JAL-4090 JAL-4281 JAL-4311 release notes

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

diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index 0c435d0..751f6ca 100644 (file)
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.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: 2022.02.07 at 04:44:47 PM GMT 
+// Generated on: 2023.11.01 at 07:03:09 PM GMT 
 //
 
 
@@ -41,6 +41,7 @@ import javax.xml.bind.annotation.XmlType;
  *           </complexType>
  *         </element>
  *         <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="Matrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/>
  *       </sequence>
  *       <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
  *       <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
@@ -56,7 +57,8 @@ import javax.xml.bind.annotation.XmlType;
     "sequence",
     "annotation",
     "sequenceSetProperties",
-    "alcodonFrame"
+    "alcodonFrame",
+    "matrix"
 })
 @XmlRootElement(name = "SequenceSet")
 public class SequenceSet {
@@ -68,6 +70,8 @@ public class SequenceSet {
     protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
     @XmlElement(name = "AlcodonFrame")
     protected List<AlcodonFrame> alcodonFrame;
+    @XmlElement(name = "Matrix")
+    protected List<MatrixType> matrix;
     @XmlAttribute(name = "gapChar", required = true)
     protected String gapChar;
     @XmlAttribute(name = "datasetId")
@@ -190,6 +194,35 @@ public class SequenceSet {
     }
 
     /**
+     * Gets the value of the matrix 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 matrix property.
+     * 
+     * &lt;p&gt;
+     * For example, to add a new item, do as follows:
+     * &lt;pre&gt;
+     *    getMatrix().add(newItem);
+     * &lt;/pre&gt;
+     * 
+     * 
+     * &lt;p&gt;
+     * Objects of the following type(s) are allowed in the list
+     * {@link MatrixType }
+     * 
+     * 
+     */
+    public List<MatrixType> getMatrix() {
+        if (matrix == null) {
+            matrix = new ArrayList<MatrixType>();
+        }
+        return this.matrix;
+    }
+
+    /**
      * Gets the value of the gapChar property.
      * 
      * @return