JAL-4124 Dataset holds list of MatrixType instances, MapOnAMatrixType allows multiple...

[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 35f78f3..dc485c5 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 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> 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2023.08.28 at 01:52:46 PM BST 
 //
 
 
@@ -42,16 +42,8 @@ import javax.xml.bind.annotation.XmlType;
  *             &lt;/complexContent>
  *           &lt;/complexType>
  *         &lt;/element>
- *         &lt;element name="property" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
+ *         &lt;element name="contactmatrix" type="{www.vamsas.ac.uk/jalview/version2}MapOnAMatrixType" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
  *       &lt;/sequence>
  *       &lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
  *       &lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
@@ -83,6 +75,7 @@ import javax.xml.bind.annotation.XmlType;
     "label",
     "description",
     "thresholdLine",
+    "contactmatrix",
     "property"
 })
 @XmlRootElement(name = "Annotation")
@@ -93,7 +86,8 @@ public class Annotation {
     protected String label;
     protected String description;
     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;
     @XmlAttribute(name = "graphType")
@@ -231,6 +225,35 @@ public class Annotation {
     }
 
     /**
+     * Gets the value of the contactmatrix property.
+     * 
+     * <p>
+     * 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 <CODE>set</CODE> method for the contactmatrix property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getContactmatrix().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * 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.
      * 
      * <p>
@@ -248,13 +271,13 @@ public class Annotation {
      * 
      * <p>
      * 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;
     }
@@ -681,84 +704,6 @@ public class Annotation {
      * &lt;complexType>
      *   &lt;complexContent>
      *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
-     * 
-     * 
-     */
-    @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;
-        }
-
-    }
-
-
-    /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
      *       &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
      *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
      *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />