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extend XML model for graduated feature colours, group associated manual/auto annotati...
[jalview.git] / src / jalview / schemabinding / version2 / descriptors / AnnotationDescriptor.java
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
index cdbfceb..f2c6fcf 100644 (file)
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationDescriptor.java
@@ -195,6 +195,43 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes
             typeValidator.setWhiteSpace("preserve");\r
         }\r
         desc.setValidator(fieldValidator);\r
+        //-- _groupRef\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_groupRef", "groupRef", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc.setImmutable(true);\r
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                return target.getGroupRef();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    target.setGroupRef( (java.lang.String) value);\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
+            }\r
+        };\r
+        desc.setHandler(handler);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _groupRef\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            org.exolab.castor.xml.validators.StringValidator typeValidator;\r
+            typeValidator = new org.exolab.castor.xml.validators.StringValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+            typeValidator.setWhiteSpace("preserve");\r
+        }\r
+        desc.setValidator(fieldValidator);\r
         //-- _graphColour\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_graphColour", "graphColour", org.exolab.castor.xml.NodeType.Attribute);\r
         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
@@ -443,6 +480,170 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
+        //-- _centreColLabels\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_centreColLabels", "centreColLabels", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                if (!target.hasCentreColLabels()) { return null; }\r
+                return (target.getCentreColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteCentreColLabels();\r
+                        return;\r
+                    }\r
+                    target.setCentreColLabels( ((java.lang.Boolean) value).booleanValue());\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
+            }\r
+        };\r
+        desc.setHandler(handler);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _centreColLabels\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _scaleColLabels\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_scaleColLabels", "scaleColLabels", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                if (!target.hasScaleColLabels()) { return null; }\r
+                return (target.getScaleColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteScaleColLabels();\r
+                        return;\r
+                    }\r
+                    target.setScaleColLabels( ((java.lang.Boolean) value).booleanValue());\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
+            }\r
+        };\r
+        desc.setHandler(handler);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _scaleColLabels\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _showAllColLabels\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showAllColLabels", "showAllColLabels", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                if (!target.hasShowAllColLabels()) { return null; }\r
+                return (target.getShowAllColLabels() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteShowAllColLabels();\r
+                        return;\r
+                    }\r
+                    target.setShowAllColLabels( ((java.lang.Boolean) value).booleanValue());\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
+            }\r
+        };\r
+        desc.setHandler(handler);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _showAllColLabels\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _autoCalculated\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_autoCalculated", "autoCalculated", org.exolab.castor.xml.NodeType.Attribute);\r
+        handler = new org.exolab.castor.xml.XMLFieldHandler() {\r
+            public java.lang.Object getValue( java.lang.Object object ) \r
+                throws IllegalStateException\r
+            {\r
+                Annotation target = (Annotation) object;\r
+                if (!target.hasAutoCalculated()) { return null; }\r
+                return (target.getAutoCalculated() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Annotation target = (Annotation) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteAutoCalculated();\r
+                        return;\r
+                    }\r
+                    target.setAutoCalculated( ((java.lang.Boolean) value).booleanValue());\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
+            }\r
+        };\r
+        desc.setHandler(handler);\r
+        desc.setMultivalued(false);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _autoCalculated\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            org.exolab.castor.xml.validators.BooleanValidator typeValidator;\r
+            typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
         //-- initialize element descriptors\r
         \r
         //-- _annotationElementList\r