X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FSequence.java;fp=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FSequence.java;h=200184531823d56b909d5fce35a2bc358c77f0e6;hb=d043ce47fc710d3eb2629ba926a8a7417bd67d8c;hp=5381c3267aa51023ea604ffc0dd4e28e4a7fe44a;hpb=49db0dff1da16c3355b43a41498c1fc93ef47e91;p=jalview.git

diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
index 5381c32..2001845 100644
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -5,7 +5,6 @@
 // Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,332 +16,325 @@ 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;
+  @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;
 
     /**
-     * Gets the value of the dbRef property.
+     * Gets the value of the mapping 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.
+     * @return possible object is {@link Mapping }
      * 
-     * &lt;p&gt;
-     * For example, to add a new item, do as follows:
-     * &lt;pre&gt;
-     *    getDBRef().add(newItem);
-     * &lt;/pre&gt;
+     */
+    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 }
      * 
-     * &lt;p&gt;
-     * Objects of the following type(s) are allowed in the list
-     * {@link Sequence.DBRef }
+     */
+    public String getSource()
+    {
+      return source;
+    }
+
+    /**
+     * Sets the value of the source property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    public List<Sequence.DBRef> getDBRef() {
-        if (dbRef == null) {
-            dbRef = new ArrayList<Sequence.DBRef>();
-        }
-        return this.dbRef;
+    public void setSource(String value)
+    {
+      this.source = value;
     }
 
     /**
-     * Gets the value of the dsseqid property.
+     * Gets the value of the version property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getDsseqid() {
-        return dsseqid;
+    public String getVersion()
+    {
+      return version;
     }
 
     /**
-     * Sets the value of the dsseqid property.
+     * Sets the value of the version property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
+     *          allowed object is {@link String }
+     * 
      */
-    public void setDsseqid(String value) {
-        this.dsseqid = value;
+    public void setVersion(String value)
+    {
+      this.version = value;
     }
 
     /**
-     * Gets the value of the biotype property.
+     * Gets the value of the accessionId property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getBiotype() {
-        return biotype;
+    public String getAccessionId()
+    {
+      return accessionId;
     }
 
     /**
-     * Sets the value of the biotype property.
+     * Sets the value of the accessionId property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
+     *          allowed object is {@link String }
+     * 
      */
-    public void setBiotype(String value) {
-        this.biotype = value;
+    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;
+      }
+    }
 
     /**
-     * &lt;p&gt;Java class for anonymous complex type.
+     * Sets the value of the locus property.
      * 
-     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
+     * @param value
+     *          allowed object is {@link Boolean }
      * 
-     * &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;
+     */
+    public void setLocus(Boolean value)
+    {
+      this.locus = value;
+    }
+
+    /**
+     * Gets the value of the canonical property.
      * 
+     * @return possible object is {@link Boolean }
      * 
      */
-    @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;
-        }
+    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;
     }
 
+  }
+
 }