made vamsas a proper root element in schema and added example document.

[vamsas.git] / src / org / vamsas / objects / core / SequenceSetDescriptor.java

diff --git a/src/org/vamsas/objects/core/SequenceSetDescriptor.java b/src/org/vamsas/objects/core/SequenceSetDescriptor.java
index f6d090e..722e429 100644 (file)
--- a/src/org/vamsas/objects/core/SequenceSetDescriptor.java
+++ b/src/org/vamsas/objects/core/SequenceSetDescriptor.java
@@ -1,6 +1,6 @@
 /*
  * This class was automatically generated with 
- * <a href="http://www.castor.org">Castor 0.9.9M1</a>, using an XML
+ * <a href="http://www.castor.org">Castor 0.9.9M2</a>, using an XML
  * Schema.
  * $Id$
  */
@@ -66,85 +66,38 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;
         //-- initialize attribute descriptors
         
-        //-- _gapChar
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_gapChar", "gapChar", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
+        //-- _id
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_id", "id", org.exolab.castor.xml.NodeType.Attribute);
+        this.identity = desc;
         handler = new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 SequenceSet target = (SequenceSet) object;
-                return target.getGapChar();
+                return target.getId();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
                     SequenceSet target = (SequenceSet) object;
-                    target.setGapChar( (java.lang.String) value);
+                    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: _gapChar
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
-        { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
-            fieldValidator.setValidator(typeValidator);
-        }
-        desc.setValidator(fieldValidator);
-        //-- _aligned
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);
-        handler = new org.exolab.castor.xml.XMLFieldHandler() {
-            public java.lang.Object getValue( java.lang.Object object ) 
-                throws IllegalStateException
-            {
-                SequenceSet target = (SequenceSet) object;
-                if(!target.hasAligned())
-                    return null;
-                return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
-            }
-            public void setValue( java.lang.Object object, java.lang.Object value) 
-                throws IllegalStateException, IllegalArgumentException
-            {
-                try {
-                    SequenceSet target = (SequenceSet) object;
-                    // if null, use delete method for optional primitives 
-                    if (value == null) {
-                        target.deleteAligned();
-                        return;
-                    }
-                    target.setAligned( ((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;
+                return new java.lang.String();
             }
         };
         desc.setHandler(handler);
         desc.setMultivalued(false);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _aligned
+        //-- validation code for: _id
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
-            BooleanValidator typeValidator = new BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
         //-- initialize element descriptors
@@ -255,8 +208,8 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         { //-- local scope
         }
         desc.setValidator(fieldValidator);
-        //-- _tree
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_tree", "tree", org.exolab.castor.xml.NodeType.Element);
+        //-- _treeList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(org.vamsas.objects.core.Tree.class, "_treeList", "Tree", org.exolab.castor.xml.NodeType.Element);
         handler = new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
@@ -269,7 +222,7 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             {
                 try {
                     SequenceSet target = (SequenceSet) object;
-                    target.setTree( (org.vamsas.objects.core.Tree) value);
+                    target.addTree( (org.vamsas.objects.core.Tree) value);
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -281,13 +234,12 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         };
         desc.setHandler(handler);
         desc.setNameSpaceURI("http://www.vamsas.org");
-        desc.setRequired(true);
-        desc.setMultivalued(false);
+        desc.setMultivalued(true);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _tree
+        //-- validation code for: _treeList
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
+        fieldValidator.setMinOccurs(0);
         { //-- local scope
         }
         desc.setValidator(fieldValidator);