X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemabinding%2Fversion2%2FViewportDescriptor.java;h=09544efabf88298d48b56e89608a55324f7ed973;hb=1c6e3aa5ffd0d3fbbfe5bffbdeaa9c4f54a61cd3;hp=66a3d7744cde674d5d5552a3cca9b3b4fbaf9e66;hpb=65df62f4b048a1615d32ea2c3576082ad2b63af8;p=jalview.git

diff --git a/src/jalview/schemabinding/version2/ViewportDescriptor.java b/src/jalview/schemabinding/version2/ViewportDescriptor.java
index 66a3d77..09544ef 100755
--- a/src/jalview/schemabinding/version2/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/ViewportDescriptor.java
@@ -57,6 +57,9 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         super();
         nsURI = "www.jalview.org";
         xmlName = "Viewport";
+        
+        //-- set grouping compositor
+        setCompositorAsSequence();
         org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;
         org.exolab.castor.xml.XMLFieldHandler              handler        = null;
         org.exolab.castor.xml.FieldValidator               fieldValidator = null;
@@ -339,6 +342,47 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
+        //-- _rightAlignIds
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_rightAlignIds", "rightAlignIds", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasRightAlignIds())
+                    return null;
+                return (target.getRightAlignIds() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteRightAlignIds();
+                        return;
+                    }
+                    target.setRightAlignIds( ((java.lang.Boolean)value).booleanValue());
+                }
+                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: _rightAlignIds
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            BooleanValidator typeValidator = new BooleanValidator();
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
         //-- _showText
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showText", "showText", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
@@ -626,16 +670,16 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _showConservation
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConservation", "showConservation", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _xpos
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasShowConservation())
+                if(!target.hasXpos())
                     return null;
-                return (target.getShowConservation() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+                return new java.lang.Integer(target.getXpos());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -644,10 +688,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteShowConservation();
+                        target.deleteXpos();
                         return;
                     }
-                    target.setShowConservation( ((java.lang.Boolean)value).booleanValue());
+                    target.setXpos( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -660,23 +704,23 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _showConservation
+        //-- validation code for: _xpos
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
-            BooleanValidator typeValidator = new BooleanValidator();
+            IntegerValidator typeValidator= new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _showQuality
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showQuality", "showQuality", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _ypos
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasShowQuality())
+                if(!target.hasYpos())
                     return null;
-                return (target.getShowQuality() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+                return new java.lang.Integer(target.getYpos());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -685,10 +729,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteShowQuality();
+                        target.deleteYpos();
                         return;
                     }
-                    target.setShowQuality( ((java.lang.Boolean)value).booleanValue());
+                    target.setYpos( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -701,23 +745,23 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _showQuality
+        //-- validation code for: _ypos
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
-            BooleanValidator typeValidator = new BooleanValidator();
+            IntegerValidator typeValidator= new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _showIdentity
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showIdentity", "showIdentity", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _width
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasShowIdentity())
+                if(!target.hasWidth())
                     return null;
-                return (target.getShowIdentity() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
+                return new java.lang.Integer(target.getWidth());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -726,10 +770,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteShowIdentity();
+                        target.deleteWidth();
                         return;
                     }
-                    target.setShowIdentity( ((java.lang.Boolean)value).booleanValue());
+                    target.setWidth( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -742,23 +786,23 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _showIdentity
+        //-- validation code for: _width
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
-            BooleanValidator typeValidator = new BooleanValidator();
+            IntegerValidator typeValidator= new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _xpos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _height
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasXpos())
+                if(!target.hasHeight())
                     return null;
-                return new java.lang.Integer(target.getXpos());
+                return new java.lang.Integer(target.getHeight());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -767,10 +811,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteXpos();
+                        target.deleteHeight();
                         return;
                     }
-                    target.setXpos( ((java.lang.Integer)value).intValue());
+                    target.setHeight( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -783,23 +827,23 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _xpos
+        //-- validation code for: _height
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
             IntegerValidator typeValidator= new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _ypos
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_ypos", "ypos", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _startRes
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasYpos())
+                if(!target.hasStartRes())
                     return null;
-                return new java.lang.Integer(target.getYpos());
+                return new java.lang.Integer(target.getStartRes());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -808,10 +852,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteYpos();
+                        target.deleteStartRes();
                         return;
                     }
-                    target.setYpos( ((java.lang.Integer)value).intValue());
+                    target.setStartRes( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -824,23 +868,23 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _ypos
+        //-- validation code for: _startRes
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
             IntegerValidator typeValidator= new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _width
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_width", "width", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _startSeq
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasWidth())
+                if(!target.hasStartSeq())
                     return null;
-                return new java.lang.Integer(target.getWidth());
+                return new java.lang.Integer(target.getStartSeq());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -849,10 +893,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteWidth();
+                        target.deleteStartSeq();
                         return;
                     }
-                    target.setWidth( ((java.lang.Integer)value).intValue());
+                    target.setStartSeq( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -865,23 +909,59 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _width
+        //-- validation code for: _startSeq
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
             IntegerValidator typeValidator= new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _height
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_height", "height", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _fontName
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", 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
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasHeight())
+                return target.getFontName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    target.setFontName( (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: _fontName
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _fontSize
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasFontSize())
                     return null;
-                return new java.lang.Integer(target.getHeight());
+                return new java.lang.Integer(target.getFontSize());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -890,10 +970,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteHeight();
+                        target.deleteFontSize();
                         return;
                     }
-                    target.setHeight( ((java.lang.Integer)value).intValue());
+                    target.setFontSize( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -906,23 +986,23 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _height
+        //-- validation code for: _fontSize
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
             IntegerValidator typeValidator= new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _startRes
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startRes", "startRes", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _fontStyle
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasStartRes())
+                if(!target.hasFontStyle())
                     return null;
-                return new java.lang.Integer(target.getStartRes());
+                return new java.lang.Integer(target.getFontStyle());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -931,10 +1011,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteStartRes();
+                        target.deleteFontStyle();
                         return;
                     }
-                    target.setStartRes( ((java.lang.Integer)value).intValue());
+                    target.setFontStyle( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -947,23 +1027,95 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _startRes
+        //-- validation code for: _fontStyle
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
             IntegerValidator typeValidator= new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _startSeq
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_startSeq", "startSeq", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _viewName
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_viewName", "viewName", 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
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasStartSeq())
+                return target.getViewName();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    target.setViewName( (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: _viewName
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _sequenceSetId
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_sequenceSetId", "sequenceSetId", 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
+            {
+                Viewport target = (Viewport) object;
+                return target.getSequenceSetId();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    target.setSequenceSetId( (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: _sequenceSetId
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+            StringValidator typeValidator = new StringValidator();
+            typeValidator.setWhiteSpace("preserve");
+            fieldValidator.setValidator(typeValidator);
+        }
+        desc.setValidator(fieldValidator);
+        //-- _gatheredViews
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_gatheredViews", "gatheredViews", org.exolab.castor.xml.NodeType.Attribute);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                if(!target.hasGatheredViews())
                     return null;
-                return new java.lang.Integer(target.getStartSeq());
+                return (target.getGatheredViews() ? java.lang.Boolean.TRUE : java.lang.Boolean.FALSE);
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -972,10 +1124,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteStartSeq();
+                        target.deleteGatheredViews();
                         return;
                     }
-                    target.setStartSeq( ((java.lang.Integer)value).intValue());
+                    target.setGatheredViews( ((java.lang.Boolean)value).booleanValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -988,29 +1140,35 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _startSeq
+        //-- validation code for: _gatheredViews
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
+            BooleanValidator typeValidator = new BooleanValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _fontName
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_fontName", "fontName", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
+        //-- _textCol1
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol1", "textCol1", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 Viewport target = (Viewport) object;
-                return target.getFontName();
+                if(!target.hasTextCol1())
+                    return null;
+                return new java.lang.Integer(target.getTextCol1());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
                     Viewport target = (Viewport) object;
-                    target.setFontName( (java.lang.String) value);
+                    // if null, use delete method for optional primitives 
+                    if (value == null) {
+                        target.deleteTextCol1();
+                        return;
+                    }
+                    target.setTextCol1( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -1023,24 +1181,23 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _fontName
+        //-- validation code for: _textCol1
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
+            IntegerValidator typeValidator= new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _fontSize
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontSize", "fontSize", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _textCol2
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textCol2", "textCol2", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasFontSize())
+                if(!target.hasTextCol2())
                     return null;
-                return new java.lang.Integer(target.getFontSize());
+                return new java.lang.Integer(target.getTextCol2());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -1049,10 +1206,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteFontSize();
+                        target.deleteTextCol2();
                         return;
                     }
-                    target.setFontSize( ((java.lang.Integer)value).intValue());
+                    target.setTextCol2( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -1065,23 +1222,23 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _fontSize
+        //-- validation code for: _textCol2
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
             IntegerValidator typeValidator= new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
-        //-- _fontStyle
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_fontStyle", "fontStyle", org.exolab.castor.xml.NodeType.Attribute);
+        //-- _textColThreshold
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_textColThreshold", "textColThreshold", org.exolab.castor.xml.NodeType.Attribute);
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 Viewport target = (Viewport) object;
-                if(!target.hasFontStyle())
+                if(!target.hasTextColThreshold())
                     return null;
-                return new java.lang.Integer(target.getFontStyle());
+                return new java.lang.Integer(target.getTextColThreshold());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
@@ -1090,10 +1247,10 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
                     Viewport target = (Viewport) object;
                     // if null, use delete method for optional primitives 
                     if (value == null) {
-                        target.deleteFontStyle();
+                        target.deleteTextColThreshold();
                         return;
                     }
-                    target.setFontStyle( ((java.lang.Integer)value).intValue());
+                    target.setTextColThreshold( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -1106,7 +1263,7 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setHandler(handler);
         addFieldDescriptor(desc);
         
-        //-- validation code for: _fontStyle
+        //-- validation code for: _textColThreshold
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         { //-- local scope
             IntegerValidator typeValidator= new IntegerValidator();
@@ -1115,6 +1272,75 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
         desc.setValidator(fieldValidator);
         //-- initialize element descriptors
         
+        //-- _annotationColours
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.AnnotationColours.class, "_annotationColours", "AnnotationColours", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                return target.getAnnotationColours();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    target.setAnnotationColours( (jalview.schemabinding.version2.AnnotationColours) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.AnnotationColours();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(false);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _annotationColours
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
+        //-- _hiddenColumnsList
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.HiddenColumns.class, "_hiddenColumnsList", "hiddenColumns", org.exolab.castor.xml.NodeType.Element);
+        handler = (new org.exolab.castor.xml.XMLFieldHandler() {
+            public java.lang.Object getValue( java.lang.Object object ) 
+                throws IllegalStateException
+            {
+                Viewport target = (Viewport) object;
+                return target.getHiddenColumns();
+            }
+            public void setValue( java.lang.Object object, java.lang.Object value) 
+                throws IllegalStateException, IllegalArgumentException
+            {
+                try {
+                    Viewport target = (Viewport) object;
+                    target.addHiddenColumns( (jalview.schemabinding.version2.HiddenColumns) value);
+                }
+                catch (java.lang.Exception ex) {
+                    throw new IllegalStateException(ex.toString());
+                }
+            }
+            public java.lang.Object newInstance( java.lang.Object parent ) {
+                return new jalview.schemabinding.version2.HiddenColumns();
+            }
+        } );
+        desc.setHandler(handler);
+        desc.setNameSpaceURI("www.jalview.org");
+        desc.setMultivalued(true);
+        addFieldDescriptor(desc);
+        
+        //-- validation code for: _hiddenColumnsList
+        fieldValidator = new org.exolab.castor.xml.FieldValidator();
+        fieldValidator.setMinOccurs(0);
+        { //-- local scope
+        }
+        desc.setValidator(fieldValidator);
     } //-- jalview.schemabinding.version2.ViewportDescriptor()