propagate changes from schema update.

git-svn-id: https://svn.lifesci.dundee.ac.uk/svn/repository/trunk@83 be28352e-c001-0410-b1a7-c7978e42abec

diff --git a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java b/src/org/vamsas/objects/core/AnnotationElementDescriptor.java
index fd3d521..943bb99 100644 (file)
--- a/src/org/vamsas/objects/core/AnnotationElementDescriptor.java
+++ b/src/org/vamsas/objects/core/AnnotationElementDescriptor.java
@@ -104,7 +104,7 @@ public class AnnotationElementDescriptor extends org.exolab.castor.xml.util.XMLC
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         fieldValidator.setMinOccurs(1);
         { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
+            IntegerValidator typeValidator = new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);

diff --git a/src/org/vamsas/objects/core/DataSetAnnotations.java b/src/org/vamsas/objects/core/DataSetAnnotations.java
index 60f2d84..cea5a3b 100644 (file)
--- a/src/org/vamsas/objects/core/DataSetAnnotations.java
+++ b/src/org/vamsas/objects/core/DataSetAnnotations.java
@@ -45,12 +45,22 @@ implements java.io.Serializable
     /**
      * Field _end
      */
-    private java.lang.String _end;
+    private int _end;
+
+    /**
+     * keeps track of state for field: _end
+     */
+    private boolean _has_end;
 
     /**
      * Field _begin
      */
-    private java.lang.String _begin;
+    private int _begin;
+
+    /**
+     * keeps track of state for field: _begin
+     */
+    private boolean _has_begin;
 
     /**
      * Field _seqRef
@@ -154,6 +164,24 @@ implements java.io.Serializable
     } //-- void addProvenance(int, org.vamsas.objects.core.Provenance) 
 
     /**
+     * Method deleteBegin
+     * 
+     */
+    public void deleteBegin()
+    {
+        this._has_begin= false;
+    } //-- void deleteBegin() 
+
+    /**
+     * Method deleteEnd
+     * 
+     */
+    public void deleteEnd()
+    {
+        this._has_end= false;
+    } //-- void deleteEnd() 
+
+    /**
      * Method enumerateAnnotationElement
      * 
      * 
@@ -201,19 +229,13 @@ implements java.io.Serializable
             }
             else if (temp._type != null)
                 return false;
-            if (this._end != null) {
-                if (temp._end == null) return false;
-                else if (!(this._end.equals(temp._end))) 
-                    return false;
-            }
-            else if (temp._end != null)
+            if (this._end != temp._end)
                 return false;
-            if (this._begin != null) {
-                if (temp._begin == null) return false;
-                else if (!(this._begin.equals(temp._begin))) 
-                    return false;
-            }
-            else if (temp._begin != null)
+            if (this._has_end != temp._has_end)
+                return false;
+            if (this._begin != temp._begin)
+                return false;
+            if (this._has_begin != temp._has_begin)
                 return false;
             if (this._seqRef != null) {
                 if (temp._seqRef == null) return false;
@@ -313,13 +335,13 @@ implements java.io.Serializable
     /**
      * Returns the value of field 'begin'.
      * 
-     * @return String
+     * @return int
      * @return the value of field 'begin'.
      */
-    public java.lang.String getBegin()
+    public int getBegin()
     {
         return this._begin;
-    } //-- java.lang.String getBegin() 
+    } //-- int getBegin() 
 
     /**
      * Returns the value of field 'description'.
@@ -335,13 +357,13 @@ implements java.io.Serializable
     /**
      * Returns the value of field 'end'.
      * 
-     * @return String
+     * @return int
      * @return the value of field 'end'.
      */
-    public java.lang.String getEnd()
+    public int getEnd()
     {
         return this._end;
-    } //-- java.lang.String getEnd() 
+    } //-- int getEnd() 
 
     /**
      * Returns the value of field 'id'.
@@ -436,6 +458,30 @@ implements java.io.Serializable
     } //-- java.lang.String getType() 
 
     /**
+     * Method hasBegin
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasBegin()
+    {
+        return this._has_begin;
+    } //-- boolean hasBegin() 
+
+    /**
+     * Method hasEnd
+     * 
+     * 
+     * 
+     * @return boolean
+     */
+    public boolean hasEnd()
+    {
+        return this._has_end;
+    } //-- boolean hasEnd() 
+
+    /**
      * Method isValid
      * 
      * 
@@ -568,10 +614,11 @@ implements java.io.Serializable
      * 
      * @param begin the value of field 'begin'.
      */
-    public void setBegin(java.lang.String begin)
+    public void setBegin(int begin)
     {
         this._begin = begin;
-    } //-- void setBegin(java.lang.String) 
+        this._has_begin = true;
+    } //-- void setBegin(int) 
 
     /**
      * Sets the value of field 'description'.
@@ -588,10 +635,11 @@ implements java.io.Serializable
      * 
      * @param end the value of field 'end'.
      */
-    public void setEnd(java.lang.String end)
+    public void setEnd(int end)
     {
         this._end = end;
-    } //-- void setEnd(java.lang.String) 
+        this._has_end = true;
+    } //-- void setEnd(int) 
 
     /**
      * Sets the value of field 'id'.

diff --git a/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java b/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java
index 064823f..f74d6bc 100644 (file)
--- a/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java
+++ b/src/org/vamsas/objects/core/DataSetAnnotationsDescriptor.java
@@ -106,21 +106,25 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
         }
         desc.setValidator(fieldValidator);
         //-- _end
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_end", "end", org.exolab.castor.xml.NodeType.Attribute);
         handler = new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 DataSetAnnotations target = (DataSetAnnotations) object;
-                return target.getEnd();
+                if(!target.hasEnd())
+                    return null;
+                return new java.lang.Integer(target.getEnd());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
                     DataSetAnnotations target = (DataSetAnnotations) object;
-                    target.setEnd( (java.lang.String) value);
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setEnd( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -139,27 +143,30 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         fieldValidator.setMinOccurs(1);
         { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
+            IntegerValidator typeValidator = new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
         //-- _begin
-        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.String.class, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);
-        desc.setImmutable(true);
+        desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(java.lang.Integer.TYPE, "_begin", "begin", org.exolab.castor.xml.NodeType.Attribute);
         handler = new org.exolab.castor.xml.XMLFieldHandler() {
             public java.lang.Object getValue( java.lang.Object object ) 
                 throws IllegalStateException
             {
                 DataSetAnnotations target = (DataSetAnnotations) object;
-                return target.getBegin();
+                if(!target.hasBegin())
+                    return null;
+                return new java.lang.Integer(target.getBegin());
             }
             public void setValue( java.lang.Object object, java.lang.Object value) 
                 throws IllegalStateException, IllegalArgumentException
             {
                 try {
                     DataSetAnnotations target = (DataSetAnnotations) object;
-                    target.setBegin( (java.lang.String) value);
+                    // ignore null values for non optional primitives
+                    if (value == null) return;
+                    
+                    target.setBegin( ((java.lang.Integer)value).intValue());
                 }
                 catch (java.lang.Exception ex) {
                     throw new IllegalStateException(ex.toString());
@@ -178,8 +185,7 @@ public class DataSetAnnotationsDescriptor extends org.exolab.castor.xml.util.XML
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         fieldValidator.setMinOccurs(1);
         { //-- local scope
-            StringValidator typeValidator = new StringValidator();
-            typeValidator.setWhiteSpace("preserve");
+            IntegerValidator typeValidator = new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);

diff --git a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java
index 0c4ded0..d7c39fc 100644 (file)
--- a/src/org/vamsas/objects/core/SequenceTypeDescriptor.java
+++ b/src/org/vamsas/objects/core/SequenceTypeDescriptor.java
@@ -104,7 +104,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         fieldValidator.setMinOccurs(1);
         { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
+            IntegerValidator typeValidator = new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);
@@ -146,7 +146,7 @@ public class SequenceTypeDescriptor extends org.exolab.castor.xml.util.XMLClassD
         fieldValidator = new org.exolab.castor.xml.FieldValidator();
         fieldValidator.setMinOccurs(1);
         { //-- local scope
-            IntegerValidator typeValidator= new IntegerValidator();
+            IntegerValidator typeValidator = new IntegerValidator();
             fieldValidator.setValidator(typeValidator);
         }
         desc.setValidator(fieldValidator);