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

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

diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java
index 8d66aa3..26e9124 100644 (file)
--- a/src/jalview/xml/binding/jalview/Annotation.java
+++ b/src/jalview/xml/binding/jalview/Annotation.java
@@ -2,7 +2,7 @@
 // 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: 2021.08.30 at 11:05:22 AM BST 
+// Generated on: 2023.11.01 at 07:03:09 PM GMT 
 //
 
 package jalview.xml.binding.jalview;
@@ -39,27 +39,23 @@ import javax.xml.bind.annotation.XmlType;
  * type="{http://www.w3.org/2001/XMLSchema}int" />
  * </restriction> </complexContent>
  * </complexType> </element> <element
- * name="property" maxOccurs="unbounded" minOccurs="0">
- * <complexType> <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * /> <attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction> </complexContent>
- * </complexType> </element>
- * </sequence> <attribute name="graph" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
- * name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="sequenceRef"
- * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
- * name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="graphColour"
+ * name="contactmatrix"
+ * type="{www.vamsas.ac.uk/jalview/version2}MapOnAMatrixType"
+ * maxOccurs="unbounded" minOccurs="0"/> <element name="property"
+ * type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded"
+ * minOccurs="0"/> </sequence> <attribute
+ * name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * /> <attribute name="graphType"
  * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
- * name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="graphHeight"
+ * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="groupRef"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
+ * name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="graphGroup"
  * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
- * name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="scoreOnly"
+ * name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
+ * /> <attribute name="scoreOnly"
  * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
  * <attribute name="score"
  * type="{http://www.w3.org/2001/XMLSchema}double" /> <attribute
@@ -84,7 +80,7 @@ import javax.xml.bind.annotation.XmlType;
   name = "",
   propOrder =
   { "annotationElement", "label", "description", "thresholdLine",
-      "property" })
+      "contactmatrix", "property" })
 @XmlRootElement(name = "Annotation")
 public class Annotation
 {
@@ -98,7 +94,9 @@ public class Annotation
 
   protected Annotation.ThresholdLine thresholdLine;
 
-  protected List<Annotation.Property> property;
+  protected List<MapOnAMatrixType> contactmatrix;
+
+  protected List<Property> property;
 
   @XmlAttribute(name = "graph", required = true)
   protected boolean graph;
@@ -247,6 +245,32 @@ public class Annotation
   }
 
   /**
+   * Gets the value of the contactmatrix property.
+   * 
+   * &lt;p&gt; This accessor method returns a reference to the live list, not a
+   * snapshot. Therefore any modification you make to the returned list will be
+   * present inside the JAXB object. This is why there is not a
+   * &lt;CODE&gt;set&lt;/CODE&gt; method for the contactmatrix property.
+   * 
+   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+   * getContactmatrix().add(newItem); &lt;/pre&gt;
+   * 
+   * 
+   * &lt;p&gt; Objects of the following type(s) are allowed in the list
+   * {@link MapOnAMatrixType }
+   * 
+   * 
+   */
+  public List<MapOnAMatrixType> getContactmatrix()
+  {
+    if (contactmatrix == null)
+    {
+      contactmatrix = new ArrayList<MapOnAMatrixType>();
+    }
+    return this.contactmatrix;
+  }
+
+  /**
    * Gets the value of the property property.
    * 
    * &lt;p&gt; This accessor method returns a reference to the live list, not a
@@ -259,15 +283,15 @@ public class Annotation
    * 
    * 
    * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Annotation.Property }
+   * {@link Property }
    * 
    * 
    */
-  public List<Annotation.Property> getProperty()
+  public List<Property> getProperty()
   {
     if (property == null)
     {
-      property = new ArrayList<Annotation.Property>();
+      property = new ArrayList<Property>();
     }
     return this.property;
   }
@@ -688,82 +712,6 @@ public class Annotation
    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
    * &amp;lt;restriction
    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
-   * name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="value"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
-   * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Property
-  {
-
-    @XmlAttribute(name = "name")
-    protected String name;
-
-    @XmlAttribute(name = "value")
-    protected String value;
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getName()
-    {
-      return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setName(String value)
-    {
-      this.name = value;
-    }
-
-    /**
-     * Gets the value of the value property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getValue()
-    {
-      return value;
-    }
-
-    /**
-     * Sets the value of the value property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setValue(String value)
-    {
-      this.value = value;
-    }
-
-  }
-
-  /**
-   * &lt;p&gt;Java class for anonymous complex type.
-   * 
-   * &lt;p&gt;The following schema fragment specifies the expected content
-   * contained within this class.
-   * 
-   * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
-   * &amp;lt;restriction
-   * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
    * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
    * &amp;lt;attribute name="value"
    * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute