JAL-4366 avoid corrupting map when no complete mapping available for chain to sequence

[jalview.git] / src / jalview / xml / binding / jalview / ObjectFactory.java

diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
index 993adae..27d9e41 100644 (file)
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
+// See https://eclipse-ee4j.github.io/jaxb-ri 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.11.01 at 07:03:09 PM GMT 
 //
 
 package jalview.xml.binding.jalview;
@@ -15,27 +15,26 @@ import javax.xml.namespace.QName;
 /**
  * This object contains factory methods for each Java content interface and Java
  * element interface generated in the jalview.xml.binding.jalview package.
- * <p>
- * An ObjectFactory allows you to programatically construct new instances of the
- * Java representation for XML content. The Java representation of XML content
- * can consist of schema derived interfaces and classes representing the binding
- * of schema type definitions, element declarations and model groups. Factory
- * methods for each of these are provided in this class.
+ * &lt;p&gt;An ObjectFactory allows you to programatically construct new
+ * instances of the Java representation for XML content. The Java representation
+ * of XML content can consist of schema derived interfaces and classes
+ * representing the binding of schema type definitions, element declarations and
+ * model groups. Factory methods for each of these are provided in this class.
  * 
  */
 @XmlRegistry
 public class ObjectFactory
 {
 
-  private final static QName _WebServiceParameterSet_QNAME = new QName(
-          "www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
-
   private final static QName _JalviewModel_QNAME = new QName(
           "www.jalview.org", "JalviewModel");
 
   private final static QName _JalviewUserColours_QNAME = new QName(
           "www.jalview.org/colours", "JalviewUserColours");
 
+  private final static QName _WebServiceParameterSet_QNAME = new QName(
+          "www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
+
   /**
    * Create a new ObjectFactory that can be used to create new instances of
    * schema derived classes for package: jalview.xml.binding.jalview
@@ -46,15 +45,6 @@ public class ObjectFactory
   }
 
   /**
-   * Create an instance of {@link AlcodonFrame }
-   * 
-   */
-  public AlcodonFrame createAlcodonFrame()
-  {
-    return new AlcodonFrame();
-  }
-
-  /**
    * Create an instance of {@link MapListType }
    * 
    */
@@ -73,6 +63,15 @@ public class ObjectFactory
   }
 
   /**
+   * Create an instance of {@link AlcodonFrame }
+   * 
+   */
+  public AlcodonFrame createAlcodonFrame()
+  {
+    return new AlcodonFrame();
+  }
+
+  /**
    * Create an instance of {@link Annotation }
    * 
    */
@@ -190,15 +189,6 @@ public class ObjectFactory
   }
 
   /**
-   * Create an instance of {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix createDoubleMatrix()
-  {
-    return new DoubleMatrix();
-  }
-
-  /**
    * Create an instance of {@link AnnotationColourScheme }
    * 
    */
@@ -226,30 +216,12 @@ public class ObjectFactory
   }
 
   /**
-   * Create an instance of {@link AlcodonFrame.Alcodon }
-   * 
-   */
-  public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
-  {
-    return new AlcodonFrame.Alcodon();
-  }
-
-  /**
-   * Create an instance of {@link AlcodonFrame.AlcodMap }
-   * 
-   */
-  public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
-  {
-    return new AlcodonFrame.AlcodMap();
-  }
-
-  /**
-   * Create an instance of {@link AnnotationElement }
+   * Create an instance of {@link DoubleMatrix }
    * 
    */
-  public AnnotationElement createAnnotationElement()
+  public DoubleMatrix createDoubleMatrix()
   {
-    return new AnnotationElement();
+    return new DoubleMatrix();
   }
 
   /**
@@ -298,6 +270,33 @@ public class ObjectFactory
   }
 
   /**
+   * Create an instance of {@link AlcodonFrame.Alcodon }
+   * 
+   */
+  public AlcodonFrame.Alcodon createAlcodonFrameAlcodon()
+  {
+    return new AlcodonFrame.Alcodon();
+  }
+
+  /**
+   * Create an instance of {@link AlcodonFrame.AlcodMap }
+   * 
+   */
+  public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap()
+  {
+    return new AlcodonFrame.AlcodMap();
+  }
+
+  /**
+   * Create an instance of {@link AnnotationElement }
+   * 
+   */
+  public AnnotationElement createAnnotationElement()
+  {
+    return new AnnotationElement();
+  }
+
+  /**
    * Create an instance of {@link Annotation.ThresholdLine }
    * 
    */
@@ -307,12 +306,12 @@ public class ObjectFactory
   }
 
   /**
-   * Create an instance of {@link MatrixType }
+   * Create an instance of {@link MapOnAMatrixType }
    * 
    */
-  public MatrixType createMatrixType()
+  public MapOnAMatrixType createMapOnAMatrixType()
   {
-    return new MatrixType();
+    return new MapOnAMatrixType();
   }
 
   /**
@@ -334,6 +333,15 @@ public class ObjectFactory
   }
 
   /**
+   * Create an instance of {@link MatrixType }
+   * 
+   */
+  public MatrixType createMatrixType()
+  {
+    return new MatrixType();
+  }
+
+  /**
    * Create an instance of {@link VAMSAS }
    * 
    */
@@ -533,25 +541,13 @@ public class ObjectFactory
   }
 
   /**
-   * Create an instance of {@link JAXBElement
-   * }{@code <}{@link WebServiceParameterSet }{@code >}}
-   * 
-   */
-  @XmlElementDecl(
-    namespace = "www.jalview.org/xml/wsparamset",
-    name = "WebServiceParameterSet")
-  public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(
-          WebServiceParameterSet value)
-  {
-    return new JAXBElement<WebServiceParameterSet>(
-            _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
-            null, value);
-  }
-
-  /**
    * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
-   * }{@code >}}
+   * }{@code >}
    * 
+   * @param value
+   *          Java instance representing xml element's value.
+   * @return the new instance of {@link JAXBElement
+   *         }{@code <}{@link JalviewModel }{@code >}
    */
   @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
   public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value)
@@ -562,8 +558,12 @@ public class ObjectFactory
 
   /**
    * Create an instance of {@link JAXBElement
-   * }{@code <}{@link JalviewUserColours }{@code >}}
+   * }{@code <}{@link JalviewUserColours }{@code >}
    * 
+   * @param value
+   *          Java instance representing xml element's value.
+   * @return the new instance of {@link JAXBElement
+   *         }{@code <}{@link JalviewUserColours }{@code >}
    */
   @XmlElementDecl(
     namespace = "www.jalview.org/colours",
@@ -575,4 +575,24 @@ public class ObjectFactory
             JalviewUserColours.class, null, value);
   }
 
+  /**
+   * Create an instance of {@link JAXBElement
+   * }{@code <}{@link WebServiceParameterSet }{@code >}
+   * 
+   * @param value
+   *          Java instance representing xml element's value.
+   * @return the new instance of {@link JAXBElement
+   *         }{@code <}{@link WebServiceParameterSet }{@code >}
+   */
+  @XmlElementDecl(
+    namespace = "www.jalview.org/xml/wsparamset",
+    name = "WebServiceParameterSet")
+  public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(
+          WebServiceParameterSet value)
+  {
+    return new JAXBElement<WebServiceParameterSet>(
+            _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
+            null, value);
+  }
+
 }