Save seqset properties

[jalview.git] / src / jalview / schemabinding / version2 / SequenceSetDescriptor.java

diff --git a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
index 1e6c7b5..22e00c3 100755 (executable)
--- 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);\r
         }\r
         desc.setValidator(fieldValidator);\r
-        //-- _aligned\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_aligned", "aligned", org.exolab.castor.xml.NodeType.Attribute);\r
+        //-- initialize element descriptors\r
+        \r
+        //-- _sequenceList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", 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
                 SequenceSet target = (SequenceSet) object;\r
-                if(!target.hasAligned())\r
-                    return null;\r
-                return (target.getAligned() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+                return target.getSequence();\r
             }\r
             public void setValue( java.lang.Object object, java.lang.Object value) \r
                 throws IllegalStateException, IllegalArgumentException\r
             {\r
                 try {\r
                     SequenceSet target = (SequenceSet) object;\r
-                    // if null, use delete method for optional primitives \r
-                    if (value == null) {\r
-                        target.deleteAligned();\r
-                        return;\r
-                    }\r
-                    target.setAligned( ((java.lang.Boolean)value).booleanValue());\r
+                    target.addSequence( (jalview.schemabinding.version2.Sequence) 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
+                return new jalview.schemabinding.version2.Sequence();\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: _aligned\r
+        //-- validation code for: _sequenceList\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        fieldValidator.setMinOccurs(0);\r
         { //-- local scope\r
-            BooleanValidator typeValidator = new BooleanValidator();\r
-            fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
-        //-- initialize element descriptors\r
-        \r
-        //-- _sequenceList\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Sequence.class, "_sequenceList", "Sequence", org.exolab.castor.xml.NodeType.Element);\r
+        //-- _annotationList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "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
                 SequenceSet target = (SequenceSet) object;\r
-                return target.getSequence();\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
                     SequenceSet target = (SequenceSet) object;\r
-                    target.addSequence( (jalview.schemabinding.version2.Sequence) value);\r
+                    target.addAnnotation( (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.Sequence();\r
+                return new jalview.schemabinding.version2.Annotation();\r
             }\r
         } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-        desc.setRequired(true);\r
         desc.setMultivalued(true);\r
         addFieldDescriptor(desc);\r
         \r
-        //-- validation code for: _sequenceList\r
+        //-- validation code for: _annotationList\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-        fieldValidator.setMinOccurs(1);\r
+        fieldValidator.setMinOccurs(0);\r
         { //-- local scope\r
         }\r
         desc.setValidator(fieldValidator);\r
-        //-- _annotationList\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.Annotation.class, "_annotationList", "Annotation", org.exolab.castor.xml.NodeType.Element);\r
+        //-- _sequenceSetPropertiesList\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.SequenceSetProperties.class, "_sequenceSetPropertiesList", "sequenceSetProperties", 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
                 SequenceSet target = (SequenceSet) object;\r
-                return target.getAnnotation();\r
+                return target.getSequenceSetProperties();\r
             }\r
             public void setValue( java.lang.Object object, java.lang.Object value) \r
                 throws IllegalStateException, IllegalArgumentException\r
             {\r
                 try {\r
                     SequenceSet target = (SequenceSet) object;\r
-                    target.addAnnotation( (jalview.schemabinding.version2.Annotation) value);\r
+                    target.addSequenceSetProperties( (jalview.schemabinding.version2.SequenceSetProperties) 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
+                return new jalview.schemabinding.version2.SequenceSetProperties();\r
             }\r
         } );\r
         desc.setHandler(handler);\r
@@ -211,7 +204,7 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         desc.setMultivalued(true);\r
         addFieldDescriptor(desc);\r
         \r
-        //-- validation code for: _annotationList\r
+        //-- validation code for: _sequenceSetPropertiesList\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         fieldValidator.setMinOccurs(0);\r
         { //-- local scope\r