X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FSequenceSet.java;h=751f6cab1f427ae6c9badc741d9c07bde8a64c12;hb=051cab343aed415a342a787e10ebd075f05243f6;hp=d6464b3551cecfd84c563aa4273cc1a6f6b3c5ba;hpb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;p=jalview.git

diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index d6464b3..751f6ca 100644
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -2,9 +2,10 @@
 // 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;
 
 import java.util.ArrayList;
@@ -16,287 +17,335 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * <p>Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre> <complexType> <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence> <element
- * ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded"
- * minOccurs="0"/> <element
- * ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded"
- * minOccurs="0"/> <element name="sequenceSetProperties"
- * maxOccurs="unbounded" minOccurs="0"> <complexType>
- * <complexContent> <restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"> <attribute
- * name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="value"
- * type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction> </complexContent>
- * </complexType> </element> <element
- * ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" 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" />
- * </restriction> </complexContent>
- * </complexType> </pre>
+ * <pre>
+ * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </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" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
+@XmlType(name = "", propOrder = {
+    "sequence",
+    "annotation",
+    "sequenceSetProperties",
+    "alcodonFrame",
+    "matrix"
+})
 @XmlRootElement(name = "SequenceSet")
-public class SequenceSet
-{
-
-  @XmlElement(name = "Sequence")
-  protected List<Sequence> sequence;
-
-  @XmlElement(name = "Annotation")
-  protected List<Annotation> annotation;
-
-  protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+public class SequenceSet {
 
-  @XmlElement(name = "AlcodonFrame")
-  protected List<AlcodonFrame> alcodonFrame;
+    @XmlElement(name = "Sequence")
+    protected List<Sequence> sequence;
+    @XmlElement(name = "Annotation")
+    protected List<Annotation> annotation;
+    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")
+    protected String datasetId;
 
-  @XmlAttribute(name = "gapChar", required = true)
-  protected String gapChar;
-
-  @XmlAttribute(name = "datasetId")
-  protected String datasetId;
-
-  /**
-   * Gets the value of the sequence 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 sequence property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getSequence().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Sequence }
-   * 
-   * 
-   */
-  public List<Sequence> getSequence()
-  {
-    if (sequence == null)
-    {
-      sequence = new ArrayList<Sequence>();
+    /**
+     * Gets the value of the sequence 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 sequence property.
+     * 
+     * &lt;p&gt;
+     * For example, to add a new item, do as follows:
+     * &lt;pre&gt;
+     *    getSequence().add(newItem);
+     * &lt;/pre&gt;
+     * 
+     * 
+     * &lt;p&gt;
+     * Objects of the following type(s) are allowed in the list
+     * {@link Sequence }
+     * 
+     * 
+     */
+    public List<Sequence> getSequence() {
+        if (sequence == null) {
+            sequence = new ArrayList<Sequence>();
+        }
+        return this.sequence;
     }
-    return this.sequence;
-  }
 
-  /**
-   * Gets the value of the annotation 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 annotation property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getAnnotation().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Annotation }
-   * 
-   * 
-   */
-  public List<Annotation> getAnnotation()
-  {
-    if (annotation == null)
-    {
-      annotation = new ArrayList<Annotation>();
+    /**
+     * Gets the value of the annotation 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 annotation property.
+     * 
+     * &lt;p&gt;
+     * For example, to add a new item, do as follows:
+     * &lt;pre&gt;
+     *    getAnnotation().add(newItem);
+     * &lt;/pre&gt;
+     * 
+     * 
+     * &lt;p&gt;
+     * Objects of the following type(s) are allowed in the list
+     * {@link Annotation }
+     * 
+     * 
+     */
+    public List<Annotation> getAnnotation() {
+        if (annotation == null) {
+            annotation = new ArrayList<Annotation>();
+        }
+        return this.annotation;
     }
-    return this.annotation;
-  }
 
-  /**
-   * Gets the value of the sequenceSetProperties 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 sequenceSetProperties property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getSequenceSetProperties().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link SequenceSet.SequenceSetProperties }
-   * 
-   * 
-   */
-  public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties()
-  {
-    if (sequenceSetProperties == null)
-    {
-      sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
+    /**
+     * Gets the value of the sequenceSetProperties 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 sequenceSetProperties property.
+     * 
+     * &lt;p&gt;
+     * For example, to add a new item, do as follows:
+     * &lt;pre&gt;
+     *    getSequenceSetProperties().add(newItem);
+     * &lt;/pre&gt;
+     * 
+     * 
+     * &lt;p&gt;
+     * Objects of the following type(s) are allowed in the list
+     * {@link SequenceSet.SequenceSetProperties }
+     * 
+     * 
+     */
+    public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() {
+        if (sequenceSetProperties == null) {
+            sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
+        }
+        return this.sequenceSetProperties;
     }
-    return this.sequenceSetProperties;
-  }
 
-  /**
-   * Gets the value of the alcodonFrame 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 alcodonFrame property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getAlcodonFrame().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame }
-   * 
-   * 
-   */
-  public List<AlcodonFrame> getAlcodonFrame()
-  {
-    if (alcodonFrame == null)
-    {
-      alcodonFrame = new ArrayList<AlcodonFrame>();
+    /**
+     * Gets the value of the alcodonFrame 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 alcodonFrame property.
+     * 
+     * &lt;p&gt;
+     * For example, to add a new item, do as follows:
+     * &lt;pre&gt;
+     *    getAlcodonFrame().add(newItem);
+     * &lt;/pre&gt;
+     * 
+     * 
+     * &lt;p&gt;
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame }
+     * 
+     * 
+     */
+    public List<AlcodonFrame> getAlcodonFrame() {
+        if (alcodonFrame == null) {
+            alcodonFrame = new ArrayList<AlcodonFrame>();
+        }
+        return this.alcodonFrame;
     }
-    return this.alcodonFrame;
-  }
-
-  /**
-   * Gets the value of the gapChar property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getGapChar()
-  {
-    return gapChar;
-  }
-
-  /**
-   * Sets the value of the gapChar property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setGapChar(String value)
-  {
-    this.gapChar = value;
-  }
-
-  /**
-   * Gets the value of the datasetId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDatasetId()
-  {
-    return datasetId;
-  }
-
-  /**
-   * Sets the value of the datasetId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDatasetId(String value)
-  {
-    this.datasetId = 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="key" 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 SequenceSetProperties
-  {
-
-    @XmlAttribute(name = "key")
-    protected String key;
-
-    @XmlAttribute(name = "value")
-    protected String value;
 
     /**
-     * Gets the value of the key property.
+     * 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 }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getKey()
-    {
-      return key;
+    public List<MatrixType> getMatrix() {
+        if (matrix == null) {
+            matrix = new ArrayList<MatrixType>();
+        }
+        return this.matrix;
     }
 
     /**
-     * Sets the value of the key property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
+     * Gets the value of the gapChar property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setKey(String value)
-    {
-      this.key = value;
+    public String getGapChar() {
+        return gapChar;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the gapChar property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setGapChar(String value) {
+        this.gapChar = value;
+    }
+
+    /**
+     * Gets the value of the datasetId property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public String getDatasetId() {
+        return datasetId;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the datasetId property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public void setDatasetId(String value) {
+        this.datasetId = 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="key" 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 SequenceSetProperties {
+
+        @XmlAttribute(name = "key")
+        protected String key;
+        @XmlAttribute(name = "value")
+        protected String value;
+
+        /**
+         * Gets the value of the key property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getKey() {
+            return key;
+        }
+
+        /**
+         * Sets the value of the key property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setKey(String value) {
+            this.key = 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;
+        }
+
+    }
 
 }