X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FSequenceSetDescriptor.java;h=22e00c38549e47ecd1f0ff9935ff0dc84d8c5ef6;hb=682c69b6a050a742d20f643459d8d8fbfecf40e1;hp=1e6c7b5d5371c55c3d2f0cff24816bb21d12dd68;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
index 1e6c7b5..22e00c3 100755
--- a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
@@ -103,107 +103,100 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
             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);
+        //-- initialize element descriptors
+        
+        //-- _sequenceList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);
         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);
+                return target.getSequence();
             }
             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());
+                    target.addSequence( (jalview.schemabinding.version2.Sequence) value);
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
                 }
             }
             public java.lang.Object newInstance( java.lang.Object parent ) {
-                return null;
+                return new jalview.schemabinding.version2.Sequence();
             }
         } );
         desc.setHandler(handler);
+        desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
+        desc.setMultivalued(true);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _aligned
+        //-- validation code for: _sequenceList
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
         { //-- local scope
-            BooleanValidator typeValidator = new BooleanValidator();
-            fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- initialize element descriptors
-        
-        //-- _sequenceList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);
+        //-- _annotationList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 SequenceSet target = (SequenceSet) object;
-                return target.getSequence();
+                return target.getAnnotation();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
                     SequenceSet target = (SequenceSet) object;
-                    target.addSequence( (jalview.schemabinding.version2.Sequence) value);
+                    target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
                 }
             }
             public java.lang.Object newInstance( java.lang.Object parent ) {
-                return new jalview.schemabinding.version2.Sequence();
+                return new jalview.schemabinding.version2.Annotation();
             }
         } );
         desc.setHandler(handler);
         desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");
-        desc.setRequired(true);
         desc.setMultivalued(true);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _sequenceList
+        //-- validation code for: _annotationList
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
-        fieldValidator.setMinOccurs(1);
+        fieldValidator.setMinOccurs(0);
         { //-- local scope
         }
         desc.setValidator(fieldValidator);
-        //-- _annotationList
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);
+        //-- _sequenceSetPropertiesList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", org.exolab.castor.xml.NodeType.Element);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 SequenceSet target = (SequenceSet) object;
-                return target.getAnnotation();
+                return target.getSequenceSetProperties();
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
                     SequenceSet target = (SequenceSet) object;
-                    target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);
+                    target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) value);
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
                 }
             }
             public java.lang.Object newInstance( java.lang.Object parent ) {
-                return new jalview.schemabinding.version2.Annotation();
+                return new jalview.schemabinding.version2.SequenceSetProperties();
             }
         } );
         desc.setHandler(handler);
@@ -211,7 +204,7 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         desc.setMultivalued(true);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _annotationList
+        //-- validation code for: _sequenceSetPropertiesList
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         fieldValidator.setMinOccurs(0);
         { //-- local scope