From a2a842580f86bd847b07cd2f75b26c74ec752fd7 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Wed, 10 May 2006 12:52:11 +0000
Subject: [PATCH] Save seqref with annotations

---
 src/jalview/schemabinding/version2/Annotation.java |   26 ++++++++++++++
 .../version2/AnnotationDescriptor.java             |   36 ++++++++++++++++++++
 2 files changed, 62 insertions(+)

diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 6003b86..e6c8e5a 100755
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -56,6 +56,11 @@ public class Annotation implements java.io.Serializable {
     private boolean _has_graphType;
 
     /**
+     * Field _sequenceRef
+     */
+    private java.lang.String _sequenceRef;
+
+    /**
      * Field _annotationElementList
      */
     private java.util.Vector _annotationElementList;
@@ -240,6 +245,17 @@ public class Annotation implements java.io.Serializable {
     } //-- java.lang.String getLabel() 
 
     /**
+     * Returns the value of field 'sequenceRef'.
+     * 
+     * @return String
+     * @return the value of field 'sequenceRef'.
+     */
+    public java.lang.String getSequenceRef()
+    {
+        return this._sequenceRef;
+    } //-- java.lang.String getSequenceRef() 
+
+    /**
      * Returns the value of field 'thresholdLine'.
      * 
      * @return ThresholdLine
@@ -421,6 +437,16 @@ public class Annotation implements java.io.Serializable {
     } //-- void setLabel(java.lang.String) 
 
     /**
+     * Sets the value of field 'sequenceRef'.
+     * 
+     * @param sequenceRef the value of field 'sequenceRef'.
+     */
+    public void setSequenceRef(java.lang.String sequenceRef)
+    {
+        this._sequenceRef = sequenceRef;
+    } //-- void setSequenceRef(java.lang.String) 
+
+    /**
      * Sets the value of field 'thresholdLine'.
      * 
      * @param thresholdLine the value of field 'thresholdLine'.
diff --git a/src/jalview/schemabinding/version2/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/AnnotationDescriptor.java
index 9e34a53..b3125c3 100755
--- a/src/jalview/schemabinding/version2/AnnotationDescriptor.java
+++ b/src/jalview/schemabinding/version2/AnnotationDescriptor.java
@@ -147,6 +147,42 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
+        //-- _sequenceRef
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceRef", "sequenceRef", org.exolab.castor.xml.NodeType.Attribute);
+        desc.setImmutable(true);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Annotation target = (Annotation) object;
+                return target.getSequenceRef();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Annotation target = (Annotation) object;
+                    target.setSequenceRef( (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);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _sequenceRef
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
         //-- initialize element descriptors
         
         //-- _annotationElementList
-- 
1.7.10.2