total annotation score is a double for maximum precision.

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index 1a24509..9ba7919 100755 (executable)
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -48,7 +48,7 @@
                                                <xs:attribute name="graphGroup" type="xs:int" use="optional"/>
                                                <xs:attribute name="id" type="xs:string" use="optional"/>
                                                <xs:attribute name="scoreOnly" type="xs:boolean" use="optional" default="false"/>
-                                               <xs:attribute name="score" type="xs:float" use="optional"/>
+                                               <xs:attribute name="score" type="xs:double" use="optional"/>
                                        </xs:complexType>
                                </xs:element>
                        </xs:sequence>

diff --git a/src/jalview/schemabinding/version2/Annotation.java b/src/jalview/schemabinding/version2/Annotation.java
index 9eb6907..021fa8b 100755 (executable)
--- a/src/jalview/schemabinding/version2/Annotation.java
+++ b/src/jalview/schemabinding/version2/Annotation.java
@@ -98,7 +98,7 @@ public class Annotation implements java.io.Serializable {
     /**\r
      * Field _score\r
      */\r
-    private float _score;\r
+    private double _score;\r
 \r
     /**\r
      * keeps track of state for field: _score\r
@@ -361,13 +361,13 @@ public class Annotation implements java.io.Serializable {
     /**\r
      * Returns the value of field 'score'.\r
      * \r
-     * @return float\r
+     * @return double\r
      * @return the value of field 'score'.\r
      */\r
-    public float getScore()\r
+    public double getScore()\r
     {\r
         return this._score;\r
-    } //-- float getScore() \r
+    } //-- double getScore() \r
 \r
     /**\r
      * Returns the value of field 'scoreOnly'.\r
@@ -657,11 +657,11 @@ public class Annotation implements java.io.Serializable {
      * \r
      * @param score the value of field 'score'.\r
      */\r
-    public void setScore(float score)\r
+    public void setScore(double score)\r
     {\r
         this._score = score;\r
         this._has_score = true;\r
-    } //-- void setScore(float) \r
+    } //-- void setScore(double) \r
 \r
     /**\r
      * Sets the value of field 'scoreOnly'.\r

diff --git a/src/jalview/schemabinding/version2/AnnotationDescriptor.java b/src/jalview/schemabinding/version2/AnnotationDescriptor.java
index e0061ae..28ceec1 100755 (executable)
--- a/src/jalview/schemabinding/version2/AnnotationDescriptor.java
+++ b/src/jalview/schemabinding/version2/AnnotationDescriptor.java
@@ -343,7 +343,7 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes
         }\r
         desc.setValidator(fieldValidator);\r
         //-- _score\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(float.class, "_score", "score", org.exolab.castor.xml.NodeType.Attribute);\r
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Double.TYPE, "_score", "score", 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
@@ -351,7 +351,7 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes
                 Annotation target = (Annotation) object;\r
                 if(!target.hasScore())\r
                     return null;\r
-                return new java.lang.Float(target.getScore());\r
+                return new java.lang.Double(target.getScore());\r
             }\r
             public void setValue( java.lang.Object object, java.lang.Object value) \r
                 throws IllegalStateException, IllegalArgumentException\r
@@ -363,7 +363,7 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes
                         target.deleteScore();\r
                         return;\r
                     }\r
-                    target.setScore( ((java.lang.Float)value).floatValue());\r
+                    target.setScore( ((java.lang.Double)value).doubleValue());\r
                 }\r
                 catch (java.lang.Exception ex) {\r
                     throw new IllegalStateException(ex.toString());\r
@@ -379,7 +379,7 @@ public class AnnotationDescriptor extends org.exolab.castor.xml.util.XMLClassDes
         //-- validation code for: _score\r
         fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
         { //-- local scope\r
-            FloatValidator typeValidator = new FloatValidator();\r
+            DoubleValidator typeValidator = new DoubleValidator();\r
             fieldValidator.setValidator(typeValidator);\r
         }\r
         desc.setValidator(fieldValidator);\r

diff --git a/src/jalview/schemabinding/version2/PdbidsItem.java b/src/jalview/schemabinding/version2/PdbidsItem.java
deleted file mode 100644 (file)
index 0c5c10f..0000000
--- a/src/jalview/schemabinding/version2/PdbidsItem.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
-  //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import java.io.Serializable;\r
-import org.exolab.castor.xml.Marshaller;\r
-import org.exolab.castor.xml.Unmarshaller;\r
-\r
-/**\r
- * Class PdbidsItem.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class PdbidsItem implements java.io.Serializable {\r
-\r
-\r
-      //--------------------------/\r
-     //- Class/Member Variables -/\r
-    //--------------------------/\r
-\r
-    /**\r
-     * Field _structureState\r
-     */\r
-    private jalview.schemabinding.version2.StructureState _structureState;\r
-\r
-\r
-      //----------------/\r
-     //- Constructors -/\r
-    //----------------/\r
-\r
-    public PdbidsItem() {\r
-        super();\r
-    } //-- jalview.schemabinding.version2.PdbidsItem()\r
-\r
-\r
-      //-----------/\r
-     //- Methods -/\r
-    //-----------/\r
-\r
-    /**\r
-     * Returns the value of field 'structureState'.\r
-     * \r
-     * @return StructureState\r
-     * @return the value of field 'structureState'.\r
-     */\r
-    public jalview.schemabinding.version2.StructureState getStructureState()\r
-    {\r
-        return this._structureState;\r
-    } //-- jalview.schemabinding.version2.StructureState getStructureState() \r
-\r
-    /**\r
-     * Sets the value of field 'structureState'.\r
-     * \r
-     * @param structureState the value of field 'structureState'.\r
-     */\r
-    public void setStructureState(jalview.schemabinding.version2.StructureState structureState)\r
-    {\r
-        this._structureState = structureState;\r
-    } //-- void setStructureState(jalview.schemabinding.version2.StructureState) \r
-\r
-}\r

diff --git a/src/jalview/schemabinding/version2/PdbidsItemDescriptor.java b/src/jalview/schemabinding/version2/PdbidsItemDescriptor.java
deleted file mode 100644 (file)
index 9128920..0000000
--- a/src/jalview/schemabinding/version2/PdbidsItemDescriptor.java
+++ /dev/null
@@ -1,207 +0,0 @@
-/*\r
- * This class was automatically generated with \r
- * <a href="http://www.castor.org">Castor 0.9.6</a>, using an XML\r
- * Schema.\r
- * $Id$\r
- */\r
-\r
-package jalview.schemabinding.version2;\r
-\r
-  //---------------------------------/\r
- //- Imported classes and packages -/\r
-//---------------------------------/\r
-\r
-import org.exolab.castor.mapping.AccessMode;\r
-import org.exolab.castor.xml.TypeValidator;\r
-import org.exolab.castor.xml.XMLFieldDescriptor;\r
-import org.exolab.castor.xml.validators.*;\r
-\r
-/**\r
- * Class PdbidsItemDescriptor.\r
- * \r
- * @version $Revision$ $Date$\r
- */\r
-public class PdbidsItemDescriptor extends org.exolab.castor.xml.util.XMLClassDescriptorImpl {\r
-\r
-\r
-      //--------------------------/\r
-     //- Class/Member Variables -/\r
-    //--------------------------/\r
-\r
-    /**\r
-     * Field nsPrefix\r
-     */\r
-    private java.lang.String nsPrefix;\r
-\r
-    /**\r
-     * Field nsURI\r
-     */\r
-    private java.lang.String nsURI;\r
-\r
-    /**\r
-     * Field xmlName\r
-     */\r
-    private java.lang.String xmlName;\r
-\r
-    /**\r
-     * Field identity\r
-     */\r
-    private org.exolab.castor.xml.XMLFieldDescriptor identity;\r
-\r
-\r
-      //----------------/\r
-     //- Constructors -/\r
-    //----------------/\r
-\r
-    public PdbidsItemDescriptor() {\r
-        super();\r
-        nsURI = "www.jalview.org";\r
-        xmlName = "pdbids";\r
-        \r
-        //-- set grouping compositor\r
-        setCompositorAsSequence();\r
-        org.exolab.castor.xml.util.XMLFieldDescriptorImpl  desc           = null;\r
-        org.exolab.castor.xml.XMLFieldHandler              handler        = null;\r
-        org.exolab.castor.xml.FieldValidator               fieldValidator = null;\r
-        //-- initialize attribute descriptors\r
-        \r
-        //-- initialize element descriptors\r
-        \r
-        //-- _structureState\r
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(jalview.schemabinding.version2.StructureState.class, "_structureState", "structureState", org.exolab.castor.xml.NodeType.Element);\r
-        handler = (new org.exolab.castor.xml.XMLFieldHandler() {\r
-            public java.lang.Object getValue( java.lang.Object object ) \r
-                throws IllegalStateException\r
-            {\r
-                PdbidsItem target = (PdbidsItem) object;\r
-                return target.getStructureState();\r
-            }\r
-            public void setValue( java.lang.Object object, java.lang.Object value) \r
-                throws IllegalStateException, IllegalArgumentException\r
-            {\r
-                try {\r
-                    PdbidsItem target = (PdbidsItem) object;\r
-                    target.setStructureState( (jalview.schemabinding.version2.StructureState) 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 new jalview.schemabinding.version2.StructureState();\r
-            }\r
-        } );\r
-        desc.setHandler(handler);\r
-        desc.setNameSpaceURI("www.jalview.org");\r
-        desc.setMultivalued(false);\r
-        addFieldDescriptor(desc);\r
-        \r
-        //-- validation code for: _structureState\r
-        fieldValidator = new org.exolab.castor.xml.FieldValidator();\r
-        { //-- local scope\r
-        }\r
-        desc.setValidator(fieldValidator);\r
-    } //-- jalview.schemabinding.version2.PdbidsItemDescriptor()\r
-\r
-\r
-      //-----------/\r
-     //- Methods -/\r
-    //-----------/\r
-\r
-    /**\r
-     * Method getAccessMode\r
-     * \r
-     * \r
-     * \r
-     * @return AccessMode\r
-     */\r
-    public org.exolab.castor.mapping.AccessMode getAccessMode()\r
-    {\r
-        return null;\r
-    } //-- org.exolab.castor.mapping.AccessMode getAccessMode() \r
-\r
-    /**\r
-     * Method getExtends\r
-     * \r
-     * \r
-     * \r
-     * @return ClassDescriptor\r
-     */\r
-    public org.exolab.castor.mapping.ClassDescriptor getExtends()\r
-    {\r
-        return null;\r
-    } //-- org.exolab.castor.mapping.ClassDescriptor getExtends() \r
-\r
-    /**\r
-     * Method getIdentity\r
-     * \r
-     * \r
-     * \r
-     * @return FieldDescriptor\r
-     */\r
-    public org.exolab.castor.mapping.FieldDescriptor getIdentity()\r
-    {\r
-        return identity;\r
-    } //-- org.exolab.castor.mapping.FieldDescriptor getIdentity() \r
-\r
-    /**\r
-     * Method getJavaClass\r
-     * \r
-     * \r
-     * \r
-     * @return Class\r
-     */\r
-    public java.lang.Class getJavaClass()\r
-    {\r
-        return jalview.schemabinding.version2.PdbidsItem.class;\r
-    } //-- java.lang.Class getJavaClass() \r
-\r
-    /**\r
-     * Method getNameSpacePrefix\r
-     * \r
-     * \r
-     * \r
-     * @return String\r
-     */\r
-    public java.lang.String getNameSpacePrefix()\r
-    {\r
-        return nsPrefix;\r
-    } //-- java.lang.String getNameSpacePrefix() \r
-\r
-    /**\r
-     * Method getNameSpaceURI\r
-     * \r
-     * \r
-     * \r
-     * @return String\r
-     */\r
-    public java.lang.String getNameSpaceURI()\r
-    {\r
-        return nsURI;\r
-    } //-- java.lang.String getNameSpaceURI() \r
-\r
-    /**\r
-     * Method getValidator\r
-     * \r
-     * \r
-     * \r
-     * @return TypeValidator\r
-     */\r
-    public org.exolab.castor.xml.TypeValidator getValidator()\r
-    {\r
-        return this;\r
-    } //-- org.exolab.castor.xml.TypeValidator getValidator() \r
-\r
-    /**\r
-     * Method getXMLName\r
-     * \r
-     * \r
-     * \r
-     * @return String\r
-     */\r
-    public java.lang.String getXMLName()\r
-    {\r
-        return xmlName;\r
-    } //-- java.lang.String getXMLName() \r
-\r
-}\r