X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FAlcodonFrame.java;fp=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FAlcodonFrame.java;h=bb263038a90303639d936d8c80bc14beb82e7992;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=c412c36eeb78e9c02b21c1c196aea46e78f1ca9d;hpb=cb31e23d9138e481479623374aed7767bf8934d2;p=jalview.git

diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java
index c412c36..bb26303 100644
--- a/src/jalview/xml/binding/jalview/AlcodonFrame.java
+++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java
@@ -5,7 +5,6 @@
 // Generated on: 2023.11.01 at 07:03:09 PM GMT 
 //
 
-
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -18,314 +17,288 @@ 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 {
+public class AlcodonFrame
+{
+
+  protected List<AlcodonFrame.Alcodon> alcodon;
+
+  protected List<AlcodonFrame.AlcodMap> alcodMap;
 
-    protected List<AlcodonFrame.Alcodon> alcodon;
-    protected List<AlcodonFrame.AlcodMap> alcodMap;
+  /**
+   * 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;
 
     /**
-     * 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.
+     * a Mapping entry and an associated protein sequence
      * 
-     * &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 }
      * 
+     * @return possible object is {@link Mapping }
      * 
      */
-    public List<AlcodonFrame.Alcodon> getAlcodon() {
-        if (alcodon == null) {
-            alcodon = new ArrayList<AlcodonFrame.Alcodon>();
-        }
-        return this.alcodon;
+    public Mapping getMapping()
+    {
+      return mapping;
     }
 
     /**
-     * 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 }
+     * Sets the value of the mapping property.
      * 
+     * @param value
+     *          allowed object is {@link Mapping }
      * 
      */
-    public List<AlcodonFrame.AlcodMap> getAlcodMap() {
-        if (alcodMap == null) {
-            alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
-        }
-        return this.alcodMap;
+    public void setMapping(Mapping value)
+    {
+      this.mapping = value;
     }
 
-
     /**
-     * &lt;p&gt;Java class for anonymous complex type.
+     * Gets the value of the dnasq property.
      * 
-     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link String }
      * 
-     * &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;
+     */
+    public String getDnasq()
+    {
+      return dnasq;
+    }
+
+    /**
+     * Sets the value of the dnasq property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = {
-        "mapping"
-    })
-    public static class AlcodMap {
+    public void setDnasq(String value)
+    {
+      this.dnasq = value;
+    }
 
-        @XmlElement(name = "Mapping", required = true)
-        protected Mapping mapping;
-        @XmlAttribute(name = "dnasq", required = true)
-        protected String dnasq;
+  }
 
-        /**
-         * 
-         * 										a Mapping entry and an associated protein
-         * 										sequence
-         * 									
-         * 
-         * @return
-         *     possible object is
-         *     {@link Mapping }
-         *     
-         */
-        public Mapping getMapping() {
-            return mapping;
-        }
+  /**
+   * 
+   * 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
+  {
 
-        /**
-         * Sets the value of the mapping property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link Mapping }
-         *     
-         */
-        public void setMapping(Mapping value) {
-            this.mapping = value;
-        }
+    @XmlAttribute(name = "pos1")
+    protected BigInteger pos1;
 
-        /**
-         * Gets the value of the dnasq property.
-         * 
-         * @return
-         *     possible object is
-         *     {@link String }
-         *     
-         */
-        public String getDnasq() {
-            return dnasq;
-        }
+    @XmlAttribute(name = "pos2")
+    protected BigInteger pos2;
 
-        /**
-         * Sets the value of the dnasq property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link String }
-         *     
-         */
-        public void setDnasq(String value) {
-            this.dnasq = value;
-        }
+    @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.
      * 
-     * 								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).
-     * 							
+     * @param value
+     *          allowed object is {@link BigInteger }
      * 
-     * &lt;p&gt;Java class for anonymous complex type.
+     */
+    public void setPos1(BigInteger value)
+    {
+      this.pos1 = value;
+    }
+
+    /**
+     * Gets the value of the pos2 property.
      * 
-     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
+     * @return possible object is {@link BigInteger }
      * 
-     * &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;
+     */
+    public BigInteger getPos2()
+    {
+      return pos2;
+    }
+
+    /**
+     * Sets the value of the pos2 property.
      * 
+     * @param value
+     *          allowed object is {@link BigInteger }
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Alcodon {
-
-        @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;
-        }
+    public void setPos2(BigInteger value)
+    {
+      this.pos2 = value;
+    }
 
-        /**
-         * Sets the value of the pos3 property.
-         * 
-         * @param value
-         *     allowed object is
-         *     {@link BigInteger }
-         *     
-         */
-        public void setPos3(BigInteger value) {
-            this.pos3 = 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;
     }
 
+  }
+
 }