JAL-3863 add canonical DBRefEntry flag to Jalview project

diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd
index 20c19dd..333a4e4 100755 (executable)
--- a/schemas/vamsas.xsd
+++ b/schemas/vamsas.xsd
@@ -173,6 +173,13 @@
                                                                                </xs:documentation>
                                                                        </xs:annotation>
                                                                </xs:attribute>
+                                                               <xs:attribute name="canonical" type="xs:boolean" default="false">
+                                                                       <xs:annotation>
+                                                                               <xs:documentation>
+                                                                                       true for the representative accession for databases where multiple accessions map to the same entry (eg. Uniprot)
+                                                                               </xs:documentation>
+                                                                       </xs:annotation>
+                                                               </xs:attribute>
                                                        </xs:complexType>
                                                </xs:element>
                                        </xs:sequence>

diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java
index 64b3a9c..ffd942f 100644 (file)
--- a/src/jalview/project/Jalview2XML.java
+++ b/src/jalview/project/Jalview2XML.java
@@ -2529,6 +2529,7 @@ public class Jalview2XML
         dbref.setSource(ref.getSource());
         dbref.setVersion(ref.getVersion());
         dbref.setAccessionId(ref.getAccessionId());
+        dbref.setCanonical(ref.isCanonical());
         if (ref instanceof GeneLocus)
         {
           dbref.setLocus(true);
@@ -5622,6 +5623,7 @@ public class Jalview2XML
       {
         entry.setMap(addMapping(dr.getMapping()));
       }
+      entry.setCanonical(dr.isCanonical());
       datasetSequence.addDBRef(entry);
     }
   }

diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java
index cb90984..e52eefb 100644 (file)
--- a/src/jalview/xml/binding/jalview/AlcodonFrame.java
+++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -20,43 +20,43 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for anonymous complex type.
+ * &lt;p&gt;Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType>
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="alcodon" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
- *                 &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
- *                 &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *         &lt;element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;sequence>
- *                   &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
- *                 &lt;/sequence>
- *                 &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *       &lt;/sequence>
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &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 name="alcodon" maxOccurs="unbounded" minOccurs="0"&amp;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;
+ *         &amp;lt;/element&amp;gt;
+ *         &amp;lt;element name="alcodMap" maxOccurs="unbounded" minOccurs="0"&amp;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;
+ *         &amp;lt;/element&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -74,20 +74,20 @@ public class AlcodonFrame {
     /**
      * Gets the value of the alcodon property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the alcodon property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the alcodon property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getAlcodon().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link AlcodonFrame.Alcodon }
      * 
@@ -103,20 +103,20 @@ public class AlcodonFrame {
     /**
      * Gets the value of the alcodMap property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the alcodMap property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the alcodMap property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getAlcodMap().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link AlcodonFrame.AlcodMap }
      * 
@@ -131,22 +131,22 @@ public class AlcodonFrame {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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;
      * 
      * 
      */
@@ -220,21 +220,21 @@ public class AlcodonFrame {
      *                                                                 Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
      *                                                         
      * 
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *       &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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;
      * 
      * 
      */

diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java
index 35f78f3..6c1573f 100644 (file)
--- a/src/jalview/xml/binding/jalview/Annotation.java
+++ b/src/jalview/xml/binding/jalview/Annotation.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -19,61 +19,61 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for anonymous complex type.
+ * &lt;p&gt;Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType>
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
- *         &lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- *         &lt;element name="thresholdLine" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                 &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *         &lt;element name="property" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *       &lt;/sequence>
- *       &lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *       &lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *       &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
- *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *       &lt;attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *       &lt;attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *       &lt;attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *       &lt;attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *       &lt;attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *       &lt;attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &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}annotationElement" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+ *         &amp;lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="thresholdLine" minOccurs="0"&amp;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="label" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                 &amp;lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                 &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *               &amp;lt;/restriction&amp;gt;
+ *             &amp;lt;/complexContent&amp;gt;
+ *           &amp;lt;/complexType&amp;gt;
+ *         &amp;lt;/element&amp;gt;
+ *         &amp;lt;element name="property" maxOccurs="unbounded" minOccurs="0"&amp;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="name" 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;
+ *         &amp;lt;/element&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *       &amp;lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *       &amp;lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" /&amp;gt;
+ *       &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *       &amp;lt;attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *       &amp;lt;attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *       &amp;lt;attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *       &amp;lt;attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *       &amp;lt;attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *       &amp;lt;attribute name="calcId" 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;
  * 
  * 
  */
@@ -132,20 +132,20 @@ public class Annotation {
     /**
      * Gets the value of the annotationElement property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the annotationElement property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the annotationElement property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getAnnotationElement().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link AnnotationElement }
      * 
@@ -233,20 +233,20 @@ public class Annotation {
     /**
      * Gets the value of the property property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the property property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the property property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getProperty().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link Annotation.Property }
      * 
@@ -673,20 +673,20 @@ public class Annotation {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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="name" 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;
      * 
      * 
      */
@@ -751,21 +751,21 @@ public class Annotation {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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="label" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *       &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */

diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
index 6f5ef65..1b31b22 100644 (file)
--- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
+++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -15,26 +15,26 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for AnnotationColourScheme complex type.
+ * &lt;p&gt;Java class for AnnotationColourScheme complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="AnnotationColourScheme">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *       &lt;attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *       &lt;attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="AnnotationColourScheme"&amp;gt;
+ *   &amp;lt;complexContent&amp;gt;
+ *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *       &amp;lt;attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *       &amp;lt;attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *       &amp;lt;attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */

diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java
index 6780323..d141272 100644 (file)
--- a/src/jalview/xml/binding/jalview/AnnotationElement.java
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -16,32 +16,32 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for anonymous complex type.
+ * &lt;p&gt;Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType>
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- *         &lt;element name="secondaryStructure" minOccurs="0">
- *           &lt;simpleType>
- *             &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
- *               &lt;length value="1"/>
- *             &lt;/restriction>
- *           &lt;/simpleType>
- *         &lt;/element>
- *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/>
- *       &lt;/sequence>
- *       &lt;attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &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 name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="secondaryStructure" minOccurs="0"&amp;gt;
+ *           &amp;lt;simpleType&amp;gt;
+ *             &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt;
+ *               &amp;lt;length value="1"/&amp;gt;
+ *             &amp;lt;/restriction&amp;gt;
+ *           &amp;lt;/simpleType&amp;gt;
+ *         &amp;lt;/element&amp;gt;
+ *         &amp;lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */

diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java
index 5edb2e8..bff4959 100644 (file)
--- a/src/jalview/xml/binding/jalview/DoubleMatrix.java
+++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -18,25 +18,25 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for DoubleMatrix complex type.
+ * &lt;p&gt;Java class for DoubleMatrix complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="DoubleMatrix">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/>
- *         &lt;element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
- *         &lt;element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/>
- *       &lt;/sequence>
- *       &lt;attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="DoubleMatrix"&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 name="row" type="{www.jalview.org}DoubleVector" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="D" type="{www.jalview.org}DoubleVector" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="E" type="{www.jalview.org}DoubleVector" minOccurs="0"/&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="rows" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="columns" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -61,20 +61,20 @@ public class DoubleMatrix {
     /**
      * Gets the value of the row property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the row property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the row property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getRow().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link DoubleVector }
      * 

diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java
index 68ebf9b..a255c74 100644 (file)
--- a/src/jalview/xml/binding/jalview/DoubleVector.java
+++ b/src/jalview/xml/binding/jalview/DoubleVector.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -17,21 +17,21 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for DoubleVector complex type.
+ * &lt;p&gt;Java class for DoubleVector complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="DoubleVector">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/>
- *       &lt;/sequence>
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="DoubleVector"&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 name="v" type="{http://www.w3.org/2001/XMLSchema}double" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -47,20 +47,20 @@ public class DoubleVector {
     /**
      * Gets the value of the v property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the v property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the v property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getV().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link Double }
      * 

diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java
index 39fc0c3..73468c9 100644 (file)
--- a/src/jalview/xml/binding/jalview/Feature.java
+++ b/src/jalview/xml/binding/jalview/Feature.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -17,38 +17,38 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for feature complex type.
+ * &lt;p&gt;Java class for feature complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="feature">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="otherData" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *       &lt;/sequence>
- *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="feature"&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 name="otherData" maxOccurs="unbounded" minOccurs="0"&amp;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" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                 &amp;lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                 &amp;lt;attribute name="value" 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;
+ *         &amp;lt;/element&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *       &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -77,20 +77,20 @@ public class Feature {
     /**
      * Gets the value of the otherData property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the otherData property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the otherData property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getOtherData().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link Feature.OtherData }
      * 
@@ -257,21 +257,21 @@ public class Feature {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="value" 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;
      * 
      * 
      */

diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java
index c92f72c..dee9bc1 100644 (file)
--- a/src/jalview/xml/binding/jalview/FeatureMatcher.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -18,24 +18,24 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for FeatureMatcher complex type.
+ * &lt;p&gt;Java class for FeatureMatcher complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="FeatureMatcher">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- *         &lt;element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *       &lt;/sequence>
- *       &lt;attribute name="by" type="{www.jalview.org/colours}FilterBy" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="FeatureMatcher"&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 name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+ *         &amp;lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="by" type="{www.jalview.org/colours}FilterBy" /&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -59,20 +59,20 @@ public class FeatureMatcher {
     /**
      * Gets the value of the attributeName property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the attributeName property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getAttributeName().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link String }
      * 

diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
index 0c21215..4c0848f 100644 (file)
--- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -20,33 +20,33 @@ import javax.xml.bind.annotation.XmlType;
 /**
  * A feature match condition, which may be simple or compound
  * 
- * <p>Java class for FeatureMatcherSet complex type.
+ * &lt;p&gt;Java class for FeatureMatcherSet complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="FeatureMatcherSet">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;choice>
- *         &lt;element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
- *         &lt;element name="compoundMatcher">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;sequence>
- *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
- *                 &lt;/sequence>
- *                 &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *       &lt;/choice>
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="FeatureMatcherSet"&amp;gt;
+ *   &amp;lt;complexContent&amp;gt;
+ *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *       &amp;lt;choice&amp;gt;
+ *         &amp;lt;element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/&amp;gt;
+ *         &amp;lt;element name="compoundMatcher"&amp;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 name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&amp;gt;
+ *                 &amp;lt;/sequence&amp;gt;
+ *                 &amp;lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *               &amp;lt;/restriction&amp;gt;
+ *             &amp;lt;/complexContent&amp;gt;
+ *           &amp;lt;/complexType&amp;gt;
+ *         &amp;lt;/element&amp;gt;
+ *       &amp;lt;/choice&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -112,22 +112,22 @@ public class FeatureMatcherSet {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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 name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -145,20 +145,20 @@ public class FeatureMatcherSet {
         /**
          * Gets the value of the matcherSet property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the matcherSet property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the matcherSet property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getMatcherSet().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link FeatureMatcherSet }
          * 

diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java
index 36b454f..bbb84a4 100644 (file)
--- a/src/jalview/xml/binding/jalview/FilterBy.java
+++ b/src/jalview/xml/binding/jalview/FilterBy.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -14,19 +14,18 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for FilterBy.
+ * &lt;p&gt;Java class for FilterBy.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <p>
- * <pre>
- * &lt;simpleType name="FilterBy">
- *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
- *     &lt;enumeration value="byLabel"/>
- *     &lt;enumeration value="byScore"/>
- *     &lt;enumeration value="byAttribute"/>
- *   &lt;/restriction>
- * &lt;/simpleType>
- * </pre>
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
+ * &lt;pre&gt;
+ * &amp;lt;simpleType name="FilterBy"&amp;gt;
+ *   &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt;
+ *     &amp;lt;enumeration value="byLabel"/&amp;gt;
+ *     &amp;lt;enumeration value="byScore"/&amp;gt;
+ *     &amp;lt;enumeration value="byAttribute"/&amp;gt;
+ *   &amp;lt;/restriction&amp;gt;
+ * &amp;lt;/simpleType&amp;gt;
+ * &lt;/pre&gt;
  * 
  */
 @XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")

diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index 0ea2491..90819d7 100644 (file)
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -24,341 +24,341 @@ import javax.xml.datatype.XMLGregorianCalendar;
 
 
 /**
- * <p>Java class for JalviewModel complex type.
+ * &lt;p&gt;Java class for JalviewModel complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="JalviewModel">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
- *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
- *         &lt;sequence>
- *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;extension base="{www.jalview.org}pdbentry">
- *                             &lt;sequence>
- *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
- *                                 &lt;complexType>
- *                                   &lt;simpleContent>
- *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
- *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     &lt;/extension>
- *                                   &lt;/simpleContent>
- *                                 &lt;/complexType>
- *                               &lt;/element>
- *                             &lt;/sequence>
- *                           &lt;/extension>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;sequence>
- *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
- *                                 &lt;complexType>
- *                                   &lt;complexContent>
- *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     &lt;/restriction>
- *                                   &lt;/complexContent>
- *                                 &lt;/complexType>
- *                               &lt;/element>
- *                             &lt;/sequence>
- *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                   &lt;/sequence>
- *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                   &lt;/sequence>
- *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           &lt;/extension>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                   &lt;/sequence>
- *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- *                   &lt;/sequence>
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence minOccurs="0">
- *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *                   &lt;/sequence>
- *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attGroup ref="{www.jalview.org}position"/>
- *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attGroup ref="{www.jalview.org}position"/>
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="seqPointMin">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attGroup ref="{www.jalview.org}position"/>
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="seqPointMax">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attGroup ref="{www.jalview.org}position"/>
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
- *                   &lt;/sequence>
- *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
- *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="FeatureSettings" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;sequence>
- *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- *                             &lt;/sequence>
- *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                   &lt;/sequence>
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *         &lt;/sequence>
- *       &lt;/sequence>
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="JalviewModel"&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 name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&amp;gt;
+ *         &amp;lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+ *         &amp;lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&amp;gt;
+ *         &amp;lt;sequence&amp;gt;
+ *           &amp;lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&amp;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 name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *                     &amp;lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
+ *                             &amp;lt;sequence&amp;gt;
+ *                               &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *                                 &amp;lt;complexType&amp;gt;
+ *                                   &amp;lt;simpleContent&amp;gt;
+ *                                     &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
+ *                                       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+ *                                       &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                                       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                                       &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                                       &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                                       &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                                       &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                                     &amp;lt;/extension&amp;gt;
+ *                                   &amp;lt;/simpleContent&amp;gt;
+ *                                 &amp;lt;/complexType&amp;gt;
+ *                               &amp;lt;/element&amp;gt;
+ *                             &amp;lt;/sequence&amp;gt;
+ *                           &amp;lt;/extension&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *                     &amp;lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&amp;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 name="secondaryStructure" maxOccurs="unbounded"&amp;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="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                                       &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                                       &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                                       &amp;lt;attribute name="viewerState" 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;
+ *                               &amp;lt;/element&amp;gt;
+ *                             &amp;lt;/sequence&amp;gt;
+ *                             &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+ *                             &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                             &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                             &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                             &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                 &amp;lt;/restriction&amp;gt;
+ *               &amp;lt;/complexContent&amp;gt;
+ *             &amp;lt;/complexType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&amp;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 name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&amp;gt;
+ *                     &amp;lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="id" 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;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&amp;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 name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
+ *                     &amp;lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&amp;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="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                             &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
+ *                             &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                             &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                             &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                           &amp;lt;/extension&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+ *                   &amp;lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
+ *                   &amp;lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="showComplementFeaturesOnTop" 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;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&amp;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 name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attribute name="id" 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;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&amp;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 minOccurs="0"&amp;gt;
+ *                     &amp;lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+ *                     &amp;lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+ *                   &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                   &amp;lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
+ *                   &amp;lt;attribute name="linkToAllViews" 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;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&amp;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 name="sequencePoint" maxOccurs="unbounded"&amp;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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+ *                             &amp;lt;attribute name="sequenceRef" 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;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="axis" maxOccurs="3" minOccurs="3"&amp;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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="seqPointMin"&amp;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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="seqPointMax"&amp;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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+ *                   &amp;lt;attGroup ref="{www.jalview.org}SimilarityParams"/&amp;gt;
+ *                   &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                   &amp;lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                 &amp;lt;/restriction&amp;gt;
+ *               &amp;lt;/complexContent&amp;gt;
+ *             &amp;lt;/complexType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="FeatureSettings" minOccurs="0"&amp;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 name="setting" maxOccurs="unbounded" minOccurs="0"&amp;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 name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
+ *                               &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
+ *                             &amp;lt;/sequence&amp;gt;
+ *                             &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                             &amp;lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                             &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                             &amp;lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                             &amp;lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                             &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
+ *                             &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                             &amp;lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                             &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                             &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                             &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                             &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="group" maxOccurs="unbounded" minOccurs="0"&amp;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="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                             &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                 &amp;lt;/restriction&amp;gt;
+ *               &amp;lt;/complexContent&amp;gt;
+ *             &amp;lt;/complexType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *         &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -473,20 +473,20 @@ public class JalviewModel {
     /**
      * Gets the value of the jSeq property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the jSeq property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the jSeq property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getJSeq().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.JSeq }
      * 
@@ -502,20 +502,20 @@ public class JalviewModel {
     /**
      * Gets the value of the jGroup property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the jGroup property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the jGroup property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getJGroup().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.JGroup }
      * 
@@ -531,20 +531,20 @@ public class JalviewModel {
     /**
      * Gets the value of the viewport property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the viewport property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the viewport property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getViewport().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.Viewport }
      * 
@@ -560,20 +560,20 @@ public class JalviewModel {
     /**
      * Gets the value of the userColours property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the userColours property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the userColours property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getUserColours().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.UserColours }
      * 
@@ -589,20 +589,20 @@ public class JalviewModel {
     /**
      * Gets the value of the tree property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the tree property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the tree property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getTree().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.Tree }
      * 
@@ -618,20 +618,20 @@ public class JalviewModel {
     /**
      * Gets the value of the pcaViewer property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the pcaViewer property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the pcaViewer property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getPcaViewer().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.PcaViewer }
      * 
@@ -670,54 +670,54 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;sequence>
-     *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-     *                 &lt;/sequence>
-     *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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 name="setting" maxOccurs="unbounded" minOccurs="0"&amp;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 name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
+     *                   &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
+     *                 &amp;lt;/sequence&amp;gt;
+     *                 &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                 &amp;lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *                 &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *                 &amp;lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *                 &amp;lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *                 &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
+     *                 &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *                 &amp;lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *                 &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *                 &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *                 &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *                 &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="group" maxOccurs="unbounded" minOccurs="0"&amp;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="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                 &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -736,20 +736,20 @@ public class JalviewModel {
         /**
          * Gets the value of the setting property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the setting property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the setting property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getSetting().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.FeatureSettings.Setting }
          * 
@@ -765,20 +765,20 @@ public class JalviewModel {
         /**
          * Gets the value of the group property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the group property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the group property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getGroup().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.FeatureSettings.Group }
          * 
@@ -793,20 +793,20 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &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="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *       &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -863,34 +863,34 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;sequence>
-         *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-         *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-         *       &lt;/sequence>
-         *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-         *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &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 name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
+         *         &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
+         *       &amp;lt;/sequence&amp;gt;
+         *       &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *       &amp;lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *       &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *       &amp;lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+         *       &amp;lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *       &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
+         *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+         *       &amp;lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *       &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+         *       &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+         *       &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *       &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -933,20 +933,20 @@ public class JalviewModel {
             /**
              * Gets the value of the attributeName property.
              * 
-             * <p>
+             * &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 <CODE>set</CODE> method for the attributeName property.
+             * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
              * 
-             * <p>
+             * &lt;p&gt;
              * For example, to add a new item, do as follows:
-             * <pre>
+             * &lt;pre&gt;
              *    getAttributeName().add(newItem);
-             * </pre>
+             * &lt;/pre&gt;
              * 
              * 
-             * <p>
+             * &lt;p&gt;
              * Objects of the following type(s) are allowed in the list
              * {@link String }
              * 
@@ -1265,41 +1265,41 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-     *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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 name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&amp;gt;
+     *         &amp;lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="id" 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;
      * 
      * 
      */
@@ -1356,20 +1356,20 @@ public class JalviewModel {
         /**
          * Gets the value of the seq property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the seq property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the seq property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getSeq().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link String }
          * 
@@ -1882,80 +1882,80 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;extension base="{www.jalview.org}pdbentry">
-     *                 &lt;sequence>
-     *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
-     *                     &lt;complexType>
-     *                       &lt;simpleContent>
-     *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-     *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         &lt;/extension>
-     *                       &lt;/simpleContent>
-     *                     &lt;/complexType>
-     *                   &lt;/element>
-     *                 &lt;/sequence>
-     *               &lt;/extension>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;sequence>
-     *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
-     *                     &lt;complexType>
-     *                       &lt;complexContent>
-     *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         &lt;/restriction>
-     *                       &lt;/complexContent>
-     *                     &lt;/complexType>
-     *                   &lt;/element>
-     *                 &lt;/sequence>
-     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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 name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+     *         &amp;lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
+     *                 &amp;lt;sequence&amp;gt;
+     *                   &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+     *                     &amp;lt;complexType&amp;gt;
+     *                       &amp;lt;simpleContent&amp;gt;
+     *                         &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
+     *                           &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+     *                           &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *                           &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                           &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *                           &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *                           &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *                           &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                         &amp;lt;/extension&amp;gt;
+     *                       &amp;lt;/simpleContent&amp;gt;
+     *                     &amp;lt;/complexType&amp;gt;
+     *                   &amp;lt;/element&amp;gt;
+     *                 &amp;lt;/sequence&amp;gt;
+     *               &amp;lt;/extension&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+     *         &amp;lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&amp;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 name="secondaryStructure" maxOccurs="unbounded"&amp;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="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                           &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                           &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *                           &amp;lt;attribute name="viewerState" 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;
+     *                   &amp;lt;/element&amp;gt;
+     *                 &amp;lt;/sequence&amp;gt;
+     *                 &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+     *                 &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                 &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                 &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *                 &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -1992,20 +1992,20 @@ public class JalviewModel {
         /**
          * Gets the value of the features property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the features property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the features property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getFeatures().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link Feature }
          * 
@@ -2021,20 +2021,20 @@ public class JalviewModel {
         /**
          * Gets the value of the pdbids property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the pdbids property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the pdbids property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getPdbids().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.JSeq.Pdbids }
          * 
@@ -2050,20 +2050,20 @@ public class JalviewModel {
         /**
          * Gets the value of the hiddenSequences property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the hiddenSequences property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenSequences property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getHiddenSequences().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link Integer }
          * 
@@ -2079,20 +2079,20 @@ public class JalviewModel {
         /**
          * Gets the value of the rnaViewer property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the rnaViewer property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the rnaViewer property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getRnaViewer().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.JSeq.RnaViewer }
          * 
@@ -2235,35 +2235,35 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;extension base="{www.jalview.org}pdbentry">
-         *       &lt;sequence>
-         *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
-         *           &lt;complexType>
-         *             &lt;simpleContent>
-         *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-         *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-         *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-         *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-         *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *               &lt;/extension>
-         *             &lt;/simpleContent>
-         *           &lt;/complexType>
-         *         &lt;/element>
-         *       &lt;/sequence>
-         *     &lt;/extension>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
+         *       &amp;lt;sequence&amp;gt;
+         *         &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+         *           &amp;lt;complexType&amp;gt;
+         *             &amp;lt;simpleContent&amp;gt;
+         *               &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
+         *                 &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+         *                 &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *                 &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *                 &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+         *                 &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+         *                 &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+         *                 &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *               &amp;lt;/extension&amp;gt;
+         *             &amp;lt;/simpleContent&amp;gt;
+         *           &amp;lt;/complexType&amp;gt;
+         *         &amp;lt;/element&amp;gt;
+         *       &amp;lt;/sequence&amp;gt;
+         *     &amp;lt;/extension&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -2281,20 +2281,20 @@ public class JalviewModel {
             /**
              * Gets the value of the structureState property.
              * 
-             * <p>
+             * &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 <CODE>set</CODE> method for the structureState property.
+             * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the structureState property.
              * 
-             * <p>
+             * &lt;p&gt;
              * For example, to add a new item, do as follows:
-             * <pre>
+             * &lt;pre&gt;
              *    getStructureState().add(newItem);
-             * </pre>
+             * &lt;/pre&gt;
              * 
              * 
-             * <p>
+             * &lt;p&gt;
              * Objects of the following type(s) are allowed in the list
              * {@link JalviewModel.JSeq.Pdbids.StructureState }
              * 
@@ -2309,25 +2309,25 @@ public class JalviewModel {
 
 
             /**
-             * <p>Java class for anonymous complex type.
+             * &lt;p&gt;Java class for anonymous complex type.
              * 
-             * <p>The following schema fragment specifies the expected content contained within this class.
+             * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
              * 
-             * <pre>
-             * &lt;complexType>
-             *   &lt;simpleContent>
-             *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-             *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-             *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-             *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     &lt;/extension>
-             *   &lt;/simpleContent>
-             * &lt;/complexType>
-             * </pre>
+             * &lt;pre&gt;
+             * &amp;lt;complexType&amp;gt;
+             *   &amp;lt;simpleContent&amp;gt;
+             *     &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
+             *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+             *       &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+             *       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+             *       &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+             *       &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+             *       &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+             *       &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+             *     &amp;lt;/extension&amp;gt;
+             *   &amp;lt;/simpleContent&amp;gt;
+             * &amp;lt;/complexType&amp;gt;
+             * &lt;/pre&gt;
              * 
              * 
              */
@@ -2642,37 +2642,37 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;sequence>
-         *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
-         *           &lt;complexType>
-         *             &lt;complexContent>
-         *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *               &lt;/restriction>
-         *             &lt;/complexContent>
-         *           &lt;/complexType>
-         *         &lt;/element>
-         *       &lt;/sequence>
-         *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-         *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &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 name="secondaryStructure" maxOccurs="unbounded"&amp;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="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *                 &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *                 &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *                 &amp;lt;attribute name="viewerState" 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;
+         *         &amp;lt;/element&amp;gt;
+         *       &amp;lt;/sequence&amp;gt;
+         *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+         *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *       &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *       &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -2704,20 +2704,20 @@ public class JalviewModel {
             /**
              * Gets the value of the secondaryStructure property.
              * 
-             * <p>
+             * &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 <CODE>set</CODE> method for the secondaryStructure property.
+             * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the secondaryStructure property.
              * 
-             * <p>
+             * &lt;p&gt;
              * For example, to add a new item, do as follows:
-             * <pre>
+             * &lt;pre&gt;
              *    getSecondaryStructure().add(newItem);
-             * </pre>
+             * &lt;/pre&gt;
              * 
              * 
-             * <p>
+             * &lt;p&gt;
              * Objects of the following type(s) are allowed in the list
              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
              * 
@@ -2924,22 +2924,22 @@ public class JalviewModel {
 
 
             /**
-             * <p>Java class for anonymous complex type.
+             * &lt;p&gt;Java class for anonymous complex type.
              * 
-             * <p>The following schema fragment specifies the expected content contained within this class.
+             * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
              * 
-             * <pre>
-             * &lt;complexType>
-             *   &lt;complexContent>
-             *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     &lt;/restriction>
-             *   &lt;/complexContent>
-             * &lt;/complexType>
-             * </pre>
+             * &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="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+             *       &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+             *       &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+             *       &amp;lt;attribute name="viewerState" 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;
              * 
              * 
              */
@@ -3060,69 +3060,69 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="sequencePoint" maxOccurs="unbounded">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="seqPointMin">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="seqPointMax">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
-     *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
-     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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 name="sequencePoint" maxOccurs="unbounded"&amp;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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+     *                 &amp;lt;attribute name="sequenceRef" 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;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="axis" maxOccurs="3" minOccurs="3"&amp;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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="seqPointMin"&amp;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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="seqPointMax"&amp;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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+     *       &amp;lt;attGroup ref="{www.jalview.org}SimilarityParams"/&amp;gt;
+     *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *       &amp;lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -3184,20 +3184,20 @@ public class JalviewModel {
         /**
          * Gets the value of the sequencePoint property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the sequencePoint property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the sequencePoint property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getSequencePoint().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.PcaViewer.SequencePoint }
          * 
@@ -3213,20 +3213,20 @@ public class JalviewModel {
         /**
          * Gets the value of the axis property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the axis property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the axis property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getAxis().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.PcaViewer.Axis }
          * 
@@ -3721,19 +3721,19 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -3824,19 +3824,19 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -3927,19 +3927,19 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -4030,20 +4030,20 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &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;attGroup ref="{www.jalview.org}position"/&amp;gt;
+         *       &amp;lt;attribute name="sequenceRef" 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;
          * 
          * 
          */
@@ -4162,34 +4162,34 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence minOccurs="0">
-     *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-     *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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 minOccurs="0"&amp;gt;
+     *         &amp;lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+     *         &amp;lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+     *       &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *       &amp;lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
+     *       &amp;lt;attribute name="linkToAllViews" 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;
      * 
      * 
      */
@@ -4654,22 +4654,22 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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 name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="id" 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;
      * 
      * 
      */
@@ -4736,86 +4736,86 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-     *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               &lt;/extension>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-     *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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 name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
+     *         &amp;lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&amp;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="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *                 &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
+     *                 &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                 &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *                 &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *               &amp;lt;/extension&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+     *       &amp;lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
+     *       &amp;lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="showComplementFeaturesOnTop" 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;
      * 
      * 
      */
@@ -4958,20 +4958,20 @@ public class JalviewModel {
         /**
          * Gets the value of the hiddenColumns property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the hiddenColumns property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenColumns property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getHiddenColumns().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.Viewport.HiddenColumns }
          * 
@@ -4987,20 +4987,20 @@ public class JalviewModel {
         /**
          * Gets the value of the calcIdParam property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the calcIdParam property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the calcIdParam property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getCalcIdParam().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.Viewport.CalcIdParam }
          * 
@@ -6195,21 +6195,21 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-         *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     &lt;/extension>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
+         *       &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *       &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+         *       &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *     &amp;lt;/extension&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -6298,20 +6298,20 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &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="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *       &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */

diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java
index c43e04c..e1ee27e 100644 (file)
--- a/src/jalview/xml/binding/jalview/JalviewUserColours.java
+++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -18,55 +18,55 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for JalviewUserColours complex type.
+ * &lt;p&gt;Java class for JalviewUserColours complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="JalviewUserColours">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- *         &lt;element name="colour" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;sequence>
- *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- *                 &lt;/sequence>
- *                 &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- *                 &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
- *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *         &lt;element name="filter" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;sequence>
- *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
- *                 &lt;/sequence>
- *                 &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *       &lt;/sequence>
- *       &lt;attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="JalviewUserColours"&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 name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="colour" maxOccurs="unbounded" minOccurs="0"&amp;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 name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
+ *                 &amp;lt;/sequence&amp;gt;
+ *                 &amp;lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                 &amp;lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                 &amp;lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                 &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
+ *                 &amp;lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&amp;gt;
+ *                 &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                 &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                 &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                 &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                 &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *               &amp;lt;/restriction&amp;gt;
+ *             &amp;lt;/complexContent&amp;gt;
+ *           &amp;lt;/complexType&amp;gt;
+ *         &amp;lt;/element&amp;gt;
+ *         &amp;lt;element name="filter" maxOccurs="unbounded" minOccurs="0"&amp;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 name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&amp;gt;
+ *                 &amp;lt;/sequence&amp;gt;
+ *                 &amp;lt;attribute name="featureType" 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;
+ *         &amp;lt;/element&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="schemeName" 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;
  * 
  * 
  */
@@ -114,20 +114,20 @@ public class JalviewUserColours {
     /**
      * Gets the value of the colour property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the colour property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the colour property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getColour().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewUserColours.Colour }
      * 
@@ -143,20 +143,20 @@ public class JalviewUserColours {
     /**
      * Gets the value of the filter property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the filter property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the filter property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getFilter().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewUserColours.Filter }
      * 
@@ -195,31 +195,31 @@ public class JalviewUserColours {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *       &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
-     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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 name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
+     *       &amp;lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&amp;gt;
+     *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *       &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *       &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *       &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -255,20 +255,20 @@ public class JalviewUserColours {
         /**
          * Gets the value of the attributeName property.
          * 
-         * <p>
+         * &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 <CODE>set</CODE> method for the attributeName property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getAttributeName().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link String }
          * 
@@ -529,22 +529,22 @@ public class JalviewUserColours {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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 name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="featureType" 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;
      * 
      * 
      */

diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java
index 1a31d82..c93112c 100644 (file)
--- a/src/jalview/xml/binding/jalview/MapListType.java
+++ b/src/jalview/xml/binding/jalview/MapListType.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -24,42 +24,42 @@ import javax.xml.bind.annotation.XmlType;
  *                             This effectively represents a java.util.MapList object
  *                     
  * 
- * <p>Java class for mapListType complex type.
+ * &lt;p&gt;Java class for mapListType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="mapListType">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="mapListFrom" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                 &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *         &lt;element name="mapListTo" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                 &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *       &lt;/sequence>
- *       &lt;attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
- *       &lt;attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="mapListType"&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 name="mapListFrom" maxOccurs="unbounded" minOccurs="0"&amp;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="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                 &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *               &amp;lt;/restriction&amp;gt;
+ *             &amp;lt;/complexContent&amp;gt;
+ *           &amp;lt;/complexType&amp;gt;
+ *         &amp;lt;/element&amp;gt;
+ *         &amp;lt;element name="mapListTo" maxOccurs="unbounded" minOccurs="0"&amp;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="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                 &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *               &amp;lt;/restriction&amp;gt;
+ *             &amp;lt;/complexContent&amp;gt;
+ *           &amp;lt;/complexType&amp;gt;
+ *         &amp;lt;/element&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&amp;gt;
+ *       &amp;lt;attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" /&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -85,20 +85,20 @@ public class MapListType {
     /**
      * Gets the value of the mapListFrom property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the mapListFrom property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the mapListFrom property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getMapListFrom().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link MapListType.MapListFrom }
      * 
@@ -114,20 +114,20 @@ public class MapListType {
     /**
      * Gets the value of the mapListTo property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the mapListTo property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the mapListTo property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getMapListTo().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link MapListType.MapListTo }
      * 
@@ -190,20 +190,20 @@ public class MapListType {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -252,20 +252,20 @@ public class MapListType {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */

diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java
index 5ebeb7e..24f5b01 100644 (file)
--- a/src/jalview/xml/binding/jalview/Mapping.java
+++ b/src/jalview/xml/binding/jalview/Mapping.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -23,30 +23,30 @@ import javax.xml.bind.annotation.XmlType;
  *                                     to the sequence set (which will mean they are then added to the alignment too).
  *                             
  * 
- * <p>Java class for anonymous complex type.
+ * &lt;p&gt;Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType>
- *   &lt;complexContent>
- *     &lt;extension base="{www.vamsas.ac.uk/jalview/version2}mapListType">
- *       &lt;sequence>
- *         &lt;choice minOccurs="0">
- *           &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/>
- *           &lt;element name="dseqFor">
- *             &lt;simpleType>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
- *               &lt;/restriction>
- *             &lt;/simpleType>
- *           &lt;/element>
- *         &lt;/choice>
- *       &lt;/sequence>
- *       &lt;attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     &lt;/extension>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType&amp;gt;
+ *   &amp;lt;complexContent&amp;gt;
+ *     &amp;lt;extension base="{www.vamsas.ac.uk/jalview/version2}mapListType"&amp;gt;
+ *       &amp;lt;sequence&amp;gt;
+ *         &amp;lt;choice minOccurs="0"&amp;gt;
+ *           &amp;lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/&amp;gt;
+ *           &amp;lt;element name="dseqFor"&amp;gt;
+ *             &amp;lt;simpleType&amp;gt;
+ *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt;
+ *               &amp;lt;/restriction&amp;gt;
+ *             &amp;lt;/simpleType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *         &amp;lt;/choice&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="mappingType" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *     &amp;lt;/extension&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */

diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java
index 9db4ea3..7e42db8 100644 (file)
--- a/src/jalview/xml/binding/jalview/NoValueColour.java
+++ b/src/jalview/xml/binding/jalview/NoValueColour.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -14,19 +14,18 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for NoValueColour.
+ * &lt;p&gt;Java class for NoValueColour.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <p>
- * <pre>
- * &lt;simpleType name="NoValueColour">
- *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
- *     &lt;enumeration value="None"/>
- *     &lt;enumeration value="Min"/>
- *     &lt;enumeration value="Max"/>
- *   &lt;/restriction>
- * &lt;/simpleType>
- * </pre>
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
+ * &lt;pre&gt;
+ * &amp;lt;simpleType name="NoValueColour"&amp;gt;
+ *   &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt;
+ *     &amp;lt;enumeration value="None"/&amp;gt;
+ *     &amp;lt;enumeration value="Min"/&amp;gt;
+ *     &amp;lt;enumeration value="Max"/&amp;gt;
+ *   &amp;lt;/restriction&amp;gt;
+ * &amp;lt;/simpleType&amp;gt;
+ * &lt;/pre&gt;
  * 
  */
 @XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")

diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
index e0b2127..b6ea489 100644 (file)
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -18,7 +18,7 @@ import javax.xml.namespace.QName;
  * This object contains factory methods for each 
  * Java content interface and Java element interface 
  * generated in the jalview.xml.binding.jalview package. 
- * <p>An ObjectFactory allows you to programatically 
+ * &lt;p&gt;An ObjectFactory allows you to programatically 
  * construct new instances of the Java representation 
  * for XML content. The Java representation of XML 
  * content can consist of schema derived interfaces 
@@ -31,9 +31,9 @@ import javax.xml.namespace.QName;
 @XmlRegistry
 public class ObjectFactory {
 
-    private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
     private final static QName _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
     private final static QName _JalviewUserColours_QNAME = new QName("www.jalview.org/colours", "JalviewUserColours");
+    private final static QName _WebServiceParameterSet_QNAME = new QName("www.jalview.org/xml/wsparamset", "WebServiceParameterSet");
 
     /**
      * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
@@ -43,14 +43,6 @@ public class ObjectFactory {
     }
 
     /**
-     * Create an instance of {@link AlcodonFrame }
-     * 
-     */
-    public AlcodonFrame createAlcodonFrame() {
-        return new AlcodonFrame();
-    }
-
-    /**
      * Create an instance of {@link MapListType }
      * 
      */
@@ -67,6 +59,14 @@ public class ObjectFactory {
     }
 
     /**
+     * Create an instance of {@link AlcodonFrame }
+     * 
+     */
+    public AlcodonFrame createAlcodonFrame() {
+        return new AlcodonFrame();
+    }
+
+    /**
      * Create an instance of {@link Annotation }
      * 
      */
@@ -171,14 +171,6 @@ public class ObjectFactory {
     }
 
     /**
-     * Create an instance of {@link DoubleMatrix }
-     * 
-     */
-    public DoubleMatrix createDoubleMatrix() {
-        return new DoubleMatrix();
-    }
-
-    /**
      * Create an instance of {@link AnnotationColourScheme }
      * 
      */
@@ -203,27 +195,11 @@ public class ObjectFactory {
     }
 
     /**
-     * Create an instance of {@link AlcodonFrame.Alcodon }
-     * 
-     */
-    public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
-        return new AlcodonFrame.Alcodon();
-    }
-
-    /**
-     * Create an instance of {@link AlcodonFrame.AlcodMap }
-     * 
-     */
-    public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
-        return new AlcodonFrame.AlcodMap();
-    }
-
-    /**
-     * Create an instance of {@link AnnotationElement }
+     * Create an instance of {@link DoubleMatrix }
      * 
      */
-    public AnnotationElement createAnnotationElement() {
-        return new AnnotationElement();
+    public DoubleMatrix createDoubleMatrix() {
+        return new DoubleMatrix();
     }
 
     /**
@@ -267,6 +243,30 @@ public class ObjectFactory {
     }
 
     /**
+     * Create an instance of {@link AlcodonFrame.Alcodon }
+     * 
+     */
+    public AlcodonFrame.Alcodon createAlcodonFrameAlcodon() {
+        return new AlcodonFrame.Alcodon();
+    }
+
+    /**
+     * Create an instance of {@link AlcodonFrame.AlcodMap }
+     * 
+     */
+    public AlcodonFrame.AlcodMap createAlcodonFrameAlcodMap() {
+        return new AlcodonFrame.AlcodMap();
+    }
+
+    /**
+     * Create an instance of {@link AnnotationElement }
+     * 
+     */
+    public AnnotationElement createAnnotationElement() {
+        return new AnnotationElement();
+    }
+
+    /**
      * Create an instance of {@link Annotation.ThresholdLine }
      * 
      */
@@ -459,17 +459,12 @@ public class ObjectFactory {
     }
 
     /**
-     * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}}
-     * 
-     */
-    @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
-    public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
-        return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
-    }
-
-    /**
-     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}}
+     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
      * 
+     * @param value
+     *     Java instance representing xml element's value.
+     * @return
+     *     the new instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}
      */
     @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
     public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
@@ -477,12 +472,29 @@ public class ObjectFactory {
     }
 
     /**
-     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}}
+     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
      * 
+     * @param value
+     *     Java instance representing xml element's value.
+     * @return
+     *     the new instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}
      */
     @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
     public JAXBElement<JalviewUserColours> createJalviewUserColours(JalviewUserColours value) {
         return new JAXBElement<JalviewUserColours>(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
     }
 
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
+     * 
+     * @param value
+     *     Java instance representing xml element's value.
+     * @return
+     *     the new instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}
+     */
+    @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
+    public JAXBElement<WebServiceParameterSet> createWebServiceParameterSet(WebServiceParameterSet value) {
+        return new JAXBElement<WebServiceParameterSet>(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
+    }
+
 }

diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java
index 6234f32..717ce89 100644 (file)
--- a/src/jalview/xml/binding/jalview/PcaDataType.java
+++ b/src/jalview/xml/binding/jalview/PcaDataType.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -19,23 +19,23 @@ import javax.xml.bind.annotation.XmlType;
  *                             The results of a PCA calculation
  *                     
  * 
- * <p>Java class for PcaDataType complex type.
+ * &lt;p&gt;Java class for PcaDataType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="PcaDataType">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/>
- *         &lt;element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/>
- *         &lt;element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/>
- *       &lt;/sequence>
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="PcaDataType"&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 name="pairwiseMatrix" type="{www.jalview.org}DoubleMatrix"/&amp;gt;
+ *         &amp;lt;element name="tridiagonalMatrix" type="{www.jalview.org}DoubleMatrix"/&amp;gt;
+ *         &amp;lt;element name="eigenMatrix" type="{www.jalview.org}DoubleMatrix"/&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */

diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java
index d5132ab..6983c04 100644 (file)
--- a/src/jalview/xml/binding/jalview/Pdbentry.java
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -18,33 +18,33 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for pdbentry complex type.
+ * &lt;p&gt;Java class for pdbentry complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="pdbentry">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence maxOccurs="unbounded" minOccurs="0">
- *         &lt;element name="property" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *       &lt;/sequence>
- *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="pdbentry"&amp;gt;
+ *   &amp;lt;complexContent&amp;gt;
+ *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *       &amp;lt;sequence maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *         &amp;lt;element name="property" maxOccurs="unbounded" minOccurs="0"&amp;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="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                 &amp;lt;attribute name="value" 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;
+ *         &amp;lt;/element&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="file" 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;
  * 
  * 
  */
@@ -68,20 +68,20 @@ public class Pdbentry {
     /**
      * Gets the value of the property property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the property property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the property property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getProperty().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link Pdbentry.Property }
      * 
@@ -168,20 +168,20 @@ public class Pdbentry {
 
 
     /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="value" 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;
      * 
      * 
      */

diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
index b842947..5381c32 100644 (file)
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -19,37 +19,38 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for anonymous complex type.
+ * &lt;p&gt;Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType>
- *   &lt;complexContent>
- *     &lt;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
- *       &lt;sequence>
- *         &lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;sequence>
- *                   &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
- *                 &lt;/sequence>
- *                 &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *       &lt;/sequence>
- *       &lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     &lt;/extension>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType&amp;gt;
+ *   &amp;lt;complexContent&amp;gt;
+ *     &amp;lt;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&amp;gt;
+ *       &amp;lt;sequence&amp;gt;
+ *         &amp;lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0"&amp;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;
+ *         &amp;lt;/element&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *     &amp;lt;/extension&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -72,20 +73,20 @@ public class Sequence
     /**
      * Gets the value of the dbRef property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the dbRef property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the dbRef property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getDBRef().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link Sequence.DBRef }
      * 
@@ -148,25 +149,26 @@ public class Sequence
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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;
      * 
      * 
      */
@@ -186,6 +188,8 @@ public class Sequence
         protected String accessionId;
         @XmlAttribute(name = "locus")
         protected Boolean locus;
+        @XmlAttribute(name = "canonical")
+        protected Boolean canonical;
 
         /**
          * Gets the value of the mapping property.
@@ -311,6 +315,34 @@ public class Sequence
             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;
+        }
+
     }
 
 }

diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index 6aee6ac..c69334e 100644 (file)
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -19,35 +19,35 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for anonymous complex type.
+ * &lt;p&gt;Java class for anonymous complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType>
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
- *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
- *         &lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
- *           &lt;complexType>
- *             &lt;complexContent>
- *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- *               &lt;/restriction>
- *             &lt;/complexContent>
- *           &lt;/complexType>
- *         &lt;/element>
- *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
- *       &lt;/sequence>
- *       &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &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}Sequence" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0"&amp;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;
+ *         &amp;lt;/element&amp;gt;
+ *         &amp;lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="datasetId" 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;
  * 
  * 
  */
@@ -76,20 +76,20 @@ public class SequenceSet {
     /**
      * Gets the value of the sequence property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the sequence property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the sequence property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getSequence().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link Sequence }
      * 
@@ -105,20 +105,20 @@ public class SequenceSet {
     /**
      * Gets the value of the annotation property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the annotation property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the annotation property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getAnnotation().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link Annotation }
      * 
@@ -134,20 +134,20 @@ public class SequenceSet {
     /**
      * Gets the value of the sequenceSetProperties property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the sequenceSetProperties property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the sequenceSetProperties property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getSequenceSetProperties().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link SequenceSet.SequenceSetProperties }
      * 
@@ -163,20 +163,20 @@ public class SequenceSet {
     /**
      * Gets the value of the alcodonFrame property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the alcodonFrame property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the alcodonFrame property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getAlcodonFrame().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link AlcodonFrame }
      * 
@@ -239,20 +239,20 @@ public class SequenceSet {
 
 
     /**
-     * <p>Java class for anonymous complex type.
-     * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &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;
      * 
      * 
      */

diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java
index aef7543..29982ae 100644 (file)
--- a/src/jalview/xml/binding/jalview/SequenceType.java
+++ b/src/jalview/xml/binding/jalview/SequenceType.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -16,24 +16,24 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for SequenceType complex type.
+ * &lt;p&gt;Java class for SequenceType complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="SequenceType">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- *         &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- *       &lt;/sequence>
- *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="SequenceType"&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 name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *       &amp;lt;attribute name="description" 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;
  * 
  * 
  */

diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java
index 1b3d6d4..edb9152 100644 (file)
--- a/src/jalview/xml/binding/jalview/ThresholdType.java
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -13,19 +13,18 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for ThresholdType.
+ * &lt;p&gt;Java class for ThresholdType.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
- * <p>
- * <pre>
- * &lt;simpleType name="ThresholdType">
- *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
- *     &lt;enumeration value="NONE"/>
- *     &lt;enumeration value="ABOVE"/>
- *     &lt;enumeration value="BELOW"/>
- *   &lt;/restriction>
- * &lt;/simpleType>
- * </pre>
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
+ * &lt;pre&gt;
+ * &amp;lt;simpleType name="ThresholdType"&amp;gt;
+ *   &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&amp;gt;
+ *     &amp;lt;enumeration value="NONE"/&amp;gt;
+ *     &amp;lt;enumeration value="ABOVE"/&amp;gt;
+ *     &amp;lt;enumeration value="BELOW"/&amp;gt;
+ *   &amp;lt;/restriction&amp;gt;
+ * &amp;lt;/simpleType&amp;gt;
+ * &lt;/pre&gt;
  * 
  */
 @XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")

diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java
index 5d341c3..48b2012 100644 (file)
--- a/src/jalview/xml/binding/jalview/VAMSAS.java
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -17,22 +17,22 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for VAMSAS complex type.
+ * &lt;p&gt;Java class for VAMSAS complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="VAMSAS">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
- *       &lt;/sequence>
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="VAMSAS"&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 name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -51,20 +51,20 @@ public class VAMSAS {
     /**
      * Gets the value of the tree property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the tree property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the tree property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getTree().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link String }
      * 
@@ -80,20 +80,20 @@ public class VAMSAS {
     /**
      * Gets the value of the sequenceSet property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the sequenceSet property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the sequenceSet property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getSequenceSet().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link SequenceSet }
      * 

diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
index 659eab9..87e275d 100644 (file)
--- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
+++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -20,25 +20,25 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * <p>Java class for WebServiceParameterSet complex type.
+ * &lt;p&gt;Java class for WebServiceParameterSet complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="WebServiceParameterSet">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
- *         &lt;element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/>
- *         &lt;element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *       &lt;/sequence>
- *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="WebServiceParameterSet"&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 name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&amp;gt;
+ *         &amp;lt;element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/&amp;gt;
+ *         &amp;lt;element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;attribute name="name" 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;
  * 
  * 
  */
@@ -117,20 +117,20 @@ public class WebServiceParameterSet {
     /**
      * Gets the value of the serviceURL property.
      * 
-     * <p>
+     * &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 <CODE>set</CODE> method for the serviceURL property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the serviceURL property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getServiceURL().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link String }
      * 

diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java
index 3ed532d..2700ffa 100644 (file)
--- a/src/jalview/xml/binding/jalview/package-info.java
+++ b/src/jalview/xml/binding/jalview/package-info.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// 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: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)