showqual, showcons never used

diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java
index a38c530..056555a 100755 (executable)
--- a/src/jalview/gui/Jalview2XML.java
+++ b/src/jalview/gui/Jalview2XML.java
@@ -645,10 +645,7 @@ public class Jalview2XML
         view.setShowAnnotation(av.getShowAnnotation());
         view.setShowBoxes(av.getShowBoxes());
         view.setShowColourText(av.getColourText());
-        view.setShowConservation(av.showConservation);
         view.setShowFullId(av.getShowJVSuffix());
-        view.setShowIdentity(av.showIdentity);
-        view.setShowQuality(av.showQuality);
         view.setShowSequenceFeatures(av.showSequenceFeatures);
         view.setShowText(av.getShowText());
         view.setWrapAlignment(av.getWrapAlignment());
@@ -1341,9 +1338,10 @@ public class Jalview2XML
         af.viewport.setStartRes(view.getStartRes());
         af.viewport.setStartSeq(view.getStartSeq());
         af.viewport.setShowAnnotation(view.getShowAnnotation());
-        af.viewport.showConservation = view.getShowConservation();
-        af.viewport.showQuality = view.getShowQuality();
-        af.viewport.showIdentity = view.getShowIdentity();
+        af.viewport.showConservation = !hideConservation;
+        af.viewport.showQuality = !hideQuality;
+        af.viewport.showIdentity = !hideConsensus;
+
         af.viewport.setAbovePIDThreshold(view.getPidSelected());
         af.abovePIDThreshold.setSelected(view.getPidSelected());
         af.viewport.setColourText(view.getShowColourText());

diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index 428789f..1d52819 100755 (executable)
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -336,9 +336,6 @@ public class Jalview2XML_V1
         af.viewport.setStartRes(view.getStartRes());\r
         af.viewport.setStartSeq(view.getStartSeq());\r
         af.viewport.setShowAnnotation(view.getShowAnnotation());\r
-        af.viewport.showConservation = view.getShowConservation();\r
-        af.viewport.showQuality = view.getShowQuality();\r
-        af.viewport.showIdentity = view.getShowIdentity();\r
         af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
         af.abovePIDThreshold.setSelected(view.getPidSelected());\r
         af.viewport.setColourText(view.getShowColourText());\r

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 24adba5..7562424 100755 (executable)
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -166,36 +166,6 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showAnnotation;\r
 \r
     /**\r
-     * Field _showConservation\r
-     */\r
-    private boolean _showConservation;\r
-\r
-    /**\r
-     * keeps track of state for field: _showConservation\r
-     */\r
-    private boolean _has_showConservation;\r
-\r
-    /**\r
-     * Field _showQuality\r
-     */\r
-    private boolean _showQuality;\r
-\r
-    /**\r
-     * keeps track of state for field: _showQuality\r
-     */\r
-    private boolean _has_showQuality;\r
-\r
-    /**\r
-     * Field _showIdentity\r
-     */\r
-    private boolean _showIdentity;\r
-\r
-    /**\r
-     * keeps track of state for field: _showIdentity\r
-     */\r
-    private boolean _has_showIdentity;\r
-\r
-    /**\r
      * Field _xpos\r
      */\r
     private int _xpos;\r
@@ -461,15 +431,6 @@ public class Viewport implements java.io.Serializable {
     } //-- void deleteShowColourText() \r
 \r
     /**\r
-     * Method deleteShowConservation\r
-     * \r
-     */\r
-    public void deleteShowConservation()\r
-    {\r
-        this._has_showConservation= false;\r
-    } //-- void deleteShowConservation() \r
-\r
-    /**\r
      * Method deleteShowFullId\r
      * \r
      */\r
@@ -479,24 +440,6 @@ public class Viewport implements java.io.Serializable {
     } //-- void deleteShowFullId() \r
 \r
     /**\r
-     * Method deleteShowIdentity\r
-     * \r
-     */\r
-    public void deleteShowIdentity()\r
-    {\r
-        this._has_showIdentity= false;\r
-    } //-- void deleteShowIdentity() \r
-\r
-    /**\r
-     * Method deleteShowQuality\r
-     * \r
-     */\r
-    public void deleteShowQuality()\r
-    {\r
-        this._has_showQuality= false;\r
-    } //-- void deleteShowQuality() \r
-\r
-    /**\r
      * Method deleteShowSequenceFeatures\r
      * \r
      */\r
@@ -805,17 +748,6 @@ public class Viewport implements java.io.Serializable {
     } //-- boolean getShowColourText() \r
 \r
     /**\r
-     * Returns the value of field 'showConservation'.\r
-     * \r
-     * @return boolean\r
-     * @return the value of field 'showConservation'.\r
-     */\r
-    public boolean getShowConservation()\r
-    {\r
-        return this._showConservation;\r
-    } //-- boolean getShowConservation() \r
-\r
-    /**\r
      * Returns the value of field 'showFullId'.\r
      * \r
      * @return boolean\r
@@ -827,28 +759,6 @@ public class Viewport implements java.io.Serializable {
     } //-- boolean getShowFullId() \r
 \r
     /**\r
-     * Returns the value of field 'showIdentity'.\r
-     * \r
-     * @return boolean\r
-     * @return the value of field 'showIdentity'.\r
-     */\r
-    public boolean getShowIdentity()\r
-    {\r
-        return this._showIdentity;\r
-    } //-- boolean getShowIdentity() \r
-\r
-    /**\r
-     * Returns the value of field 'showQuality'.\r
-     * \r
-     * @return boolean\r
-     * @return the value of field 'showQuality'.\r
-     */\r
-    public boolean getShowQuality()\r
-    {\r
-        return this._showQuality;\r
-    } //-- boolean getShowQuality() \r
-\r
-    /**\r
      * Returns the value of field 'showSequenceFeatures'.\r
      * \r
      * @return boolean\r
@@ -1103,18 +1013,6 @@ public class Viewport implements java.io.Serializable {
     } //-- boolean hasShowColourText() \r
 \r
     /**\r
-     * Method hasShowConservation\r
-     * \r
-     * \r
-     * \r
-     * @return boolean\r
-     */\r
-    public boolean hasShowConservation()\r
-    {\r
-        return this._has_showConservation;\r
-    } //-- boolean hasShowConservation() \r
-\r
-    /**\r
      * Method hasShowFullId\r
      * \r
      * \r
@@ -1127,30 +1025,6 @@ public class Viewport implements java.io.Serializable {
     } //-- boolean hasShowFullId() \r
 \r
     /**\r
-     * Method hasShowIdentity\r
-     * \r
-     * \r
-     * \r
-     * @return boolean\r
-     */\r
-    public boolean hasShowIdentity()\r
-    {\r
-        return this._has_showIdentity;\r
-    } //-- boolean hasShowIdentity() \r
-\r
-    /**\r
-     * Method hasShowQuality\r
-     * \r
-     * \r
-     * \r
-     * @return boolean\r
-     */\r
-    public boolean hasShowQuality()\r
-    {\r
-        return this._has_showQuality;\r
-    } //-- boolean hasShowQuality() \r
-\r
-    /**\r
      * Method hasShowSequenceFeatures\r
      * \r
      * \r
@@ -1525,17 +1399,6 @@ public class Viewport implements java.io.Serializable {
     } //-- void setShowColourText(boolean) \r
 \r
     /**\r
-     * Sets the value of field 'showConservation'.\r
-     * \r
-     * @param showConservation the value of field 'showConservation'\r
-     */\r
-    public void setShowConservation(boolean showConservation)\r
-    {\r
-        this._showConservation = showConservation;\r
-        this._has_showConservation = true;\r
-    } //-- void setShowConservation(boolean) \r
-\r
-    /**\r
      * Sets the value of field 'showFullId'.\r
      * \r
      * @param showFullId the value of field 'showFullId'.\r
@@ -1547,28 +1410,6 @@ public class Viewport implements java.io.Serializable {
     } //-- void setShowFullId(boolean) \r
 \r
     /**\r
-     * Sets the value of field 'showIdentity'.\r
-     * \r
-     * @param showIdentity the value of field 'showIdentity'.\r
-     */\r
-    public void setShowIdentity(boolean showIdentity)\r
-    {\r
-        this._showIdentity = showIdentity;\r
-        this._has_showIdentity = true;\r
-    } //-- void setShowIdentity(boolean) \r
-\r
-    /**\r
-     * Sets the value of field 'showQuality'.\r
-     * \r
-     * @param showQuality the value of field 'showQuality'.\r
-     */\r
-    public void setShowQuality(boolean showQuality)\r
-    {\r
-        this._showQuality = showQuality;\r
-        this._has_showQuality = true;\r
-    } //-- void setShowQuality(boolean) \r
-\r
-    /**\r
      * Sets the value of field 'showSequenceFeatures'.\r
      * \r
      * @param showSequenceFeatures the value of field\r

diff --git a/src/jalview/schemabinding/version2/ViewportDescriptor.java b/src/jalview/schemabinding/version2/ViewportDescriptor.java
index 9f2ad90..00167ad 100755 (executable)
--- a/src/jalview/schemabinding/version2/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/ViewportDescriptor.java
@@ -629,129 +629,6 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
-        //-- _showConservation\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showConservation", "showConservation", 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.hasShowConservation())\r
-                    return null;\r
-                return (target.getShowConservation() ? 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.deleteShowConservation();\r
-                        return;\r
-                    }\r
-                    target.setShowConservation( ((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: _showConservation\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
-        //-- _showQuality\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showQuality", "showQuality", 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.hasShowQuality())\r
-                    return null;\r
-                return (target.getShowQuality() ? 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.deleteShowQuality();\r
-                        return;\r
-                    }\r
-                    target.setShowQuality( ((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: _showQuality\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
-        //-- _showIdentity\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showIdentity", "showIdentity", 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.hasShowIdentity())\r
-                    return null;\r
-                return (target.getShowIdentity() ? 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.deleteShowIdentity();\r
-                        return;\r
-                    }\r
-                    target.setShowIdentity( ((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: _showIdentity\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
         //-- _xpos\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_xpos", "xpos", org.exolab.castor.xml.NodeType.Attribute);\r
         handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r