Sequenceset may be empty, multiple views

diff --git a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
index 1e6c7b5..81946b5 100755 (executable)
--- a/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceSetDescriptor.java
@@ -172,13 +172,12 @@ public class SequenceSetDescriptor extends org.exolab.castor.xml.util.XMLClassDe
         } );\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
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-        fieldValidator.setMinOccurs(1);\r
+        fieldValidator.setMinOccurs(0);\r
         { //-- local scope\r
         }\r
         desc.setValidator(fieldValidator);\r

diff --git a/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java b/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
index 9977ea3..ef6c636 100755 (executable)
--- a/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
+++ b/src/jalview/schemabinding/version2/SequenceTypeDescriptor.java
@@ -166,13 +166,11 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
         } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-        desc.setRequired(true);\r
         desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _sequence\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-        fieldValidator.setMinOccurs(1);\r
         { //-- local scope\r
             StringValidator typeValidator = new StringValidator();\r
             typeValidator.setWhiteSpace("preserve");\r
@@ -206,13 +204,11 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
         } );\r
         desc.setHandler(handler);\r
         desc.setNameSpaceURI("www.vamsas.ac.uk/jalview/version2");\r
-        desc.setRequired(true);\r
         desc.setMultivalued(false);\r
         addFieldDescriptor(desc);\r
         \r
         //-- validation code for: _name\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-        fieldValidator.setMinOccurs(1);\r
         { //-- local scope\r
             StringValidator typeValidator = new StringValidator();\r
             typeValidator.setWhiteSpace("preserve");\r

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 557e454..24adba5 100755 (executable)
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -281,6 +281,26 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_fontStyle;\r
 \r
     /**\r
+     * Field _viewName\r
+     */\r
+    private java.lang.String _viewName;\r
+\r
+    /**\r
+     * Field _sequenceSetId\r
+     */\r
+    private java.lang.String _sequenceSetId;\r
+\r
+    /**\r
+     * Field _gatheredViews\r
+     */\r
+    private boolean _gatheredViews;\r
+\r
+    /**\r
+     * keeps track of state for field: _gatheredViews\r
+     */\r
+    private boolean _has_gatheredViews;\r
+\r
+    /**\r
      * Field _annotationColours\r
      */\r
     private jalview.schemabinding.version2.AnnotationColours _annotationColours;\r
@@ -369,6 +389,15 @@ public class Viewport implements java.io.Serializable {
     } //-- void deleteFontStyle() \r
 \r
     /**\r
+     * Method deleteGatheredViews\r
+     * \r
+     */\r
+    public void deleteGatheredViews()\r
+    {\r
+        this._has_gatheredViews= false;\r
+    } //-- void deleteGatheredViews() \r
+\r
+    /**\r
      * Method deleteHeight\r
      * \r
      */\r
@@ -629,6 +658,17 @@ public class Viewport implements java.io.Serializable {
     } //-- int getFontStyle() \r
 \r
     /**\r
+     * Returns the value of field 'gatheredViews'.\r
+     * \r
+     * @return boolean\r
+     * @return the value of field 'gatheredViews'.\r
+     */\r
+    public boolean getGatheredViews()\r
+    {\r
+        return this._gatheredViews;\r
+    } //-- boolean getGatheredViews() \r
+\r
+    /**\r
      * Returns the value of field 'height'.\r
      * \r
      * @return int\r
@@ -721,6 +761,17 @@ public class Viewport implements java.io.Serializable {
     } //-- boolean getRenderGaps() \r
 \r
     /**\r
+     * Returns the value of field 'sequenceSetId'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'sequenceSetId'.\r
+     */\r
+    public java.lang.String getSequenceSetId()\r
+    {\r
+        return this._sequenceSetId;\r
+    } //-- java.lang.String getSequenceSetId() \r
+\r
+    /**\r
      * Returns the value of field 'showAnnotation'.\r
      * \r
      * @return boolean\r
@@ -853,6 +904,17 @@ public class Viewport implements java.io.Serializable {
     } //-- java.lang.String getTitle() \r
 \r
     /**\r
+     * Returns the value of field 'viewName'.\r
+     * \r
+     * @return String\r
+     * @return the value of field 'viewName'.\r
+     */\r
+    public java.lang.String getViewName()\r
+    {\r
+        return this._viewName;\r
+    } //-- java.lang.String getViewName() \r
+\r
+    /**\r
      * Returns the value of field 'width'.\r
      * \r
      * @return int\r
@@ -945,6 +1007,18 @@ public class Viewport implements java.io.Serializable {
     } //-- boolean hasFontStyle() \r
 \r
     /**\r
+     * Method hasGatheredViews\r
+     * \r
+     * \r
+     * \r
+     * @return boolean\r
+     */\r
+    public boolean hasGatheredViews()\r
+    {\r
+        return this._has_gatheredViews;\r
+    } //-- boolean hasGatheredViews() \r
+\r
+    /**\r
      * Method hasHeight\r
      * \r
      * \r
@@ -1319,6 +1393,17 @@ public class Viewport implements java.io.Serializable {
     } //-- void setFontStyle(int) \r
 \r
     /**\r
+     * Sets the value of field 'gatheredViews'.\r
+     * \r
+     * @param gatheredViews the value of field 'gatheredViews'.\r
+     */\r
+    public void setGatheredViews(boolean gatheredViews)\r
+    {\r
+        this._gatheredViews = gatheredViews;\r
+        this._has_gatheredViews = true;\r
+    } //-- void setGatheredViews(boolean) \r
+\r
+    /**\r
      * Sets the value of field 'height'.\r
      * \r
      * @param height the value of field 'height'.\r
@@ -1397,6 +1482,16 @@ public class Viewport implements java.io.Serializable {
     } //-- void setRenderGaps(boolean) \r
 \r
     /**\r
+     * Sets the value of field 'sequenceSetId'.\r
+     * \r
+     * @param sequenceSetId the value of field 'sequenceSetId'.\r
+     */\r
+    public void setSequenceSetId(java.lang.String sequenceSetId)\r
+    {\r
+        this._sequenceSetId = sequenceSetId;\r
+    } //-- void setSequenceSetId(java.lang.String) \r
+\r
+    /**\r
      * Sets the value of field 'showAnnotation'.\r
      * \r
      * @param showAnnotation the value of field 'showAnnotation'.\r
@@ -1529,6 +1624,16 @@ public class Viewport implements java.io.Serializable {
     } //-- void setTitle(java.lang.String) \r
 \r
     /**\r
+     * Sets the value of field 'viewName'.\r
+     * \r
+     * @param viewName the value of field 'viewName'.\r
+     */\r
+    public void setViewName(java.lang.String viewName)\r
+    {\r
+        this._viewName = viewName;\r
+    } //-- void setViewName(java.lang.String) \r
+\r
+    /**\r
      * Sets the value of field 'width'.\r
      * \r
      * @param width the value of field 'width'.\r

diff --git a/src/jalview/schemabinding/version2/ViewportDescriptor.java b/src/jalview/schemabinding/version2/ViewportDescriptor.java
index b98f97b..9f2ad90 100755 (executable)
--- a/src/jalview/schemabinding/version2/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/ViewportDescriptor.java
@@ -1116,6 +1116,119 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
+        //-- _viewName\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", 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
+                Viewport target = (Viewport) object;\r
+                return target.getViewName();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    target.setViewName( (java.lang.String) 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
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _viewName\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _sequenceSetId\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", 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
+                Viewport target = (Viewport) object;\r
+                return target.getSequenceSetId();\r
+            }\r
+            public void setValue( java.lang.Object object, java.lang.Object value) \r
+                throws IllegalStateException, IllegalArgumentException\r
+            {\r
+                try {\r
+                    Viewport target = (Viewport) object;\r
+                    target.setSequenceSetId( (java.lang.String) 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
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _sequenceSetId\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            StringValidator typeValidator = new StringValidator();\r
+            typeValidator.setWhiteSpace("preserve");\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
+        //-- _gatheredViews\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", 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
+                Viewport target = (Viewport) object;\r
+                if(!target.hasGatheredViews())\r
+                    return null;\r
+                return (target.getGatheredViews() ? 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
+                    Viewport target = (Viewport) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteGatheredViews();\r
+                        return;\r
+                    }\r
+                    target.setGatheredViews( ((java.lang.Boolean)value).booleanValue());\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
+            }\r
+        } );\r
+        desc.setHandler(handler);\r
+        addFieldDescriptor(desc);\r
+        \r
+        //-- validation code for: _gatheredViews\r
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
+        { //-- local scope\r
+            BooleanValidator typeValidator = new BooleanValidator();\r
+            fieldValidator.setValidator(typeValidator);\r
+        }\r
+        desc.setValidator(fieldValidator);\r
         //-- initialize element descriptors\r
         \r
         //-- _annotationColours\r