From: jprocter <Jim Procter>
Date: Fri, 13 Jul 2007 14:54:00 +0000 (+0000)
Subject: moved to castor-1.1-cycle - a specially patched version of castor relating to jira... 
X-Git-Tag: Release_2_4~363
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=81c0d443543fea0b28237b6e2bd7973517780030;p=jalview.git

moved to castor-1.1-cycle - a specially patched version of castor relating to jira bugs : jira.codehaus.org/browse/CASTOR-2027 http://jira.codehaus.org/browse/CASTOR-2012 http://jira.codehaus.org/browse/CASTOR-2011
---

diff --git a/build.xml b/build.xml
index aa0ca67..c872cfe 100755
--- a/build.xml
+++ b/build.xml
@@ -68,6 +68,8 @@
 		<property name="outputDir" value="classes" />
 		<property name="packageDir" value="dist" />
 		<property name="outputJar" value="jalview.jar" />
+                <!-- Jalview Applet JMol Jar Dependency -->
+                <property name="jmolJar" value="Jmol-11.0.2.jar" />
 		<!-- Jalview Web Service Clients - see the comments in 'buildextclients' for details -->
 		<property name="wsdl.File" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred?wsdl" />
 		<property name="wsdl.Files" value="http://www.compbio.dundee.ac.uk/JalviewWS/services/vamsas?wsdlFiles" />
@@ -89,12 +91,16 @@
 		</path>
 		<!-- The Location of the java 1.1.8 jdk -->
 		<property name="java118.home" value="C:\Sun\jdk1.1.8" />
+		<property name="applet.jre.tools" value="${java118.home}/lib/classes.zip"/>
+		<!-- jre for 1.4 version
+		<property name="applet.jre.tools" value="${java.home}/lib/rt.jar"/>
+		-->
 		<!-- the classpath for building the 1.1 applet -->
 		<path id="jalviewlite.deps">
 			<fileset dir="${java118.home}">
 				<include name="lib/classes.zip"/>
 			</fileset>
-	   	<pathelement location="lib/jmol.jar"/>
+	   	<pathelement location="lib/${jmolJar}"/>
 	  </path>
 	</target>
 
@@ -346,7 +352,7 @@
     target="1.1"
     srcdir="${sourceDir}" 
     destdir="${outputDir}"
-    classpath="lib/JmolApplet.jar"
+    classpath="lib/${jmolJar}"
        includes="jalview/appletgui/**"
        excludes="ext/**,MCview/**,org/**,vamsas/**"
        />
@@ -371,13 +377,27 @@
   </target>
 
   <target name="obfuscate" depends="packageApplet">
+    <path id="obfuscateDeps.path">
+    <pathelement location="${applet.jre.tools}"/>
+    <pathelement location="lib/${jmolJar}"/>
+    </path>
     <taskdef resource="proguard/ant/task.properties" classpath="utils/proguard.jar" />
     <proguard>
-      -libraryjars "${java.home}/lib/rt.jar";lib/JmolApplet.jar
+      <injar file="in.jar"/>
+      <outjar file="jalviewApplet.jar"/>
+      <libraryjar refid="obfuscateDeps.path"/>
+      <keep access="public" type="class"
+      name="jalview.bin.JalviewLite">
+        <field access="public"/>
+        <method access="public"/>
+        <constructor access="public"/>
+      </keep>
+<!--      -libraryjars "${obfuscateDeps}"
       -injars      in.jar
       -outjars     jalviewApplet.jar
       -keep public class jalview.bin.JalviewLite
        { public * ; }
+       -->
     </proguard>
     <delete file="in.jar"/>
   </target>
diff --git a/lib/castor-1.1-xml.jar b/lib/castor-1.1-cycle-xml.jar
similarity index 91%
rename from lib/castor-1.1-xml.jar
rename to lib/castor-1.1-cycle-xml.jar
index 9427fed..6702de9 100644
Binary files a/lib/castor-1.1-xml.jar and b/lib/castor-1.1-cycle-xml.jar differ
diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr
index 24ffdfa..cb20022 100644
--- a/src/jalview/schemabinding/version2/.castor.cdr
+++ b/src/jalview/schemabinding/version2/.castor.cdr
@@ -1,4 +1,4 @@
-#Thu May 24 16:17:26 BST 2007
+#Sun Jun 17 14:17:08 BST 2007
 jalview.schemabinding.version2.AnnotationColours=jalview.schemabinding.version2.descriptors.AnnotationColoursDescriptor
 jalview.schemabinding.version2.Sequence=jalview.schemabinding.version2.descriptors.SequenceDescriptor
 jalview.schemabinding.version2.SequenceType=jalview.schemabinding.version2.descriptors.SequenceTypeDescriptor
@@ -15,18 +15,18 @@ jalview.schemabinding.version2.JalviewModelSequence=jalview.schemabinding.versio
 jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor
 jalview.schemabinding.version2.SequenceSet=jalview.schemabinding.version2.descriptors.SequenceSetDescriptor
 jalview.schemabinding.version2.DBRef=jalview.schemabinding.version2.descriptors.DBRefDescriptor
-jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor
 jalview.schemabinding.version2.Colour=jalview.schemabinding.version2.descriptors.ColourDescriptor
+jalview.schemabinding.version2.Feature=jalview.schemabinding.version2.descriptors.FeatureDescriptor
 jalview.schemabinding.version2.Viewport=jalview.schemabinding.version2.descriptors.ViewportDescriptor
-jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor
 jalview.schemabinding.version2.JalviewModel=jalview.schemabinding.version2.descriptors.JalviewModelDescriptor
+jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor
 jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor
 jalview.schemabinding.version2.UserColourScheme=jalview.schemabinding.version2.descriptors.UserColourSchemeDescriptor
-jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor
-jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor
 jalview.schemabinding.version2.Pdbids=jalview.schemabinding.version2.descriptors.PdbidsDescriptor
-jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor
+jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor
+jalview.schemabinding.version2.Group=jalview.schemabinding.version2.descriptors.GroupDescriptor
 jalview.schemabinding.version2.Tree=jalview.schemabinding.version2.descriptors.TreeDescriptor
+jalview.schemabinding.version2.Setting=jalview.schemabinding.version2.descriptors.SettingDescriptor
 jalview.schemabinding.version2.UserColours=jalview.schemabinding.version2.descriptors.UserColoursDescriptor
 jalview.schemabinding.version2.JSeq=jalview.schemabinding.version2.descriptors.JSeqDescriptor
 jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
index 4474867..3d32ff6 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
@@ -45,11 +45,6 @@ public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLC
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -338,7 +333,7 @@ public class AnnotationColoursDescriptor extends org.exolab.castor.xml.util.XMLC
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
index e06c62c..44576ee 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
@@ -45,11 +45,6 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -617,7 +612,7 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
index 7441e9e..61221a1 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationElementDescriptor.java
@@ -45,11 +45,6 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -340,7 +335,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
index 8dee424..bdd9739 100644
--- a/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ColourDescriptor.java
@@ -45,11 +45,6 @@ public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -167,7 +162,7 @@ public class ColourDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
index 9a348b0..877f931 100644
--- a/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/DBRefDescriptor.java
@@ -45,11 +45,6 @@ public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -203,7 +198,7 @@ public class DBRefDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
index b5ac5f5..92c919e 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureDescriptor.java
@@ -45,11 +45,6 @@ public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -416,7 +411,7 @@ public class FeatureDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
index 6097bfa..930aac9 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeatureSettingsDescriptor.java
@@ -45,11 +45,6 @@ public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLCla
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -179,7 +174,7 @@ public class FeatureSettingsDescriptor extends org.exolab.castor.xml.util.XMLCla
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
index 6ebbb34..380d46e 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
@@ -45,11 +45,6 @@ public class FeaturesDescriptor extends jalview.schemabinding.version2.descripto
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -86,10 +81,7 @@ public class FeaturesDescriptor extends jalview.schemabinding.version2.descripto
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        if (_identity == null) {
-            return super.getIdentity();
-        }
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
index a0bacc0..417dbbb 100644
--- a/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/GroupDescriptor.java
@@ -45,11 +45,6 @@ public class GroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -172,7 +167,7 @@ public class GroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescript
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
index 90ef5ab..f307ee4 100644
--- a/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/HiddenColumnsDescriptor.java
@@ -45,11 +45,6 @@ public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClass
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -178,7 +173,7 @@ public class HiddenColumnsDescriptor extends org.exolab.castor.xml.util.XMLClass
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
index 1ab08a2..adde010 100644
--- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
@@ -45,11 +45,6 @@ public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -687,7 +682,7 @@ public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
index 3d3a4f5..738d4fc 100644
--- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
@@ -45,11 +45,6 @@ public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -442,7 +437,7 @@ public class JSeqDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
index eb5e0dd..9aad95c 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelDescriptor.java
@@ -45,11 +45,6 @@ public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassD
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -247,7 +242,7 @@ public class JalviewModelDescriptor extends org.exolab.castor.xml.util.XMLClassD
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
index 2bbb1ff..d6fd0ba 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewModelSequenceDescriptor.java
@@ -45,11 +45,6 @@ public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.X
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -339,7 +334,7 @@ public class JalviewModelSequenceDescriptor extends org.exolab.castor.xml.util.X
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
index 1b12b63..dd155dd 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
@@ -11,8 +11,9 @@ package jalview.schemabinding.version2.descriptors;
  //- Imported classes and packages -/
 //---------------------------------/
 
+import jalview.schemabinding.version2.Colour;
 import jalview.schemabinding.version2.JalviewUserColours;
-import jalview.schemabinding.version2.Colour; // Added Manually
+
 /**
  * Class JalviewUserColoursDescriptor.
  * 
@@ -45,11 +46,6 @@ public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XML
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -174,7 +170,7 @@ public class JalviewUserColoursDescriptor extends org.exolab.castor.xml.util.XML
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
index e5dc0b8..46f6682 100644
--- a/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/OtherDataDescriptor.java
@@ -45,11 +45,6 @@ public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -170,7 +165,7 @@ public class OtherDataDescriptor extends org.exolab.castor.xml.util.XMLClassDesc
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
index 97fedd9..dbf0c3a 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbentryDescriptor.java
@@ -45,11 +45,6 @@ public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -247,7 +242,7 @@ public class PdbentryDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
index ccd26c1..693ad61 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbentryItemDescriptor.java
@@ -45,11 +45,6 @@ public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassD
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -137,7 +132,7 @@ public class PdbentryItemDescriptor extends org.exolab.castor.xml.util.XMLClassD
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
index 265e907..2547f1d 100644
--- a/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PdbidsDescriptor.java
@@ -45,11 +45,6 @@ public class PdbidsDescriptor extends jalview.schemabinding.version2.descriptors
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -138,10 +133,7 @@ public class PdbidsDescriptor extends jalview.schemabinding.version2.descriptors
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        if (_identity == null) {
-            return super.getIdentity();
-        }
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
index 1bdcf5f..15f2e37 100644
--- a/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/PropertyDescriptor.java
@@ -45,11 +45,6 @@ public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -170,7 +165,7 @@ public class PropertyDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
index 9f2da96..15a81e2 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceDescriptor.java
@@ -45,11 +45,6 @@ public class SequenceDescriptor extends jalview.schemabinding.version2.descripto
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -138,10 +133,7 @@ public class SequenceDescriptor extends jalview.schemabinding.version2.descripto
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        if (_identity == null) {
-            return super.getIdentity();
-        }
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
index 2801940..ca59cf3 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetDescriptor.java
@@ -45,11 +45,6 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -260,7 +255,7 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
index af6975d..9c3c578 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceSetPropertiesDescriptor.java
@@ -45,11 +45,6 @@ public class SequenceSetPropertiesDescriptor extends org.exolab.castor.xml.util.
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -166,7 +161,7 @@ public class SequenceSetPropertiesDescriptor extends org.exolab.castor.xml.util.
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
index 9d7d579..fa73621 100644
--- a/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SequenceTypeDescriptor.java
@@ -45,11 +45,6 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -245,7 +240,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
index 8214765..23783bb 100644
--- a/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/SettingDescriptor.java
@@ -45,11 +45,6 @@ public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -258,7 +253,7 @@ public class SettingDescriptor extends org.exolab.castor.xml.util.XMLClassDescri
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
index 31f2389..8584429 100644
--- a/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/StructureStateDescriptor.java
@@ -45,11 +45,6 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -341,7 +336,7 @@ public class StructureStateDescriptor extends org.exolab.castor.xml.util.XMLClas
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
index e43b8cc..951e7ca 100644
--- a/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ThresholdLineDescriptor.java
@@ -45,11 +45,6 @@ public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClass
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -215,7 +210,7 @@ public class ThresholdLineDescriptor extends org.exolab.castor.xml.util.XMLClass
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
index 8ac65d0..9d508a4 100644
--- a/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/TreeDescriptor.java
@@ -45,11 +45,6 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -714,7 +709,7 @@ public class TreeDescriptor extends org.exolab.castor.xml.util.XMLClassDescripto
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
index 634239f..be7012a 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
@@ -45,11 +45,6 @@ public class UserColourSchemeDescriptor extends jalview.schemabinding.version2.d
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -86,10 +81,7 @@ public class UserColourSchemeDescriptor extends jalview.schemabinding.version2.d
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        if (_identity == null) {
-            return super.getIdentity();
-        }
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
index 32382a4..bda1c5e 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColoursDescriptor.java
@@ -45,11 +45,6 @@ public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDe
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -167,7 +162,7 @@ public class UserColoursDescriptor extends org.exolab.castor.xml.util.XMLClassDe
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
index f8d9ba8..375f435 100644
--- a/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VAMSASDescriptor.java
@@ -45,11 +45,6 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -184,7 +179,7 @@ public class VAMSASDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
index 5f46219..bc14cfd 100644
--- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
@@ -45,11 +45,6 @@ public class VamsasModelDescriptor extends jalview.schemabinding.version2.descri
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -86,10 +81,7 @@ public class VamsasModelDescriptor extends jalview.schemabinding.version2.descri
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        if (_identity == null) {
-            return super.getIdentity();
-        }
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
index f1fe49e..4faa6c1 100644
--- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
@@ -45,11 +45,6 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
      */
     private java.lang.String _xmlName;
 
-    /**
-     * Field _identity.
-     */
-    private org.exolab.castor.xml.XMLFieldDescriptor _identity;
-
 
       //----------------/
      //- Constructors -/
@@ -1406,7 +1401,7 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
      */
     public org.exolab.castor.mapping.FieldDescriptor getIdentity(
     ) {
-        return _identity;
+        return super.getIdentity();
     }
 
     /**
diff --git a/utils/castor-1.1-codegen.jar b/utils/castor-1.1-codegen.jar
deleted file mode 100644
index d8fbb88..0000000
Binary files a/utils/castor-1.1-codegen.jar and /dev/null differ
diff --git a/utils/castor-1.1-codegen-anttask.jar b/utils/castor-1.1-cycle-codegen-anttask.jar
similarity index 86%
rename from utils/castor-1.1-codegen-anttask.jar
rename to utils/castor-1.1-cycle-codegen-anttask.jar
index 16287b5..5c59416 100644
Binary files a/utils/castor-1.1-codegen-anttask.jar and b/utils/castor-1.1-cycle-codegen-anttask.jar differ
diff --git a/utils/castor-1.1-cycle-codegen.jar b/utils/castor-1.1-cycle-codegen.jar
new file mode 100644
index 0000000..74ad927
Binary files /dev/null and b/utils/castor-1.1-cycle-codegen.jar differ