X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FSequenceSet.java;h=d6464b3551cecfd84c563aa4273cc1a6f6b3c5ba;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=c69334e14d76d6337e255d93fd22228190be52d4;hpb=e7338a61f3ce96dadf44ac80b2b32cc5ba4b94c8;p=jalview.git

diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index c69334e..d6464b3 100644
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.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;
@@ -17,302 +16,287 @@ 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"/> </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" })
 @XmlRootElement(name = "SequenceSet")
-public class SequenceSet {
+public class SequenceSet
+{
 
-    @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;
-    @XmlAttribute(name = "gapChar", required = true)
-    protected String gapChar;
-    @XmlAttribute(name = "datasetId")
-    protected String datasetId;
+  @XmlElement(name = "Sequence")
+  protected List<Sequence> 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;
+  @XmlElement(name = "Annotation")
+  protected List<Annotation> annotation;
+
+  protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+
+  @XmlElement(name = "AlcodonFrame")
+  protected List<AlcodonFrame> alcodonFrame;
+
+  @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>();
     }
+    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>();
-        }
-        return this.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;
+  }
 
-    /**
-     * 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;
+  /**
+   * 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;
+  }
 
-    /**
-     * 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;
+  /**
+   * 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;
+  }
+
+  /**
+   * 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 gapChar property.
+     * Gets the value of the key property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getGapChar() {
-        return gapChar;
+    public String getKey()
+    {
+      return key;
     }
 
     /**
-     * Sets the value of the gapChar property.
+     * Sets the value of the key property.
      * 
      * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
-     */
-    public void setGapChar(String value) {
-        this.gapChar = value;
-    }
-
-    /**
-     * Gets the value of the datasetId property.
+     *          allowed object is {@link String }
      * 
-     * @return
-     *     possible object is
-     *     {@link String }
-     *     
      */
-    public String getDatasetId() {
-        return datasetId;
+    public void setKey(String value)
+    {
+      this.key = value;
     }
 
     /**
-     * Sets the value of the datasetId property.
+     * Gets the value of the value property.
+     * 
+     * @return possible object is {@link String }
      * 
-     * @param value
-     *     allowed object is
-     *     {@link String }
-     *     
      */
-    public void setDatasetId(String value) {
-        this.datasetId = value;
+    public String getValue()
+    {
+      return 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;
+     * Sets the value of the value property.
      * 
+     * @param value
+     *          allowed object is {@link String }
      * 
      */
-    @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;
-        }
-
+    public void setValue(String value)
+    {
+      this.value = value;
     }
 
+  }
+
 }