added showUnconserved property to group and view attributes

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 06473bc..72c1270 100755 (executable)
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -73,6 +73,8 @@
                                                <xs:attribute name="textCol1" type="xs:int"/>
                                                <xs:attribute name="textCol2" type="xs:int"/>
                                                <xs:attribute name="textColThreshold" type="xs:int"/>
+                                               <xs:attribute name="showUnconserved" type="xs:boolean" use="optional"/>
+                                               
                                        </xs:complexType>
                                </xs:element>
                                <xs:element name="Viewport" maxOccurs="unbounded">
@@ -105,6 +107,7 @@
                                                <xs:attribute name="rightAlignIds" type="xs:boolean"/>
                                                <xs:attribute name="showText" type="xs:boolean"/>
                                                <xs:attribute name="showColourText" type="xs:boolean"/>
+                                               <xs:attribute name="showUnconserved" type="xs:boolean" use="optional"/>
                                                <xs:attribute name="showBoxes" type="xs:boolean"/>
                                                <xs:attribute name="wrapAlignment" type="xs:boolean"/>
                                                <xs:attribute name="renderGaps" type="xs:boolean"/>

diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr
index 7e3a754..92a62c4 100644 (file)
--- a/src/jalview/schemabinding/version2/.castor.cdr
+++ b/src/jalview/schemabinding/version2/.castor.cdr
@@ -1,4 +1,4 @@
-#Sun Dec 14 18:51:51 GMT 2008\r
+#Fri Feb 06 14:21:53 GMT 2009\r
 jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor\r
 jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor\r
 jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor\r
@@ -33,12 +33,12 @@ jalview.schemabinding.version2.MapListFrom=jalview.schemabinding.version2.descri
 jalview.schemabinding.version2.PdbentryItem=jalview.schemabinding.version2.descriptors.PdbentryItemDescriptor\r
 jalview.schemabinding.version2.FeatureSettings=jalview.schemabinding.version2.descriptors.FeatureSettingsDescriptor\r
 jalview.schemabinding.version2.JGroup=jalview.schemabinding.version2.descriptors.JGroupDescriptor\r
-jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor\r
-jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor\r
 jalview.schemabinding.version2.VamsasModel=jalview.schemabinding.version2.descriptors.VamsasModelDescriptor\r
+jalview.schemabinding.version2.JalviewUserColours=jalview.schemabinding.version2.descriptors.JalviewUserColoursDescriptor\r
+jalview.schemabinding.version2.MapListTo=jalview.schemabinding.version2.descriptors.MapListToDescriptor\r
 jalview.schemabinding.version2.Pdbentry=jalview.schemabinding.version2.descriptors.PdbentryDescriptor\r
 jalview.schemabinding.version2.HiddenColumns=jalview.schemabinding.version2.descriptors.HiddenColumnsDescriptor\r
-jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor\r
 jalview.schemabinding.version2.Features=jalview.schemabinding.version2.descriptors.FeaturesDescriptor\r
+jalview.schemabinding.version2.DseqFor=jalview.schemabinding.version2.descriptors.DseqForDescriptor\r
 jalview.schemabinding.version2.VAMSAS=jalview.schemabinding.version2.descriptors.VAMSASDescriptor\r
 jalview.schemabinding.version2.MappingChoiceItem=jalview.schemabinding.version2.descriptors.MappingChoiceItemDescriptor\r

diff --git a/src/jalview/schemabinding/version2/JGroup.java b/src/jalview/schemabinding/version2/JGroup.java
index ca77ed2..3563186 100755 (executable)
--- a/src/jalview/schemabinding/version2/JGroup.java
+++ b/src/jalview/schemabinding/version2/JGroup.java
@@ -147,6 +147,16 @@ public class JGroup implements java.io.Serializable {
     private boolean _has_textColThreshold;\r
 \r
     /**\r
+     * Field _showUnconserved.\r
+     */\r
+    private boolean _showUnconserved;\r
+\r
+    /**\r
+     * keeps track of state for field: _showUnconserved\r
+     */\r
+    private boolean _has_showUnconserved;\r
+\r
+    /**\r
      * Field _seqList.\r
      */\r
     private java.util.Vector _seqList;\r
@@ -245,6 +255,13 @@ public class JGroup implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteShowUnconserved(\r
+    ) {\r
+        this._has_showUnconserved= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteStart(\r
     ) {\r
         this._has_start= false;\r
@@ -416,6 +433,16 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showUnconserved'.\r
+     * \r
+     * @return the value of field 'ShowUnconserved'.\r
+     */\r
+    public boolean getShowUnconserved(\r
+    ) {\r
+        return this._showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'start'.\r
      * \r
      * @return the value of field 'Start'.\r
@@ -526,6 +553,16 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasShowUnconserved.\r
+     * \r
+     * @return true if at least one ShowUnconserved has been added\r
+     */\r
+    public boolean hasShowUnconserved(\r
+    ) {\r
+        return this._has_showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Method hasStart.\r
      * \r
      * @return true if at least one Start has been added\r
@@ -596,6 +633,16 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showUnconserved'.\r
+     * \r
+     * @return the value of field 'ShowUnconserved'.\r
+     */\r
+    public boolean isShowUnconserved(\r
+    ) {\r
+        return this._showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Method isValid.\r
      * \r
      * @return true if this object is valid according to the schema\r
@@ -806,6 +853,17 @@ public class JGroup implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'showUnconserved'.\r
+     * \r
+     * @param showUnconserved the value of field 'showUnconserved'.\r
+     */\r
+    public void setShowUnconserved(\r
+            final boolean showUnconserved) {\r
+        this._showUnconserved = showUnconserved;\r
+        this._has_showUnconserved = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'start'.\r
      * \r
      * @param start the value of field 'start'.\r

diff --git a/src/jalview/schemabinding/version2/Viewport.java b/src/jalview/schemabinding/version2/Viewport.java
index 07ddd65..d212e84 100755 (executable)
--- a/src/jalview/schemabinding/version2/Viewport.java
+++ b/src/jalview/schemabinding/version2/Viewport.java
@@ -117,6 +117,16 @@ public class Viewport implements java.io.Serializable {
     private boolean _has_showColourText;\r
 \r
     /**\r
+     * Field _showUnconserved.\r
+     */\r
+    private boolean _showUnconserved;\r
+\r
+    /**\r
+     * keeps track of state for field: _showUnconserved\r
+     */\r
+    private boolean _has_showUnconserved;\r
+\r
+    /**\r
      * Field _showBoxes.\r
      */\r
     private boolean _showBoxes;\r
@@ -475,6 +485,13 @@ public class Viewport implements java.io.Serializable {
 \r
     /**\r
      */\r
+    public void deleteShowUnconserved(\r
+    ) {\r
+        this._has_showUnconserved= false;\r
+    }\r
+\r
+    /**\r
+     */\r
     public void deleteStartRes(\r
     ) {\r
         this._has_startRes= false;\r
@@ -808,6 +825,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showUnconserved'.\r
+     * \r
+     * @return the value of field 'ShowUnconserved'.\r
+     */\r
+    public boolean getShowUnconserved(\r
+    ) {\r
+        return this._showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Returns the value of field 'startRes'.\r
      * \r
      * @return the value of field 'StartRes'.\r
@@ -1080,6 +1107,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Method hasShowUnconserved.\r
+     * \r
+     * @return true if at least one ShowUnconserved has been added\r
+     */\r
+    public boolean hasShowUnconserved(\r
+    ) {\r
+        return this._has_showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Method hasStartRes.\r
      * \r
      * @return true if at least one StartRes has been added\r
@@ -1280,6 +1317,16 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Returns the value of field 'showUnconserved'.\r
+     * \r
+     * @return the value of field 'ShowUnconserved'.\r
+     */\r
+    public boolean isShowUnconserved(\r
+    ) {\r
+        return this._showUnconserved;\r
+    }\r
+\r
+    /**\r
      * Method isValid.\r
      * \r
      * @return true if this object is valid according to the schema\r
@@ -1635,6 +1682,17 @@ public class Viewport implements java.io.Serializable {
     }\r
 \r
     /**\r
+     * Sets the value of field 'showUnconserved'.\r
+     * \r
+     * @param showUnconserved the value of field 'showUnconserved'.\r
+     */\r
+    public void setShowUnconserved(\r
+            final boolean showUnconserved) {\r
+        this._showUnconserved = showUnconserved;\r
+        this._has_showUnconserved = true;\r
+    }\r
+\r
+    /**\r
      * Sets the value of field 'startRes'.\r
      * \r
      * @param startRes the value of field 'startRes'.\r

diff --git a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
index 21b3b67..e6ebec7 100644 (file)
--- a/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JGroupDescriptor.java
@@ -604,6 +604,47 @@ public class JGroupDescriptor extends org.exolab.castor.xml.util.XMLClassDescrip
             typeValidator.setMaxInclusive(2147483647);\r
         }\r
         desc.setValidator(fieldValidator);\r
+        //-- _showUnconserved\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", 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
+                JGroup target = (JGroup) object;\r
+                if (!target.hasShowUnconserved()) { return null; }\r
+                return (target.getShowUnconserved() ? 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
+                    JGroup target = (JGroup) object;\r
+                    // if null, use delete method for optional primitives \r
+                    if (value == null) {\r
+                        target.deleteShowUnconserved();\r
+                        return;\r
+                    }\r
+                    target.setShowUnconserved( ((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: _showUnconserved\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
         //-- _seqList\r

diff --git a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
index f00cb21..e9b93d4 100644 (file)
--- a/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/ViewportDescriptor.java
@@ -469,6 +469,47 @@ public class ViewportDescriptor extends org.exolab.castor.xml.util.XMLClassDescr
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r
+        //-- _showUnconserved\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showUnconserved", "showUnconserved", 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.hasShowUnconserved()) { return null; }\r
+                return (target.getShowUnconserved() ? 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.deleteShowUnconserved();\r
+                        return;\r
+                    }\r
+                    target.setShowUnconserved( ((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: _showUnconserved\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
         //-- _showBoxes\r
         desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Boolean.TYPE, "_showBoxes", "showBoxes", org.exolab.castor.xml.NodeType.Attribute);\r
         handler = new org.exolab.castor.xml.XMLFieldHandler() {\r