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Merge branch 'develop' into releases/Release_2_11_3_Branch
[jalview.git] / src / jalview / xml / binding / jalview / AlcodonFrame.java
diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java
index 9a2c488..c412c36 100644 (file)
--- a/src/jalview/xml/binding/jalview/AlcodonFrame.java
+++ b/src/jalview/xml/binding/jalview/AlcodonFrame.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.math.BigInteger;
@@ -17,288 +18,314 @@ 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 name="alcodon" maxOccurs="unbounded"
- * minOccurs="0"> <complexType>
- * <complexContent> <restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"> <attribute
- * name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * <attribute name="pos2"
- * type="{http://www.w3.org/2001/XMLSchema}integer" /> <attribute
- * name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
- * </restriction> </complexContent>
- * </complexType> </element> <element
- * name="alcodMap" maxOccurs="unbounded" minOccurs="0">
- * <complexType> <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <sequence> <element
- * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
- * </sequence> <attribute name="dnasq" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction> </complexContent>
- * </complexType> </element>
- * </sequence> </restriction>
- * </complexContent> </complexType> </pre>
+ * <pre>
+ * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="alcodon" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <sequence>
+ *                   <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+ *                 </sequence>
+ *                 <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
+@XmlType(name = "", propOrder = {
+    "alcodon",
+    "alcodMap"
+})
 @XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame
-{
-
-  protected List<AlcodonFrame.Alcodon> alcodon;
-
-  protected List<AlcodonFrame.AlcodMap> alcodMap;
+public class AlcodonFrame {
 
-  /**
-   * Gets the value of the alcodon 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 alcodon property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getAlcodon().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame.Alcodon }
-   * 
-   * 
-   */
-  public List<AlcodonFrame.Alcodon> getAlcodon()
-  {
-    if (alcodon == null)
-    {
-      alcodon = new ArrayList<AlcodonFrame.Alcodon>();
-    }
-    return this.alcodon;
-  }
-
-  /**
-   * Gets the value of the alcodMap 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 alcodMap property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getAlcodMap().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame.AlcodMap }
-   * 
-   * 
-   */
-  public List<AlcodonFrame.AlcodMap> getAlcodMap()
-  {
-    if (alcodMap == null)
-    {
-      alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
-    }
-    return this.alcodMap;
-  }
-
-  /**
-   * &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;sequence&amp;gt; &amp;lt;element
-   * ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="dnasq" use="required"
-   * 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 = "", propOrder = { "mapping" })
-  public static class AlcodMap
-  {
-
-    @XmlElement(name = "Mapping", required = true)
-    protected Mapping mapping;
-
-    @XmlAttribute(name = "dnasq", required = true)
-    protected String dnasq;
+    protected List<AlcodonFrame.Alcodon> alcodon;
+    protected List<AlcodonFrame.AlcodMap> alcodMap;
 
     /**
+     * Gets the value of the alcodon property.
      * 
-     * a Mapping entry and an associated protein sequence
+     * &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 alcodon property.
      * 
+     * &lt;p&gt;
+     * For example, to add a new item, do as follows:
+     * &lt;pre&gt;
+     *    getAlcodon().add(newItem);
+     * &lt;/pre&gt;
      * 
-     * @return possible object is {@link Mapping }
      * 
-     */
-    public Mapping getMapping()
-    {
-      return mapping;
-    }
-
-    /**
-     * Sets the value of the mapping property.
+     * &lt;p&gt;
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame.Alcodon }
      * 
-     * @param value
-     *          allowed object is {@link Mapping }
      * 
      */
-    public void setMapping(Mapping value)
-    {
-      this.mapping = value;
+    public List<AlcodonFrame.Alcodon> getAlcodon() {
+        if (alcodon == null) {
+            alcodon = new ArrayList<AlcodonFrame.Alcodon>();
+        }
+        return this.alcodon;
     }
 
     /**
-     * Gets the value of the dnasq property.
+     * Gets the value of the alcodMap 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 alcodMap property.
+     * 
+     * &lt;p&gt;
+     * For example, to add a new item, do as follows:
+     * &lt;pre&gt;
+     *    getAlcodMap().add(newItem);
+     * &lt;/pre&gt;
+     * 
+     * 
+     * &lt;p&gt;
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame.AlcodMap }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getDnasq()
-    {
-      return dnasq;
+    public List<AlcodonFrame.AlcodMap> getAlcodMap() {
+        if (alcodMap == null) {
+            alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
+        }
+        return this.alcodMap;
     }
 
+
     /**
-     * Sets the value of the dnasq property.
+     * &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;sequence&amp;gt;
+     *         &amp;lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="dnasq" use="required" 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;
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setDnasq(String value)
-    {
-      this.dnasq = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "mapping"
+    })
+    public static class AlcodMap {
 
-  }
+        @XmlElement(name = "Mapping", required = true)
+        protected Mapping mapping;
+        @XmlAttribute(name = "dnasq", required = true)
+        protected String dnasq;
 
-  /**
-   * 
-   * specifies a series of aligned codons from an associated DNA sequence
-   * alignment that when translated correspond to columns of a peptide
-   * alignment. Element may have either all pos1,2,3 attributes specified, or
-   * none at all (indicating a gapped column with no translated peptide).
-   * 
-   * 
-   * &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="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt;
-   * &amp;lt;attribute name="pos2"
-   * type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt;
-   * &amp;lt;attribute name="pos3"
-   * type="{http://www.w3.org/2001/XMLSchema}integer" /&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 Alcodon
-  {
+        /**
+         * 
+         *                                                                             a Mapping entry and an associated protein
+         *                                                                             sequence
+         *                                                                     
+         * 
+         * @return
+         *     possible object is
+         *     {@link Mapping }
+         *     
+         */
+        public Mapping getMapping() {
+            return mapping;
+        }
 
-    @XmlAttribute(name = "pos1")
-    protected BigInteger pos1;
+        /**
+         * Sets the value of the mapping property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Mapping }
+         *     
+         */
+        public void setMapping(Mapping value) {
+            this.mapping = value;
+        }
 
-    @XmlAttribute(name = "pos2")
-    protected BigInteger pos2;
+        /**
+         * Gets the value of the dnasq property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getDnasq() {
+            return dnasq;
+        }
 
-    @XmlAttribute(name = "pos3")
-    protected BigInteger pos3;
+        /**
+         * Sets the value of the dnasq property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setDnasq(String value) {
+            this.dnasq = value;
+        }
 
-    /**
-     * Gets the value of the pos1 property.
-     * 
-     * @return possible object is {@link BigInteger }
-     * 
-     */
-    public BigInteger getPos1()
-    {
-      return pos1;
     }
 
-    /**
-     * Sets the value of the pos1 property.
-     * 
-     * @param value
-     *          allowed object is {@link BigInteger }
-     * 
-     */
-    public void setPos1(BigInteger value)
-    {
-      this.pos1 = value;
-    }
 
     /**
-     * Gets the value of the pos2 property.
      * 
-     * @return possible object is {@link BigInteger }
+     *                                                                 specifies a series of aligned codons from an
+     *                                                                 associated DNA sequence alignment that when translated
+     *                                                                 correspond to columns of a peptide alignment.
+     *                                                                 Element may have
+     *                                                                 either all pos1,2,3 attributes specified, or none at all
+     *                                                                 (indicating a gapped column with no translated peptide).
+     *                                                         
      * 
-     */
-    public BigInteger getPos2()
-    {
-      return pos2;
-    }
-
-    /**
-     * Sets the value of the pos2 property.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link BigInteger }
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setPos2(BigInteger value)
-    {
-      this.pos2 = value;
-    }
-
-    /**
-     * Gets the value of the pos3 property.
+     * &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="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt;
+     *       &amp;lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt;
+     *       &amp;lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
-     * @return possible object is {@link BigInteger }
      * 
      */
-    public BigInteger getPos3()
-    {
-      return pos3;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Alcodon {
 
-    /**
-     * Sets the value of the pos3 property.
-     * 
-     * @param value
-     *          allowed object is {@link BigInteger }
-     * 
-     */
-    public void setPos3(BigInteger value)
-    {
-      this.pos3 = value;
-    }
+        @XmlAttribute(name = "pos1")
+        protected BigInteger pos1;
+        @XmlAttribute(name = "pos2")
+        protected BigInteger pos2;
+        @XmlAttribute(name = "pos3")
+        protected BigInteger pos3;
+
+        /**
+         * Gets the value of the pos1 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos1() {
+            return pos1;
+        }
 
-  }
+        /**
+         * Sets the value of the pos1 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos1(BigInteger value) {
+            this.pos1 = value;
+        }
+
+        /**
+         * Gets the value of the pos2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos2() {
+            return pos2;
+        }
+
+        /**
+         * Sets the value of the pos2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos2(BigInteger value) {
+            this.pos2 = value;
+        }
+
+        /**
+         * Gets the value of the pos3 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos3() {
+            return pos3;
+        }
+
+        /**
+         * Sets the value of the pos3 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos3(BigInteger value) {
+            this.pos3 = value;
+        }
+
+    }
 
 }