From: Jim Procter <jprocter@issues.jalview.org>
Date: Mon, 20 Jun 2016 20:38:41 +0000 (+0100)
Subject: JAL-1369 updated project schema - flag on JSeq to mark view’s reference seq
X-Git-Tag: Release_2_10_0~161^2~5^2~9
X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=cdb40eae73b3a9a7ca68c9b882e38a2e1dd3d03e

JAL-1369 updated project schema - flag on JSeq to mark view’s reference seq
---

diff --git a/schemas/jalview.xsd b/schemas/jalview.xsd
index 850b223..f0bd638 100755
--- a/schemas/jalview.xsd
+++ b/schemas/jalview.xsd
@@ -293,6 +293,7 @@
 						<xs:attribute name="end" type="xs:int" use="required" />
 						<xs:attribute name="id" type="xs:string" use="required" />
 						<xs:attribute name="hidden" type="xs:boolean" />
+						<xs:attribute name="viewreference" type="xs:boolean" use="optional"/>
 					</xs:complexType>
 				</xs:element>
 				<xs:element name="JGroup" minOccurs="0" maxOccurs="unbounded">
diff --git a/src/jalview/schemabinding/version2/.castor.cdr b/src/jalview/schemabinding/version2/.castor.cdr
index 361fb7c..0a01103 100644
--- a/src/jalview/schemabinding/version2/.castor.cdr
+++ b/src/jalview/schemabinding/version2/.castor.cdr
@@ -1,4 +1,4 @@
-#Thu Sep 03 10:55:37 BST 2015
+#Mon Jun 20 15:44:52 BST 2016
 jalview.schemabinding.version2.ThresholdLine=jalview.schemabinding.version2.descriptors.ThresholdLineDescriptor
 jalview.schemabinding.version2.SequenceSetProperties=jalview.schemabinding.version2.descriptors.SequenceSetPropertiesDescriptor
 jalview.schemabinding.version2.StructureState=jalview.schemabinding.version2.descriptors.StructureStateDescriptor
diff --git a/src/jalview/schemabinding/version2/JSeq.java b/src/jalview/schemabinding/version2/JSeq.java
index 9ca6708..7c6308e 100644
--- a/src/jalview/schemabinding/version2/JSeq.java
+++ b/src/jalview/schemabinding/version2/JSeq.java
@@ -72,6 +72,16 @@ public class JSeq implements java.io.Serializable
   private boolean _has_hidden;
 
   /**
+   * Field _viewreference.
+   */
+  private boolean _viewreference;
+
+  /**
+   * keeps track of state for field: _viewreference
+   */
+  private boolean _has_viewreference;
+
+  /**
    * Field _featuresList.
    */
   private java.util.Vector _featuresList;
@@ -256,6 +266,13 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+     */
+  public void deleteViewreference()
+  {
+    this._has_viewreference = false;
+  }
+
+  /**
    * Method enumerateFeatures.
    * 
    * @return an Enumeration over all jalview.schemabinding.version2.Features
@@ -549,6 +566,16 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+   * Returns the value of field 'viewreference'.
+   * 
+   * @return the value of field 'Viewreference'.
+   */
+  public boolean getViewreference()
+  {
+    return this._viewreference;
+  }
+
+  /**
    * Method hasColour.
    * 
    * @return true if at least one Colour has been added
@@ -589,6 +616,16 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+   * Method hasViewreference.
+   * 
+   * @return true if at least one Viewreference has been added
+   */
+  public boolean hasViewreference()
+  {
+    return this._has_viewreference;
+  }
+
+  /**
    * Returns the value of field 'hidden'.
    * 
    * @return the value of field 'Hidden'.
@@ -616,6 +653,16 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+   * Returns the value of field 'viewreference'.
+   * 
+   * @return the value of field 'Viewreference'.
+   */
+  public boolean isViewreference()
+  {
+    return this._viewreference;
+  }
+
+  /**
    * 
    * 
    * @param out
@@ -1004,6 +1051,18 @@ public class JSeq implements java.io.Serializable
   }
 
   /**
+   * Sets the value of field 'viewreference'.
+   * 
+   * @param viewreference
+   *          the value of field 'viewreference'.
+   */
+  public void setViewreference(final boolean viewreference)
+  {
+    this._viewreference = viewreference;
+    this._has_viewreference = true;
+  }
+
+  /**
    * Method unmarshal.
    * 
    * @param reader
diff --git a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
index 1d2aad3..5739d90 100644
--- a/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/AnnotationColoursDescriptor.java
@@ -11,6 +11,8 @@ package jalview.schemabinding.version2.descriptors;
 //- Imported classes and packages -/
 //---------------------------------/
 
+import jalview.schemabinding.version2.AnnotationColours;
+
 /**
  * Class AnnotationColoursDescriptor.
  * 
diff --git a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
index a7ffaba..107c06d 100644
--- a/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/FeaturesDescriptor.java
@@ -11,6 +11,8 @@ package jalview.schemabinding.version2.descriptors;
 //- Imported classes and packages -/
 //---------------------------------/
 
+import jalview.schemabinding.version2.Features;
+
 /**
  * Class FeaturesDescriptor.
  * 
diff --git a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
index 0f000bb..28f23b26 100644
--- a/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JSeqDescriptor.java
@@ -334,6 +334,61 @@ public class JSeqDescriptor extends
       fieldValidator.setValidator(typeValidator);
     }
     desc.setValidator(fieldValidator);
+    // -- _viewreference
+    desc = new org.exolab.castor.xml.util.XMLFieldDescriptorImpl(
+            java.lang.Boolean.TYPE, "_viewreference", "viewreference",
+            org.exolab.castor.xml.NodeType.Attribute);
+    handler = new org.exolab.castor.xml.XMLFieldHandler()
+    {
+      public java.lang.Object getValue(java.lang.Object object)
+              throws IllegalStateException
+      {
+        JSeq target = (JSeq) object;
+        if (!target.hasViewreference())
+        {
+          return null;
+        }
+        return (target.getViewreference() ? java.lang.Boolean.TRUE
+                : java.lang.Boolean.FALSE);
+      }
+
+      public void setValue(java.lang.Object object, java.lang.Object value)
+              throws IllegalStateException, IllegalArgumentException
+      {
+        try
+        {
+          JSeq target = (JSeq) object;
+          // if null, use delete method for optional primitives
+          if (value == null)
+          {
+            target.deleteViewreference();
+            return;
+          }
+          target.setViewreference(((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);
+    desc.setMultivalued(false);
+    addFieldDescriptor(desc);
+
+    // -- validation code for: _viewreference
+    fieldValidator = new org.exolab.castor.xml.FieldValidator();
+    { // -- local scope
+      org.exolab.castor.xml.validators.BooleanValidator typeValidator;
+      typeValidator = new org.exolab.castor.xml.validators.BooleanValidator();
+      fieldValidator.setValidator(typeValidator);
+    }
+    desc.setValidator(fieldValidator);
     // -- initialize element descriptors
 
     // -- _featuresList
diff --git a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
index 77efa7e..d65de13 100644
--- a/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/JalviewUserColoursDescriptor.java
@@ -72,6 +72,7 @@ public class JalviewUserColoursDescriptor extends
     desc.setImmutable(true);
     handler = new org.exolab.castor.xml.XMLFieldHandler()
     {
+      @Override
       public java.lang.Object getValue(java.lang.Object object)
               throws IllegalStateException
       {
@@ -79,6 +80,7 @@ public class JalviewUserColoursDescriptor extends
         return target.getSchemeName();
       }
 
+      @Override
       public void setValue(java.lang.Object object, java.lang.Object value)
               throws IllegalStateException, IllegalArgumentException
       {
@@ -92,6 +94,7 @@ public class JalviewUserColoursDescriptor extends
         }
       }
 
+      @Override
       public java.lang.Object newInstance(java.lang.Object parent)
       {
         return null;
@@ -119,6 +122,7 @@ public class JalviewUserColoursDescriptor extends
     desc.setImmutable(true);
     handler = new org.exolab.castor.xml.XMLFieldHandler()
     {
+      @Override
       public java.lang.Object getValue(java.lang.Object object)
               throws IllegalStateException
       {
@@ -126,6 +130,7 @@ public class JalviewUserColoursDescriptor extends
         return target.getVersion();
       }
 
+      @Override
       public void setValue(java.lang.Object object, java.lang.Object value)
               throws IllegalStateException, IllegalArgumentException
       {
@@ -139,6 +144,7 @@ public class JalviewUserColoursDescriptor extends
         }
       }
 
+      @Override
       public java.lang.Object newInstance(java.lang.Object parent)
       {
         return null;
@@ -163,6 +169,7 @@ public class JalviewUserColoursDescriptor extends
             org.exolab.castor.xml.NodeType.Element);
     handler = new org.exolab.castor.xml.XMLFieldHandler()
     {
+      @Override
       public java.lang.Object getValue(java.lang.Object object)
               throws IllegalStateException
       {
@@ -170,6 +177,7 @@ public class JalviewUserColoursDescriptor extends
         return target.getColour();
       }
 
+      @Override
       public void setValue(java.lang.Object object, java.lang.Object value)
               throws IllegalStateException, IllegalArgumentException
       {
@@ -183,6 +191,7 @@ public class JalviewUserColoursDescriptor extends
         }
       }
 
+      @Override
       public void resetValue(Object object) throws IllegalStateException,
               IllegalArgumentException
       {
@@ -196,6 +205,7 @@ public class JalviewUserColoursDescriptor extends
         }
       }
 
+      @Override
       public java.lang.Object newInstance(java.lang.Object parent)
       {
         return new Colour();
@@ -222,6 +232,7 @@ public class JalviewUserColoursDescriptor extends
    * 
    * @return the access mode specified for this class.
    */
+  @Override
   public org.exolab.castor.mapping.AccessMode getAccessMode()
   {
     return null;
@@ -232,6 +243,7 @@ public class JalviewUserColoursDescriptor extends
    * 
    * @return the identity field, null if this class has no identity.
    */
+  @Override
   public org.exolab.castor.mapping.FieldDescriptor getIdentity()
   {
     return super.getIdentity();
@@ -242,6 +254,7 @@ public class JalviewUserColoursDescriptor extends
    * 
    * @return the Java class represented by this descriptor.
    */
+  @Override
   public java.lang.Class getJavaClass()
   {
     return jalview.schemabinding.version2.JalviewUserColours.class;
@@ -252,6 +265,7 @@ public class JalviewUserColoursDescriptor extends
    * 
    * @return the namespace prefix to use when marshaling as XML.
    */
+  @Override
   public java.lang.String getNameSpacePrefix()
   {
     return _nsPrefix;
@@ -262,6 +276,7 @@ public class JalviewUserColoursDescriptor extends
    * 
    * @return the namespace URI used when marshaling and unmarshaling as XML.
    */
+  @Override
   public java.lang.String getNameSpaceURI()
   {
     return _nsURI;
@@ -273,6 +288,7 @@ public class JalviewUserColoursDescriptor extends
    * @return a specific validator for the class described by this
    *         ClassDescriptor.
    */
+  @Override
   public org.exolab.castor.xml.TypeValidator getValidator()
   {
     return this;
@@ -283,6 +299,7 @@ public class JalviewUserColoursDescriptor extends
    * 
    * @return the XML Name for the Class being described.
    */
+  @Override
   public java.lang.String getXMLName()
   {
     return _xmlName;
@@ -294,6 +311,7 @@ public class JalviewUserColoursDescriptor extends
    * @return true if XML schema definition of this Class is that of a global
    *         element or element with anonymous type definition.
    */
+  @Override
   public boolean isElementDefinition()
   {
     return _elementDefinition;
diff --git a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
index ece728a..df9ab07 100644
--- a/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/UserColourSchemeDescriptor.java
@@ -11,6 +11,8 @@ package jalview.schemabinding.version2.descriptors;
 //- Imported classes and packages -/
 //---------------------------------/
 
+import jalview.schemabinding.version2.UserColourScheme;
+
 /**
  * Class UserColourSchemeDescriptor.
  * 
diff --git a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
index 86e6992..3e26611 100644
--- a/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
+++ b/src/jalview/schemabinding/version2/descriptors/VamsasModelDescriptor.java
@@ -11,6 +11,8 @@ package jalview.schemabinding.version2.descriptors;
 //- Imported classes and packages -/
 //---------------------------------/
 
+import jalview.schemabinding.version2.VamsasModel;
+
 /**
  * Class VamsasModelDescriptor.
  *