Merge branch 'develop' into features/JAL-518_justify_seqs_in_region

[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 d6464b3..c45fe81 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: 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;
@@ -38,6 +38,8 @@ import javax.xml.bind.annotation.XmlType;
  * </restriction> </complexContent>
  * </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"
@@ -51,7 +53,8 @@ import javax.xml.bind.annotation.XmlType;
 @XmlType(
   name = "",
   propOrder =
-  { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
+  { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame",
+      "matrix" })
 @XmlRootElement(name = "SequenceSet")
 public class SequenceSet
 {
@@ -67,6 +70,9 @@ public class SequenceSet
   @XmlElement(name = "AlcodonFrame")
   protected List<AlcodonFrame> alcodonFrame;
 
+  @XmlElement(name = "Matrix")
+  protected List<MatrixType> matrix;
+
   @XmlAttribute(name = "gapChar", required = true)
   protected String gapChar;
 
@@ -178,6 +184,32 @@ 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 possible object is {@link String }