Merge branch 'patch/JAL-4311_import_pLDDT_scores_from_nonAlphaFold_sources' into...

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

diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
index 2001845..76b4f1a 100644 (file)
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.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: 2023.09.01 at 02:16:11 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,325 +17,332 @@ 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>
- * <extension
- * base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
- * <sequence> <element name="DBRef" 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" minOccurs="0"/>
- * </sequence> <attribute name="source"
- * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
- * name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
- * <attribute name="accessionId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
- * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
- * /> <attribute name="canonical"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- * </restriction> </complexContent>
- * </complexType> </element>
- * </sequence> <attribute name="dsseqid"
- * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
- * name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </extension> </complexContent>
- * </complexType> </pre>
+ * <pre>
+ * <complexType>
+ *   <complexContent>
+ *     <extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
+ *       <sequence>
+ *         <element name="DBRef" 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" minOccurs="0"/>
+ *                 </sequence>
+ *                 <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                 <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *       <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </extension>
+ *   </complexContent>
+ * </complexType>
+ * </pre>
  * 
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "dbRef" })
+@XmlType(name = "", propOrder = {
+    "dbRef"
+})
 @XmlRootElement(name = "Sequence")
-public class Sequence extends SequenceType
+public class Sequence
+    extends SequenceType
 {
 
-  @XmlElement(name = "DBRef")
-  protected List<Sequence.DBRef> dbRef;
-
-  @XmlAttribute(name = "dsseqid")
-  protected String dsseqid;
-
-  @XmlAttribute(name = "biotype")
-  protected String biotype;
-
-  /**
-   * Gets the value of the dbRef 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 dbRef property.
-   * 
-   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
-   * getDBRef().add(newItem); &lt;/pre&gt;
-   * 
-   * 
-   * &lt;p&gt; Objects of the following type(s) are allowed in the list
-   * {@link Sequence.DBRef }
-   * 
-   * 
-   */
-  public List<Sequence.DBRef> getDBRef()
-  {
-    if (dbRef == null)
-    {
-      dbRef = new ArrayList<Sequence.DBRef>();
-    }
-    return this.dbRef;
-  }
-
-  /**
-   * Gets the value of the dsseqid property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDsseqid()
-  {
-    return dsseqid;
-  }
-
-  /**
-   * Sets the value of the dsseqid property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDsseqid(String value)
-  {
-    this.dsseqid = value;
-  }
-
-  /**
-   * Gets the value of the biotype property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getBiotype()
-  {
-    return biotype;
-  }
-
-  /**
-   * Sets the value of the biotype property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setBiotype(String value)
-  {
-    this.biotype = 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;sequence&amp;gt; &amp;lt;element
-   * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&amp;gt;
-   * &amp;lt;/sequence&amp;gt; &amp;lt;attribute name="source"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
-   * &amp;lt;attribute name="accessionId"
-   * type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt; &amp;lt;attribute
-   * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean"
-   * default="false" /&amp;gt; &amp;lt;attribute name="canonical"
-   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&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 DBRef
-  {
-
-    @XmlElement(name = "Mapping")
-    protected Mapping mapping;
-
-    @XmlAttribute(name = "source")
-    protected String source;
-
-    @XmlAttribute(name = "version")
-    protected String version;
-
-    @XmlAttribute(name = "accessionId")
-    protected String accessionId;
-
-    @XmlAttribute(name = "locus")
-    protected Boolean locus;
-
-    @XmlAttribute(name = "canonical")
-    protected Boolean canonical;
+    @XmlElement(name = "DBRef")
+    protected List<Sequence.DBRef> dbRef;
+    @XmlAttribute(name = "dsseqid")
+    protected String dsseqid;
+    @XmlAttribute(name = "biotype")
+    protected String biotype;
 
     /**
-     * Gets the value of the mapping property.
+     * Gets the value of the dbRef property.
      * 
-     * @return possible object is {@link Mapping }
+     * &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 dbRef property.
      * 
-     */
-    public Mapping getMapping()
-    {
-      return mapping;
-    }
-
-    /**
-     * Sets the value of the mapping property.
-     * 
-     * @param value
-     *          allowed object is {@link Mapping }
-     * 
-     */
-    public void setMapping(Mapping value)
-    {
-      this.mapping = value;
-    }
-
-    /**
-     * Gets the value of the source property.
+     * &lt;p&gt;
+     * For example, to add a new item, do as follows:
+     * &lt;pre&gt;
+     *    getDBRef().add(newItem);
+     * &lt;/pre&gt;
      * 
-     * @return possible object is {@link String }
      * 
-     */
-    public String getSource()
-    {
-      return source;
-    }
-
-    /**
-     * Sets the value of the source property.
+     * &lt;p&gt;
+     * Objects of the following type(s) are allowed in the list
+     * {@link Sequence.DBRef }
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setSource(String value)
-    {
-      this.source = value;
+    public List<Sequence.DBRef> getDBRef() {
+        if (dbRef == null) {
+            dbRef = new ArrayList<Sequence.DBRef>();
+        }
+        return this.dbRef;
     }
 
     /**
-     * Gets the value of the version property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the dsseqid property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getVersion()
-    {
-      return version;
+    public String getDsseqid() {
+        return dsseqid;
     }
 
     /**
-     * Sets the value of the version property.
+     * Sets the value of the dsseqid property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setVersion(String value)
-    {
-      this.version = value;
+    public void setDsseqid(String value) {
+        this.dsseqid = value;
     }
 
     /**
-     * Gets the value of the accessionId property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the biotype property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getAccessionId()
-    {
-      return accessionId;
+    public String getBiotype() {
+        return biotype;
     }
 
     /**
-     * Sets the value of the accessionId property.
+     * Sets the value of the biotype property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setAccessionId(String value)
-    {
-      this.accessionId = value;
+    public void setBiotype(String value) {
+        this.biotype = value;
     }
 
-    /**
-     * Gets the value of the locus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isLocus()
-    {
-      if (locus == null)
-      {
-        return false;
-      }
-      else
-      {
-        return locus;
-      }
-    }
 
     /**
-     * Sets the value of the locus property.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setLocus(Boolean value)
-    {
-      this.locus = value;
-    }
-
-    /**
-     * Gets the value of the canonical 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;sequence&amp;gt;
+     *         &amp;lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&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 Boolean }
      * 
      */
-    public boolean isCanonical()
-    {
-      if (canonical == null)
-      {
-        return false;
-      }
-      else
-      {
-        return canonical;
-      }
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "mapping"
+    })
+    public static class DBRef {
+
+        @XmlElement(name = "Mapping")
+        protected Mapping mapping;
+        @XmlAttribute(name = "source")
+        protected String source;
+        @XmlAttribute(name = "version")
+        protected String version;
+        @XmlAttribute(name = "accessionId")
+        protected String accessionId;
+        @XmlAttribute(name = "locus")
+        protected Boolean locus;
+        @XmlAttribute(name = "canonical")
+        protected Boolean canonical;
+
+        /**
+         * Gets the value of the mapping property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Mapping }
+         *     
+         */
+        public Mapping getMapping() {
+            return mapping;
+        }
+
+        /**
+         * Sets the value of the mapping property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Mapping }
+         *     
+         */
+        public void setMapping(Mapping value) {
+            this.mapping = value;
+        }
+
+        /**
+         * Gets the value of the source property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getSource() {
+            return source;
+        }
+
+        /**
+         * Sets the value of the source property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setSource(String value) {
+            this.source = value;
+        }
+
+        /**
+         * Gets the value of the version property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getVersion() {
+            return version;
+        }
+
+        /**
+         * Sets the value of the version property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setVersion(String value) {
+            this.version = value;
+        }
+
+        /**
+         * Gets the value of the accessionId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getAccessionId() {
+            return accessionId;
+        }
+
+        /**
+         * Sets the value of the accessionId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setAccessionId(String value) {
+            this.accessionId = value;
+        }
+
+        /**
+         * Gets the value of the locus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isLocus() {
+            if (locus == null) {
+                return false;
+            } else {
+                return locus;
+            }
+        }
+
+        /**
+         * Sets the value of the locus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setLocus(Boolean value) {
+            this.locus = value;
+        }
+
+        /**
+         * Gets the value of the canonical property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isCanonical() {
+            if (canonical == null) {
+                return false;
+            } else {
+                return canonical;
+            }
+        }
+
+        /**
+         * Sets the value of the canonical property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCanonical(Boolean value) {
+            this.canonical = value;
+        }
 
-    /**
-     * Sets the value of the canonical property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCanonical(Boolean value)
-    {
-      this.canonical = value;
     }
 
-  }
-
 }