45,11 +45,6 @@ public class SequenceMappingDescriptor extends org.exolab.castor.xml.util.XMLCla
      */\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
@@ -57,6 +52,7 @@ public class SequenceMappingDescriptor extends org.exolab.castor.xml.util.XMLCla
 \r
     public SequenceMappingDescriptor() {\r
         super();\r
+        setExtendsWithoutFlatten(new uk.ac.vamsas.objects.core.descriptors.MapTypeDescriptor());\r
         _nsURI = "http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes";\r
         _xmlName = "sequenceMapping";\r
         _elementDefinition = true;\r
@@ -68,22 +64,22 @@ public class SequenceMappingDescriptor extends org.exolab.castor.xml.util.XMLCla
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
         //-- initialize attribute descriptors\r
         \r
-        //-- _sequenceA\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_sequenceA", "sequenceA", org.exolab.castor.xml.NodeType.Attribute);\r
+        //-- _loc\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_loc", "loc", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setReference(true);\r
         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
                 SequenceMapping target = (SequenceMapping) object;\r
-                return target.getSequenceA();\r
+                return target.getLoc();\r
             }\r
             public void setValue( java.lang.Object object, java.lang.Object value) \r
                 throws IllegalStateException, IllegalArgumentException\r
             {\r
                 try {\r
                     SequenceMapping target = (SequenceMapping) object;\r
-                    target.setSequenceA( (java.lang.Object) value);\r
+                    target.setLoc( (java.lang.Object) value);\r
                 } catch (java.lang.Exception ex) {\r
                     throw new IllegalStateException(ex.toString());\r
                 }\r
@@ -97,7 +93,7 @@ public class SequenceMappingDescriptor extends org.exolab.castor.xml.util.XMLCla
         desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
-        //-- validation code for: _sequenceA\r
+        //-- validation code for: _loc\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         fieldValidator.setMinOccurs(1);\r
         { //-- local scope\r
@@ -106,22 +102,22 @@ public class SequenceMappingDescriptor extends org.exolab.castor.xml.util.XMLCla
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
-        //-- _sequenceB\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_sequenceB", "sequenceB", org.exolab.castor.xml.NodeType.Attribute);\r
+        //-- _map\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Object.class, "_map", "map", org.exolab.castor.xml.NodeType.Attribute);\r
         desc.setReference(true);\r
         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
             {\r
                 SequenceMapping target = (SequenceMapping) object;\r
-                return target.getSequenceB();\r
+                return target.getMap();\r
             }\r
             public void setValue( java.lang.Object object, java.lang.Object value) \r
                 throws IllegalStateException, IllegalArgumentException\r
             {\r
                 try {\r
                     SequenceMapping target = (SequenceMapping) object;\r
-                    target.setSequenceB( (java.lang.Object) value);\r
+                    target.setMap( (java.lang.Object) value);\r
                 } catch (java.lang.Exception ex) {\r
                     throw new IllegalStateException(ex.toString());\r
                 }\r
@@ -135,7 +131,7 @@ public class SequenceMappingDescriptor extends org.exolab.castor.xml.util.XMLCla
         desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
-        //-- validation code for: _sequenceB\r
+        //-- validation code for: _map\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         fieldValidator.setMinOccurs(1);\r
         { //-- local scope\r
@@ -146,7 +142,7 @@ public class SequenceMappingDescriptor extends org.exolab.castor.xml.util.XMLCla
         desc.setValidator(fieldValidator);\r
         //-- _id\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);\r
-        this._identity = desc;\r
+        super.setIdentity(desc);\r
         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
             public java.lang.Object getValue( java.lang.Object object ) \r
                 throws IllegalStateException\r
@@ -182,49 +178,6 @@ public class SequenceMappingDescriptor extends org.exolab.castor.xml.util.XMLCla
         desc.setValidator(fieldValidator);\r
         //-- initialize element descriptors\r
         \r
-        //-- _rangeList\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(uk.ac.vamsas.objects.core.Range.class, "_rangeList", "range", 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
-                SequenceMapping target = (SequenceMapping) object;\r
-                return target.getRange();\r
-            }\r
-            public void setValue( java.lang.Object object, java.lang.Object value) \r
-                throws IllegalStateException, IllegalArgumentException\r
-            {\r
-                try {\r
-                    SequenceMapping target = (SequenceMapping) object;\r
-                    target.addRange( (uk.ac.vamsas.objects.core.Range) value);\r
-                } catch (java.lang.Exception ex) {\r
-                    throw new IllegalStateException(ex.toString());\r
-                }\r
-            }\r
-            public void resetValue(Object object) throws IllegalStateException, IllegalArgumentException {\r
-                try {\r
-                    SequenceMapping target = (SequenceMapping) object;\r
-                    target.removeAllRange();\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 uk.ac.vamsas.objects.core.Range();\r
-            }\r
-        };\r
-        desc.setHandler(handler);\r
-        desc.setNameSpaceURI("http://www.vamsas.ac.uk/schemas/1.0/vamsasTypes");\r
-        desc.setRequired(true);\r
-        desc.setMultivalued(true);\r
-        addFieldDescriptor(desc);\r
-        \r
-        //-- validation code for: _rangeList\r
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-        fieldValidator.setMinOccurs(1);\r
-        { //-- local scope\r
-        }\r
-        desc.setValidator(fieldValidator);\r
         //-- _provenance\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(uk.ac.vamsas.objects.core.Provenance.class, "_provenance", "Provenance", org.exolab.castor.xml.NodeType.Element);\r
         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
@@ -285,7 +238,7 @@ public class SequenceMappingDescriptor extends org.exolab.castor.xml.util.XMLCla
      */\r
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(\r
     ) {\r
-        return _identity;\r
+        return super.getIdentity();\r
     }\r
 \r
     /**\r