From 7a48066cfd16ea943eb3dfcc8b2fe353d33ae15a Mon Sep 17 00:00:00 2001 From: James Procter Date: Tue, 18 Jul 2023 17:39:32 +0100 Subject: [PATCH] exploring making PAE storage in projects more efficient --- schemas/vamsas.xsd | 28 +- src/jalview/project/Jalview2XML.java | 137 +- src/jalview/xml/binding/jalview/AlcodonFrame.java | 458 +- src/jalview/xml/binding/jalview/Annotation.java | 1397 ++- .../binding/jalview/AnnotationColourScheme.java | 431 +- .../xml/binding/jalview/AnnotationElement.java | 316 +- src/jalview/xml/binding/jalview/DoubleMatrix.java | 295 +- src/jalview/xml/binding/jalview/DoubleVector.java | 82 +- src/jalview/xml/binding/jalview/Feature.java | 557 +- .../xml/binding/jalview/FeatureMatcher.java | 228 +- .../xml/binding/jalview/FeatureMatcherSet.java | 259 +- src/jalview/xml/binding/jalview/FilterBy.java | 63 +- src/jalview/xml/binding/jalview/JalviewModel.java |11880 ++++++++++---------- .../xml/binding/jalview/JalviewUserColours.java | 973 +- src/jalview/xml/binding/jalview/MapListType.java | 446 +- .../xml/binding/jalview/MapOnAMatrixType.java | 156 + src/jalview/xml/binding/jalview/Mapping.java | 168 +- src/jalview/xml/binding/jalview/MatrixType.java | 587 +- src/jalview/xml/binding/jalview/NoValueColour.java | 63 +- src/jalview/xml/binding/jalview/ObjectFactory.java | 1052 +- src/jalview/xml/binding/jalview/PcaDataType.java | 171 +- src/jalview/xml/binding/jalview/Pdbentry.java | 353 +- src/jalview/xml/binding/jalview/Property.java | 109 +- src/jalview/xml/binding/jalview/Sequence.java | 505 +- src/jalview/xml/binding/jalview/SequenceSet.java | 515 +- src/jalview/xml/binding/jalview/SequenceType.java | 228 +- src/jalview/xml/binding/jalview/ThresholdType.java | 33 +- src/jalview/xml/binding/jalview/VAMSAS.java | 141 +- .../binding/jalview/WebServiceParameterSet.java | 302 +- src/jalview/xml/binding/jalview/package-info.java | 6 +- 30 files changed, 10883 insertions(+), 11056 deletions(-) create mode 100644 src/jalview/xml/binding/jalview/MapOnAMatrixType.java diff --git a/schemas/vamsas.xsd b/schemas/vamsas.xsd index fedbae3..c4a5d3e 100755 --- a/schemas/vamsas.xsd +++ b/schemas/vamsas.xsd @@ -269,6 +269,7 @@ + @@ -349,9 +350,34 @@ use="optional" /> - + + + + + + + mapping from the matrix row and column positions + to + associated reference frame + + + + + + + + + reference to the matrix type this Map refers to + + + + + diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index 6f26036..b9e1f46 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -283,6 +283,12 @@ public class Jalview2XML * entry names */ private Map rnaSessions = new HashMap<>(); + + /** + * map from contact matrices to their XML ids + */ + private Map contactMatrices = new HashMap<>(); + private Map contactMatrixRefs = new HashMap<>(); /** * A helper method for safely using the value of an optional attribute that @@ -2315,64 +2321,7 @@ public class Jalview2XML .getContactMatrixFor(annotation); if (cm != null) { - MatrixType xmlmat = new MatrixType(); - xmlmat.setType(cm.getType()); - xmlmat.setRows(BigInteger.valueOf(cm.getWidth())); - xmlmat.setCols(BigInteger.valueOf(cm.getHeight())); - // consider using an opaque to/from -> allow instance to control - // its representation ? - xmlmat.setElements(ContactMatrix.contactToFloatString(cm)); - if (cm.hasGroups()) - { - for (BitSet gp : cm.getGroups()) - { - xmlmat.getGroups().add(stringifyBitset(gp)); - } - } - if (cm.hasTree()) - { - // provenance object for tree ? - xmlmat.getNewick().add(cm.getNewick()); - xmlmat.setTreeMethod(cm.getTreeMethod()); - } - if (cm.hasCutHeight()) - { - xmlmat.setCutHeight(cm.getCutHeight()); - } - // set/get properties - if (cm instanceof MappableContactMatrixI) - { - jalview.util.MapList mlst = ((MappableContactMatrixI) cm) - .getMapFor(annotation.sequenceRef); - if (mlst != null) - { - MapListType mp = new MapListType(); - List r = mlst.getFromRanges(); - for (int[] range : r) - { - MapListFrom mfrom = new MapListFrom(); - mfrom.setStart(range[0]); - mfrom.setEnd(range[1]); - // mp.addMapListFrom(mfrom); - mp.getMapListFrom().add(mfrom); - } - r = mlst.getToRanges(); - for (int[] range : r) - { - MapListTo mto = new MapListTo(); - mto.setStart(range[0]); - mto.setEnd(range[1]); - // mp.addMapListTo(mto); - mp.getMapListTo().add(mto); - } - mp.setMapFromUnit( - BigInteger.valueOf(mlst.getFromRatio())); - mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio())); - xmlmat.setMapping(mp); - } - } - // and add to model - an.getContactmatrix().add(xmlmat); + storeMatrixFor(vamsasSet, an,annotation, cm); } } } @@ -2479,6 +2428,78 @@ public class Jalview2XML } + private void storeMatrixFor(SequenceSet root, Annotation an, AlignmentAnnotation annotation, ContactMatrixI cm) + { + String cmId = contactMatrices.get(cm); + MatrixType xmlmat=null; + if (cmId==null) + { +xmlmat = new MatrixType(); + xmlmat.setType(cm.getType()); + xmlmat.setRows(BigInteger.valueOf(cm.getWidth())); + xmlmat.setCols(BigInteger.valueOf(cm.getHeight())); + // consider using an opaque to/from -> allow instance to control + // its representation ? + xmlmat.setElements(ContactMatrix.contactToFloatString(cm)); + if (cm.hasGroups()) + { + for (BitSet gp : cm.getGroups()) + { + xmlmat.getGroups().add(stringifyBitset(gp)); + } + } + if (cm.hasTree()) + { + // provenance object for tree ? + xmlmat.getNewick().add(cm.getNewick()); + xmlmat.setTreeMethod(cm.getTreeMethod()); + } + if (cm.hasCutHeight()) + { + xmlmat.setCutHeight(cm.getCutHeight()); + } + xmlmat.setId(makeHashCode(cm, cm.get)); + root.getMatrices().add(xmlmat); + } + else { + + } + // set/get properties + if (cm instanceof MappableContactMatrixI) + { + jalview.util.MapList mlst = ((MappableContactMatrixI) cm) + .getMapFor(annotation.sequenceRef); + if (mlst != null) + { + MapListType mp = new MapListType(); + List r = mlst.getFromRanges(); + for (int[] range : r) + { + MapListFrom mfrom = new MapListFrom(); + mfrom.setStart(range[0]); + mfrom.setEnd(range[1]); + // mp.addMapListFrom(mfrom); + mp.getMapListFrom().add(mfrom); + } + r = mlst.getToRanges(); + for (int[] range : r) + { + MapListTo mto = new MapListTo(); + mto.setStart(range[0]); + mto.setEnd(range[1]); + // mp.addMapListTo(mto); + mp.getMapListTo().add(mto); + } + mp.setMapFromUnit( + BigInteger.valueOf(mlst.getFromRatio())); + mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio())); + xmlmat.setMapping(mp); + } + } + // and add to model + an.getContactmatrix().add(xmlmat); + } + private String stringifyBitset(BitSet gp) { StringBuilder sb = new StringBuilder(); diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index 6b98b6a..77ea749 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -2,9 +2,10 @@ // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 // See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2023.05.13 at 06:58:41 PM BST +// Generated on: 2023.07.18 at 05:07:54 PM BST // + package jalview.xml.binding.jalview; import java.math.BigInteger; @@ -17,13 +18,11 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; + /** - *

- * Java class for anonymous complex type. + *

Java class for anonymous complex type. * - *

- * The following schema fragment specifies the expected content contained within - * this class. + *

The following schema fragment specifies the expected content contained within this class. * * 

  * <complexType>
@@ -62,275 +61,266 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
+@XmlType(name = "", propOrder = {
+    "alcodon",
+    "alcodMap"
+})
 @XmlRootElement(name = "AlcodonFrame")
-public class AlcodonFrame
-{
-
-  protected List alcodon;
-
-  protected List alcodMap;
+public class AlcodonFrame {
 
-  /**
-   * Gets the value of the alcodon property.
-   * 
-   * 

-   * 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 set method
-   * for the alcodon property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getAlcodon().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame.Alcodon }
-   * 
-   * 
-   */
-  public List getAlcodon()
-  {
-    if (alcodon == null)
-    {
-      alcodon = new ArrayList();
-    }
-    return this.alcodon;
-  }
-
-  /**
-   * Gets the value of the alcodMap property.
-   * 
-   * 

-   * 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 set method
-   * for the alcodMap property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getAlcodMap().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame.AlcodMap }
-   * 
-   * 
-   */
-  public List getAlcodMap()
-  {
-    if (alcodMap == null)
-    {
-      alcodMap = new ArrayList();
-    }
-    return this.alcodMap;
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
-   *       </sequence>
-   *       <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "mapping" })
-  public static class AlcodMap
-  {
-
-    @XmlElement(name = "Mapping", required = true)
-    protected Mapping mapping;
-
-    @XmlAttribute(name = "dnasq", required = true)
-    protected String dnasq;
+    protected List alcodon;
+    protected List alcodMap;
 
     /**
+     * Gets the value of the alcodon property.
      * 
-     * a Mapping entry and an associated protein sequence
+     * 

+     * 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 set method for the alcodon property.
      * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getAlcodon().add(newItem);
+     * 

      * 
-     * @return possible object is {@link Mapping }
      * 
-     */
-    public Mapping getMapping()
-    {
-      return mapping;
-    }
-
-    /**
-     * Sets the value of the mapping property.
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame.Alcodon }
      * 
-     * @param value
-     *          allowed object is {@link Mapping }
      * 
      */
-    public void setMapping(Mapping value)
-    {
-      this.mapping = value;
+    public List getAlcodon() {
+        if (alcodon == null) {
+            alcodon = new ArrayList();
+        }
+        return this.alcodon;
     }
 
     /**
-     * Gets the value of the dnasq property.
+     * Gets the value of the alcodMap property.
+     * 
+     * 

+     * 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 set method for the alcodMap property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getAlcodMap().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame.AlcodMap }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getDnasq()
-    {
-      return dnasq;
+    public List getAlcodMap() {
+        if (alcodMap == null) {
+            alcodMap = new ArrayList();
+        }
+        return this.alcodMap;
     }
 
+
     /**
-     * Sets the value of the dnasq property.
+     * 
Java class for anonymous complex type.
+     * 
+     * 
The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+     *       </sequence>
+     *       <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setDnasq(String value)
-    {
-      this.dnasq = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "mapping"
+    })
+    public static class AlcodMap {
 
-  }
+        @XmlElement(name = "Mapping", required = true)
+        protected Mapping mapping;
+        @XmlAttribute(name = "dnasq", required = true)
+        protected String dnasq;
 
-  /**
-   * 
-   * specifies a series of aligned codons from an associated DNA sequence
-   * alignment that when translated correspond to columns of a peptide
-   * alignment. Element may have either all pos1,2,3 attributes specified, or
-   * none at all (indicating a gapped column with no translated peptide).
-   * 
-   * 
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *       <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *       <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Alcodon
-  {
+        /**
+         * 
+         * 										a Mapping entry and an associated protein sequence
+         * 									
+         * 
+         * @return
+         *     possible object is
+         *     {@link Mapping }
+         *     
+         */
+        public Mapping getMapping() {
+            return mapping;
+        }
 
-    @XmlAttribute(name = "pos1")
-    protected BigInteger pos1;
+        /**
+         * Sets the value of the mapping property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Mapping }
+         *     
+         */
+        public void setMapping(Mapping value) {
+            this.mapping = value;
+        }
 
-    @XmlAttribute(name = "pos2")
-    protected BigInteger pos2;
+        /**
+         * Gets the value of the dnasq property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getDnasq() {
+            return dnasq;
+        }
 
-    @XmlAttribute(name = "pos3")
-    protected BigInteger pos3;
+        /**
+         * Sets the value of the dnasq property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setDnasq(String value) {
+            this.dnasq = value;
+        }
 
-    /**
-     * Gets the value of the pos1 property.
-     * 
-     * @return possible object is {@link BigInteger }
-     * 
-     */
-    public BigInteger getPos1()
-    {
-      return pos1;
     }
 
-    /**
-     * Sets the value of the pos1 property.
-     * 
-     * @param value
-     *          allowed object is {@link BigInteger }
-     * 
-     */
-    public void setPos1(BigInteger value)
-    {
-      this.pos1 = value;
-    }
 
     /**
-     * Gets the value of the pos2 property.
      * 
-     * @return possible object is {@link BigInteger }
+     * 								specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment.
+     * 								Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide).
+     * 							
      * 
-     */
-    public BigInteger getPos2()
-    {
-      return pos2;
-    }
-
-    /**
-     * Sets the value of the pos2 property.
+     * 
Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link BigInteger }
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setPos2(BigInteger value)
-    {
-      this.pos2 = value;
-    }
-
-    /**
-     * Gets the value of the pos3 property.
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

      * 
-     * @return possible object is {@link BigInteger }
      * 
      */
-    public BigInteger getPos3()
-    {
-      return pos3;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Alcodon {
 
-    /**
-     * Sets the value of the pos3 property.
-     * 
-     * @param value
-     *          allowed object is {@link BigInteger }
-     * 
-     */
-    public void setPos3(BigInteger value)
-    {
-      this.pos3 = value;
-    }
+        @XmlAttribute(name = "pos1")
+        protected BigInteger pos1;
+        @XmlAttribute(name = "pos2")
+        protected BigInteger pos2;
+        @XmlAttribute(name = "pos3")
+        protected BigInteger pos3;
+
+        /**
+         * Gets the value of the pos1 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos1() {
+            return pos1;
+        }
 
-  }
+        /**
+         * Sets the value of the pos1 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos1(BigInteger value) {
+            this.pos1 = value;
+        }
+
+        /**
+         * Gets the value of the pos2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos2() {
+            return pos2;
+        }
+
+        /**
+         * Sets the value of the pos2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos2(BigInteger value) {
+            this.pos2 = value;
+        }
+
+        /**
+         * Gets the value of the pos3 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos3() {
+            return pos3;
+        }
+
+        /**
+         * Sets the value of the pos3 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos3(BigInteger value) {
+            this.pos3 = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Annotation.java b/src/jalview/xml/binding/jalview/Annotation.java
index 2feda64..8a5d9b2 100644
--- a/src/jalview/xml/binding/jalview/Annotation.java
+++ b/src/jalview/xml/binding/jalview/Annotation.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,13 +17,11 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for anonymous complex type.
+ * 
Java class for anonymous complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType>
@@ -71,755 +70,733 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "annotationElement", "label", "description", "thresholdLine",
-      "contactmatrix", "property" })
+@XmlType(name = "", propOrder = {
+    "annotationElement",
+    "label",
+    "description",
+    "thresholdLine",
+    "contactmatrix",
+    "property"
+})
 @XmlRootElement(name = "Annotation")
-public class Annotation
-{
+public class Annotation {
 
-  protected List annotationElement;
+    protected List annotationElement;
+    @XmlElement(required = true)
+    protected String label;
+    protected String description;
+    protected Annotation.ThresholdLine thresholdLine;
+    protected List contactmatrix;
+    protected List property;
+    @XmlAttribute(name = "graph", required = true)
+    protected boolean graph;
+    @XmlAttribute(name = "graphType")
+    protected Integer graphType;
+    @XmlAttribute(name = "sequenceRef")
+    protected String sequenceRef;
+    @XmlAttribute(name = "groupRef")
+    protected String groupRef;
+    @XmlAttribute(name = "graphColour")
+    protected Integer graphColour;
+    @XmlAttribute(name = "graphGroup")
+    protected Integer graphGroup;
+    @XmlAttribute(name = "graphHeight")
+    protected Integer graphHeight;
+    @XmlAttribute(name = "id")
+    protected String id;
+    @XmlAttribute(name = "scoreOnly")
+    protected Boolean scoreOnly;
+    @XmlAttribute(name = "score")
+    protected Double score;
+    @XmlAttribute(name = "visible")
+    protected Boolean visible;
+    @XmlAttribute(name = "centreColLabels")
+    protected Boolean centreColLabels;
+    @XmlAttribute(name = "scaleColLabels")
+    protected Boolean scaleColLabels;
+    @XmlAttribute(name = "showAllColLabels")
+    protected Boolean showAllColLabels;
+    @XmlAttribute(name = "autoCalculated")
+    protected Boolean autoCalculated;
+    @XmlAttribute(name = "belowAlignment")
+    protected Boolean belowAlignment;
+    @XmlAttribute(name = "calcId")
+    protected String calcId;
 
-  @XmlElement(required = true)
-  protected String label;
-
-  protected String description;
+    /**
+     * Gets the value of the annotationElement property.
+     * 
+     * 

+     * 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 set method for the annotationElement property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getAnnotationElement().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link AnnotationElement }
+     * 
+     * 
+     */
+    public List getAnnotationElement() {
+        if (annotationElement == null) {
+            annotationElement = new ArrayList();
+        }
+        return this.annotationElement;
+    }
 
-  protected Annotation.ThresholdLine thresholdLine;
-
-  protected List contactmatrix;
-
-  protected List property;
-
-  @XmlAttribute(name = "graph", required = true)
-  protected boolean graph;
-
-  @XmlAttribute(name = "graphType")
-  protected Integer graphType;
-
-  @XmlAttribute(name = "sequenceRef")
-  protected String sequenceRef;
-
-  @XmlAttribute(name = "groupRef")
-  protected String groupRef;
-
-  @XmlAttribute(name = "graphColour")
-  protected Integer graphColour;
-
-  @XmlAttribute(name = "graphGroup")
-  protected Integer graphGroup;
-
-  @XmlAttribute(name = "graphHeight")
-  protected Integer graphHeight;
-
-  @XmlAttribute(name = "id")
-  protected String id;
-
-  @XmlAttribute(name = "scoreOnly")
-  protected Boolean scoreOnly;
-
-  @XmlAttribute(name = "score")
-  protected Double score;
-
-  @XmlAttribute(name = "visible")
-  protected Boolean visible;
-
-  @XmlAttribute(name = "centreColLabels")
-  protected Boolean centreColLabels;
-
-  @XmlAttribute(name = "scaleColLabels")
-  protected Boolean scaleColLabels;
-
-  @XmlAttribute(name = "showAllColLabels")
-  protected Boolean showAllColLabels;
-
-  @XmlAttribute(name = "autoCalculated")
-  protected Boolean autoCalculated;
-
-  @XmlAttribute(name = "belowAlignment")
-  protected Boolean belowAlignment;
-
-  @XmlAttribute(name = "calcId")
-  protected String calcId;
-
-  /**
-   * Gets the value of the annotationElement property.
-   * 
-   * 

-   * 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 set method
-   * for the annotationElement property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getAnnotationElement().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link AnnotationElement }
-   * 
-   * 
-   */
-  public List getAnnotationElement()
-  {
-    if (annotationElement == null)
-    {
-      annotationElement = new ArrayList();
-    }
-    return this.annotationElement;
-  }
-
-  /**
-   * Gets the value of the label property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getLabel()
-  {
-    return label;
-  }
-
-  /**
-   * Sets the value of the label property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setLabel(String value)
-  {
-    this.label = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the thresholdLine property.
-   * 
-   * @return possible object is {@link Annotation.ThresholdLine }
-   * 
-   */
-  public Annotation.ThresholdLine getThresholdLine()
-  {
-    return thresholdLine;
-  }
-
-  /**
-   * Sets the value of the thresholdLine property.
-   * 
-   * @param value
-   *          allowed object is {@link Annotation.ThresholdLine }
-   * 
-   */
-  public void setThresholdLine(Annotation.ThresholdLine value)
-  {
-    this.thresholdLine = value;
-  }
-
-  /**
-   * Gets the value of the contactmatrix property.
-   * 
-   * 

-   * 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 set method
-   * for the contactmatrix property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getContactmatrix().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link MatrixType
-   * }
-   * 
-   * 
-   */
-  public List getContactmatrix()
-  {
-    if (contactmatrix == null)
-    {
-      contactmatrix = new ArrayList();
-    }
-    return this.contactmatrix;
-  }
-
-  /**
-   * Gets the value of the property property.
-   * 
-   * 

-   * 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 set method
-   * for the property property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getProperty().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link Property }
-   * 
-   * 
-   */
-  public List getProperty()
-  {
-    if (property == null)
-    {
-      property = new ArrayList();
-    }
-    return this.property;
-  }
-
-  /**
-   * Gets the value of the graph property.
-   * 
-   */
-  public boolean isGraph()
-  {
-    return graph;
-  }
-
-  /**
-   * Sets the value of the graph property.
-   * 
-   */
-  public void setGraph(boolean value)
-  {
-    this.graph = value;
-  }
-
-  /**
-   * Gets the value of the graphType property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphType()
-  {
-    return graphType;
-  }
-
-  /**
-   * Sets the value of the graphType property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphType(Integer value)
-  {
-    this.graphType = value;
-  }
-
-  /**
-   * Gets the value of the sequenceRef property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSequenceRef()
-  {
-    return sequenceRef;
-  }
-
-  /**
-   * Sets the value of the sequenceRef property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSequenceRef(String value)
-  {
-    this.sequenceRef = value;
-  }
-
-  /**
-   * Gets the value of the groupRef property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getGroupRef()
-  {
-    return groupRef;
-  }
-
-  /**
-   * Sets the value of the groupRef property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setGroupRef(String value)
-  {
-    this.groupRef = value;
-  }
-
-  /**
-   * Gets the value of the graphColour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphColour()
-  {
-    return graphColour;
-  }
-
-  /**
-   * Sets the value of the graphColour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphColour(Integer value)
-  {
-    this.graphColour = value;
-  }
-
-  /**
-   * Gets the value of the graphGroup property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphGroup()
-  {
-    return graphGroup;
-  }
-
-  /**
-   * Sets the value of the graphGroup property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphGroup(Integer value)
-  {
-    this.graphGroup = value;
-  }
-
-  /**
-   * Gets the value of the graphHeight property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getGraphHeight()
-  {
-    return graphHeight;
-  }
-
-  /**
-   * Sets the value of the graphHeight property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setGraphHeight(Integer value)
-  {
-    this.graphHeight = value;
-  }
-
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
-
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
-
-  /**
-   * Gets the value of the scoreOnly property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public boolean isScoreOnly()
-  {
-    if (scoreOnly == null)
-    {
-      return false;
-    }
-    else
-    {
-      return scoreOnly;
-    }
-  }
-
-  /**
-   * Sets the value of the scoreOnly property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setScoreOnly(Boolean value)
-  {
-    this.scoreOnly = value;
-  }
-
-  /**
-   * Gets the value of the score property.
-   * 
-   * @return possible object is {@link Double }
-   * 
-   */
-  public Double getScore()
-  {
-    return score;
-  }
-
-  /**
-   * Sets the value of the score property.
-   * 
-   * @param value
-   *          allowed object is {@link Double }
-   * 
-   */
-  public void setScore(Double value)
-  {
-    this.score = value;
-  }
-
-  /**
-   * Gets the value of the visible property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isVisible()
-  {
-    return visible;
-  }
-
-  /**
-   * Sets the value of the visible property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setVisible(Boolean value)
-  {
-    this.visible = value;
-  }
-
-  /**
-   * Gets the value of the centreColLabels property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isCentreColLabels()
-  {
-    return centreColLabels;
-  }
-
-  /**
-   * Sets the value of the centreColLabels property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setCentreColLabels(Boolean value)
-  {
-    this.centreColLabels = value;
-  }
-
-  /**
-   * Gets the value of the scaleColLabels property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isScaleColLabels()
-  {
-    return scaleColLabels;
-  }
-
-  /**
-   * Sets the value of the scaleColLabels property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setScaleColLabels(Boolean value)
-  {
-    this.scaleColLabels = value;
-  }
-
-  /**
-   * Gets the value of the showAllColLabels property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isShowAllColLabels()
-  {
-    return showAllColLabels;
-  }
-
-  /**
-   * Sets the value of the showAllColLabels property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setShowAllColLabels(Boolean value)
-  {
-    this.showAllColLabels = value;
-  }
-
-  /**
-   * Gets the value of the autoCalculated property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public boolean isAutoCalculated()
-  {
-    if (autoCalculated == null)
-    {
-      return false;
-    }
-    else
-    {
-      return autoCalculated;
-    }
-  }
-
-  /**
-   * Sets the value of the autoCalculated property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setAutoCalculated(Boolean value)
-  {
-    this.autoCalculated = value;
-  }
-
-  /**
-   * Gets the value of the belowAlignment property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public boolean isBelowAlignment()
-  {
-    if (belowAlignment == null)
-    {
-      return true;
-    }
-    else
-    {
-      return belowAlignment;
-    }
-  }
-
-  /**
-   * Sets the value of the belowAlignment property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setBelowAlignment(Boolean value)
-  {
-    this.belowAlignment = value;
-  }
-
-  /**
-   * Gets the value of the calcId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCalcId()
-  {
-    return calcId;
-  }
-
-  /**
-   * Sets the value of the calcId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCalcId(String value)
-  {
-    this.calcId = value;
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class ThresholdLine
-  {
-
-    @XmlAttribute(name = "label")
-    protected String label;
+    /**
+     * Gets the value of the label property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getLabel() {
+        return label;
+    }
+
+    /**
+     * Sets the value of the label property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setLabel(String value) {
+        this.label = value;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
 
-    @XmlAttribute(name = "value")
-    protected Float value;
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
 
-    @XmlAttribute(name = "colour")
-    protected Integer colour;
+    /**
+     * Gets the value of the thresholdLine property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Annotation.ThresholdLine }
+     *     
+     */
+    public Annotation.ThresholdLine getThresholdLine() {
+        return thresholdLine;
+    }
 
     /**
-     * Gets the value of the label property.
+     * Sets the value of the thresholdLine property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Annotation.ThresholdLine }
+     *     
+     */
+    public void setThresholdLine(Annotation.ThresholdLine value) {
+        this.thresholdLine = value;
+    }
+
+    /**
+     * Gets the value of the contactmatrix property.
+     * 
+     * 

+     * 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 set method for the contactmatrix property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getContactmatrix().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link MatrixType }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getLabel()
-    {
-      return label;
+    public List getContactmatrix() {
+        if (contactmatrix == null) {
+            contactmatrix = new ArrayList();
+        }
+        return this.contactmatrix;
     }
 
     /**
-     * Sets the value of the label property.
+     * Gets the value of the property property.
+     * 
+     * 

+     * 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 set method for the property property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getProperty().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link Property }
+     * 
+     * 
+     */
+    public List getProperty() {
+        if (property == null) {
+            property = new ArrayList();
+        }
+        return this.property;
+    }
+
+    /**
+     * Gets the value of the graph property.
+     * 
+     */
+    public boolean isGraph() {
+        return graph;
+    }
+
+    /**
+     * Sets the value of the graph property.
+     * 
+     */
+    public void setGraph(boolean value) {
+        this.graph = value;
+    }
+
+    /**
+     * Gets the value of the graphType property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getGraphType() {
+        return graphType;
+    }
+
+    /**
+     * Sets the value of the graphType property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphType(Integer value) {
+        this.graphType = value;
+    }
+
+    /**
+     * Gets the value of the sequenceRef property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSequenceRef() {
+        return sequenceRef;
+    }
+
+    /**
+     * Sets the value of the sequenceRef property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSequenceRef(String value) {
+        this.sequenceRef = value;
+    }
+
+    /**
+     * Gets the value of the groupRef property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setLabel(String value)
-    {
-      this.label = value;
+    public String getGroupRef() {
+        return groupRef;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the groupRef property.
      * 
-     * @return possible object is {@link Float }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setGroupRef(String value) {
+        this.groupRef = value;
+    }
+
+    /**
+     * Gets the value of the graphColour property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
      */
-    public Float getValue()
-    {
-      return value;
+    public Integer getGraphColour() {
+        return graphColour;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the graphColour property.
      * 
      * @param value
-     *          allowed object is {@link Float }
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphColour(Integer value) {
+        this.graphColour = value;
+    }
+
+    /**
+     * Gets the value of the graphGroup property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
      */
-    public void setValue(Float value)
-    {
-      this.value = value;
+    public Integer getGraphGroup() {
+        return graphGroup;
     }
 
     /**
-     * Gets the value of the colour property.
+     * Sets the value of the graphGroup property.
      * 
-     * @return possible object is {@link Integer }
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphGroup(Integer value) {
+        this.graphGroup = value;
+    }
+
+    /**
+     * Gets the value of the graphHeight property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
      */
-    public Integer getColour()
-    {
-      return colour;
+    public Integer getGraphHeight() {
+        return graphHeight;
     }
 
     /**
-     * Sets the value of the colour property.
+     * Sets the value of the graphHeight property.
      * 
      * @param value
-     *          allowed object is {@link Integer }
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setGraphHeight(Integer value) {
+        this.graphHeight = value;
+    }
+
+    /**
+     * Gets the value of the id property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setColour(Integer value)
-    {
-      this.colour = value;
+    public String getId() {
+        return id;
     }
 
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
+    /**
+     * Gets the value of the scoreOnly property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public boolean isScoreOnly() {
+        if (scoreOnly == null) {
+            return false;
+        } else {
+            return scoreOnly;
+        }
+    }
+
+    /**
+     * Sets the value of the scoreOnly property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setScoreOnly(Boolean value) {
+        this.scoreOnly = value;
+    }
+
+    /**
+     * Gets the value of the score property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Double }
+     *     
+     */
+    public Double getScore() {
+        return score;
+    }
+
+    /**
+     * Sets the value of the score property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Double }
+     *     
+     */
+    public void setScore(Double value) {
+        this.score = value;
+    }
+
+    /**
+     * Gets the value of the visible property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isVisible() {
+        return visible;
+    }
+
+    /**
+     * Sets the value of the visible property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setVisible(Boolean value) {
+        this.visible = value;
+    }
+
+    /**
+     * Gets the value of the centreColLabels property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isCentreColLabels() {
+        return centreColLabels;
+    }
+
+    /**
+     * Sets the value of the centreColLabels property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setCentreColLabels(Boolean value) {
+        this.centreColLabels = value;
+    }
+
+    /**
+     * Gets the value of the scaleColLabels property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isScaleColLabels() {
+        return scaleColLabels;
+    }
+
+    /**
+     * Sets the value of the scaleColLabels property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setScaleColLabels(Boolean value) {
+        this.scaleColLabels = value;
+    }
+
+    /**
+     * Gets the value of the showAllColLabels property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isShowAllColLabels() {
+        return showAllColLabels;
+    }
+
+    /**
+     * Sets the value of the showAllColLabels property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setShowAllColLabels(Boolean value) {
+        this.showAllColLabels = value;
+    }
+
+    /**
+     * Gets the value of the autoCalculated property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public boolean isAutoCalculated() {
+        if (autoCalculated == null) {
+            return false;
+        } else {
+            return autoCalculated;
+        }
+    }
+
+    /**
+     * Sets the value of the autoCalculated property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setAutoCalculated(Boolean value) {
+        this.autoCalculated = value;
+    }
+
+    /**
+     * Gets the value of the belowAlignment property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public boolean isBelowAlignment() {
+        if (belowAlignment == null) {
+            return true;
+        } else {
+            return belowAlignment;
+        }
+    }
+
+    /**
+     * Sets the value of the belowAlignment property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setBelowAlignment(Boolean value) {
+        this.belowAlignment = value;
+    }
+
+    /**
+     * Gets the value of the calcId property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCalcId() {
+        return calcId;
+    }
+
+    /**
+     * Sets the value of the calcId property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCalcId(String value) {
+        this.calcId = value;
+    }
+
+
+    /**
+     * 
Java class for anonymous complex type.
+     * 
+     * 
The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class ThresholdLine {
+
+        @XmlAttribute(name = "label")
+        protected String label;
+        @XmlAttribute(name = "value")
+        protected Float value;
+        @XmlAttribute(name = "colour")
+        protected Integer colour;
+
+        /**
+         * Gets the value of the label property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getLabel() {
+            return label;
+        }
+
+        /**
+         * Sets the value of the label property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setLabel(String value) {
+            this.label = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setValue(Float value) {
+            this.value = value;
+        }
+
+        /**
+         * Gets the value of the colour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getColour() {
+            return colour;
+        }
+
+        /**
+         * Sets the value of the colour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setColour(Integer value) {
+            this.colour = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
index c820076..a9f545d 100644
--- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
+++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,13 +13,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for AnnotationColourScheme complex type.
+ * 
Java class for AnnotationColourScheme complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="AnnotationColourScheme">
@@ -41,215 +40,215 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "AnnotationColourScheme", namespace = "www.jalview.org")
-public class AnnotationColourScheme
-{
-
-  @XmlAttribute(name = "aboveThreshold")
-  protected Integer aboveThreshold;
-
-  @XmlAttribute(name = "annotation")
-  protected String annotation;
-
-  @XmlAttribute(name = "minColour")
-  protected Integer minColour;
-
-  @XmlAttribute(name = "maxColour")
-  protected Integer maxColour;
-
-  @XmlAttribute(name = "colourScheme")
-  protected String colourScheme;
-
-  @XmlAttribute(name = "threshold")
-  protected Float threshold;
-
-  @XmlAttribute(name = "perSequence")
-  protected Boolean perSequence;
-
-  @XmlAttribute(name = "predefinedColours")
-  protected Boolean predefinedColours;
-
-  /**
-   * Gets the value of the aboveThreshold property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getAboveThreshold()
-  {
-    return aboveThreshold;
-  }
-
-  /**
-   * Sets the value of the aboveThreshold property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setAboveThreshold(Integer value)
-  {
-    this.aboveThreshold = value;
-  }
-
-  /**
-   * Gets the value of the annotation property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getAnnotation()
-  {
-    return annotation;
-  }
-
-  /**
-   * Sets the value of the annotation property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setAnnotation(String value)
-  {
-    this.annotation = value;
-  }
-
-  /**
-   * Gets the value of the minColour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getMinColour()
-  {
-    return minColour;
-  }
-
-  /**
-   * Sets the value of the minColour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setMinColour(Integer value)
-  {
-    this.minColour = value;
-  }
-
-  /**
-   * Gets the value of the maxColour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getMaxColour()
-  {
-    return maxColour;
-  }
-
-  /**
-   * Sets the value of the maxColour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setMaxColour(Integer value)
-  {
-    this.maxColour = value;
-  }
-
-  /**
-   * Gets the value of the colourScheme property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getColourScheme()
-  {
-    return colourScheme;
-  }
-
-  /**
-   * Sets the value of the colourScheme property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setColourScheme(String value)
-  {
-    this.colourScheme = value;
-  }
-
-  /**
-   * Gets the value of the threshold property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getThreshold()
-  {
-    return threshold;
-  }
-
-  /**
-   * Sets the value of the threshold property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setThreshold(Float value)
-  {
-    this.threshold = value;
-  }
-
-  /**
-   * Gets the value of the perSequence property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isPerSequence()
-  {
-    return perSequence;
-  }
-
-  /**
-   * Sets the value of the perSequence property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setPerSequence(Boolean value)
-  {
-    this.perSequence = value;
-  }
-
-  /**
-   * Gets the value of the predefinedColours property.
-   * 
-   * @return possible object is {@link Boolean }
-   * 
-   */
-  public Boolean isPredefinedColours()
-  {
-    return predefinedColours;
-  }
-
-  /**
-   * Sets the value of the predefinedColours property.
-   * 
-   * @param value
-   *          allowed object is {@link Boolean }
-   * 
-   */
-  public void setPredefinedColours(Boolean value)
-  {
-    this.predefinedColours = value;
-  }
+public class AnnotationColourScheme {
+
+    @XmlAttribute(name = "aboveThreshold")
+    protected Integer aboveThreshold;
+    @XmlAttribute(name = "annotation")
+    protected String annotation;
+    @XmlAttribute(name = "minColour")
+    protected Integer minColour;
+    @XmlAttribute(name = "maxColour")
+    protected Integer maxColour;
+    @XmlAttribute(name = "colourScheme")
+    protected String colourScheme;
+    @XmlAttribute(name = "threshold")
+    protected Float threshold;
+    @XmlAttribute(name = "perSequence")
+    protected Boolean perSequence;
+    @XmlAttribute(name = "predefinedColours")
+    protected Boolean predefinedColours;
+
+    /**
+     * Gets the value of the aboveThreshold property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getAboveThreshold() {
+        return aboveThreshold;
+    }
+
+    /**
+     * Sets the value of the aboveThreshold property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setAboveThreshold(Integer value) {
+        this.aboveThreshold = value;
+    }
+
+    /**
+     * Gets the value of the annotation property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getAnnotation() {
+        return annotation;
+    }
+
+    /**
+     * Sets the value of the annotation property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setAnnotation(String value) {
+        this.annotation = value;
+    }
+
+    /**
+     * Gets the value of the minColour property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getMinColour() {
+        return minColour;
+    }
+
+    /**
+     * Sets the value of the minColour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setMinColour(Integer value) {
+        this.minColour = value;
+    }
+
+    /**
+     * Gets the value of the maxColour property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getMaxColour() {
+        return maxColour;
+    }
+
+    /**
+     * Sets the value of the maxColour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setMaxColour(Integer value) {
+        this.maxColour = value;
+    }
+
+    /**
+     * Gets the value of the colourScheme property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getColourScheme() {
+        return colourScheme;
+    }
+
+    /**
+     * Sets the value of the colourScheme property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setColourScheme(String value) {
+        this.colourScheme = value;
+    }
+
+    /**
+     * Gets the value of the threshold property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
+     */
+    public Float getThreshold() {
+        return threshold;
+    }
+
+    /**
+     * Sets the value of the threshold property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setThreshold(Float value) {
+        this.threshold = value;
+    }
+
+    /**
+     * Gets the value of the perSequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isPerSequence() {
+        return perSequence;
+    }
+
+    /**
+     * Sets the value of the perSequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setPerSequence(Boolean value) {
+        this.perSequence = value;
+    }
+
+    /**
+     * Gets the value of the predefinedColours property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Boolean }
+     *     
+     */
+    public Boolean isPredefinedColours() {
+        return predefinedColours;
+    }
+
+    /**
+     * Sets the value of the predefinedColours property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Boolean }
+     *     
+     */
+    public void setPredefinedColours(Boolean value) {
+        this.predefinedColours = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java
index 087667a..912be73 100644
--- a/src/jalview/xml/binding/jalview/AnnotationElement.java
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,13 +14,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for anonymous complex type.
+ * 
Java class for anonymous complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType>
@@ -47,159 +46,158 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "displayCharacter", "description", "secondaryStructure", "value" })
+@XmlType(name = "", propOrder = {
+    "displayCharacter",
+    "description",
+    "secondaryStructure",
+    "value"
+})
 @XmlRootElement(name = "annotationElement")
-public class AnnotationElement
-{
-
-  protected String displayCharacter;
-
-  protected String description;
-
-  protected String secondaryStructure;
-
-  protected Float value;
-
-  @XmlAttribute(name = "position", required = true)
-  protected int position;
-
-  @XmlAttribute(name = "colour")
-  protected Integer colour;
-
-  /**
-   * Gets the value of the displayCharacter property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDisplayCharacter()
-  {
-    return displayCharacter;
-  }
-
-  /**
-   * Sets the value of the displayCharacter property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDisplayCharacter(String value)
-  {
-    this.displayCharacter = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the secondaryStructure property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSecondaryStructure()
-  {
-    return secondaryStructure;
-  }
-
-  /**
-   * Sets the value of the secondaryStructure property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSecondaryStructure(String value)
-  {
-    this.secondaryStructure = value;
-  }
-
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getValue()
-  {
-    return value;
-  }
-
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setValue(Float value)
-  {
-    this.value = value;
-  }
-
-  /**
-   * Gets the value of the position property.
-   * 
-   */
-  public int getPosition()
-  {
-    return position;
-  }
-
-  /**
-   * Sets the value of the position property.
-   * 
-   */
-  public void setPosition(int value)
-  {
-    this.position = value;
-  }
-
-  /**
-   * Gets the value of the colour property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getColour()
-  {
-    return colour;
-  }
-
-  /**
-   * Sets the value of the colour property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setColour(Integer value)
-  {
-    this.colour = value;
-  }
+public class AnnotationElement {
+
+    protected String displayCharacter;
+    protected String description;
+    protected String secondaryStructure;
+    protected Float value;
+    @XmlAttribute(name = "position", required = true)
+    protected int position;
+    @XmlAttribute(name = "colour")
+    protected Integer colour;
+
+    /**
+     * Gets the value of the displayCharacter property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDisplayCharacter() {
+        return displayCharacter;
+    }
+
+    /**
+     * Sets the value of the displayCharacter property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDisplayCharacter(String value) {
+        this.displayCharacter = value;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
+
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the secondaryStructure property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSecondaryStructure() {
+        return secondaryStructure;
+    }
+
+    /**
+     * Sets the value of the secondaryStructure property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSecondaryStructure(String value) {
+        this.secondaryStructure = value;
+    }
+
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
+     */
+    public Float getValue() {
+        return value;
+    }
+
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setValue(Float value) {
+        this.value = value;
+    }
+
+    /**
+     * Gets the value of the position property.
+     * 
+     */
+    public int getPosition() {
+        return position;
+    }
+
+    /**
+     * Sets the value of the position property.
+     * 
+     */
+    public void setPosition(int value) {
+        this.position = value;
+    }
+
+    /**
+     * Gets the value of the colour property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getColour() {
+        return colour;
+    }
+
+    /**
+     * Sets the value of the colour property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setColour(Integer value) {
+        this.colour = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleMatrix.java b/src/jalview/xml/binding/jalview/DoubleMatrix.java
index b42a170..cb0fe86 100644
--- a/src/jalview/xml/binding/jalview/DoubleMatrix.java
+++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for DoubleMatrix complex type.
+ * 
Java class for DoubleMatrix complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="DoubleMatrix">
@@ -42,150 +41,146 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "DoubleMatrix",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "row", "d", "e" })
-public class DoubleMatrix
-{
-
-  protected List row;
-
-  @XmlElement(name = "D")
-  protected DoubleVector d;
-
-  @XmlElement(name = "E")
-  protected DoubleVector e;
-
-  @XmlAttribute(name = "rows")
-  protected Integer rows;
-
-  @XmlAttribute(name = "columns")
-  protected Integer columns;
-
-  /**
-   * Gets the value of the row property.
-   * 
-   * 

-   * 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 set method
-   * for the row property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getRow().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link DoubleVector }
-   * 
-   * 
-   */
-  public List getRow()
-  {
-    if (row == null)
-    {
-      row = new ArrayList();
+@XmlType(name = "DoubleMatrix", namespace = "www.jalview.org", propOrder = {
+    "row",
+    "d",
+    "e"
+})
+public class DoubleMatrix {
+
+    protected List row;
+    @XmlElement(name = "D")
+    protected DoubleVector d;
+    @XmlElement(name = "E")
+    protected DoubleVector e;
+    @XmlAttribute(name = "rows")
+    protected Integer rows;
+    @XmlAttribute(name = "columns")
+    protected Integer columns;
+
+    /**
+     * Gets the value of the row property.
+     * 
+     * 

+     * 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 set method for the row property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getRow().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link DoubleVector }
+     * 
+     * 
+     */
+    public List getRow() {
+        if (row == null) {
+            row = new ArrayList();
+        }
+        return this.row;
+    }
+
+    /**
+     * Gets the value of the d property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public DoubleVector getD() {
+        return d;
+    }
+
+    /**
+     * Sets the value of the d property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public void setD(DoubleVector value) {
+        this.d = value;
+    }
+
+    /**
+     * Gets the value of the e property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public DoubleVector getE() {
+        return e;
+    }
+
+    /**
+     * Sets the value of the e property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleVector }
+     *     
+     */
+    public void setE(DoubleVector value) {
+        this.e = value;
+    }
+
+    /**
+     * Gets the value of the rows property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getRows() {
+        return rows;
+    }
+
+    /**
+     * Sets the value of the rows property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setRows(Integer value) {
+        this.rows = value;
+    }
+
+    /**
+     * Gets the value of the columns property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Integer }
+     *     
+     */
+    public Integer getColumns() {
+        return columns;
+    }
+
+    /**
+     * Sets the value of the columns property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Integer }
+     *     
+     */
+    public void setColumns(Integer value) {
+        this.columns = value;
     }
-    return this.row;
-  }
-
-  /**
-   * Gets the value of the d property.
-   * 
-   * @return possible object is {@link DoubleVector }
-   * 
-   */
-  public DoubleVector getD()
-  {
-    return d;
-  }
-
-  /**
-   * Sets the value of the d property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleVector }
-   * 
-   */
-  public void setD(DoubleVector value)
-  {
-    this.d = value;
-  }
-
-  /**
-   * Gets the value of the e property.
-   * 
-   * @return possible object is {@link DoubleVector }
-   * 
-   */
-  public DoubleVector getE()
-  {
-    return e;
-  }
-
-  /**
-   * Sets the value of the e property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleVector }
-   * 
-   */
-  public void setE(DoubleVector value)
-  {
-    this.e = value;
-  }
-
-  /**
-   * Gets the value of the rows property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getRows()
-  {
-    return rows;
-  }
-
-  /**
-   * Sets the value of the rows property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setRows(Integer value)
-  {
-    this.rows = value;
-  }
-
-  /**
-   * Gets the value of the columns property.
-   * 
-   * @return possible object is {@link Integer }
-   * 
-   */
-  public Integer getColumns()
-  {
-    return columns;
-  }
-
-  /**
-   * Sets the value of the columns property.
-   * 
-   * @param value
-   *          allowed object is {@link Integer }
-   * 
-   */
-  public void setColumns(Integer value)
-  {
-    this.columns = value;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/DoubleVector.java b/src/jalview/xml/binding/jalview/DoubleVector.java
index 3b449fe..83a2476 100644
--- a/src/jalview/xml/binding/jalview/DoubleVector.java
+++ b/src/jalview/xml/binding/jalview/DoubleVector.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -14,13 +15,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for DoubleVector complex type.
+ * 
Java class for DoubleVector complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="DoubleVector">
@@ -37,46 +36,41 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "DoubleVector",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "v" })
-public class DoubleVector
-{
+@XmlType(name = "DoubleVector", namespace = "www.jalview.org", propOrder = {
+    "v"
+})
+public class DoubleVector {
 
-  @XmlElement(type = Double.class)
-  protected List v;
+    @XmlElement(type = Double.class)
+    protected List v;
 
-  /**
-   * Gets the value of the v property.
-   * 
-   * 

-   * 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 set method
-   * for the v property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getV().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link Double }
-   * 
-   * 
-   */
-  public List getV()
-  {
-    if (v == null)
-    {
-      v = new ArrayList();
+    /**
+     * Gets the value of the v property.
+     * 
+     * 

+     * 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 set method for the v property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getV().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link Double }
+     * 
+     * 
+     */
+    public List getV() {
+        if (v == null) {
+            v = new ArrayList();
+        }
+        return this.v;
     }
-    return this.v;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java
index afedb4c..5902d10 100644
--- a/src/jalview/xml/binding/jalview/Feature.java
+++ b/src/jalview/xml/binding/jalview/Feature.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -14,13 +15,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for feature complex type.
+ * 
Java class for feature complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="feature">
@@ -54,325 +53,311 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "feature",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "otherData" })
-public class Feature
-{
-
-  protected List otherData;
-
-  @XmlAttribute(name = "begin", required = true)
-  protected int begin;
-
-  @XmlAttribute(name = "end", required = true)
-  protected int end;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "description")
-  protected String description;
-
-  @XmlAttribute(name = "status")
-  protected String status;
-
-  @XmlAttribute(name = "featureGroup")
-  protected String featureGroup;
-
-  @XmlAttribute(name = "score")
-  protected Float score;
-
-  /**
-   * Gets the value of the otherData property.
-   * 
-   * 

-   * 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 set method
-   * for the otherData property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getOtherData().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link Feature.OtherData }
-   * 
-   * 
-   */
-  public List getOtherData()
-  {
-    if (otherData == null)
-    {
-      otherData = new ArrayList();
+@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
+    "otherData"
+})
+public class Feature {
+
+    protected List otherData;
+    @XmlAttribute(name = "begin", required = true)
+    protected int begin;
+    @XmlAttribute(name = "end", required = true)
+    protected int end;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "description")
+    protected String description;
+    @XmlAttribute(name = "status")
+    protected String status;
+    @XmlAttribute(name = "featureGroup")
+    protected String featureGroup;
+    @XmlAttribute(name = "score")
+    protected Float score;
+
+    /**
+     * Gets the value of the otherData property.
+     * 
+     * 

+     * 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 set method for the otherData property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getOtherData().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link Feature.OtherData }
+     * 
+     * 
+     */
+    public List getOtherData() {
+        if (otherData == null) {
+            otherData = new ArrayList();
+        }
+        return this.otherData;
     }
-    return this.otherData;
-  }
-
-  /**
-   * Gets the value of the begin property.
-   * 
-   */
-  public int getBegin()
-  {
-    return begin;
-  }
-
-  /**
-   * Sets the value of the begin property.
-   * 
-   */
-  public void setBegin(int value)
-  {
-    this.begin = value;
-  }
-
-  /**
-   * Gets the value of the end property.
-   * 
-   */
-  public int getEnd()
-  {
-    return end;
-  }
-
-  /**
-   * Sets the value of the end property.
-   * 
-   */
-  public void setEnd(int value)
-  {
-    this.end = value;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the status property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getStatus()
-  {
-    return status;
-  }
-
-  /**
-   * Sets the value of the status property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setStatus(String value)
-  {
-    this.status = value;
-  }
-
-  /**
-   * Gets the value of the featureGroup property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getFeatureGroup()
-  {
-    return featureGroup;
-  }
-
-  /**
-   * Sets the value of the featureGroup property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setFeatureGroup(String value)
-  {
-    this.featureGroup = value;
-  }
-
-  /**
-   * Gets the value of the score property.
-   * 
-   * @return possible object is {@link Float }
-   * 
-   */
-  public Float getScore()
-  {
-    return score;
-  }
-
-  /**
-   * Sets the value of the score property.
-   * 
-   * @param value
-   *          allowed object is {@link Float }
-   * 
-   */
-  public void setScore(Float value)
-  {
-    this.score = value;
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class OtherData
-  {
-
-    @XmlAttribute(name = "key", required = true)
-    protected String key;
-
-    @XmlAttribute(name = "key2")
-    protected String key2;
-
-    @XmlAttribute(name = "value", required = true)
-    protected String value;
 
     /**
-     * Gets the value of the key property.
+     * Gets the value of the begin property.
      * 
-     * @return possible object is {@link String }
+     */
+    public int getBegin() {
+        return begin;
+    }
+
+    /**
+     * Sets the value of the begin property.
      * 
      */
-    public String getKey()
-    {
-      return key;
+    public void setBegin(int value) {
+        this.begin = value;
     }
 
     /**
-     * Sets the value of the key property.
+     * Gets the value of the end property.
      * 
-     * @param value
-     *          allowed object is {@link String }
+     */
+    public int getEnd() {
+        return end;
+    }
+
+    /**
+     * Sets the value of the end property.
+     * 
+     */
+    public void setEnd(int value) {
+        this.end = value;
+    }
+
+    /**
+     * Gets the value of the type property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setKey(String value)
-    {
-      this.key = value;
+    public String getType() {
+        return type;
     }
 
     /**
-     * Gets the value of the key2 property.
+     * Sets the value of the type property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the description property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getKey2()
-    {
-      return key2;
+    public String getDescription() {
+        return description;
     }
 
     /**
-     * Sets the value of the key2 property.
+     * Sets the value of the description property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the status property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setKey2(String value)
-    {
-      this.key2 = value;
+    public String getStatus() {
+        return status;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the status property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setStatus(String value) {
+        this.status = value;
+    }
+
+    /**
+     * Gets the value of the featureGroup property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public String getFeatureGroup() {
+        return featureGroup;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the featureGroup property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setFeatureGroup(String value) {
+        this.featureGroup = value;
+    }
+
+    /**
+     * Gets the value of the score property.
      * 
+     * @return
+     *     possible object is
+     *     {@link Float }
+     *     
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public Float getScore() {
+        return score;
     }
 
-  }
+    /**
+     * Sets the value of the score property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Float }
+     *     
+     */
+    public void setScore(Float value) {
+        this.score = value;
+    }
+
+
+    /**
+     * 
Java class for anonymous complex type.
+     * 
+     * 
The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class OtherData {
+
+        @XmlAttribute(name = "key", required = true)
+        protected String key;
+        @XmlAttribute(name = "key2")
+        protected String key2;
+        @XmlAttribute(name = "value", required = true)
+        protected String value;
+
+        /**
+         * Gets the value of the key property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getKey() {
+            return key;
+        }
+
+        /**
+         * Sets the value of the key property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setKey(String value) {
+            this.key = value;
+        }
+
+        /**
+         * Gets the value of the key2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getKey2() {
+            return key2;
+        }
+
+        /**
+         * Sets the value of the key2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setKey2(String value) {
+            this.key2 = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcher.java b/src/jalview/xml/binding/jalview/FeatureMatcher.java
index fa80569..9d28efa 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcher.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for FeatureMatcher complex type.
+ * 
Java class for FeatureMatcher complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="FeatureMatcher">
@@ -41,124 +40,121 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "FeatureMatcher",
-  namespace = "www.jalview.org/colours",
-  propOrder =
-  { "attributeName", "condition", "value" })
-public class FeatureMatcher
-{
-
-  @XmlElement(namespace = "")
-  protected List attributeName;
+@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
+    "attributeName",
+    "condition",
+    "value"
+})
+public class FeatureMatcher {
 
-  @XmlElement(namespace = "", required = true)
-  protected String condition;
+    @XmlElement(namespace = "")
+    protected List attributeName;
+    @XmlElement(namespace = "", required = true)
+    protected String condition;
+    @XmlElement(namespace = "", required = true)
+    protected String value;
+    @XmlAttribute(name = "by")
+    protected FilterBy by;
 
-  @XmlElement(namespace = "", required = true)
-  protected String value;
-
-  @XmlAttribute(name = "by")
-  protected FilterBy by;
-
-  /**
-   * Gets the value of the attributeName property.
-   * 
-   * 

-   * 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 set method
-   * for the attributeName property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getAttributeName().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getAttributeName()
-  {
-    if (attributeName == null)
-    {
-      attributeName = new ArrayList();
+    /**
+     * Gets the value of the attributeName property.
+     * 
+     * 

+     * 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 set method for the attributeName property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getAttributeName().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getAttributeName() {
+        if (attributeName == null) {
+            attributeName = new ArrayList();
+        }
+        return this.attributeName;
     }
-    return this.attributeName;
-  }
 
-  /**
-   * Gets the value of the condition property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getCondition()
-  {
-    return condition;
-  }
+    /**
+     * Gets the value of the condition property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getCondition() {
+        return condition;
+    }
 
-  /**
-   * Sets the value of the condition property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setCondition(String value)
-  {
-    this.condition = value;
-  }
+    /**
+     * Sets the value of the condition property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setCondition(String value) {
+        this.condition = value;
+    }
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
-  /**
-   * Gets the value of the by property.
-   * 
-   * @return possible object is {@link FilterBy }
-   * 
-   */
-  public FilterBy getBy()
-  {
-    return by;
-  }
+    /**
+     * Gets the value of the by property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link FilterBy }
+     *     
+     */
+    public FilterBy getBy() {
+        return by;
+    }
 
-  /**
-   * Sets the value of the by property.
-   * 
-   * @param value
-   *          allowed object is {@link FilterBy }
-   * 
-   */
-  public void setBy(FilterBy value)
-  {
-    this.by = value;
-  }
+    /**
+     * Sets the value of the by property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link FilterBy }
+     *     
+     */
+    public void setBy(FilterBy value) {
+        this.by = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
index 45077af..6499485 100644
--- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,15 +16,13 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * A feature match condition, which may be simple or compound
  * 
- * 

- * Java class for FeatureMatcherSet complex type.
+ * 
Java class for FeatureMatcherSet complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="FeatureMatcherSet">
@@ -52,150 +51,142 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "FeatureMatcherSet",
-  namespace = "www.jalview.org/colours",
-  propOrder =
-  { "matchCondition", "compoundMatcher" })
-public class FeatureMatcherSet
-{
-
-  @XmlElement(namespace = "")
-  protected FeatureMatcher matchCondition;
-
-  @XmlElement(namespace = "")
-  protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
-
-  /**
-   * Gets the value of the matchCondition property.
-   * 
-   * @return possible object is {@link FeatureMatcher }
-   * 
-   */
-  public FeatureMatcher getMatchCondition()
-  {
-    return matchCondition;
-  }
-
-  /**
-   * Sets the value of the matchCondition property.
-   * 
-   * @param value
-   *          allowed object is {@link FeatureMatcher }
-   * 
-   */
-  public void setMatchCondition(FeatureMatcher value)
-  {
-    this.matchCondition = value;
-  }
-
-  /**
-   * Gets the value of the compoundMatcher property.
-   * 
-   * @return possible object is {@link FeatureMatcherSet.CompoundMatcher }
-   * 
-   */
-  public FeatureMatcherSet.CompoundMatcher getCompoundMatcher()
-  {
-    return compoundMatcher;
-  }
-
-  /**
-   * Sets the value of the compoundMatcher property.
-   * 
-   * @param value
-   *          allowed object is {@link FeatureMatcherSet.CompoundMatcher }
-   * 
-   */
-  public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value)
-  {
-    this.compoundMatcher = value;
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
-   *       </sequence>
-   *       <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "matcherSet" })
-  public static class CompoundMatcher
-  {
-
-    @XmlElement(namespace = "", required = true)
-    protected List matcherSet;
-
-    @XmlAttribute(name = "and", required = true)
-    protected boolean and;
+@XmlType(name = "FeatureMatcherSet", namespace = "www.jalview.org/colours", propOrder = {
+    "matchCondition",
+    "compoundMatcher"
+})
+public class FeatureMatcherSet {
+
+    @XmlElement(namespace = "")
+    protected FeatureMatcher matchCondition;
+    @XmlElement(namespace = "")
+    protected FeatureMatcherSet.CompoundMatcher compoundMatcher;
 
     /**
-     * Gets the value of the matcherSet property.
-     * 
-     * 

-     * 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
-     * set method for the matcherSet property.
-     * 
-     * 

-     * For example, to add a new item, do as follows:
-     * 
-     * 
-     * getMatcherSet().add(newItem);
-     * 

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link FeatureMatcherSet }
+     * Gets the value of the matchCondition property.
      * 
+     * @return
+     *     possible object is
+     *     {@link FeatureMatcher }
+     *     
+     */
+    public FeatureMatcher getMatchCondition() {
+        return matchCondition;
+    }
+
+    /**
+     * Sets the value of the matchCondition property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link FeatureMatcher }
+     *     
      */
-    public List getMatcherSet()
-    {
-      if (matcherSet == null)
-      {
-        matcherSet = new ArrayList();
-      }
-      return this.matcherSet;
+    public void setMatchCondition(FeatureMatcher value) {
+        this.matchCondition = value;
     }
 
     /**
-     * Gets the value of the and property.
+     * Gets the value of the compoundMatcher property.
      * 
+     * @return
+     *     possible object is
+     *     {@link FeatureMatcherSet.CompoundMatcher }
+     *     
      */
-    public boolean isAnd()
-    {
-      return and;
+    public FeatureMatcherSet.CompoundMatcher getCompoundMatcher() {
+        return compoundMatcher;
     }
 
     /**
-     * Sets the value of the and property.
+     * Sets the value of the compoundMatcher property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link FeatureMatcherSet.CompoundMatcher }
+     *     
      */
-    public void setAnd(boolean value)
-    {
-      this.and = value;
+    public void setCompoundMatcher(FeatureMatcherSet.CompoundMatcher value) {
+        this.compoundMatcher = value;
     }
 
-  }
+
+    /**
+     * 
Java class for anonymous complex type.
+     * 
+     * 
The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+     *       </sequence>
+     *       <attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "matcherSet"
+    })
+    public static class CompoundMatcher {
+
+        @XmlElement(namespace = "", required = true)
+        protected List matcherSet;
+        @XmlAttribute(name = "and", required = true)
+        protected boolean and;
+
+        /**
+         * Gets the value of the matcherSet property.
+         * 
+         * 

+         * 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 set method for the matcherSet property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getMatcherSet().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link FeatureMatcherSet }
+         * 
+         * 
+         */
+        public List getMatcherSet() {
+            if (matcherSet == null) {
+                matcherSet = new ArrayList();
+            }
+            return this.matcherSet;
+        }
+
+        /**
+         * Gets the value of the and property.
+         * 
+         */
+        public boolean isAnd() {
+            return and;
+        }
+
+        /**
+         * Sets the value of the and property.
+         * 
+         */
+        public void setAnd(boolean value) {
+            this.and = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/FilterBy.java b/src/jalview/xml/binding/jalview/FilterBy.java
index 76fc6cd..f2b113f 100644
--- a/src/jalview/xml/binding/jalview/FilterBy.java
+++ b/src/jalview/xml/binding/jalview/FilterBy.java
@@ -2,24 +2,22 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlEnumValue;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for FilterBy.
+ * 
Java class for FilterBy.
  * 
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 

- * The following schema fragment specifies the expected content contained within
- * this class.
- * 

- * 
  * 
  * <simpleType name="FilterBy">
  *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
@@ -33,36 +31,31 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "FilterBy", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum FilterBy
-{
-
-  @XmlEnumValue("byLabel")
-  BY_LABEL("byLabel"), @XmlEnumValue("byScore")
-  BY_SCORE("byScore"), @XmlEnumValue("byAttribute")
-  BY_ATTRIBUTE("byAttribute");
-
-  private final String value;
-
-  FilterBy(String v)
-  {
-    value = v;
-  }
+public enum FilterBy {
+
+    @XmlEnumValue("byLabel")
+    BY_LABEL("byLabel"),
+    @XmlEnumValue("byScore")
+    BY_SCORE("byScore"),
+    @XmlEnumValue("byAttribute")
+    BY_ATTRIBUTE("byAttribute");
+    private final String value;
+
+    FilterBy(String v) {
+        value = v;
+    }
 
-  public String value()
-  {
-    return value;
-  }
+    public String value() {
+        return value;
+    }
 
-  public static FilterBy fromValue(String v)
-  {
-    for (FilterBy c : FilterBy.values())
-    {
-      if (c.value.equals(v))
-      {
-        return c;
-      }
+    public static FilterBy fromValue(String v) {
+        for (FilterBy c: FilterBy.values()) {
+            if (c.value.equals(v)) {
+                return c;
+            }
+        }
+        throw new IllegalArgumentException(v);
     }
-    throw new IllegalArgumentException(v);
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index 94f9373..9241fdd 100644
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -21,13 +22,11 @@ import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
 import javax.xml.datatype.XMLGregorianCalendar;
 
+
 /**
- * 

- * Java class for JalviewModel complex type.
+ * 
Java class for JalviewModel complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="JalviewModel">
@@ -382,3475 +381,2762 @@ import javax.xml.datatype.XMLGregorianCalendar;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "JalviewModel",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport",
-      "userColours", "tree", "pcaViewer", "featureSettings" })
-public class JalviewModel
-{
-
-  @XmlElement(required = true)
-  @XmlSchemaType(name = "dateTime")
-  protected XMLGregorianCalendar creationDate;
-
-  @XmlElement(required = true)
-  protected String version;
-
-  @XmlElement(required = true)
-  protected VAMSAS vamsasModel;
-
-  @XmlElement(name = "JSeq")
-  protected List jSeq;
-
-  @XmlElement(name = "JGroup")
-  protected List jGroup;
-
-  @XmlElement(name = "Viewport")
-  protected List viewport;
-
-  @XmlElement(name = "UserColours")
-  protected List userColours;
-
-  protected List tree;
-
-  @XmlElement(name = "PcaViewer")
-  protected List pcaViewer;
-
-  @XmlElement(name = "FeatureSettings")
-  protected JalviewModel.FeatureSettings featureSettings;
-
-  /**
-   * Gets the value of the creationDate property.
-   * 
-   * @return possible object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public XMLGregorianCalendar getCreationDate()
-  {
-    return creationDate;
-  }
-
-  /**
-   * Sets the value of the creationDate property.
-   * 
-   * @param value
-   *          allowed object is {@link XMLGregorianCalendar }
-   * 
-   */
-  public void setCreationDate(XMLGregorianCalendar value)
-  {
-    this.creationDate = value;
-  }
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the vamsasModel property.
-   * 
-   * @return possible object is {@link VAMSAS }
-   * 
-   */
-  public VAMSAS getVamsasModel()
-  {
-    return vamsasModel;
-  }
-
-  /**
-   * Sets the value of the vamsasModel property.
-   * 
-   * @param value
-   *          allowed object is {@link VAMSAS }
-   * 
-   */
-  public void setVamsasModel(VAMSAS value)
-  {
-    this.vamsasModel = value;
-  }
-
-  /**
-   * Gets the value of the jSeq property.
-   * 
-   * 

-   * 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 set method
-   * for the jSeq property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getJSeq().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.JSeq }
-   * 
-   * 
-   */
-  public List getJSeq()
-  {
-    if (jSeq == null)
-    {
-      jSeq = new ArrayList();
-    }
-    return this.jSeq;
-  }
-
-  /**
-   * Gets the value of the jGroup property.
-   * 
-   * 

-   * 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 set method
-   * for the jGroup property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getJGroup().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.JGroup }
-   * 
-   * 
-   */
-  public List getJGroup()
-  {
-    if (jGroup == null)
-    {
-      jGroup = new ArrayList();
+@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
+    "creationDate",
+    "version",
+    "vamsasModel",
+    "jSeq",
+    "jGroup",
+    "viewport",
+    "userColours",
+    "tree",
+    "pcaViewer",
+    "featureSettings"
+})
+public class JalviewModel {
+
+    @XmlElement(required = true)
+    @XmlSchemaType(name = "dateTime")
+    protected XMLGregorianCalendar creationDate;
+    @XmlElement(required = true)
+    protected String version;
+    @XmlElement(required = true)
+    protected VAMSAS vamsasModel;
+    @XmlElement(name = "JSeq")
+    protected List jSeq;
+    @XmlElement(name = "JGroup")
+    protected List jGroup;
+    @XmlElement(name = "Viewport")
+    protected List viewport;
+    @XmlElement(name = "UserColours")
+    protected List userColours;
+    protected List tree;
+    @XmlElement(name = "PcaViewer")
+    protected List pcaViewer;
+    @XmlElement(name = "FeatureSettings")
+    protected JalviewModel.FeatureSettings featureSettings;
+
+    /**
+     * Gets the value of the creationDate property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public XMLGregorianCalendar getCreationDate() {
+        return creationDate;
+    }
+
+    /**
+     * Sets the value of the creationDate property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link XMLGregorianCalendar }
+     *     
+     */
+    public void setCreationDate(XMLGregorianCalendar value) {
+        this.creationDate = value;
     }
-    return this.jGroup;
-  }
-
-  /**
-   * Gets the value of the viewport property.
-   * 
-   * 

-   * 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 set method
-   * for the viewport property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getViewport().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.Viewport }
-   * 
-   * 
-   */
-  public List getViewport()
-  {
-    if (viewport == null)
-    {
-      viewport = new ArrayList();
+
+    /**
+     * Gets the value of the version property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getVersion() {
+        return version;
     }
-    return this.viewport;
-  }
-
-  /**
-   * Gets the value of the userColours property.
-   * 
-   * 

-   * 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 set method
-   * for the userColours property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getUserColours().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.UserColours }
-   * 
-   * 
-   */
-  public List getUserColours()
-  {
-    if (userColours == null)
-    {
-      userColours = new ArrayList();
+
+    /**
+     * Sets the value of the version property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setVersion(String value) {
+        this.version = value;
     }
-    return this.userColours;
-  }
-
-  /**
-   * Gets the value of the tree property.
-   * 
-   * 

-   * 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 set method
-   * for the tree property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getTree().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.Tree }
-   * 
-   * 
-   */
-  public List getTree()
-  {
-    if (tree == null)
-    {
-      tree = new ArrayList();
+
+    /**
+     * Gets the value of the vamsasModel property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link VAMSAS }
+     *     
+     */
+    public VAMSAS getVamsasModel() {
+        return vamsasModel;
     }
-    return this.tree;
-  }
-
-  /**
-   * Gets the value of the pcaViewer property.
-   * 
-   * 

-   * 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 set method
-   * for the pcaViewer property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getPcaViewer().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewModel.PcaViewer }
-   * 
-   * 
-   */
-  public List getPcaViewer()
-  {
-    if (pcaViewer == null)
-    {
-      pcaViewer = new ArrayList();
+
+    /**
+     * Sets the value of the vamsasModel property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link VAMSAS }
+     *     
+     */
+    public void setVamsasModel(VAMSAS value) {
+        this.vamsasModel = value;
     }
-    return this.pcaViewer;
-  }
-
-  /**
-   * Gets the value of the featureSettings property.
-   * 
-   * @return possible object is {@link JalviewModel.FeatureSettings }
-   * 
-   */
-  public JalviewModel.FeatureSettings getFeatureSettings()
-  {
-    return featureSettings;
-  }
-
-  /**
-   * Sets the value of the featureSettings property.
-   * 
-   * @param value
-   *          allowed object is {@link JalviewModel.FeatureSettings }
-   * 
-   */
-  public void setFeatureSettings(JalviewModel.FeatureSettings value)
-  {
-    this.featureSettings = value;
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <sequence>
-   *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-   *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-   *                 </sequence>
-   *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-   *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="group" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "setting", "group" })
-  public static class FeatureSettings
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List setting;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List group;
 
     /**
-     * Gets the value of the setting property.
+     * Gets the value of the jSeq property.
      * 
      * 

-     * 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
-     * set method for the setting property.
+     * 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 set method for the jSeq property.
      * 
      * 

      * For example, to add a new item, do as follows:
-     * 
      * 
-     * getSetting().add(newItem);
+     *    getJSeq().add(newItem);
      * 

      * 
      * 
      * 

      * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.FeatureSettings.Setting }
+     * {@link JalviewModel.JSeq }
      * 
      * 
      */
-    public List getSetting()
-    {
-      if (setting == null)
-      {
-        setting = new ArrayList();
-      }
-      return this.setting;
+    public List getJSeq() {
+        if (jSeq == null) {
+            jSeq = new ArrayList();
+        }
+        return this.jSeq;
     }
 
     /**
-     * Gets the value of the group property.
+     * Gets the value of the jGroup property.
      * 
      * 

-     * 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
-     * set method for the group property.
+     * 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 set method for the jGroup property.
      * 
      * 

      * For example, to add a new item, do as follows:
-     * 
      * 
-     * getGroup().add(newItem);
+     *    getJGroup().add(newItem);
      * 

      * 
      * 
      * 

      * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.FeatureSettings.Group }
+     * {@link JalviewModel.JGroup }
      * 
      * 
      */
-    public List getGroup()
-    {
-      if (group == null)
-      {
-        group = new ArrayList();
-      }
-      return this.group;
+    public List getJGroup() {
+        if (jGroup == null) {
+            jGroup = new ArrayList();
+        }
+        return this.jGroup;
     }
 
     /**
-     * 

-     * Java class for anonymous complex type.
+     * Gets the value of the viewport property.
      * 
      * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * 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 set method for the viewport property.
      * 
+     * 

+     * For example, to add a new item, do as follows:
      * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
+     *    getViewport().add(newItem);
      * 

      * 
      * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Group
-    {
-
-      @XmlAttribute(name = "name", required = true)
-      protected String name;
-
-      @XmlAttribute(name = "display", required = true)
-      protected boolean display;
-
-      /**
-       * Gets the value of the name property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getName()
-      {
-        return name;
-      }
-
-      /**
-       * Sets the value of the name property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setName(String value)
-      {
-        this.name = value;
-      }
-
-      /**
-       * Gets the value of the display property.
-       * 
-       */
-      public boolean isDisplay()
-      {
-        return display;
-      }
-
-      /**
-       * Sets the value of the display property.
-       * 
-       */
-      public void setDisplay(boolean value)
-      {
-        this.display = value;
-      }
-
-    }
-
-    /**
-     * 

-     * Java class for anonymous complex type.
-     * 
      * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.Viewport }
      * 
      * 
      */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
-    public static class Setting
-    {
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected List attributeName;
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected FeatureMatcherSet matcherSet;
-
-      @XmlAttribute(name = "type", required = true)
-      protected String type;
-
-      @XmlAttribute(name = "colour", required = true)
-      protected int colour;
-
-      @XmlAttribute(name = "display", required = true)
-      protected boolean display;
-
-      @XmlAttribute(name = "order")
-      protected Float order;
-
-      @XmlAttribute(name = "mincolour")
-      protected Integer mincolour;
-
-      @XmlAttribute(name = "noValueColour")
-      protected NoValueColour noValueColour;
-
-      @XmlAttribute(name = "threshold")
-      protected Float threshold;
-
-      @XmlAttribute(name = "threshstate")
-      protected Integer threshstate;
-
-      @XmlAttribute(name = "max")
-      protected Float max;
-
-      @XmlAttribute(name = "min")
-      protected Float min;
-
-      @XmlAttribute(name = "colourByLabel")
-      protected Boolean colourByLabel;
-
-      @XmlAttribute(name = "autoScale")
-      protected Boolean autoScale;
-
-      /**
-       * Gets the value of the attributeName property.
-       * 
-       * 

-       * 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
-       * set method for the attributeName property.
-       * 
-       * 

-       * For example, to add a new item, do as follows:
-       * 
-       * 
-       * getAttributeName().add(newItem);
-       * 

-       * 
-       * 
-       * 

-       * Objects of the following type(s) are allowed in the list {@link String
-       * }
-       * 
-       * 
-       */
-      public List getAttributeName()
-      {
-        if (attributeName == null)
-        {
-          attributeName = new ArrayList();
-        }
-        return this.attributeName;
-      }
-
-      /**
-       * Gets the value of the matcherSet property.
-       * 
-       * @return possible object is {@link FeatureMatcherSet }
-       * 
-       */
-      public FeatureMatcherSet getMatcherSet()
-      {
-        return matcherSet;
-      }
-
-      /**
-       * Sets the value of the matcherSet property.
-       * 
-       * @param value
-       *          allowed object is {@link FeatureMatcherSet }
-       * 
-       */
-      public void setMatcherSet(FeatureMatcherSet value)
-      {
-        this.matcherSet = value;
-      }
-
-      /**
-       * Gets the value of the type property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getType()
-      {
-        return type;
-      }
-
-      /**
-       * Sets the value of the type property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setType(String value)
-      {
-        this.type = value;
-      }
-
-      /**
-       * Gets the value of the colour property.
-       * 
-       */
-      public int getColour()
-      {
-        return colour;
-      }
-
-      /**
-       * Sets the value of the colour property.
-       * 
-       */
-      public void setColour(int value)
-      {
-        this.colour = value;
-      }
-
-      /**
-       * Gets the value of the display property.
-       * 
-       */
-      public boolean isDisplay()
-      {
-        return display;
-      }
-
-      /**
-       * Sets the value of the display property.
-       * 
-       */
-      public void setDisplay(boolean value)
-      {
-        this.display = value;
-      }
-
-      /**
-       * Gets the value of the order property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getOrder()
-      {
-        return order;
-      }
-
-      /**
-       * Sets the value of the order property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setOrder(Float value)
-      {
-        this.order = value;
-      }
-
-      /**
-       * Gets the value of the mincolour property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getMincolour()
-      {
-        return mincolour;
-      }
-
-      /**
-       * Sets the value of the mincolour property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setMincolour(Integer value)
-      {
-        this.mincolour = value;
-      }
-
-      /**
-       * Gets the value of the noValueColour property.
-       * 
-       * @return possible object is {@link NoValueColour }
-       * 
-       */
-      public NoValueColour getNoValueColour()
-      {
-        if (noValueColour == null)
-        {
-          return NoValueColour.MIN;
+    public List getViewport() {
+        if (viewport == null) {
+            viewport = new ArrayList();
         }
-        else
-        {
-          return noValueColour;
-        }
-      }
-
-      /**
-       * Sets the value of the noValueColour property.
-       * 
-       * @param value
-       *          allowed object is {@link NoValueColour }
-       * 
-       */
-      public void setNoValueColour(NoValueColour value)
-      {
-        this.noValueColour = value;
-      }
-
-      /**
-       * Gets the value of the threshold property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getThreshold()
-      {
-        return threshold;
-      }
-
-      /**
-       * Sets the value of the threshold property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setThreshold(Float value)
-      {
-        this.threshold = value;
-      }
-
-      /**
-       * Gets the value of the threshstate property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getThreshstate()
-      {
-        return threshstate;
-      }
-
-      /**
-       * Sets the value of the threshstate property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setThreshstate(Integer value)
-      {
-        this.threshstate = value;
-      }
-
-      /**
-       * Gets the value of the max property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getMax()
-      {
-        return max;
-      }
-
-      /**
-       * Sets the value of the max property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setMax(Float value)
-      {
-        this.max = value;
-      }
-
-      /**
-       * Gets the value of the min property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getMin()
-      {
-        return min;
-      }
-
-      /**
-       * Sets the value of the min property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setMin(Float value)
-      {
-        this.min = value;
-      }
-
-      /**
-       * Gets the value of the colourByLabel property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isColourByLabel()
-      {
-        return colourByLabel;
-      }
-
-      /**
-       * Sets the value of the colourByLabel property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setColourByLabel(Boolean value)
-      {
-        this.colourByLabel = value;
-      }
-
-      /**
-       * Gets the value of the autoScale property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isAutoScale()
-      {
-        return autoScale;
-      }
-
-      /**
-       * Sets the value of the autoScale property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setAutoScale(Boolean value)
-      {
-        this.autoScale = value;
-      }
-
+        return this.viewport;
     }
 
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-   *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-   *       </sequence>
-   *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "seq", "annotationColours" })
-  public static class JGroup
-  {
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List seq;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected AnnotationColourScheme annotationColours;
-
-    @XmlAttribute(name = "start")
-    protected Integer start;
-
-    @XmlAttribute(name = "end")
-    protected Integer end;
-
-    @XmlAttribute(name = "name")
-    protected String name;
-
-    @XmlAttribute(name = "colour")
-    protected String colour;
-
-    @XmlAttribute(name = "consThreshold")
-    protected Integer consThreshold;
-
-    @XmlAttribute(name = "pidThreshold")
-    protected Integer pidThreshold;
-
-    @XmlAttribute(name = "outlineColour")
-    protected Integer outlineColour;
-
-    @XmlAttribute(name = "displayBoxes")
-    protected Boolean displayBoxes;
-
-    @XmlAttribute(name = "displayText")
-    protected Boolean displayText;
-
-    @XmlAttribute(name = "colourText")
-    protected Boolean colourText;
-
-    @XmlAttribute(name = "textCol1")
-    protected Integer textCol1;
-
-    @XmlAttribute(name = "textCol2")
-    protected Integer textCol2;
-
-    @XmlAttribute(name = "textColThreshold")
-    protected Integer textColThreshold;
-
-    @XmlAttribute(name = "showUnconserved")
-    protected Boolean showUnconserved;
-
-    @XmlAttribute(name = "ignoreGapsinConsensus")
-    protected Boolean ignoreGapsinConsensus;
-
-    @XmlAttribute(name = "showConsensusHistogram")
-    protected Boolean showConsensusHistogram;
-
-    @XmlAttribute(name = "showSequenceLogo")
-    protected Boolean showSequenceLogo;
-
-    @XmlAttribute(name = "normaliseSequenceLogo")
-    protected Boolean normaliseSequenceLogo;
-
-    @XmlAttribute(name = "id")
-    protected String id;
-
     /**
-     * Gets the value of the seq property.
+     * Gets the value of the userColours property.
      * 
      * 

-     * 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
-     * set method for the seq property.
+     * 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 set method for the userColours property.
      * 
      * 

      * For example, to add a new item, do as follows:
-     * 
      * 
-     * getSeq().add(newItem);
+     *    getUserColours().add(newItem);
      * 

      * 
      * 
      * 

-     * Objects of the following type(s) are allowed in the list {@link String }
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.UserColours }
      * 
      * 
      */
-    public List getSeq()
-    {
-      if (seq == null)
-      {
-        seq = new ArrayList();
-      }
-      return this.seq;
+    public List getUserColours() {
+        if (userColours == null) {
+            userColours = new ArrayList();
+        }
+        return this.userColours;
     }
 
     /**
-     * Gets the value of the annotationColours property.
+     * Gets the value of the tree property.
      * 
-     * @return possible object is {@link AnnotationColourScheme }
+     * 

+     * 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 set method for the tree property.
      * 
-     */
-    public AnnotationColourScheme getAnnotationColours()
-    {
-      return annotationColours;
-    }
-
-    /**
-     * Sets the value of the annotationColours property.
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getTree().add(newItem);
+     * 

      * 
-     * @param value
-     *          allowed object is {@link AnnotationColourScheme }
      * 
-     */
-    public void setAnnotationColours(AnnotationColourScheme value)
-    {
-      this.annotationColours = value;
-    }
-
-    /**
-     * Gets the value of the start property.
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.Tree }
      * 
-     * @return possible object is {@link Integer }
      * 
      */
-    public Integer getStart()
-    {
-      return start;
+    public List getTree() {
+        if (tree == null) {
+            tree = new ArrayList();
+        }
+        return this.tree;
     }
 
     /**
-     * Sets the value of the start property.
+     * Gets the value of the pcaViewer property.
      * 
-     * @param value
-     *          allowed object is {@link Integer }
+     * 

+     * 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 set method for the pcaViewer property.
      * 
-     */
-    public void setStart(Integer value)
-    {
-      this.start = value;
-    }
-
-    /**
-     * Gets the value of the end property.
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getPcaViewer().add(newItem);
+     * 

      * 
-     * @return possible object is {@link Integer }
      * 
-     */
-    public Integer getEnd()
-    {
-      return end;
-    }
-
-    /**
-     * Sets the value of the end property.
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.PcaViewer }
      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
      */
-    public void setEnd(Integer value)
-    {
-      this.end = value;
+    public List getPcaViewer() {
+        if (pcaViewer == null) {
+            pcaViewer = new ArrayList();
+        }
+        return this.pcaViewer;
     }
 
     /**
-     * Gets the value of the name property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the featureSettings property.
      * 
+     * @return
+     *     possible object is
+     *     {@link JalviewModel.FeatureSettings }
+     *     
      */
-    public String getName()
-    {
-      return name;
+    public JalviewModel.FeatureSettings getFeatureSettings() {
+        return featureSettings;
     }
 
     /**
-     * Sets the value of the name property.
+     * Sets the value of the featureSettings property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link JalviewModel.FeatureSettings }
+     *     
      */
-    public void setName(String value)
-    {
-      this.name = value;
+    public void setFeatureSettings(JalviewModel.FeatureSettings value) {
+        this.featureSettings = value;
     }
 
-    /**
-     * Gets the value of the colour property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getColour()
-    {
-      return colour;
-    }
 
     /**
-     * Sets the value of the colour property.
+     * 
Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link String }
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setColour(String value)
-    {
-      this.colour = value;
-    }
-
-    /**
-     * Gets the value of the consThreshold property.
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <sequence>
+     *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *                 </sequence>
+     *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="group" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

      * 
-     * @return possible object is {@link Integer }
      * 
      */
-    public Integer getConsThreshold()
-    {
-      return consThreshold;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "setting",
+        "group"
+    })
+    public static class FeatureSettings {
 
-    /**
-     * Sets the value of the consThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setConsThreshold(Integer value)
-    {
-      this.consThreshold = value;
-    }
+        @XmlElement(namespace = "www.jalview.org")
+        protected List setting;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List group;
 
-    /**
-     * Gets the value of the pidThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getPidThreshold()
-    {
-      return pidThreshold;
-    }
+        /**
+         * Gets the value of the setting property.
+         * 
+         * 

+         * 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 set method for the setting property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getSetting().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.FeatureSettings.Setting }
+         * 
+         * 
+         */
+        public List getSetting() {
+            if (setting == null) {
+                setting = new ArrayList();
+            }
+            return this.setting;
+        }
 
-    /**
-     * Sets the value of the pidThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setPidThreshold(Integer value)
-    {
-      this.pidThreshold = value;
-    }
+        /**
+         * Gets the value of the group property.
+         * 
+         * 

+         * 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 set method for the group property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getGroup().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.FeatureSettings.Group }
+         * 
+         * 
+         */
+        public List getGroup() {
+            if (group == null) {
+                group = new ArrayList();
+            }
+            return this.group;
+        }
 
-    /**
-     * Gets the value of the outlineColour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getOutlineColour()
-    {
-      return outlineColour;
-    }
 
-    /**
-     * Sets the value of the outlineColour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setOutlineColour(Integer value)
-    {
-      this.outlineColour = value;
-    }
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Group {
+
+            @XmlAttribute(name = "name", required = true)
+            protected String name;
+            @XmlAttribute(name = "display", required = true)
+            protected boolean display;
+
+            /**
+             * Gets the value of the name property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getName() {
+                return name;
+            }
+
+            /**
+             * Sets the value of the name property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setName(String value) {
+                this.name = value;
+            }
+
+            /**
+             * Gets the value of the display property.
+             * 
+             */
+            public boolean isDisplay() {
+                return display;
+            }
+
+            /**
+             * Sets the value of the display property.
+             * 
+             */
+            public void setDisplay(boolean value) {
+                this.display = value;
+            }
 
-    /**
-     * Gets the value of the displayBoxes property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isDisplayBoxes()
-    {
-      return displayBoxes;
-    }
+        }
 
-    /**
-     * Sets the value of the displayBoxes property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setDisplayBoxes(Boolean value)
-    {
-      this.displayBoxes = value;
-    }
 
-    /**
-     * Gets the value of the displayText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isDisplayText()
-    {
-      return displayText;
-    }
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <sequence>
+         *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+         *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+         *       </sequence>
+         *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+         *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "attributeName",
+            "matcherSet"
+        })
+        public static class Setting {
+
+            @XmlElement(namespace = "www.jalview.org")
+            protected List attributeName;
+            @XmlElement(namespace = "www.jalview.org")
+            protected FeatureMatcherSet matcherSet;
+            @XmlAttribute(name = "type", required = true)
+            protected String type;
+            @XmlAttribute(name = "colour", required = true)
+            protected int colour;
+            @XmlAttribute(name = "display", required = true)
+            protected boolean display;
+            @XmlAttribute(name = "order")
+            protected Float order;
+            @XmlAttribute(name = "mincolour")
+            protected Integer mincolour;
+            @XmlAttribute(name = "noValueColour")
+            protected NoValueColour noValueColour;
+            @XmlAttribute(name = "threshold")
+            protected Float threshold;
+            @XmlAttribute(name = "threshstate")
+            protected Integer threshstate;
+            @XmlAttribute(name = "max")
+            protected Float max;
+            @XmlAttribute(name = "min")
+            protected Float min;
+            @XmlAttribute(name = "colourByLabel")
+            protected Boolean colourByLabel;
+            @XmlAttribute(name = "autoScale")
+            protected Boolean autoScale;
+
+            /**
+             * Gets the value of the attributeName property.
+             * 
+             * 

+             * 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 set method for the attributeName property.
+             * 
+             * 

+             * For example, to add a new item, do as follows:
+             * 
+             *    getAttributeName().add(newItem);
+             * 

+             * 
+             * 
+             * 

+             * Objects of the following type(s) are allowed in the list
+             * {@link String }
+             * 
+             * 
+             */
+            public List getAttributeName() {
+                if (attributeName == null) {
+                    attributeName = new ArrayList();
+                }
+                return this.attributeName;
+            }
+
+            /**
+             * Gets the value of the matcherSet property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link FeatureMatcherSet }
+             *     
+             */
+            public FeatureMatcherSet getMatcherSet() {
+                return matcherSet;
+            }
+
+            /**
+             * Sets the value of the matcherSet property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link FeatureMatcherSet }
+             *     
+             */
+            public void setMatcherSet(FeatureMatcherSet value) {
+                this.matcherSet = value;
+            }
+
+            /**
+             * Gets the value of the type property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getType() {
+                return type;
+            }
+
+            /**
+             * Sets the value of the type property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setType(String value) {
+                this.type = value;
+            }
+
+            /**
+             * Gets the value of the colour property.
+             * 
+             */
+            public int getColour() {
+                return colour;
+            }
+
+            /**
+             * Sets the value of the colour property.
+             * 
+             */
+            public void setColour(int value) {
+                this.colour = value;
+            }
+
+            /**
+             * Gets the value of the display property.
+             * 
+             */
+            public boolean isDisplay() {
+                return display;
+            }
+
+            /**
+             * Sets the value of the display property.
+             * 
+             */
+            public void setDisplay(boolean value) {
+                this.display = value;
+            }
+
+            /**
+             * Gets the value of the order property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getOrder() {
+                return order;
+            }
+
+            /**
+             * Sets the value of the order property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setOrder(Float value) {
+                this.order = value;
+            }
+
+            /**
+             * Gets the value of the mincolour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getMincolour() {
+                return mincolour;
+            }
+
+            /**
+             * Sets the value of the mincolour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setMincolour(Integer value) {
+                this.mincolour = value;
+            }
+
+            /**
+             * Gets the value of the noValueColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link NoValueColour }
+             *     
+             */
+            public NoValueColour getNoValueColour() {
+                if (noValueColour == null) {
+                    return NoValueColour.MIN;
+                } else {
+                    return noValueColour;
+                }
+            }
+
+            /**
+             * Sets the value of the noValueColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link NoValueColour }
+             *     
+             */
+            public void setNoValueColour(NoValueColour value) {
+                this.noValueColour = value;
+            }
+
+            /**
+             * Gets the value of the threshold property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getThreshold() {
+                return threshold;
+            }
+
+            /**
+             * Sets the value of the threshold property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setThreshold(Float value) {
+                this.threshold = value;
+            }
+
+            /**
+             * Gets the value of the threshstate property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getThreshstate() {
+                return threshstate;
+            }
+
+            /**
+             * Sets the value of the threshstate property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setThreshstate(Integer value) {
+                this.threshstate = value;
+            }
+
+            /**
+             * Gets the value of the max property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getMax() {
+                return max;
+            }
+
+            /**
+             * Sets the value of the max property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setMax(Float value) {
+                this.max = value;
+            }
+
+            /**
+             * Gets the value of the min property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getMin() {
+                return min;
+            }
+
+            /**
+             * Sets the value of the min property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setMin(Float value) {
+                this.min = value;
+            }
+
+            /**
+             * Gets the value of the colourByLabel property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public Boolean isColourByLabel() {
+                return colourByLabel;
+            }
+
+            /**
+             * Sets the value of the colourByLabel property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setColourByLabel(Boolean value) {
+                this.colourByLabel = value;
+            }
+
+            /**
+             * Gets the value of the autoScale property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public Boolean isAutoScale() {
+                return autoScale;
+            }
+
+            /**
+             * Sets the value of the autoScale property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setAutoScale(Boolean value) {
+                this.autoScale = value;
+            }
 
-    /**
-     * Sets the value of the displayText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setDisplayText(Boolean value)
-    {
-      this.displayText = value;
-    }
+        }
 
-    /**
-     * Gets the value of the colourText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isColourText()
-    {
-      return colourText;
     }
 
-    /**
-     * Sets the value of the colourText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setColourText(Boolean value)
-    {
-      this.colourText = value;
-    }
 
     /**
-     * Gets the value of the textCol1 property.
+     * 
Java class for anonymous complex type.
      * 
-     * @return possible object is {@link Integer }
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public Integer getTextCol1()
-    {
-      return textCol1;
-    }
-
-    /**
-     * Sets the value of the textCol1 property.
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+     *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

      * 
-     * @param value
-     *          allowed object is {@link Integer }
      * 
      */
-    public void setTextCol1(Integer value)
-    {
-      this.textCol1 = value;
-    }
-
-    /**
-     * Gets the value of the textCol2 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol2()
-    {
-      return textCol2;
-    }
-
-    /**
-     * Sets the value of the textCol2 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol2(Integer value)
-    {
-      this.textCol2 = value;
-    }
-
-    /**
-     * Gets the value of the textColThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextColThreshold()
-    {
-      return textColThreshold;
-    }
-
-    /**
-     * Sets the value of the textColThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextColThreshold(Integer value)
-    {
-      this.textColThreshold = value;
-    }
-
-    /**
-     * Gets the value of the showUnconserved property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowUnconserved()
-    {
-      return showUnconserved;
-    }
-
-    /**
-     * Sets the value of the showUnconserved property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowUnconserved(Boolean value)
-    {
-      this.showUnconserved = value;
-    }
-
-    /**
-     * Gets the value of the ignoreGapsinConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isIgnoreGapsinConsensus()
-    {
-      if (ignoreGapsinConsensus == null)
-      {
-        return true;
-      }
-      else
-      {
-        return ignoreGapsinConsensus;
-      }
-    }
-
-    /**
-     * Sets the value of the ignoreGapsinConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIgnoreGapsinConsensus(Boolean value)
-    {
-      this.ignoreGapsinConsensus = value;
-    }
-
-    /**
-     * Gets the value of the showConsensusHistogram property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowConsensusHistogram()
-    {
-      if (showConsensusHistogram == null)
-      {
-        return true;
-      }
-      else
-      {
-        return showConsensusHistogram;
-      }
-    }
-
-    /**
-     * Sets the value of the showConsensusHistogram property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowConsensusHistogram(Boolean value)
-    {
-      this.showConsensusHistogram = value;
-    }
-
-    /**
-     * Gets the value of the showSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowSequenceLogo()
-    {
-      if (showSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showSequenceLogo;
-      }
-    }
-
-    /**
-     * Sets the value of the showSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceLogo(Boolean value)
-    {
-      this.showSequenceLogo = value;
-    }
-
-    /**
-     * Gets the value of the normaliseSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isNormaliseSequenceLogo()
-    {
-      if (normaliseSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return normaliseSequenceLogo;
-      }
-    }
-
-    /**
-     * Sets the value of the normaliseSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setNormaliseSequenceLogo(Boolean value)
-    {
-      this.normaliseSequenceLogo = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <extension base="{www.jalview.org}pdbentry">
-   *                 <sequence>
-   *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
-   *                     <complexType>
-   *                       <simpleContent>
-   *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
-   *                           <attGroup ref="{www.jalview.org}swingwindow"/>
-   *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                         </extension>
-   *                       </simpleContent>
-   *                     </complexType>
-   *                   </element>
-   *                 </sequence>
-   *               </extension>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <sequence>
-   *                   <element name="secondaryStructure" maxOccurs="unbounded">
-   *                     <complexType>
-   *                       <complexContent>
-   *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                         </restriction>
-   *                       </complexContent>
-   *                     </complexType>
-   *                   </element>
-   *                 </sequence>
-   *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-   *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "features", "pdbids", "hiddenSequences", "rnaViewer" })
-  public static class JSeq
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List features;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List pdbids;
-
-    @XmlElement(namespace = "www.jalview.org", type = Integer.class)
-    protected List hiddenSequences;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List rnaViewer;
-
-    @XmlAttribute(name = "colour")
-    protected Integer colour;
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-
-    @XmlAttribute(name = "id", required = true)
-    protected String id;
-
-    @XmlAttribute(name = "hidden")
-    protected Boolean hidden;
-
-    @XmlAttribute(name = "viewreference")
-    protected Boolean viewreference;
-
-    /**
-     * Gets the value of the features property.
-     * 
-     * 

-     * 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
-     * set method for the features property.
-     * 
-     * 

-     * For example, to add a new item, do as follows:
-     * 
-     * 
-     * getFeatures().add(newItem);
-     * 

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list {@link Feature }
-     * 
-     * 
-     */
-    public List getFeatures()
-    {
-      if (features == null)
-      {
-        features = new ArrayList();
-      }
-      return this.features;
-    }
-
-    /**
-     * Gets the value of the pdbids property.
-     * 
-     * 

-     * 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
-     * set method for the pdbids property.
-     * 
-     * 

-     * For example, to add a new item, do as follows:
-     * 
-     * 
-     * getPdbids().add(newItem);
-     * 

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.JSeq.Pdbids }
-     * 
-     * 
-     */
-    public List getPdbids()
-    {
-      if (pdbids == null)
-      {
-        pdbids = new ArrayList();
-      }
-      return this.pdbids;
-    }
-
-    /**
-     * Gets the value of the hiddenSequences property.
-     * 
-     * 

-     * 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
-     * set method for the hiddenSequences property.
-     * 
-     * 

-     * For example, to add a new item, do as follows:
-     * 
-     * 
-     * getHiddenSequences().add(newItem);
-     * 

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list {@link Integer }
-     * 
-     * 
-     */
-    public List getHiddenSequences()
-    {
-      if (hiddenSequences == null)
-      {
-        hiddenSequences = new ArrayList();
-      }
-      return this.hiddenSequences;
-    }
-
-    /**
-     * Gets the value of the rnaViewer property.
-     * 
-     * 

-     * 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
-     * set method for the rnaViewer property.
-     * 
-     * 

-     * For example, to add a new item, do as follows:
-     * 
-     * 
-     * getRnaViewer().add(newItem);
-     * 

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.JSeq.RnaViewer }
-     * 
-     * 
-     */
-    public List getRnaViewer()
-    {
-      if (rnaViewer == null)
-      {
-        rnaViewer = new ArrayList();
-      }
-      return this.rnaViewer;
-    }
-
-    /**
-     * Gets the value of the colour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getColour()
-    {
-      return colour;
-    }
-
-    /**
-     * Sets the value of the colour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setColour(Integer value)
-    {
-      this.colour = value;
-    }
-
-    /**
-     * Gets the value of the start property.
-     * 
-     */
-    public int getStart()
-    {
-      return start;
-    }
-
-    /**
-     * Sets the value of the start property.
-     * 
-     */
-    public void setStart(int value)
-    {
-      this.start = value;
-    }
-
-    /**
-     * Gets the value of the end property.
-     * 
-     */
-    public int getEnd()
-    {
-      return end;
-    }
-
-    /**
-     * Sets the value of the end property.
-     * 
-     */
-    public void setEnd(int value)
-    {
-      this.end = value;
-    }
-
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
-
-    /**
-     * Gets the value of the hidden property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isHidden()
-    {
-      return hidden;
-    }
-
-    /**
-     * Sets the value of the hidden property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setHidden(Boolean value)
-    {
-      this.hidden = value;
-    }
-
-    /**
-     * Gets the value of the viewreference property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isViewreference()
-    {
-      return viewreference;
-    }
-
-    /**
-     * Sets the value of the viewreference property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setViewreference(Boolean value)
-    {
-      this.viewreference = value;
-    }
-
-    /**
-     * 

-     * Java class for anonymous complex type.
-     * 
-     * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <extension base="{www.jalview.org}pdbentry">
-     *       <sequence>
-     *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <simpleContent>
-     *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </extension>
-     *             </simpleContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *     </extension>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "structureState" })
-    public static class Pdbids extends Pdbentry
-    {
-
-      @XmlElement(namespace = "www.jalview.org")
-      protected List structureState;
-
-      /**
-       * Gets the value of the structureState property.
-       * 
-       * 

-       * 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
-       * set method for the structureState property.
-       * 
-       * 

-       * For example, to add a new item, do as follows:
-       * 
-       * 
-       * getStructureState().add(newItem);
-       * 

-       * 
-       * 
-       * 

-       * Objects of the following type(s) are allowed in the list
-       * {@link JalviewModel.JSeq.Pdbids.StructureState }
-       * 
-       * 
-       */
-      public List getStructureState()
-      {
-        if (structureState == null)
-        {
-          structureState = new ArrayList();
-        }
-        return this.structureState;
-      }
-
-      /**
-       * 

-       * Java class for anonymous complex type.
-       * 
-       * 

-       * The following schema fragment specifies the expected content contained
-       * within this class.
-       * 
-       * 
-       * <complexType>
-       *   <simpleContent>
-       *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-       *       <attGroup ref="{www.jalview.org}swingwindow"/>
-       *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-       *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-       *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-       *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-       *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *     </extension>
-       *   </simpleContent>
-       * </complexType>
-       * 

-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "", propOrder = { "value" })
-      public static class StructureState
-      {
-
-        @XmlValue
-        protected String value;
-
-        @XmlAttribute(name = "visible")
-        protected Boolean visible;
-
-        @XmlAttribute(name = "viewId")
-        protected String viewId;
-
-        @XmlAttribute(name = "alignwithAlignPanel")
-        protected Boolean alignwithAlignPanel;
-
-        @XmlAttribute(name = "colourwithAlignPanel")
-        protected Boolean colourwithAlignPanel;
-
-        @XmlAttribute(name = "colourByJmol")
-        protected Boolean colourByJmol;
-
-        @XmlAttribute(name = "type")
-        protected String type;
-
-        @XmlAttribute(name = "width")
-        protected Integer width;
-
-        @XmlAttribute(name = "height")
-        protected Integer height;
-
-        @XmlAttribute(name = "xpos")
-        protected Integer xpos;
-
-        @XmlAttribute(name = "ypos")
-        protected Integer ypos;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "seq",
+        "annotationColours"
+    })
+    public static class JGroup {
+
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List seq;
+        @XmlElement(namespace = "www.jalview.org")
+        protected AnnotationColourScheme annotationColours;
+        @XmlAttribute(name = "start")
+        protected Integer start;
+        @XmlAttribute(name = "end")
+        protected Integer end;
+        @XmlAttribute(name = "name")
+        protected String name;
+        @XmlAttribute(name = "colour")
+        protected String colour;
+        @XmlAttribute(name = "consThreshold")
+        protected Integer consThreshold;
+        @XmlAttribute(name = "pidThreshold")
+        protected Integer pidThreshold;
+        @XmlAttribute(name = "outlineColour")
+        protected Integer outlineColour;
+        @XmlAttribute(name = "displayBoxes")
+        protected Boolean displayBoxes;
+        @XmlAttribute(name = "displayText")
+        protected Boolean displayText;
+        @XmlAttribute(name = "colourText")
+        protected Boolean colourText;
+        @XmlAttribute(name = "textCol1")
+        protected Integer textCol1;
+        @XmlAttribute(name = "textCol2")
+        protected Integer textCol2;
+        @XmlAttribute(name = "textColThreshold")
+        protected Integer textColThreshold;
+        @XmlAttribute(name = "showUnconserved")
+        protected Boolean showUnconserved;
+        @XmlAttribute(name = "ignoreGapsinConsensus")
+        protected Boolean ignoreGapsinConsensus;
+        @XmlAttribute(name = "showConsensusHistogram")
+        protected Boolean showConsensusHistogram;
+        @XmlAttribute(name = "showSequenceLogo")
+        protected Boolean showSequenceLogo;
+        @XmlAttribute(name = "normaliseSequenceLogo")
+        protected Boolean normaliseSequenceLogo;
+        @XmlAttribute(name = "id")
+        protected String id;
 
         /**
-         * Gets the value of the value property.
+         * Gets the value of the seq property.
+         * 
+         * 

+         * 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 set method for the seq property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getSeq().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
          * 
-         * @return possible object is {@link String }
          * 
          */
-        public String getValue()
-        {
-          return value;
+        public List getSeq() {
+            if (seq == null) {
+                seq = new ArrayList();
+            }
+            return this.seq;
         }
 
         /**
-         * Sets the value of the value property.
-         * 
-         * @param value
-         *          allowed object is {@link String }
+         * Gets the value of the annotationColours property.
          * 
+         * @return
+         *     possible object is
+         *     {@link AnnotationColourScheme }
+         *     
          */
-        public void setValue(String value)
-        {
-          this.value = value;
+        public AnnotationColourScheme getAnnotationColours() {
+            return annotationColours;
         }
 
         /**
-         * Gets the value of the visible property.
+         * Sets the value of the annotationColours property.
          * 
-         * @return possible object is {@link Boolean }
+         * @param value
+         *     allowed object is
+         *     {@link AnnotationColourScheme }
+         *     
+         */
+        public void setAnnotationColours(AnnotationColourScheme value) {
+            this.annotationColours = value;
+        }
+
+        /**
+         * Gets the value of the start property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public Boolean isVisible()
-        {
-          return visible;
+        public Integer getStart() {
+            return start;
         }
 
         /**
-         * Sets the value of the visible property.
+         * Sets the value of the start property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setVisible(Boolean value)
-        {
-          this.visible = value;
+        public void setStart(Integer value) {
+            this.start = value;
         }
 
         /**
-         * Gets the value of the viewId property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the end property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public String getViewId()
-        {
-          return viewId;
+        public Integer getEnd() {
+            return end;
         }
 
         /**
-         * Sets the value of the viewId property.
+         * Sets the value of the end property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setViewId(String value)
-        {
-          this.viewId = value;
+        public void setEnd(Integer value) {
+            this.end = value;
         }
 
         /**
-         * Gets the value of the alignwithAlignPanel property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the name property.
          * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
          */
-        public boolean isAlignwithAlignPanel()
-        {
-          if (alignwithAlignPanel == null)
-          {
-            return true;
-          }
-          else
-          {
-            return alignwithAlignPanel;
-          }
+        public String getName() {
+            return name;
         }
 
         /**
-         * Sets the value of the alignwithAlignPanel property.
+         * Sets the value of the name property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link String }
+         *     
          */
-        public void setAlignwithAlignPanel(Boolean value)
-        {
-          this.alignwithAlignPanel = value;
+        public void setName(String value) {
+            this.name = value;
         }
 
         /**
-         * Gets the value of the colourwithAlignPanel property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the colour property.
          * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
          */
-        public boolean isColourwithAlignPanel()
-        {
-          if (colourwithAlignPanel == null)
-          {
-            return false;
-          }
-          else
-          {
-            return colourwithAlignPanel;
-          }
+        public String getColour() {
+            return colour;
         }
 
         /**
-         * Sets the value of the colourwithAlignPanel property.
+         * Sets the value of the colour property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link String }
+         *     
          */
-        public void setColourwithAlignPanel(Boolean value)
-        {
-          this.colourwithAlignPanel = value;
+        public void setColour(String value) {
+            this.colour = value;
         }
 
         /**
-         * Gets the value of the colourByJmol property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the consThreshold property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public boolean isColourByJmol()
-        {
-          if (colourByJmol == null)
-          {
-            return true;
-          }
-          else
-          {
-            return colourByJmol;
-          }
+        public Integer getConsThreshold() {
+            return consThreshold;
         }
 
         /**
-         * Sets the value of the colourByJmol property.
+         * Sets the value of the consThreshold property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setColourByJmol(Boolean value)
-        {
-          this.colourByJmol = value;
+        public void setConsThreshold(Integer value) {
+            this.consThreshold = value;
         }
 
         /**
-         * Gets the value of the type property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the pidThreshold property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public String getType()
-        {
-          return type;
+        public Integer getPidThreshold() {
+            return pidThreshold;
         }
 
         /**
-         * Sets the value of the type property.
+         * Sets the value of the pidThreshold property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setType(String value)
-        {
-          this.type = value;
+        public void setPidThreshold(Integer value) {
+            this.pidThreshold = value;
         }
 
         /**
-         * Gets the value of the width property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the outlineColour property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public Integer getWidth()
-        {
-          return width;
+        public Integer getOutlineColour() {
+            return outlineColour;
         }
 
         /**
-         * Sets the value of the width property.
+         * Sets the value of the outlineColour property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setWidth(Integer value)
-        {
-          this.width = value;
+        public void setOutlineColour(Integer value) {
+            this.outlineColour = value;
         }
 
         /**
-         * Gets the value of the height property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the displayBoxes property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Integer getHeight()
-        {
-          return height;
+        public Boolean isDisplayBoxes() {
+            return displayBoxes;
         }
 
         /**
-         * Sets the value of the height property.
+         * Sets the value of the displayBoxes property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Boolean }
+         *     
          */
-        public void setHeight(Integer value)
-        {
-          this.height = value;
+        public void setDisplayBoxes(Boolean value) {
+            this.displayBoxes = value;
         }
 
         /**
-         * Gets the value of the xpos property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the displayText property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Integer getXpos()
-        {
-          return xpos;
+        public Boolean isDisplayText() {
+            return displayText;
         }
 
         /**
-         * Sets the value of the xpos property.
+         * Sets the value of the displayText property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Boolean }
+         *     
          */
-        public void setXpos(Integer value)
-        {
-          this.xpos = value;
+        public void setDisplayText(Boolean value) {
+            this.displayText = value;
         }
 
         /**
-         * Gets the value of the ypos property.
-         * 
-         * @return possible object is {@link Integer }
+         * Gets the value of the colourText property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public Integer getYpos()
-        {
-          return ypos;
+        public Boolean isColourText() {
+            return colourText;
         }
 
         /**
-         * Sets the value of the ypos property.
+         * Sets the value of the colourText property.
          * 
          * @param value
-         *          allowed object is {@link Integer }
-         * 
+         *     allowed object is
+         *     {@link Boolean }
+         *     
          */
-        public void setYpos(Integer value)
-        {
-          this.ypos = value;
+        public void setColourText(Boolean value) {
+            this.colourText = value;
         }
 
-      }
-
-    }
-
-    /**
-     * 

-     * Java class for anonymous complex type.
-     * 
-     * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="secondaryStructure" maxOccurs="unbounded">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "", propOrder = { "secondaryStructure" })
-    public static class RnaViewer
-    {
-
-      @XmlElement(namespace = "www.jalview.org", required = true)
-      protected List secondaryStructure;
-
-      @XmlAttribute(name = "title")
-      protected String title;
-
-      @XmlAttribute(name = "viewId")
-      protected String viewId;
-
-      @XmlAttribute(name = "dividerLocation")
-      protected Integer dividerLocation;
-
-      @XmlAttribute(name = "selectedRna")
-      protected Integer selectedRna;
-
-      @XmlAttribute(name = "width")
-      protected Integer width;
-
-      @XmlAttribute(name = "height")
-      protected Integer height;
-
-      @XmlAttribute(name = "xpos")
-      protected Integer xpos;
-
-      @XmlAttribute(name = "ypos")
-      protected Integer ypos;
-
-      /**
-       * Gets the value of the secondaryStructure property.
-       * 
-       * 

-       * 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
-       * set method for the secondaryStructure property.
-       * 
-       * 

-       * For example, to add a new item, do as follows:
-       * 
-       * 
-       * getSecondaryStructure().add(newItem);
-       * 

-       * 
-       * 
-       * 

-       * Objects of the following type(s) are allowed in the list
-       * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-       * 
-       * 
-       */
-      public List getSecondaryStructure()
-      {
-        if (secondaryStructure == null)
-        {
-          secondaryStructure = new ArrayList();
-        }
-        return this.secondaryStructure;
-      }
-
-      /**
-       * Gets the value of the title property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getTitle()
-      {
-        return title;
-      }
-
-      /**
-       * Sets the value of the title property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setTitle(String value)
-      {
-        this.title = value;
-      }
-
-      /**
-       * Gets the value of the viewId property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getViewId()
-      {
-        return viewId;
-      }
-
-      /**
-       * Sets the value of the viewId property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setViewId(String value)
-      {
-        this.viewId = value;
-      }
-
-      /**
-       * Gets the value of the dividerLocation property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getDividerLocation()
-      {
-        return dividerLocation;
-      }
-
-      /**
-       * Sets the value of the dividerLocation property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setDividerLocation(Integer value)
-      {
-        this.dividerLocation = value;
-      }
-
-      /**
-       * Gets the value of the selectedRna property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getSelectedRna()
-      {
-        return selectedRna;
-      }
-
-      /**
-       * Sets the value of the selectedRna property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setSelectedRna(Integer value)
-      {
-        this.selectedRna = value;
-      }
-
-      /**
-       * Gets the value of the width property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getWidth()
-      {
-        return width;
-      }
-
-      /**
-       * Sets the value of the width property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setWidth(Integer value)
-      {
-        this.width = value;
-      }
-
-      /**
-       * Gets the value of the height property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getHeight()
-      {
-        return height;
-      }
-
-      /**
-       * Sets the value of the height property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setHeight(Integer value)
-      {
-        this.height = value;
-      }
-
-      /**
-       * Gets the value of the xpos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getXpos()
-      {
-        return xpos;
-      }
-
-      /**
-       * Sets the value of the xpos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setXpos(Integer value)
-      {
-        this.xpos = value;
-      }
-
-      /**
-       * Gets the value of the ypos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getYpos()
-      {
-        return ypos;
-      }
-
-      /**
-       * Sets the value of the ypos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setYpos(Integer value)
-      {
-        this.ypos = value;
-      }
-
-      /**
-       * 

-       * Java class for anonymous complex type.
-       * 
-       * 

-       * The following schema fragment specifies the expected content contained
-       * within this class.
-       * 
-       * 
-       * <complexType>
-       *   <complexContent>
-       *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-       *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-       *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *     </restriction>
-       *   </complexContent>
-       * </complexType>
-       * 

-       * 
-       * 
-       */
-      @XmlAccessorType(XmlAccessType.FIELD)
-      @XmlType(name = "")
-      public static class SecondaryStructure
-      {
-
-        @XmlAttribute(name = "title")
-        protected String title;
-
-        @XmlAttribute(name = "annotationId", required = true)
-        protected String annotationId;
-
-        @XmlAttribute(name = "gapped")
-        protected Boolean gapped;
-
-        @XmlAttribute(name = "viewerState")
-        protected String viewerState;
-
         /**
-         * Gets the value of the title property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the textCol1 property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public String getTitle()
-        {
-          return title;
+        public Integer getTextCol1() {
+            return textCol1;
         }
 
         /**
-         * Sets the value of the title property.
+         * Sets the value of the textCol1 property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setTitle(String value)
-        {
-          this.title = value;
+        public void setTextCol1(Integer value) {
+            this.textCol1 = value;
         }
 
         /**
-         * Gets the value of the annotationId property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the textCol2 property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public String getAnnotationId()
-        {
-          return annotationId;
+        public Integer getTextCol2() {
+            return textCol2;
         }
 
         /**
-         * Sets the value of the annotationId property.
+         * Sets the value of the textCol2 property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setAnnotationId(String value)
-        {
-          this.annotationId = value;
+        public void setTextCol2(Integer value) {
+            this.textCol2 = value;
         }
 
         /**
-         * Gets the value of the gapped property.
-         * 
-         * @return possible object is {@link Boolean }
+         * Gets the value of the textColThreshold property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
          */
-        public Boolean isGapped()
-        {
-          return gapped;
+        public Integer getTextColThreshold() {
+            return textColThreshold;
         }
 
         /**
-         * Sets the value of the gapped property.
+         * Sets the value of the textColThreshold property.
          * 
          * @param value
-         *          allowed object is {@link Boolean }
-         * 
+         *     allowed object is
+         *     {@link Integer }
+         *     
          */
-        public void setGapped(Boolean value)
-        {
-          this.gapped = value;
+        public void setTextColThreshold(Integer value) {
+            this.textColThreshold = value;
         }
 
         /**
-         * Gets the value of the viewerState property.
-         * 
-         * @return possible object is {@link String }
+         * Gets the value of the showUnconserved property.
          * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
          */
-        public String getViewerState()
-        {
-          return viewerState;
+        public Boolean isShowUnconserved() {
+            return showUnconserved;
         }
 
         /**
-         * Sets the value of the viewerState property.
+         * Sets the value of the showUnconserved property.
          * 
          * @param value
-         *          allowed object is {@link String }
-         * 
+         *     allowed object is
+         *     {@link Boolean }
+         *     
          */
-        public void setViewerState(String value)
-        {
-          this.viewerState = value;
+        public void setShowUnconserved(Boolean value) {
+            this.showUnconserved = value;
         }
 
-      }
-
-    }
-
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="sequencePoint" maxOccurs="unbounded">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attGroup ref="{www.jalview.org}position"/>
-   *                 <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="axis" maxOccurs="3" minOccurs="3">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attGroup ref="{www.jalview.org}position"/>
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="seqPointMin">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attGroup ref="{www.jalview.org}position"/>
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="seqPointMax">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attGroup ref="{www.jalview.org}position"/>
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
-   *       </sequence>
-   *       <attGroup ref="{www.jalview.org}SimilarityParams"/>
-   *       <attGroup ref="{www.jalview.org}swingwindow"/>
-   *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *       <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
-  public static class PcaViewer
-  {
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List sequencePoint;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected List axis;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
-
-    @XmlElement(namespace = "www.jalview.org", required = true)
-    protected PcaDataType pcaData;
-
-    @XmlAttribute(name = "title")
-    protected String title;
-
-    @XmlAttribute(name = "scoreModelName")
-    protected String scoreModelName;
-
-    @XmlAttribute(name = "xDim")
-    protected Integer xDim;
-
-    @XmlAttribute(name = "yDim")
-    protected Integer yDim;
-
-    @XmlAttribute(name = "zDim")
-    protected Integer zDim;
-
-    @XmlAttribute(name = "bgColour")
-    protected Integer bgColour;
-
-    @XmlAttribute(name = "scaleFactor")
-    protected Float scaleFactor;
-
-    @XmlAttribute(name = "showLabels")
-    protected Boolean showLabels;
-
-    @XmlAttribute(name = "linkToAllViews")
-    protected Boolean linkToAllViews;
-
-    @XmlAttribute(name = "includeGaps")
-    protected Boolean includeGaps;
-
-    @XmlAttribute(name = "matchGaps")
-    protected Boolean matchGaps;
-
-    @XmlAttribute(name = "includeGappedColumns")
-    protected Boolean includeGappedColumns;
-
-    @XmlAttribute(name = "denominateByShortestLength")
-    protected Boolean denominateByShortestLength;
-
-    @XmlAttribute(name = "width")
-    protected Integer width;
-
-    @XmlAttribute(name = "height")
-    protected Integer height;
-
-    @XmlAttribute(name = "xpos")
-    protected Integer xpos;
-
-    @XmlAttribute(name = "ypos")
-    protected Integer ypos;
-
-    /**
-     * Gets the value of the sequencePoint property.
-     * 
-     * 

-     * 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
-     * set method for the sequencePoint property.
-     * 
-     * 

-     * For example, to add a new item, do as follows:
-     * 
-     * 
-     * getSequencePoint().add(newItem);
-     * 

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.PcaViewer.SequencePoint }
-     * 
-     * 
-     */
-    public List getSequencePoint()
-    {
-      if (sequencePoint == null)
-      {
-        sequencePoint = new ArrayList();
-      }
-      return this.sequencePoint;
-    }
-
-    /**
-     * Gets the value of the axis property.
-     * 
-     * 

-     * 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
-     * set method for the axis property.
-     * 
-     * 

-     * For example, to add a new item, do as follows:
-     * 
-     * 
-     * getAxis().add(newItem);
-     * 

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.PcaViewer.Axis }
-     * 
-     * 
-     */
-    public List getAxis()
-    {
-      if (axis == null)
-      {
-        axis = new ArrayList();
-      }
-      return this.axis;
-    }
-
-    /**
-     * Gets the value of the seqPointMin property.
-     * 
-     * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMin }
-     * 
-     */
-    public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin()
-    {
-      return seqPointMin;
-    }
-
-    /**
-     * Sets the value of the seqPointMin property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewModel.PcaViewer.SeqPointMin }
-     * 
-     */
-    public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value)
-    {
-      this.seqPointMin = value;
-    }
+        /**
+         * Gets the value of the ignoreGapsinConsensus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isIgnoreGapsinConsensus() {
+            if (ignoreGapsinConsensus == null) {
+                return true;
+            } else {
+                return ignoreGapsinConsensus;
+            }
+        }
 
-    /**
-     * Gets the value of the seqPointMax property.
-     * 
-     * @return possible object is {@link JalviewModel.PcaViewer.SeqPointMax }
-     * 
-     */
-    public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax()
-    {
-      return seqPointMax;
-    }
+        /**
+         * Sets the value of the ignoreGapsinConsensus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIgnoreGapsinConsensus(Boolean value) {
+            this.ignoreGapsinConsensus = value;
+        }
 
-    /**
-     * Sets the value of the seqPointMax property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewModel.PcaViewer.SeqPointMax }
-     * 
-     */
-    public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value)
-    {
-      this.seqPointMax = value;
-    }
+        /**
+         * Gets the value of the showConsensusHistogram property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowConsensusHistogram() {
+            if (showConsensusHistogram == null) {
+                return true;
+            } else {
+                return showConsensusHistogram;
+            }
+        }
 
-    /**
-     * Gets the value of the pcaData property.
-     * 
-     * @return possible object is {@link PcaDataType }
-     * 
-     */
-    public PcaDataType getPcaData()
-    {
-      return pcaData;
-    }
+        /**
+         * Sets the value of the showConsensusHistogram property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowConsensusHistogram(Boolean value) {
+            this.showConsensusHistogram = value;
+        }
 
-    /**
-     * Sets the value of the pcaData property.
-     * 
-     * @param value
-     *          allowed object is {@link PcaDataType }
-     * 
-     */
-    public void setPcaData(PcaDataType value)
-    {
-      this.pcaData = value;
-    }
+        /**
+         * Gets the value of the showSequenceLogo property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowSequenceLogo() {
+            if (showSequenceLogo == null) {
+                return false;
+            } else {
+                return showSequenceLogo;
+            }
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
+        /**
+         * Sets the value of the showSequenceLogo property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowSequenceLogo(Boolean value) {
+            this.showSequenceLogo = value;
+        }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
+        /**
+         * Gets the value of the normaliseSequenceLogo property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isNormaliseSequenceLogo() {
+            if (normaliseSequenceLogo == null) {
+                return false;
+            } else {
+                return normaliseSequenceLogo;
+            }
+        }
 
-    /**
-     * Gets the value of the scoreModelName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getScoreModelName()
-    {
-      return scoreModelName;
-    }
+        /**
+         * Sets the value of the normaliseSequenceLogo property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setNormaliseSequenceLogo(Boolean value) {
+            this.normaliseSequenceLogo = value;
+        }
 
-    /**
-     * Sets the value of the scoreModelName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setScoreModelName(String value)
-    {
-      this.scoreModelName = value;
-    }
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    /**
-     * Gets the value of the xDim property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXDim()
-    {
-      return xDim;
-    }
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    /**
-     * Sets the value of the xDim property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXDim(Integer value)
-    {
-      this.xDim = value;
     }
 
-    /**
-     * Gets the value of the yDim property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYDim()
-    {
-      return yDim;
-    }
 
     /**
-     * Sets the value of the yDim property.
+     * 
Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link Integer }
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setYDim(Integer value)
-    {
-      this.yDim = value;
-    }
-
-    /**
-     * Gets the value of the zDim property.
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <extension base="{www.jalview.org}pdbentry">
+     *                 <sequence>
+     *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *                     <complexType>
+     *                       <simpleContent>
+     *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
+     *                           <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         </extension>
+     *                       </simpleContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
+     *               </extension>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+     *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <sequence>
+     *                   <element name="secondaryStructure" maxOccurs="unbounded">
+     *                     <complexType>
+     *                       <complexContent>
+     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         </restriction>
+     *                       </complexContent>
+     *                     </complexType>
+     *                   </element>
+     *                 </sequence>
+     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

      * 
-     * @return possible object is {@link Integer }
      * 
      */
-    public Integer getZDim()
-    {
-      return zDim;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "features",
+        "pdbids",
+        "hiddenSequences",
+        "rnaViewer"
+    })
+    public static class JSeq {
+
+        @XmlElement(namespace = "www.jalview.org")
+        protected List features;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List pdbids;
+        @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+        protected List hiddenSequences;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List rnaViewer;
+        @XmlAttribute(name = "colour")
+        protected Integer colour;
+        @XmlAttribute(name = "start", required = true)
+        protected int start;
+        @XmlAttribute(name = "end", required = true)
+        protected int end;
+        @XmlAttribute(name = "id", required = true)
+        protected String id;
+        @XmlAttribute(name = "hidden")
+        protected Boolean hidden;
+        @XmlAttribute(name = "viewreference")
+        protected Boolean viewreference;
 
-    /**
-     * Sets the value of the zDim property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setZDim(Integer value)
-    {
-      this.zDim = value;
-    }
+        /**
+         * Gets the value of the features property.
+         * 
+         * 

+         * 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 set method for the features property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getFeatures().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link Feature }
+         * 
+         * 
+         */
+        public List getFeatures() {
+            if (features == null) {
+                features = new ArrayList();
+            }
+            return this.features;
+        }
 
-    /**
-     * Gets the value of the bgColour property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getBgColour()
-    {
-      return bgColour;
-    }
+        /**
+         * Gets the value of the pdbids property.
+         * 
+         * 

+         * 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 set method for the pdbids property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getPdbids().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.JSeq.Pdbids }
+         * 
+         * 
+         */
+        public List getPdbids() {
+            if (pdbids == null) {
+                pdbids = new ArrayList();
+            }
+            return this.pdbids;
+        }
 
-    /**
-     * Sets the value of the bgColour property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setBgColour(Integer value)
-    {
-      this.bgColour = value;
-    }
+        /**
+         * Gets the value of the hiddenSequences property.
+         * 
+         * 

+         * 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 set method for the hiddenSequences property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getHiddenSequences().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List getHiddenSequences() {
+            if (hiddenSequences == null) {
+                hiddenSequences = new ArrayList();
+            }
+            return this.hiddenSequences;
+        }
 
-    /**
-     * Gets the value of the scaleFactor property.
-     * 
-     * @return possible object is {@link Float }
-     * 
-     */
-    public Float getScaleFactor()
-    {
-      return scaleFactor;
-    }
+        /**
+         * Gets the value of the rnaViewer property.
+         * 
+         * 

+         * 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 set method for the rnaViewer property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getRnaViewer().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.JSeq.RnaViewer }
+         * 
+         * 
+         */
+        public List getRnaViewer() {
+            if (rnaViewer == null) {
+                rnaViewer = new ArrayList();
+            }
+            return this.rnaViewer;
+        }
 
-    /**
-     * Sets the value of the scaleFactor property.
-     * 
-     * @param value
-     *          allowed object is {@link Float }
-     * 
-     */
-    public void setScaleFactor(Float value)
-    {
-      this.scaleFactor = value;
-    }
+        /**
+         * Gets the value of the colour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getColour() {
+            return colour;
+        }
 
-    /**
-     * Gets the value of the showLabels property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowLabels()
-    {
-      return showLabels;
-    }
+        /**
+         * Sets the value of the colour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setColour(Integer value) {
+            this.colour = value;
+        }
 
-    /**
-     * Sets the value of the showLabels property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowLabels(Boolean value)
-    {
-      this.showLabels = value;
-    }
+        /**
+         * Gets the value of the start property.
+         * 
+         */
+        public int getStart() {
+            return start;
+        }
 
-    /**
-     * Gets the value of the linkToAllViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isLinkToAllViews()
-    {
-      return linkToAllViews;
-    }
+        /**
+         * Sets the value of the start property.
+         * 
+         */
+        public void setStart(int value) {
+            this.start = value;
+        }
 
-    /**
-     * Sets the value of the linkToAllViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setLinkToAllViews(Boolean value)
-    {
-      this.linkToAllViews = value;
-    }
+        /**
+         * Gets the value of the end property.
+         * 
+         */
+        public int getEnd() {
+            return end;
+        }
 
-    /**
-     * Gets the value of the includeGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isIncludeGaps()
-    {
-      return includeGaps;
-    }
+        /**
+         * Sets the value of the end property.
+         * 
+         */
+        public void setEnd(int value) {
+            this.end = value;
+        }
 
-    /**
-     * Sets the value of the includeGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIncludeGaps(Boolean value)
-    {
-      this.includeGaps = value;
-    }
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    /**
-     * Gets the value of the matchGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isMatchGaps()
-    {
-      return matchGaps;
-    }
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    /**
-     * Sets the value of the matchGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setMatchGaps(Boolean value)
-    {
-      this.matchGaps = value;
-    }
+        /**
+         * Gets the value of the hidden property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isHidden() {
+            return hidden;
+        }
 
-    /**
-     * Gets the value of the includeGappedColumns property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isIncludeGappedColumns()
-    {
-      return includeGappedColumns;
-    }
+        /**
+         * Sets the value of the hidden property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setHidden(Boolean value) {
+            this.hidden = value;
+        }
 
-    /**
-     * Sets the value of the includeGappedColumns property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIncludeGappedColumns(Boolean value)
-    {
-      this.includeGappedColumns = value;
-    }
+        /**
+         * Gets the value of the viewreference property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isViewreference() {
+            return viewreference;
+        }
 
-    /**
-     * Gets the value of the denominateByShortestLength property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isDenominateByShortestLength()
-    {
-      return denominateByShortestLength;
-    }
+        /**
+         * Sets the value of the viewreference property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setViewreference(Boolean value) {
+            this.viewreference = value;
+        }
 
-    /**
-     * Sets the value of the denominateByShortestLength property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setDenominateByShortestLength(Boolean value)
-    {
-      this.denominateByShortestLength = value;
-    }
 
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <extension base="{www.jalview.org}pdbentry">
+         *       <sequence>
+         *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+         *           <complexType>
+         *             <simpleContent>
+         *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
+         *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+         *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               </extension>
+         *             </simpleContent>
+         *           </complexType>
+         *         </element>
+         *       </sequence>
+         *     </extension>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "structureState"
+        })
+        public static class Pdbids
+            extends Pdbentry
+        {
 
-    /**
-     * Sets the value of the width property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
+            @XmlElement(namespace = "www.jalview.org")
+            protected List structureState;
+
+            /**
+             * Gets the value of the structureState property.
+             * 
+             * 

+             * 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 set method for the structureState property.
+             * 
+             * 

+             * For example, to add a new item, do as follows:
+             * 
+             *    getStructureState().add(newItem);
+             * 

+             * 
+             * 
+             * 

+             * Objects of the following type(s) are allowed in the list
+             * {@link JalviewModel.JSeq.Pdbids.StructureState }
+             * 
+             * 
+             */
+            public List getStructureState() {
+                if (structureState == null) {
+                    structureState = new ArrayList();
+                }
+                return this.structureState;
+            }
+
+
+            /**
+             * 
Java class for anonymous complex type.
+             * 
+             * 
The following schema fragment specifies the expected content contained within this class.
+             * 
+             * 
+             * <complexType>
+             *   <simpleContent>
+             *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
+             *       <attGroup ref="{www.jalview.org}swingwindow"/>
+             *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+             *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     </extension>
+             *   </simpleContent>
+             * </complexType>
+             * 

+             * 
+             * 
+             */
+            @XmlAccessorType(XmlAccessType.FIELD)
+            @XmlType(name = "", propOrder = {
+                "value"
+            })
+            public static class StructureState {
+
+                @XmlValue
+                protected String value;
+                @XmlAttribute(name = "visible")
+                protected Boolean visible;
+                @XmlAttribute(name = "viewId")
+                protected String viewId;
+                @XmlAttribute(name = "alignwithAlignPanel")
+                protected Boolean alignwithAlignPanel;
+                @XmlAttribute(name = "colourwithAlignPanel")
+                protected Boolean colourwithAlignPanel;
+                @XmlAttribute(name = "colourByJmol")
+                protected Boolean colourByJmol;
+                @XmlAttribute(name = "type")
+                protected String type;
+                @XmlAttribute(name = "width")
+                protected Integer width;
+                @XmlAttribute(name = "height")
+                protected Integer height;
+                @XmlAttribute(name = "xpos")
+                protected Integer xpos;
+                @XmlAttribute(name = "ypos")
+                protected Integer ypos;
+
+                /**
+                 * Gets the value of the value property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getValue() {
+                    return value;
+                }
+
+                /**
+                 * Sets the value of the value property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setValue(String value) {
+                    this.value = value;
+                }
+
+                /**
+                 * Gets the value of the visible property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public Boolean isVisible() {
+                    return visible;
+                }
+
+                /**
+                 * Sets the value of the visible property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setVisible(Boolean value) {
+                    this.visible = value;
+                }
+
+                /**
+                 * Gets the value of the viewId property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getViewId() {
+                    return viewId;
+                }
+
+                /**
+                 * Sets the value of the viewId property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setViewId(String value) {
+                    this.viewId = value;
+                }
+
+                /**
+                 * Gets the value of the alignwithAlignPanel property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public boolean isAlignwithAlignPanel() {
+                    if (alignwithAlignPanel == null) {
+                        return true;
+                    } else {
+                        return alignwithAlignPanel;
+                    }
+                }
+
+                /**
+                 * Sets the value of the alignwithAlignPanel property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setAlignwithAlignPanel(Boolean value) {
+                    this.alignwithAlignPanel = value;
+                }
+
+                /**
+                 * Gets the value of the colourwithAlignPanel property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public boolean isColourwithAlignPanel() {
+                    if (colourwithAlignPanel == null) {
+                        return false;
+                    } else {
+                        return colourwithAlignPanel;
+                    }
+                }
+
+                /**
+                 * Sets the value of the colourwithAlignPanel property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setColourwithAlignPanel(Boolean value) {
+                    this.colourwithAlignPanel = value;
+                }
+
+                /**
+                 * Gets the value of the colourByJmol property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public boolean isColourByJmol() {
+                    if (colourByJmol == null) {
+                        return true;
+                    } else {
+                        return colourByJmol;
+                    }
+                }
+
+                /**
+                 * Sets the value of the colourByJmol property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setColourByJmol(Boolean value) {
+                    this.colourByJmol = value;
+                }
+
+                /**
+                 * Gets the value of the type property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getType() {
+                    return type;
+                }
+
+                /**
+                 * Sets the value of the type property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setType(String value) {
+                    this.type = value;
+                }
+
+                /**
+                 * Gets the value of the width property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getWidth() {
+                    return width;
+                }
+
+                /**
+                 * Sets the value of the width property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setWidth(Integer value) {
+                    this.width = value;
+                }
+
+                /**
+                 * Gets the value of the height property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getHeight() {
+                    return height;
+                }
+
+                /**
+                 * Sets the value of the height property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setHeight(Integer value) {
+                    this.height = value;
+                }
+
+                /**
+                 * Gets the value of the xpos property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getXpos() {
+                    return xpos;
+                }
+
+                /**
+                 * Sets the value of the xpos property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setXpos(Integer value) {
+                    this.xpos = value;
+                }
+
+                /**
+                 * Gets the value of the ypos property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public Integer getYpos() {
+                    return ypos;
+                }
+
+                /**
+                 * Sets the value of the ypos property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Integer }
+                 *     
+                 */
+                public void setYpos(Integer value) {
+                    this.ypos = value;
+                }
+
+            }
 
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
+        }
 
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
 
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <sequence>
+         *         <element name="secondaryStructure" maxOccurs="unbounded">
+         *           <complexType>
+         *             <complexContent>
+         *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               </restriction>
+         *             </complexContent>
+         *           </complexType>
+         *         </element>
+         *       </sequence>
+         *       <attGroup ref="{www.jalview.org}swingwindow"/>
+         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "secondaryStructure"
+        })
+        public static class RnaViewer {
+
+            @XmlElement(namespace = "www.jalview.org", required = true)
+            protected List secondaryStructure;
+            @XmlAttribute(name = "title")
+            protected String title;
+            @XmlAttribute(name = "viewId")
+            protected String viewId;
+            @XmlAttribute(name = "dividerLocation")
+            protected Integer dividerLocation;
+            @XmlAttribute(name = "selectedRna")
+            protected Integer selectedRna;
+            @XmlAttribute(name = "width")
+            protected Integer width;
+            @XmlAttribute(name = "height")
+            protected Integer height;
+            @XmlAttribute(name = "xpos")
+            protected Integer xpos;
+            @XmlAttribute(name = "ypos")
+            protected Integer ypos;
+
+            /**
+             * Gets the value of the secondaryStructure property.
+             * 
+             * 

+             * 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 set method for the secondaryStructure property.
+             * 
+             * 

+             * For example, to add a new item, do as follows:
+             * 
+             *    getSecondaryStructure().add(newItem);
+             * 

+             * 
+             * 
+             * 

+             * Objects of the following type(s) are allowed in the list
+             * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+             * 
+             * 
+             */
+            public List getSecondaryStructure() {
+                if (secondaryStructure == null) {
+                    secondaryStructure = new ArrayList();
+                }
+                return this.secondaryStructure;
+            }
+
+            /**
+             * Gets the value of the title property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getTitle() {
+                return title;
+            }
+
+            /**
+             * Sets the value of the title property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setTitle(String value) {
+                this.title = value;
+            }
+
+            /**
+             * Gets the value of the viewId property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getViewId() {
+                return viewId;
+            }
+
+            /**
+             * Sets the value of the viewId property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setViewId(String value) {
+                this.viewId = value;
+            }
+
+            /**
+             * Gets the value of the dividerLocation property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getDividerLocation() {
+                return dividerLocation;
+            }
+
+            /**
+             * Sets the value of the dividerLocation property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setDividerLocation(Integer value) {
+                this.dividerLocation = value;
+            }
+
+            /**
+             * Gets the value of the selectedRna property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getSelectedRna() {
+                return selectedRna;
+            }
+
+            /**
+             * Sets the value of the selectedRna property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setSelectedRna(Integer value) {
+                this.selectedRna = value;
+            }
+
+            /**
+             * Gets the value of the width property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getWidth() {
+                return width;
+            }
+
+            /**
+             * Sets the value of the width property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setWidth(Integer value) {
+                this.width = value;
+            }
+
+            /**
+             * Gets the value of the height property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getHeight() {
+                return height;
+            }
+
+            /**
+             * Sets the value of the height property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setHeight(Integer value) {
+                this.height = value;
+            }
+
+            /**
+             * Gets the value of the xpos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getXpos() {
+                return xpos;
+            }
+
+            /**
+             * Sets the value of the xpos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setXpos(Integer value) {
+                this.xpos = value;
+            }
+
+            /**
+             * Gets the value of the ypos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getYpos() {
+                return ypos;
+            }
+
+            /**
+             * Sets the value of the ypos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setYpos(Integer value) {
+                this.ypos = value;
+            }
+
+
+            /**
+             * 
Java class for anonymous complex type.
+             * 
+             * 
The following schema fragment specifies the expected content contained within this class.
+             * 
+             * 
+             * <complexType>
+             *   <complexContent>
+             *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     </restriction>
+             *   </complexContent>
+             * </complexType>
+             * 

+             * 
+             * 
+             */
+            @XmlAccessorType(XmlAccessType.FIELD)
+            @XmlType(name = "")
+            public static class SecondaryStructure {
+
+                @XmlAttribute(name = "title")
+                protected String title;
+                @XmlAttribute(name = "annotationId", required = true)
+                protected String annotationId;
+                @XmlAttribute(name = "gapped")
+                protected Boolean gapped;
+                @XmlAttribute(name = "viewerState")
+                protected String viewerState;
+
+                /**
+                 * Gets the value of the title property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getTitle() {
+                    return title;
+                }
+
+                /**
+                 * Sets the value of the title property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setTitle(String value) {
+                    this.title = value;
+                }
+
+                /**
+                 * Gets the value of the annotationId property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getAnnotationId() {
+                    return annotationId;
+                }
+
+                /**
+                 * Sets the value of the annotationId property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setAnnotationId(String value) {
+                    this.annotationId = value;
+                }
+
+                /**
+                 * Gets the value of the gapped property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public Boolean isGapped() {
+                    return gapped;
+                }
+
+                /**
+                 * Sets the value of the gapped property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link Boolean }
+                 *     
+                 */
+                public void setGapped(Boolean value) {
+                    this.gapped = value;
+                }
+
+                /**
+                 * Gets the value of the viewerState property.
+                 * 
+                 * @return
+                 *     possible object is
+                 *     {@link String }
+                 *     
+                 */
+                public String getViewerState() {
+                    return viewerState;
+                }
+
+                /**
+                 * Sets the value of the viewerState property.
+                 * 
+                 * @param value
+                 *     allowed object is
+                 *     {@link String }
+                 *     
+                 */
+                public void setViewerState(String value) {
+                    this.viewerState = value;
+                }
+
+            }
 
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
+        }
 
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
     }
 
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
 
     /**
-     * 

-     * Java class for anonymous complex type.
+     * 
Java class for anonymous complex type.
      * 
-     * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
      * 
      * <complexType>
      *   <complexContent>
      *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attGroup ref="{www.jalview.org}position"/>
+     *       <sequence>
+     *         <element name="sequencePoint" maxOccurs="unbounded">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *                 <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="axis" maxOccurs="3" minOccurs="3">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="seqPointMin">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="seqPointMax">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}position"/>
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}SimilarityParams"/>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
      *     </restriction>
      *   </complexContent>
      * </complexType>
@@ -3859,3130 +3145,3670 @@ public class JalviewModel
      * 
      */
     @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Axis
-    {
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+    @XmlType(name = "", propOrder = {
+        "sequencePoint",
+        "axis",
+        "seqPointMin",
+        "seqPointMax",
+        "pcaData"
+    })
+    public static class PcaViewer {
+
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List sequencePoint;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List axis;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected PcaDataType pcaData;
+        @XmlAttribute(name = "title")
+        protected String title;
+        @XmlAttribute(name = "scoreModelName")
+        protected String scoreModelName;
+        @XmlAttribute(name = "xDim")
+        protected Integer xDim;
+        @XmlAttribute(name = "yDim")
+        protected Integer yDim;
+        @XmlAttribute(name = "zDim")
+        protected Integer zDim;
+        @XmlAttribute(name = "bgColour")
+        protected Integer bgColour;
+        @XmlAttribute(name = "scaleFactor")
+        protected Float scaleFactor;
+        @XmlAttribute(name = "showLabels")
+        protected Boolean showLabels;
+        @XmlAttribute(name = "linkToAllViews")
+        protected Boolean linkToAllViews;
+        @XmlAttribute(name = "includeGaps")
+        protected Boolean includeGaps;
+        @XmlAttribute(name = "matchGaps")
+        protected Boolean matchGaps;
+        @XmlAttribute(name = "includeGappedColumns")
+        protected Boolean includeGappedColumns;
+        @XmlAttribute(name = "denominateByShortestLength")
+        protected Boolean denominateByShortestLength;
+        @XmlAttribute(name = "width")
+        protected Integer width;
+        @XmlAttribute(name = "height")
+        protected Integer height;
+        @XmlAttribute(name = "xpos")
+        protected Integer xpos;
+        @XmlAttribute(name = "ypos")
+        protected Integer ypos;
 
-    }
+        /**
+         * Gets the value of the sequencePoint property.
+         * 
+         * 

+         * 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 set method for the sequencePoint property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getSequencePoint().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.PcaViewer.SequencePoint }
+         * 
+         * 
+         */
+        public List getSequencePoint() {
+            if (sequencePoint == null) {
+                sequencePoint = new ArrayList();
+            }
+            return this.sequencePoint;
+        }
 
-    /**
-     * 

-     * Java class for anonymous complex type.
-     * 
-     * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attGroup ref="{www.jalview.org}position"/>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class SeqPointMax
-    {
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Gets the value of the axis property.
+         * 
+         * 

+         * 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 set method for the axis property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getAxis().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.PcaViewer.Axis }
+         * 
+         * 
+         */
+        public List getAxis() {
+            if (axis == null) {
+                axis = new ArrayList();
+            }
+            return this.axis;
+        }
 
-    }
+        /**
+         * Gets the value of the seqPointMin property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMin }
+         *     
+         */
+        public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
+            return seqPointMin;
+        }
 
-    /**
-     * 

-     * Java class for anonymous complex type.
-     * 
-     * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attGroup ref="{www.jalview.org}position"/>
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class SeqPointMin
-    {
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Sets the value of the seqPointMin property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMin }
+         *     
+         */
+        public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
+            this.seqPointMin = value;
+        }
 
-    }
+        /**
+         * Gets the value of the seqPointMax property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMax }
+         *     
+         */
+        public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
+            return seqPointMax;
+        }
 
-    /**
-     * 

-     * Java class for anonymous complex type.
-     * 
-     * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attGroup ref="{www.jalview.org}position"/>
-     *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class SequencePoint
-    {
-
-      @XmlAttribute(name = "sequenceRef")
-      protected String sequenceRef;
-
-      @XmlAttribute(name = "xPos")
-      protected Float xPos;
-
-      @XmlAttribute(name = "yPos")
-      protected Float yPos;
-
-      @XmlAttribute(name = "zPos")
-      protected Float zPos;
-
-      /**
-       * Gets the value of the sequenceRef property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getSequenceRef()
-      {
-        return sequenceRef;
-      }
-
-      /**
-       * Sets the value of the sequenceRef property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setSequenceRef(String value)
-      {
-        this.sequenceRef = value;
-      }
-
-      /**
-       * Gets the value of the xPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getXPos()
-      {
-        return xPos;
-      }
-
-      /**
-       * Sets the value of the xPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setXPos(Float value)
-      {
-        this.xPos = value;
-      }
-
-      /**
-       * Gets the value of the yPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getYPos()
-      {
-        return yPos;
-      }
-
-      /**
-       * Sets the value of the yPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setYPos(Float value)
-      {
-        this.yPos = value;
-      }
-
-      /**
-       * Gets the value of the zPos property.
-       * 
-       * @return possible object is {@link Float }
-       * 
-       */
-      public Float getZPos()
-      {
-        return zPos;
-      }
-
-      /**
-       * Sets the value of the zPos property.
-       * 
-       * @param value
-       *          allowed object is {@link Float }
-       * 
-       */
-      public void setZPos(Float value)
-      {
-        this.zPos = value;
-      }
+        /**
+         * Sets the value of the seqPointMax property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewModel.PcaViewer.SeqPointMax }
+         *     
+         */
+        public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
+            this.seqPointMax = value;
+        }
 
-    }
+        /**
+         * Gets the value of the pcaData property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link PcaDataType }
+         *     
+         */
+        public PcaDataType getPcaData() {
+            return pcaData;
+        }
+
+        /**
+         * Sets the value of the pcaData property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link PcaDataType }
+         *     
+         */
+        public void setPcaData(PcaDataType value) {
+            this.pcaData = value;
+        }
 
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence minOccurs="0">
-   *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *       </sequence>
-   *       <attGroup ref="{www.jalview.org}swingwindow"/>
-   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-   *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "title", "newick" })
-  public static class Tree
-  {
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected String title;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected String newick;
-
-    @XmlAttribute(name = "fontName")
-    protected String fontName;
-
-    @XmlAttribute(name = "fontSize")
-    protected Integer fontSize;
-
-    @XmlAttribute(name = "fontStyle")
-    protected Integer fontStyle;
-
-    @XmlAttribute(name = "threshold")
-    protected Float threshold;
-
-    @XmlAttribute(name = "showBootstrap")
-    protected Boolean showBootstrap;
-
-    @XmlAttribute(name = "showDistances")
-    protected Boolean showDistances;
-
-    @XmlAttribute(name = "markUnlinked")
-    protected Boolean markUnlinked;
-
-    @XmlAttribute(name = "fitToWindow")
-    protected Boolean fitToWindow;
-
-    @XmlAttribute(name = "currentTree")
-    protected Boolean currentTree;
-
-    @XmlAttribute(name = "columnWise")
-    protected Boolean columnWise;
-
-    @XmlAttribute(name = "columnReference")
-    protected String columnReference;
-
-    @XmlAttribute(name = "id")
-    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-    @XmlID
-    @XmlSchemaType(name = "ID")
-    protected String id;
-
-    @XmlAttribute(name = "linkToAllViews")
-    protected Boolean linkToAllViews;
-
-    @XmlAttribute(name = "width")
-    protected Integer width;
-
-    @XmlAttribute(name = "height")
-    protected Integer height;
-
-    @XmlAttribute(name = "xpos")
-    protected Integer xpos;
-
-    @XmlAttribute(name = "ypos")
-    protected Integer ypos;
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
+        /**
+         * Gets the value of the scoreModelName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getScoreModelName() {
+            return scoreModelName;
+        }
 
-    /**
-     * Gets the value of the newick property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getNewick()
-    {
-      return newick;
-    }
+        /**
+         * Sets the value of the scoreModelName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setScoreModelName(String value) {
+            this.scoreModelName = value;
+        }
+
+        /**
+         * Gets the value of the xDim property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXDim() {
+            return xDim;
+        }
+
+        /**
+         * Sets the value of the xDim property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXDim(Integer value) {
+            this.xDim = value;
+        }
+
+        /**
+         * Gets the value of the yDim property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYDim() {
+            return yDim;
+        }
+
+        /**
+         * Sets the value of the yDim property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYDim(Integer value) {
+            this.yDim = value;
+        }
+
+        /**
+         * Gets the value of the zDim property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getZDim() {
+            return zDim;
+        }
 
-    /**
-     * Sets the value of the newick property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setNewick(String value)
-    {
-      this.newick = value;
-    }
+        /**
+         * Sets the value of the zDim property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setZDim(Integer value) {
+            this.zDim = value;
+        }
 
-    /**
-     * Gets the value of the fontName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFontName()
-    {
-      return fontName;
-    }
+        /**
+         * Gets the value of the bgColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getBgColour() {
+            return bgColour;
+        }
 
-    /**
-     * Sets the value of the fontName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFontName(String value)
-    {
-      this.fontName = value;
-    }
+        /**
+         * Sets the value of the bgColour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setBgColour(Integer value) {
+            this.bgColour = value;
+        }
 
-    /**
-     * Gets the value of the fontSize property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontSize()
-    {
-      return fontSize;
-    }
+        /**
+         * Gets the value of the scaleFactor property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getScaleFactor() {
+            return scaleFactor;
+        }
 
-    /**
-     * Sets the value of the fontSize property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontSize(Integer value)
-    {
-      this.fontSize = value;
-    }
+        /**
+         * Sets the value of the scaleFactor property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setScaleFactor(Float value) {
+            this.scaleFactor = value;
+        }
 
-    /**
-     * Gets the value of the fontStyle property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontStyle()
-    {
-      return fontStyle;
-    }
+        /**
+         * Gets the value of the showLabels property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowLabels() {
+            return showLabels;
+        }
 
-    /**
-     * Sets the value of the fontStyle property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontStyle(Integer value)
-    {
-      this.fontStyle = value;
-    }
+        /**
+         * Sets the value of the showLabels property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowLabels(Boolean value) {
+            this.showLabels = value;
+        }
 
-    /**
-     * Gets the value of the threshold property.
-     * 
-     * @return possible object is {@link Float }
-     * 
-     */
-    public Float getThreshold()
-    {
-      return threshold;
-    }
+        /**
+         * Gets the value of the linkToAllViews property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isLinkToAllViews() {
+            return linkToAllViews;
+        }
 
-    /**
-     * Sets the value of the threshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Float }
-     * 
-     */
-    public void setThreshold(Float value)
-    {
-      this.threshold = value;
-    }
+        /**
+         * Sets the value of the linkToAllViews property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setLinkToAllViews(Boolean value) {
+            this.linkToAllViews = value;
+        }
 
-    /**
-     * Gets the value of the showBootstrap property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowBootstrap()
-    {
-      return showBootstrap;
-    }
+        /**
+         * Gets the value of the includeGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isIncludeGaps() {
+            return includeGaps;
+        }
 
-    /**
-     * Sets the value of the showBootstrap property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowBootstrap(Boolean value)
-    {
-      this.showBootstrap = value;
-    }
+        /**
+         * Sets the value of the includeGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIncludeGaps(Boolean value) {
+            this.includeGaps = value;
+        }
 
-    /**
-     * Gets the value of the showDistances property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowDistances()
-    {
-      return showDistances;
-    }
+        /**
+         * Gets the value of the matchGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isMatchGaps() {
+            return matchGaps;
+        }
 
-    /**
-     * Sets the value of the showDistances property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowDistances(Boolean value)
-    {
-      this.showDistances = value;
-    }
+        /**
+         * Sets the value of the matchGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setMatchGaps(Boolean value) {
+            this.matchGaps = value;
+        }
 
-    /**
-     * Gets the value of the markUnlinked property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isMarkUnlinked()
-    {
-      return markUnlinked;
-    }
+        /**
+         * Gets the value of the includeGappedColumns property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isIncludeGappedColumns() {
+            return includeGappedColumns;
+        }
 
-    /**
-     * Sets the value of the markUnlinked property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setMarkUnlinked(Boolean value)
-    {
-      this.markUnlinked = value;
-    }
+        /**
+         * Sets the value of the includeGappedColumns property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIncludeGappedColumns(Boolean value) {
+            this.includeGappedColumns = value;
+        }
 
-    /**
-     * Gets the value of the fitToWindow property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isFitToWindow()
-    {
-      return fitToWindow;
-    }
+        /**
+         * Gets the value of the denominateByShortestLength property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isDenominateByShortestLength() {
+            return denominateByShortestLength;
+        }
 
-    /**
-     * Sets the value of the fitToWindow property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFitToWindow(Boolean value)
-    {
-      this.fitToWindow = value;
-    }
+        /**
+         * Sets the value of the denominateByShortestLength property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setDenominateByShortestLength(Boolean value) {
+            this.denominateByShortestLength = value;
+        }
 
-    /**
-     * Gets the value of the currentTree property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isCurrentTree()
-    {
-      return currentTree;
-    }
+        /**
+         * Gets the value of the width property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getWidth() {
+            return width;
+        }
 
-    /**
-     * Sets the value of the currentTree property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCurrentTree(Boolean value)
-    {
-      this.currentTree = value;
-    }
+        /**
+         * Sets the value of the width property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setWidth(Integer value) {
+            this.width = value;
+        }
 
-    /**
-     * Gets the value of the columnWise property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isColumnWise()
-    {
-      if (columnWise == null)
-      {
-        return false;
-      }
-      else
-      {
-        return columnWise;
-      }
-    }
+        /**
+         * Gets the value of the height property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getHeight() {
+            return height;
+        }
 
-    /**
-     * Sets the value of the columnWise property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setColumnWise(Boolean value)
-    {
-      this.columnWise = value;
-    }
+        /**
+         * Sets the value of the height property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setHeight(Integer value) {
+            this.height = value;
+        }
 
-    /**
-     * Gets the value of the columnReference property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getColumnReference()
-    {
-      return columnReference;
-    }
+        /**
+         * Gets the value of the xpos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXpos() {
+            return xpos;
+        }
 
-    /**
-     * Sets the value of the columnReference property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setColumnReference(String value)
-    {
-      this.columnReference = value;
-    }
+        /**
+         * Sets the value of the xpos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXpos(Integer value) {
+            this.xpos = value;
+        }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
+        /**
+         * Gets the value of the ypos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYpos() {
+            return ypos;
+        }
+
+        /**
+         * Sets the value of the ypos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYpos(Integer value) {
+            this.ypos = value;
+        }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
 
-    /**
-     * Gets the value of the linkToAllViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isLinkToAllViews()
-    {
-      if (linkToAllViews == null)
-      {
-        return false;
-      }
-      else
-      {
-        return linkToAllViews;
-      }
-    }
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Axis {
+
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
 
-    /**
-     * Sets the value of the linkToAllViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setLinkToAllViews(Boolean value)
-    {
-      this.linkToAllViews = value;
-    }
+        }
 
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
 
-    /**
-     * Sets the value of the width property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class SeqPointMax {
+
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
 
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
+        }
 
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
 
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class SeqPointMin {
+
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
 
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
+        }
 
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
 
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}position"/>
+         *       <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class SequencePoint {
+
+            @XmlAttribute(name = "sequenceRef")
+            protected String sequenceRef;
+            @XmlAttribute(name = "xPos")
+            protected Float xPos;
+            @XmlAttribute(name = "yPos")
+            protected Float yPos;
+            @XmlAttribute(name = "zPos")
+            protected Float zPos;
+
+            /**
+             * Gets the value of the sequenceRef property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getSequenceRef() {
+                return sequenceRef;
+            }
+
+            /**
+             * Sets the value of the sequenceRef property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setSequenceRef(String value) {
+                this.sequenceRef = value;
+            }
+
+            /**
+             * Gets the value of the xPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getXPos() {
+                return xPos;
+            }
+
+            /**
+             * Sets the value of the xPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setXPos(Float value) {
+                this.xPos = value;
+            }
+
+            /**
+             * Gets the value of the yPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getYPos() {
+                return yPos;
+            }
+
+            /**
+             * Sets the value of the yPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setYPos(Float value) {
+                this.yPos = value;
+            }
+
+            /**
+             * Gets the value of the zPos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Float }
+             *     
+             */
+            public Float getZPos() {
+                return zPos;
+            }
+
+            /**
+             * Sets the value of the zPos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Float }
+             *     
+             */
+            public void setZPos(Float value) {
+                this.zPos = value;
+            }
 
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
-   *       </sequence>
-   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "userColourScheme" })
-  public static class UserColours
-  {
-
-    @XmlElement(
-      name = "UserColourScheme",
-      namespace = "www.jalview.org",
-      required = true)
-    protected JalviewUserColours userColourScheme;
-
-    @XmlAttribute(name = "id")
-    protected String id;
+        }
 
-    /**
-     * Gets the value of the userColourScheme property.
-     * 
-     * @return possible object is {@link JalviewUserColours }
-     * 
-     */
-    public JalviewUserColours getUserColourScheme()
-    {
-      return userColourScheme;
     }
 
-    /**
-     * Sets the value of the userColourScheme property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewUserColours }
-     * 
-     */
-    public void setUserColourScheme(JalviewUserColours value)
-    {
-      this.userColourScheme = value;
-    }
 
     /**
-     * Gets the value of the id property.
+     * 
Java class for anonymous complex type.
      * 
-     * @return possible object is {@link String }
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public String getId()
-    {
-      return id;
-    }
-
-    /**
-     * Sets the value of the id property.
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence minOccurs="0">
+     *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "title",
+        "newick"
+    })
+    public static class Tree {
+
+        @XmlElement(namespace = "www.jalview.org")
+        protected String title;
+        @XmlElement(namespace = "www.jalview.org")
+        protected String newick;
+        @XmlAttribute(name = "fontName")
+        protected String fontName;
+        @XmlAttribute(name = "fontSize")
+        protected Integer fontSize;
+        @XmlAttribute(name = "fontStyle")
+        protected Integer fontStyle;
+        @XmlAttribute(name = "threshold")
+        protected Float threshold;
+        @XmlAttribute(name = "showBootstrap")
+        protected Boolean showBootstrap;
+        @XmlAttribute(name = "showDistances")
+        protected Boolean showDistances;
+        @XmlAttribute(name = "markUnlinked")
+        protected Boolean markUnlinked;
+        @XmlAttribute(name = "fitToWindow")
+        protected Boolean fitToWindow;
+        @XmlAttribute(name = "currentTree")
+        protected Boolean currentTree;
+        @XmlAttribute(name = "columnWise")
+        protected Boolean columnWise;
+        @XmlAttribute(name = "columnReference")
+        protected String columnReference;
+        @XmlAttribute(name = "id")
+        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+        @XmlID
+        @XmlSchemaType(name = "ID")
+        protected String id;
+        @XmlAttribute(name = "linkToAllViews")
+        protected Boolean linkToAllViews;
+        @XmlAttribute(name = "width")
+        protected Integer width;
+        @XmlAttribute(name = "height")
+        protected Integer height;
+        @XmlAttribute(name = "xpos")
+        protected Integer xpos;
+        @XmlAttribute(name = "ypos")
+        protected Integer ypos;
+
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-   *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-   *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               </extension>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="overview" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-   *                 <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                 <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *       <attGroup ref="{www.jalview.org}swingwindow"/>
-   *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-   *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(
-    name = "",
-    propOrder =
-    { "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
-  public static class Viewport
-  {
-
-    @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
-    protected AnnotationColourScheme annotationColours;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List hiddenColumns;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected List calcIdParam;
-
-    @XmlElement(namespace = "www.jalview.org")
-    protected JalviewModel.Viewport.Overview overview;
-
-    @XmlAttribute(name = "conservationSelected")
-    protected Boolean conservationSelected;
-
-    @XmlAttribute(name = "pidSelected")
-    protected Boolean pidSelected;
-
-    @XmlAttribute(name = "bgColour")
-    protected String bgColour;
-
-    @XmlAttribute(name = "consThreshold")
-    protected Integer consThreshold;
-
-    @XmlAttribute(name = "pidThreshold")
-    protected Integer pidThreshold;
-
-    @XmlAttribute(name = "title")
-    protected String title;
-
-    @XmlAttribute(name = "showFullId")
-    protected Boolean showFullId;
-
-    @XmlAttribute(name = "rightAlignIds")
-    protected Boolean rightAlignIds;
-
-    @XmlAttribute(name = "showText")
-    protected Boolean showText;
-
-    @XmlAttribute(name = "showColourText")
-    protected Boolean showColourText;
-
-    @XmlAttribute(name = "showUnconserved")
-    protected Boolean showUnconserved;
-
-    @XmlAttribute(name = "showBoxes")
-    protected Boolean showBoxes;
-
-    @XmlAttribute(name = "wrapAlignment")
-    protected Boolean wrapAlignment;
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    @XmlAttribute(name = "renderGaps")
-    protected Boolean renderGaps;
+        /**
+         * Gets the value of the newick property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getNewick() {
+            return newick;
+        }
 
-    @XmlAttribute(name = "showSequenceFeatures")
-    protected Boolean showSequenceFeatures;
+        /**
+         * Sets the value of the newick property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setNewick(String value) {
+            this.newick = value;
+        }
 
-    @XmlAttribute(name = "showNPfeatureTooltip")
-    protected Boolean showNPfeatureTooltip;
+        /**
+         * Gets the value of the fontName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFontName() {
+            return fontName;
+        }
 
-    @XmlAttribute(name = "showDbRefTooltip")
-    protected Boolean showDbRefTooltip;
+        /**
+         * Sets the value of the fontName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFontName(String value) {
+            this.fontName = value;
+        }
 
-    @XmlAttribute(name = "followHighlight")
-    protected Boolean followHighlight;
+        /**
+         * Gets the value of the fontSize property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontSize() {
+            return fontSize;
+        }
 
-    @XmlAttribute(name = "followSelection")
-    protected Boolean followSelection;
+        /**
+         * Sets the value of the fontSize property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontSize(Integer value) {
+            this.fontSize = value;
+        }
 
-    @XmlAttribute(name = "showAnnotation")
-    protected Boolean showAnnotation;
+        /**
+         * Gets the value of the fontStyle property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontStyle() {
+            return fontStyle;
+        }
 
-    @XmlAttribute(name = "centreColumnLabels")
-    protected Boolean centreColumnLabels;
+        /**
+         * Sets the value of the fontStyle property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontStyle(Integer value) {
+            this.fontStyle = value;
+        }
 
-    @XmlAttribute(name = "showGroupConservation")
-    protected Boolean showGroupConservation;
+        /**
+         * Gets the value of the threshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getThreshold() {
+            return threshold;
+        }
 
-    @XmlAttribute(name = "showGroupConsensus")
-    protected Boolean showGroupConsensus;
+        /**
+         * Sets the value of the threshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setThreshold(Float value) {
+            this.threshold = value;
+        }
 
-    @XmlAttribute(name = "showConsensusHistogram")
-    protected Boolean showConsensusHistogram;
+        /**
+         * Gets the value of the showBootstrap property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowBootstrap() {
+            return showBootstrap;
+        }
 
-    @XmlAttribute(name = "showSequenceLogo")
-    protected Boolean showSequenceLogo;
+        /**
+         * Sets the value of the showBootstrap property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowBootstrap(Boolean value) {
+            this.showBootstrap = value;
+        }
 
-    @XmlAttribute(name = "normaliseSequenceLogo")
-    protected Boolean normaliseSequenceLogo;
+        /**
+         * Gets the value of the showDistances property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowDistances() {
+            return showDistances;
+        }
 
-    @XmlAttribute(name = "ignoreGapsinConsensus")
-    protected Boolean ignoreGapsinConsensus;
+        /**
+         * Sets the value of the showDistances property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowDistances(Boolean value) {
+            this.showDistances = value;
+        }
 
-    @XmlAttribute(name = "startRes")
-    protected Integer startRes;
+        /**
+         * Gets the value of the markUnlinked property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isMarkUnlinked() {
+            return markUnlinked;
+        }
 
-    @XmlAttribute(name = "startSeq")
-    protected Integer startSeq;
+        /**
+         * Sets the value of the markUnlinked property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setMarkUnlinked(Boolean value) {
+            this.markUnlinked = value;
+        }
 
-    @XmlAttribute(name = "charWidth")
-    protected Integer charWidth;
+        /**
+         * Gets the value of the fitToWindow property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isFitToWindow() {
+            return fitToWindow;
+        }
 
-    @XmlAttribute(name = "charHeight")
-    protected Integer charHeight;
+        /**
+         * Sets the value of the fitToWindow property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFitToWindow(Boolean value) {
+            this.fitToWindow = value;
+        }
 
-    @XmlAttribute(name = "fontName")
-    protected String fontName;
+        /**
+         * Gets the value of the currentTree property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isCurrentTree() {
+            return currentTree;
+        }
 
-    @XmlAttribute(name = "fontSize")
-    protected Integer fontSize;
+        /**
+         * Sets the value of the currentTree property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCurrentTree(Boolean value) {
+            this.currentTree = value;
+        }
 
-    @XmlAttribute(name = "fontStyle")
-    protected Integer fontStyle;
+        /**
+         * Gets the value of the columnWise property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isColumnWise() {
+            if (columnWise == null) {
+                return false;
+            } else {
+                return columnWise;
+            }
+        }
 
-    @XmlAttribute(name = "scaleProteinAsCdna")
-    protected Boolean scaleProteinAsCdna;
+        /**
+         * Sets the value of the columnWise property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setColumnWise(Boolean value) {
+            this.columnWise = value;
+        }
 
-    @XmlAttribute(name = "viewName")
-    protected String viewName;
+        /**
+         * Gets the value of the columnReference property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getColumnReference() {
+            return columnReference;
+        }
 
-    @XmlAttribute(name = "sequenceSetId")
-    protected String sequenceSetId;
+        /**
+         * Sets the value of the columnReference property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setColumnReference(String value) {
+            this.columnReference = value;
+        }
 
-    @XmlAttribute(name = "gatheredViews")
-    protected Boolean gatheredViews;
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    @XmlAttribute(name = "textCol1")
-    protected Integer textCol1;
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    @XmlAttribute(name = "textCol2")
-    protected Integer textCol2;
+        /**
+         * Gets the value of the linkToAllViews property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isLinkToAllViews() {
+            if (linkToAllViews == null) {
+                return false;
+            } else {
+                return linkToAllViews;
+            }
+        }
 
-    @XmlAttribute(name = "textColThreshold")
-    protected Integer textColThreshold;
+        /**
+         * Sets the value of the linkToAllViews property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setLinkToAllViews(Boolean value) {
+            this.linkToAllViews = value;
+        }
 
-    @XmlAttribute(name = "id")
-    @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
-    @XmlID
-    @XmlSchemaType(name = "ID")
-    protected String id;
+        /**
+         * Gets the value of the width property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getWidth() {
+            return width;
+        }
 
-    @XmlAttribute(name = "complementId")
-    protected String complementId;
+        /**
+         * Sets the value of the width property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setWidth(Integer value) {
+            this.width = value;
+        }
 
-    @XmlAttribute(name = "showComplementFeatures")
-    protected Boolean showComplementFeatures;
+        /**
+         * Gets the value of the height property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getHeight() {
+            return height;
+        }
 
-    @XmlAttribute(name = "showComplementFeaturesOnTop")
-    protected Boolean showComplementFeaturesOnTop;
+        /**
+         * Sets the value of the height property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setHeight(Integer value) {
+            this.height = value;
+        }
 
-    @XmlAttribute(name = "width")
-    protected Integer width;
+        /**
+         * Gets the value of the xpos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXpos() {
+            return xpos;
+        }
 
-    @XmlAttribute(name = "height")
-    protected Integer height;
+        /**
+         * Sets the value of the xpos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXpos(Integer value) {
+            this.xpos = value;
+        }
 
-    @XmlAttribute(name = "xpos")
-    protected Integer xpos;
+        /**
+         * Gets the value of the ypos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYpos() {
+            return ypos;
+        }
 
-    @XmlAttribute(name = "ypos")
-    protected Integer ypos;
+        /**
+         * Sets the value of the ypos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYpos(Integer value) {
+            this.ypos = value;
+        }
 
-    /**
-     * Gets the value of the annotationColours property.
-     * 
-     * @return possible object is {@link AnnotationColourScheme }
-     * 
-     */
-    public AnnotationColourScheme getAnnotationColours()
-    {
-      return annotationColours;
     }
 
-    /**
-     * Sets the value of the annotationColours property.
-     * 
-     * @param value
-     *          allowed object is {@link AnnotationColourScheme }
-     * 
-     */
-    public void setAnnotationColours(AnnotationColourScheme value)
-    {
-      this.annotationColours = value;
-    }
 
     /**
-     * Gets the value of the hiddenColumns property.
-     * 
-     * 

-     * 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
-     * set method for the hiddenColumns property.
+     * 
Java class for anonymous complex type.
      * 
-     * 

-     * For example, to add a new item, do as follows:
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
      * 
-     * getHiddenColumns().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+     *       </sequence>
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 

      * 
      * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.Viewport.HiddenColumns }
-     * 
-     * 
      */
-    public List getHiddenColumns()
-    {
-      if (hiddenColumns == null)
-      {
-        hiddenColumns = new ArrayList();
-      }
-      return this.hiddenColumns;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "userColourScheme"
+    })
+    public static class UserColours {
+
+        @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
+        protected JalviewUserColours userColourScheme;
+        @XmlAttribute(name = "id")
+        protected String id;
+
+        /**
+         * Gets the value of the userColourScheme property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewUserColours }
+         *     
+         */
+        public JalviewUserColours getUserColourScheme() {
+            return userColourScheme;
+        }
+
+        /**
+         * Sets the value of the userColourScheme property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewUserColours }
+         *     
+         */
+        public void setUserColourScheme(JalviewUserColours value) {
+            this.userColourScheme = value;
+        }
+
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
+
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
+
     }
 
+
     /**
-     * Gets the value of the calcIdParam property.
-     * 
-     * 

-     * 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
-     * set method for the calcIdParam property.
+     * 
Java class for anonymous complex type.
      * 
-     * 

-     * For example, to add a new item, do as follows:
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
      * 
-     * getCalcIdParam().add(newItem);
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               </extension>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *         <element name="overview" minOccurs="0">
+     *           <complexType>
+     *             <complexContent>
+     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *               </restriction>
+     *             </complexContent>
+     *           </complexType>
+     *         </element>
+     *       </sequence>
+     *       <attGroup ref="{www.jalview.org}swingwindow"/>
+     *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
      * 

      * 
      * 
-     * 

-     * Objects of the following type(s) are allowed in the list
-     * {@link JalviewModel.Viewport.CalcIdParam }
-     * 
-     * 
      */
-    public List getCalcIdParam()
-    {
-      if (calcIdParam == null)
-      {
-        calcIdParam = new ArrayList();
-      }
-      return this.calcIdParam;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "annotationColours",
+        "hiddenColumns",
+        "calcIdParam",
+        "overview"
+    })
+    public static class Viewport {
+
+        @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+        protected AnnotationColourScheme annotationColours;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List hiddenColumns;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List calcIdParam;
+        @XmlElement(namespace = "www.jalview.org")
+        protected JalviewModel.Viewport.Overview overview;
+        @XmlAttribute(name = "conservationSelected")
+        protected Boolean conservationSelected;
+        @XmlAttribute(name = "pidSelected")
+        protected Boolean pidSelected;
+        @XmlAttribute(name = "bgColour")
+        protected String bgColour;
+        @XmlAttribute(name = "consThreshold")
+        protected Integer consThreshold;
+        @XmlAttribute(name = "pidThreshold")
+        protected Integer pidThreshold;
+        @XmlAttribute(name = "title")
+        protected String title;
+        @XmlAttribute(name = "showFullId")
+        protected Boolean showFullId;
+        @XmlAttribute(name = "rightAlignIds")
+        protected Boolean rightAlignIds;
+        @XmlAttribute(name = "showText")
+        protected Boolean showText;
+        @XmlAttribute(name = "showColourText")
+        protected Boolean showColourText;
+        @XmlAttribute(name = "showUnconserved")
+        protected Boolean showUnconserved;
+        @XmlAttribute(name = "showBoxes")
+        protected Boolean showBoxes;
+        @XmlAttribute(name = "wrapAlignment")
+        protected Boolean wrapAlignment;
+        @XmlAttribute(name = "renderGaps")
+        protected Boolean renderGaps;
+        @XmlAttribute(name = "showSequenceFeatures")
+        protected Boolean showSequenceFeatures;
+        @XmlAttribute(name = "showNPfeatureTooltip")
+        protected Boolean showNPfeatureTooltip;
+        @XmlAttribute(name = "showDbRefTooltip")
+        protected Boolean showDbRefTooltip;
+        @XmlAttribute(name = "followHighlight")
+        protected Boolean followHighlight;
+        @XmlAttribute(name = "followSelection")
+        protected Boolean followSelection;
+        @XmlAttribute(name = "showAnnotation")
+        protected Boolean showAnnotation;
+        @XmlAttribute(name = "centreColumnLabels")
+        protected Boolean centreColumnLabels;
+        @XmlAttribute(name = "showGroupConservation")
+        protected Boolean showGroupConservation;
+        @XmlAttribute(name = "showGroupConsensus")
+        protected Boolean showGroupConsensus;
+        @XmlAttribute(name = "showConsensusHistogram")
+        protected Boolean showConsensusHistogram;
+        @XmlAttribute(name = "showSequenceLogo")
+        protected Boolean showSequenceLogo;
+        @XmlAttribute(name = "normaliseSequenceLogo")
+        protected Boolean normaliseSequenceLogo;
+        @XmlAttribute(name = "ignoreGapsinConsensus")
+        protected Boolean ignoreGapsinConsensus;
+        @XmlAttribute(name = "startRes")
+        protected Integer startRes;
+        @XmlAttribute(name = "startSeq")
+        protected Integer startSeq;
+        @XmlAttribute(name = "charWidth")
+        protected Integer charWidth;
+        @XmlAttribute(name = "charHeight")
+        protected Integer charHeight;
+        @XmlAttribute(name = "fontName")
+        protected String fontName;
+        @XmlAttribute(name = "fontSize")
+        protected Integer fontSize;
+        @XmlAttribute(name = "fontStyle")
+        protected Integer fontStyle;
+        @XmlAttribute(name = "scaleProteinAsCdna")
+        protected Boolean scaleProteinAsCdna;
+        @XmlAttribute(name = "viewName")
+        protected String viewName;
+        @XmlAttribute(name = "sequenceSetId")
+        protected String sequenceSetId;
+        @XmlAttribute(name = "gatheredViews")
+        protected Boolean gatheredViews;
+        @XmlAttribute(name = "textCol1")
+        protected Integer textCol1;
+        @XmlAttribute(name = "textCol2")
+        protected Integer textCol2;
+        @XmlAttribute(name = "textColThreshold")
+        protected Integer textColThreshold;
+        @XmlAttribute(name = "id")
+        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+        @XmlID
+        @XmlSchemaType(name = "ID")
+        protected String id;
+        @XmlAttribute(name = "complementId")
+        protected String complementId;
+        @XmlAttribute(name = "showComplementFeatures")
+        protected Boolean showComplementFeatures;
+        @XmlAttribute(name = "showComplementFeaturesOnTop")
+        protected Boolean showComplementFeaturesOnTop;
+        @XmlAttribute(name = "width")
+        protected Integer width;
+        @XmlAttribute(name = "height")
+        protected Integer height;
+        @XmlAttribute(name = "xpos")
+        protected Integer xpos;
+        @XmlAttribute(name = "ypos")
+        protected Integer ypos;
 
-    /**
-     * Gets the value of the overview property.
-     * 
-     * @return possible object is {@link JalviewModel.Viewport.Overview }
-     * 
-     */
-    public JalviewModel.Viewport.Overview getOverview()
-    {
-      return overview;
-    }
+        /**
+         * Gets the value of the annotationColours property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link AnnotationColourScheme }
+         *     
+         */
+        public AnnotationColourScheme getAnnotationColours() {
+            return annotationColours;
+        }
 
-    /**
-     * Sets the value of the overview property.
-     * 
-     * @param value
-     *          allowed object is {@link JalviewModel.Viewport.Overview }
-     * 
-     */
-    public void setOverview(JalviewModel.Viewport.Overview value)
-    {
-      this.overview = value;
-    }
+        /**
+         * Sets the value of the annotationColours property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link AnnotationColourScheme }
+         *     
+         */
+        public void setAnnotationColours(AnnotationColourScheme value) {
+            this.annotationColours = value;
+        }
 
-    /**
-     * Gets the value of the conservationSelected property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isConservationSelected()
-    {
-      return conservationSelected;
-    }
+        /**
+         * Gets the value of the hiddenColumns property.
+         * 
+         * 

+         * 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 set method for the hiddenColumns property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getHiddenColumns().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.Viewport.HiddenColumns }
+         * 
+         * 
+         */
+        public List getHiddenColumns() {
+            if (hiddenColumns == null) {
+                hiddenColumns = new ArrayList();
+            }
+            return this.hiddenColumns;
+        }
 
-    /**
-     * Sets the value of the conservationSelected property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setConservationSelected(Boolean value)
-    {
-      this.conservationSelected = value;
-    }
+        /**
+         * Gets the value of the calcIdParam property.
+         * 
+         * 

+         * 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 set method for the calcIdParam property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getCalcIdParam().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.Viewport.CalcIdParam }
+         * 
+         * 
+         */
+        public List getCalcIdParam() {
+            if (calcIdParam == null) {
+                calcIdParam = new ArrayList();
+            }
+            return this.calcIdParam;
+        }
 
-    /**
-     * Gets the value of the pidSelected property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isPidSelected()
-    {
-      return pidSelected;
-    }
+        /**
+         * Gets the value of the overview property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link JalviewModel.Viewport.Overview }
+         *     
+         */
+        public JalviewModel.Viewport.Overview getOverview() {
+            return overview;
+        }
 
-    /**
-     * Sets the value of the pidSelected property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setPidSelected(Boolean value)
-    {
-      this.pidSelected = value;
-    }
+        /**
+         * Sets the value of the overview property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link JalviewModel.Viewport.Overview }
+         *     
+         */
+        public void setOverview(JalviewModel.Viewport.Overview value) {
+            this.overview = value;
+        }
 
-    /**
-     * Gets the value of the bgColour property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getBgColour()
-    {
-      return bgColour;
-    }
+        /**
+         * Gets the value of the conservationSelected property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isConservationSelected() {
+            return conservationSelected;
+        }
 
-    /**
-     * Sets the value of the bgColour property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setBgColour(String value)
-    {
-      this.bgColour = value;
-    }
+        /**
+         * Sets the value of the conservationSelected property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setConservationSelected(Boolean value) {
+            this.conservationSelected = value;
+        }
+
+        /**
+         * Gets the value of the pidSelected property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isPidSelected() {
+            return pidSelected;
+        }
+
+        /**
+         * Sets the value of the pidSelected property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setPidSelected(Boolean value) {
+            this.pidSelected = value;
+        }
 
-    /**
-     * Gets the value of the consThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getConsThreshold()
-    {
-      return consThreshold;
-    }
+        /**
+         * Gets the value of the bgColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getBgColour() {
+            return bgColour;
+        }
 
-    /**
-     * Sets the value of the consThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setConsThreshold(Integer value)
-    {
-      this.consThreshold = value;
-    }
+        /**
+         * Sets the value of the bgColour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setBgColour(String value) {
+            this.bgColour = value;
+        }
 
-    /**
-     * Gets the value of the pidThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getPidThreshold()
-    {
-      return pidThreshold;
-    }
+        /**
+         * Gets the value of the consThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getConsThreshold() {
+            return consThreshold;
+        }
 
-    /**
-     * Sets the value of the pidThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setPidThreshold(Integer value)
-    {
-      this.pidThreshold = value;
-    }
+        /**
+         * Sets the value of the consThreshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setConsThreshold(Integer value) {
+            this.consThreshold = value;
+        }
 
-    /**
-     * Gets the value of the title property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getTitle()
-    {
-      return title;
-    }
+        /**
+         * Gets the value of the pidThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getPidThreshold() {
+            return pidThreshold;
+        }
 
-    /**
-     * Sets the value of the title property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setTitle(String value)
-    {
-      this.title = value;
-    }
+        /**
+         * Sets the value of the pidThreshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setPidThreshold(Integer value) {
+            this.pidThreshold = value;
+        }
 
-    /**
-     * Gets the value of the showFullId property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowFullId()
-    {
-      return showFullId;
-    }
+        /**
+         * Gets the value of the title property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getTitle() {
+            return title;
+        }
 
-    /**
-     * Sets the value of the showFullId property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowFullId(Boolean value)
-    {
-      this.showFullId = value;
-    }
+        /**
+         * Sets the value of the title property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setTitle(String value) {
+            this.title = value;
+        }
 
-    /**
-     * Gets the value of the rightAlignIds property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isRightAlignIds()
-    {
-      return rightAlignIds;
-    }
+        /**
+         * Gets the value of the showFullId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowFullId() {
+            return showFullId;
+        }
 
-    /**
-     * Sets the value of the rightAlignIds property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setRightAlignIds(Boolean value)
-    {
-      this.rightAlignIds = value;
-    }
+        /**
+         * Sets the value of the showFullId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowFullId(Boolean value) {
+            this.showFullId = value;
+        }
 
-    /**
-     * Gets the value of the showText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowText()
-    {
-      return showText;
-    }
+        /**
+         * Gets the value of the rightAlignIds property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isRightAlignIds() {
+            return rightAlignIds;
+        }
 
-    /**
-     * Sets the value of the showText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowText(Boolean value)
-    {
-      this.showText = value;
-    }
+        /**
+         * Sets the value of the rightAlignIds property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setRightAlignIds(Boolean value) {
+            this.rightAlignIds = value;
+        }
 
-    /**
-     * Gets the value of the showColourText property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowColourText()
-    {
-      return showColourText;
-    }
+        /**
+         * Gets the value of the showText property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowText() {
+            return showText;
+        }
 
-    /**
-     * Sets the value of the showColourText property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowColourText(Boolean value)
-    {
-      this.showColourText = value;
-    }
+        /**
+         * Sets the value of the showText property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowText(Boolean value) {
+            this.showText = value;
+        }
 
-    /**
-     * Gets the value of the showUnconserved property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowUnconserved()
-    {
-      if (showUnconserved == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showUnconserved;
-      }
-    }
+        /**
+         * Gets the value of the showColourText property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowColourText() {
+            return showColourText;
+        }
 
-    /**
-     * Sets the value of the showUnconserved property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowUnconserved(Boolean value)
-    {
-      this.showUnconserved = value;
-    }
+        /**
+         * Sets the value of the showColourText property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowColourText(Boolean value) {
+            this.showColourText = value;
+        }
 
-    /**
-     * Gets the value of the showBoxes property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowBoxes()
-    {
-      return showBoxes;
-    }
+        /**
+         * Gets the value of the showUnconserved property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowUnconserved() {
+            if (showUnconserved == null) {
+                return false;
+            } else {
+                return showUnconserved;
+            }
+        }
 
-    /**
-     * Sets the value of the showBoxes property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowBoxes(Boolean value)
-    {
-      this.showBoxes = value;
-    }
+        /**
+         * Sets the value of the showUnconserved property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowUnconserved(Boolean value) {
+            this.showUnconserved = value;
+        }
 
-    /**
-     * Gets the value of the wrapAlignment property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isWrapAlignment()
-    {
-      return wrapAlignment;
-    }
+        /**
+         * Gets the value of the showBoxes property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowBoxes() {
+            return showBoxes;
+        }
 
-    /**
-     * Sets the value of the wrapAlignment property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setWrapAlignment(Boolean value)
-    {
-      this.wrapAlignment = value;
-    }
+        /**
+         * Sets the value of the showBoxes property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowBoxes(Boolean value) {
+            this.showBoxes = value;
+        }
 
-    /**
-     * Gets the value of the renderGaps property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isRenderGaps()
-    {
-      return renderGaps;
-    }
+        /**
+         * Gets the value of the wrapAlignment property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isWrapAlignment() {
+            return wrapAlignment;
+        }
 
-    /**
-     * Sets the value of the renderGaps property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setRenderGaps(Boolean value)
-    {
-      this.renderGaps = value;
-    }
+        /**
+         * Sets the value of the wrapAlignment property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setWrapAlignment(Boolean value) {
+            this.wrapAlignment = value;
+        }
 
-    /**
-     * Gets the value of the showSequenceFeatures property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowSequenceFeatures()
-    {
-      return showSequenceFeatures;
-    }
+        /**
+         * Gets the value of the renderGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isRenderGaps() {
+            return renderGaps;
+        }
 
-    /**
-     * Sets the value of the showSequenceFeatures property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceFeatures(Boolean value)
-    {
-      this.showSequenceFeatures = value;
-    }
+        /**
+         * Sets the value of the renderGaps property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setRenderGaps(Boolean value) {
+            this.renderGaps = value;
+        }
 
-    /**
-     * Gets the value of the showNPfeatureTooltip property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowNPfeatureTooltip()
-    {
-      return showNPfeatureTooltip;
-    }
+        /**
+         * Gets the value of the showSequenceFeatures property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowSequenceFeatures() {
+            return showSequenceFeatures;
+        }
+
+        /**
+         * Sets the value of the showSequenceFeatures property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowSequenceFeatures(Boolean value) {
+            this.showSequenceFeatures = value;
+        }
 
-    /**
-     * Sets the value of the showNPfeatureTooltip property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowNPfeatureTooltip(Boolean value)
-    {
-      this.showNPfeatureTooltip = value;
-    }
+        /**
+         * Gets the value of the showNPfeatureTooltip property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowNPfeatureTooltip() {
+            return showNPfeatureTooltip;
+        }
 
-    /**
-     * Gets the value of the showDbRefTooltip property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowDbRefTooltip()
-    {
-      return showDbRefTooltip;
-    }
+        /**
+         * Sets the value of the showNPfeatureTooltip property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowNPfeatureTooltip(Boolean value) {
+            this.showNPfeatureTooltip = value;
+        }
 
-    /**
-     * Sets the value of the showDbRefTooltip property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowDbRefTooltip(Boolean value)
-    {
-      this.showDbRefTooltip = value;
-    }
+        /**
+         * Gets the value of the showDbRefTooltip property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowDbRefTooltip() {
+            return showDbRefTooltip;
+        }
 
-    /**
-     * Gets the value of the followHighlight property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isFollowHighlight()
-    {
-      if (followHighlight == null)
-      {
-        return true;
-      }
-      else
-      {
-        return followHighlight;
-      }
-    }
+        /**
+         * Sets the value of the showDbRefTooltip property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowDbRefTooltip(Boolean value) {
+            this.showDbRefTooltip = value;
+        }
 
-    /**
-     * Sets the value of the followHighlight property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFollowHighlight(Boolean value)
-    {
-      this.followHighlight = value;
-    }
+        /**
+         * Gets the value of the followHighlight property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isFollowHighlight() {
+            if (followHighlight == null) {
+                return true;
+            } else {
+                return followHighlight;
+            }
+        }
 
-    /**
-     * Gets the value of the followSelection property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isFollowSelection()
-    {
-      if (followSelection == null)
-      {
-        return true;
-      }
-      else
-      {
-        return followSelection;
-      }
-    }
+        /**
+         * Sets the value of the followHighlight property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFollowHighlight(Boolean value) {
+            this.followHighlight = value;
+        }
 
-    /**
-     * Sets the value of the followSelection property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setFollowSelection(Boolean value)
-    {
-      this.followSelection = value;
-    }
+        /**
+         * Gets the value of the followSelection property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isFollowSelection() {
+            if (followSelection == null) {
+                return true;
+            } else {
+                return followSelection;
+            }
+        }
 
-    /**
-     * Gets the value of the showAnnotation property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isShowAnnotation()
-    {
-      return showAnnotation;
-    }
+        /**
+         * Sets the value of the followSelection property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFollowSelection(Boolean value) {
+            this.followSelection = value;
+        }
 
-    /**
-     * Sets the value of the showAnnotation property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowAnnotation(Boolean value)
-    {
-      this.showAnnotation = value;
-    }
+        /**
+         * Gets the value of the showAnnotation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowAnnotation() {
+            return showAnnotation;
+        }
 
-    /**
-     * Gets the value of the centreColumnLabels property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isCentreColumnLabels()
-    {
-      if (centreColumnLabels == null)
-      {
-        return false;
-      }
-      else
-      {
-        return centreColumnLabels;
-      }
-    }
+        /**
+         * Sets the value of the showAnnotation property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowAnnotation(Boolean value) {
+            this.showAnnotation = value;
+        }
 
-    /**
-     * Sets the value of the centreColumnLabels property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCentreColumnLabels(Boolean value)
-    {
-      this.centreColumnLabels = value;
-    }
+        /**
+         * Gets the value of the centreColumnLabels property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isCentreColumnLabels() {
+            if (centreColumnLabels == null) {
+                return false;
+            } else {
+                return centreColumnLabels;
+            }
+        }
 
-    /**
-     * Gets the value of the showGroupConservation property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowGroupConservation()
-    {
-      if (showGroupConservation == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showGroupConservation;
-      }
-    }
+        /**
+         * Sets the value of the centreColumnLabels property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCentreColumnLabels(Boolean value) {
+            this.centreColumnLabels = value;
+        }
 
-    /**
-     * Sets the value of the showGroupConservation property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowGroupConservation(Boolean value)
-    {
-      this.showGroupConservation = value;
-    }
+        /**
+         * Gets the value of the showGroupConservation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowGroupConservation() {
+            if (showGroupConservation == null) {
+                return false;
+            } else {
+                return showGroupConservation;
+            }
+        }
 
-    /**
-     * Gets the value of the showGroupConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowGroupConsensus()
-    {
-      if (showGroupConsensus == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showGroupConsensus;
-      }
-    }
+        /**
+         * Sets the value of the showGroupConservation property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowGroupConservation(Boolean value) {
+            this.showGroupConservation = value;
+        }
 
-    /**
-     * Sets the value of the showGroupConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowGroupConsensus(Boolean value)
-    {
-      this.showGroupConsensus = value;
-    }
+        /**
+         * Gets the value of the showGroupConsensus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowGroupConsensus() {
+            if (showGroupConsensus == null) {
+                return false;
+            } else {
+                return showGroupConsensus;
+            }
+        }
 
-    /**
-     * Gets the value of the showConsensusHistogram property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowConsensusHistogram()
-    {
-      if (showConsensusHistogram == null)
-      {
-        return true;
-      }
-      else
-      {
-        return showConsensusHistogram;
-      }
-    }
+        /**
+         * Sets the value of the showGroupConsensus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowGroupConsensus(Boolean value) {
+            this.showGroupConsensus = value;
+        }
 
-    /**
-     * Sets the value of the showConsensusHistogram property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowConsensusHistogram(Boolean value)
-    {
-      this.showConsensusHistogram = value;
-    }
+        /**
+         * Gets the value of the showConsensusHistogram property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowConsensusHistogram() {
+            if (showConsensusHistogram == null) {
+                return true;
+            } else {
+                return showConsensusHistogram;
+            }
+        }
 
-    /**
-     * Gets the value of the showSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowSequenceLogo()
-    {
-      if (showSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showSequenceLogo;
-      }
-    }
+        /**
+         * Sets the value of the showConsensusHistogram property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowConsensusHistogram(Boolean value) {
+            this.showConsensusHistogram = value;
+        }
 
-    /**
-     * Sets the value of the showSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowSequenceLogo(Boolean value)
-    {
-      this.showSequenceLogo = value;
-    }
+        /**
+         * Gets the value of the showSequenceLogo property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowSequenceLogo() {
+            if (showSequenceLogo == null) {
+                return false;
+            } else {
+                return showSequenceLogo;
+            }
+        }
 
-    /**
-     * Gets the value of the normaliseSequenceLogo property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isNormaliseSequenceLogo()
-    {
-      if (normaliseSequenceLogo == null)
-      {
-        return false;
-      }
-      else
-      {
-        return normaliseSequenceLogo;
-      }
-    }
+        /**
+         * Sets the value of the showSequenceLogo property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowSequenceLogo(Boolean value) {
+            this.showSequenceLogo = value;
+        }
 
-    /**
-     * Sets the value of the normaliseSequenceLogo property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setNormaliseSequenceLogo(Boolean value)
-    {
-      this.normaliseSequenceLogo = value;
-    }
+        /**
+         * Gets the value of the normaliseSequenceLogo property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isNormaliseSequenceLogo() {
+            if (normaliseSequenceLogo == null) {
+                return false;
+            } else {
+                return normaliseSequenceLogo;
+            }
+        }
 
-    /**
-     * Gets the value of the ignoreGapsinConsensus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isIgnoreGapsinConsensus()
-    {
-      if (ignoreGapsinConsensus == null)
-      {
-        return true;
-      }
-      else
-      {
-        return ignoreGapsinConsensus;
-      }
-    }
+        /**
+         * Sets the value of the normaliseSequenceLogo property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setNormaliseSequenceLogo(Boolean value) {
+            this.normaliseSequenceLogo = value;
+        }
 
-    /**
-     * Sets the value of the ignoreGapsinConsensus property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setIgnoreGapsinConsensus(Boolean value)
-    {
-      this.ignoreGapsinConsensus = value;
-    }
+        /**
+         * Gets the value of the ignoreGapsinConsensus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isIgnoreGapsinConsensus() {
+            if (ignoreGapsinConsensus == null) {
+                return true;
+            } else {
+                return ignoreGapsinConsensus;
+            }
+        }
 
-    /**
-     * Gets the value of the startRes property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStartRes()
-    {
-      return startRes;
-    }
+        /**
+         * Sets the value of the ignoreGapsinConsensus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setIgnoreGapsinConsensus(Boolean value) {
+            this.ignoreGapsinConsensus = value;
+        }
 
-    /**
-     * Sets the value of the startRes property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStartRes(Integer value)
-    {
-      this.startRes = value;
-    }
+        /**
+         * Gets the value of the startRes property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getStartRes() {
+            return startRes;
+        }
+
+        /**
+         * Sets the value of the startRes property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setStartRes(Integer value) {
+            this.startRes = value;
+        }
 
-    /**
-     * Gets the value of the startSeq property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getStartSeq()
-    {
-      return startSeq;
-    }
+        /**
+         * Gets the value of the startSeq property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getStartSeq() {
+            return startSeq;
+        }
 
-    /**
-     * Sets the value of the startSeq property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setStartSeq(Integer value)
-    {
-      this.startSeq = value;
-    }
+        /**
+         * Sets the value of the startSeq property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setStartSeq(Integer value) {
+            this.startSeq = value;
+        }
 
-    /**
-     * Gets the value of the charWidth property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getCharWidth()
-    {
-      return charWidth;
-    }
+        /**
+         * Gets the value of the charWidth property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getCharWidth() {
+            return charWidth;
+        }
 
-    /**
-     * Sets the value of the charWidth property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setCharWidth(Integer value)
-    {
-      this.charWidth = value;
-    }
+        /**
+         * Sets the value of the charWidth property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setCharWidth(Integer value) {
+            this.charWidth = value;
+        }
 
-    /**
-     * Gets the value of the charHeight property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getCharHeight()
-    {
-      return charHeight;
-    }
+        /**
+         * Gets the value of the charHeight property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getCharHeight() {
+            return charHeight;
+        }
 
-    /**
-     * Sets the value of the charHeight property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setCharHeight(Integer value)
-    {
-      this.charHeight = value;
-    }
+        /**
+         * Sets the value of the charHeight property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setCharHeight(Integer value) {
+            this.charHeight = value;
+        }
 
-    /**
-     * Gets the value of the fontName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getFontName()
-    {
-      return fontName;
-    }
+        /**
+         * Gets the value of the fontName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFontName() {
+            return fontName;
+        }
 
-    /**
-     * Sets the value of the fontName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFontName(String value)
-    {
-      this.fontName = value;
-    }
+        /**
+         * Sets the value of the fontName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFontName(String value) {
+            this.fontName = value;
+        }
 
-    /**
-     * Gets the value of the fontSize property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontSize()
-    {
-      return fontSize;
-    }
+        /**
+         * Gets the value of the fontSize property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontSize() {
+            return fontSize;
+        }
 
-    /**
-     * Sets the value of the fontSize property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontSize(Integer value)
-    {
-      this.fontSize = value;
-    }
+        /**
+         * Sets the value of the fontSize property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontSize(Integer value) {
+            this.fontSize = value;
+        }
 
-    /**
-     * Gets the value of the fontStyle property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getFontStyle()
-    {
-      return fontStyle;
-    }
+        /**
+         * Gets the value of the fontStyle property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getFontStyle() {
+            return fontStyle;
+        }
 
-    /**
-     * Sets the value of the fontStyle property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setFontStyle(Integer value)
-    {
-      this.fontStyle = value;
-    }
+        /**
+         * Sets the value of the fontStyle property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setFontStyle(Integer value) {
+            this.fontStyle = value;
+        }
 
-    /**
-     * Gets the value of the scaleProteinAsCdna property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isScaleProteinAsCdna()
-    {
-      if (scaleProteinAsCdna == null)
-      {
-        return true;
-      }
-      else
-      {
-        return scaleProteinAsCdna;
-      }
-    }
+        /**
+         * Gets the value of the scaleProteinAsCdna property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isScaleProteinAsCdna() {
+            if (scaleProteinAsCdna == null) {
+                return true;
+            } else {
+                return scaleProteinAsCdna;
+            }
+        }
 
-    /**
-     * Sets the value of the scaleProteinAsCdna property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setScaleProteinAsCdna(Boolean value)
-    {
-      this.scaleProteinAsCdna = value;
-    }
+        /**
+         * Sets the value of the scaleProteinAsCdna property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setScaleProteinAsCdna(Boolean value) {
+            this.scaleProteinAsCdna = value;
+        }
 
-    /**
-     * Gets the value of the viewName property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getViewName()
-    {
-      return viewName;
-    }
+        /**
+         * Gets the value of the viewName property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getViewName() {
+            return viewName;
+        }
 
-    /**
-     * Sets the value of the viewName property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setViewName(String value)
-    {
-      this.viewName = value;
-    }
+        /**
+         * Sets the value of the viewName property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setViewName(String value) {
+            this.viewName = value;
+        }
 
-    /**
-     * Gets the value of the sequenceSetId property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getSequenceSetId()
-    {
-      return sequenceSetId;
-    }
+        /**
+         * Gets the value of the sequenceSetId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getSequenceSetId() {
+            return sequenceSetId;
+        }
 
-    /**
-     * Sets the value of the sequenceSetId property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setSequenceSetId(String value)
-    {
-      this.sequenceSetId = value;
-    }
+        /**
+         * Sets the value of the sequenceSetId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setSequenceSetId(String value) {
+            this.sequenceSetId = value;
+        }
 
-    /**
-     * Gets the value of the gatheredViews property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isGatheredViews()
-    {
-      return gatheredViews;
-    }
+        /**
+         * Gets the value of the gatheredViews property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isGatheredViews() {
+            return gatheredViews;
+        }
 
-    /**
-     * Sets the value of the gatheredViews property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setGatheredViews(Boolean value)
-    {
-      this.gatheredViews = value;
-    }
+        /**
+         * Sets the value of the gatheredViews property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setGatheredViews(Boolean value) {
+            this.gatheredViews = value;
+        }
 
-    /**
-     * Gets the value of the textCol1 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol1()
-    {
-      return textCol1;
-    }
+        /**
+         * Gets the value of the textCol1 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextCol1() {
+            return textCol1;
+        }
 
-    /**
-     * Sets the value of the textCol1 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol1(Integer value)
-    {
-      this.textCol1 = value;
-    }
+        /**
+         * Sets the value of the textCol1 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextCol1(Integer value) {
+            this.textCol1 = value;
+        }
 
-    /**
-     * Gets the value of the textCol2 property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextCol2()
-    {
-      return textCol2;
-    }
+        /**
+         * Gets the value of the textCol2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextCol2() {
+            return textCol2;
+        }
 
-    /**
-     * Sets the value of the textCol2 property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextCol2(Integer value)
-    {
-      this.textCol2 = value;
-    }
+        /**
+         * Sets the value of the textCol2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextCol2(Integer value) {
+            this.textCol2 = value;
+        }
 
-    /**
-     * Gets the value of the textColThreshold property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getTextColThreshold()
-    {
-      return textColThreshold;
-    }
+        /**
+         * Gets the value of the textColThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getTextColThreshold() {
+            return textColThreshold;
+        }
+
+        /**
+         * Sets the value of the textColThreshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setTextColThreshold(Integer value) {
+            this.textColThreshold = value;
+        }
 
-    /**
-     * Sets the value of the textColThreshold property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setTextColThreshold(Integer value)
-    {
-      this.textColThreshold = value;
-    }
+        /**
+         * Gets the value of the id property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getId() {
+            return id;
+        }
 
-    /**
-     * Gets the value of the id property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getId()
-    {
-      return id;
-    }
+        /**
+         * Sets the value of the id property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setId(String value) {
+            this.id = value;
+        }
 
-    /**
-     * Sets the value of the id property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setId(String value)
-    {
-      this.id = value;
-    }
+        /**
+         * Gets the value of the complementId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getComplementId() {
+            return complementId;
+        }
 
-    /**
-     * Gets the value of the complementId property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getComplementId()
-    {
-      return complementId;
-    }
+        /**
+         * Sets the value of the complementId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setComplementId(String value) {
+            this.complementId = value;
+        }
 
-    /**
-     * Sets the value of the complementId property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setComplementId(String value)
-    {
-      this.complementId = value;
-    }
+        /**
+         * Gets the value of the showComplementFeatures property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowComplementFeatures() {
+            if (showComplementFeatures == null) {
+                return false;
+            } else {
+                return showComplementFeatures;
+            }
+        }
 
-    /**
-     * Gets the value of the showComplementFeatures property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowComplementFeatures()
-    {
-      if (showComplementFeatures == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showComplementFeatures;
-      }
-    }
+        /**
+         * Sets the value of the showComplementFeatures property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowComplementFeatures(Boolean value) {
+            this.showComplementFeatures = value;
+        }
 
-    /**
-     * Sets the value of the showComplementFeatures property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowComplementFeatures(Boolean value)
-    {
-      this.showComplementFeatures = value;
-    }
+        /**
+         * Gets the value of the showComplementFeaturesOnTop property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowComplementFeaturesOnTop() {
+            if (showComplementFeaturesOnTop == null) {
+                return false;
+            } else {
+                return showComplementFeaturesOnTop;
+            }
+        }
 
-    /**
-     * Gets the value of the showComplementFeaturesOnTop property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isShowComplementFeaturesOnTop()
-    {
-      if (showComplementFeaturesOnTop == null)
-      {
-        return false;
-      }
-      else
-      {
-        return showComplementFeaturesOnTop;
-      }
-    }
+        /**
+         * Sets the value of the showComplementFeaturesOnTop property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowComplementFeaturesOnTop(Boolean value) {
+            this.showComplementFeaturesOnTop = value;
+        }
 
-    /**
-     * Sets the value of the showComplementFeaturesOnTop property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setShowComplementFeaturesOnTop(Boolean value)
-    {
-      this.showComplementFeaturesOnTop = value;
-    }
+        /**
+         * Gets the value of the width property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getWidth() {
+            return width;
+        }
 
-    /**
-     * Gets the value of the width property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getWidth()
-    {
-      return width;
-    }
+        /**
+         * Sets the value of the width property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setWidth(Integer value) {
+            this.width = value;
+        }
 
-    /**
-     * Sets the value of the width property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setWidth(Integer value)
-    {
-      this.width = value;
-    }
+        /**
+         * Gets the value of the height property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getHeight() {
+            return height;
+        }
 
-    /**
-     * Gets the value of the height property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getHeight()
-    {
-      return height;
-    }
+        /**
+         * Sets the value of the height property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setHeight(Integer value) {
+            this.height = value;
+        }
 
-    /**
-     * Sets the value of the height property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setHeight(Integer value)
-    {
-      this.height = value;
-    }
+        /**
+         * Gets the value of the xpos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getXpos() {
+            return xpos;
+        }
 
-    /**
-     * Gets the value of the xpos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getXpos()
-    {
-      return xpos;
-    }
+        /**
+         * Sets the value of the xpos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setXpos(Integer value) {
+            this.xpos = value;
+        }
 
-    /**
-     * Sets the value of the xpos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setXpos(Integer value)
-    {
-      this.xpos = value;
-    }
+        /**
+         * Gets the value of the ypos property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getYpos() {
+            return ypos;
+        }
 
-    /**
-     * Gets the value of the ypos property.
-     * 
-     * @return possible object is {@link Integer }
-     * 
-     */
-    public Integer getYpos()
-    {
-      return ypos;
-    }
+        /**
+         * Sets the value of the ypos property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Integer }
+         *     
+         */
+        public void setYpos(Integer value) {
+            this.ypos = value;
+        }
 
-    /**
-     * Sets the value of the ypos property.
-     * 
-     * @param value
-     *          allowed object is {@link Integer }
-     * 
-     */
-    public void setYpos(Integer value)
-    {
-      this.ypos = value;
-    }
 
-    /**
-     * 

-     * Java class for anonymous complex type.
-     * 
-     * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-     *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </extension>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class CalcIdParam extends WebServiceParameterSet
-    {
-
-      @XmlAttribute(name = "calcId", required = true)
-      protected String calcId;
-
-      @XmlAttribute(name = "needsUpdate")
-      protected Boolean needsUpdate;
-
-      @XmlAttribute(name = "autoUpdate", required = true)
-      protected boolean autoUpdate;
-
-      /**
-       * Gets the value of the calcId property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getCalcId()
-      {
-        return calcId;
-      }
-
-      /**
-       * Sets the value of the calcId property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setCalcId(String value)
-      {
-        this.calcId = value;
-      }
-
-      /**
-       * Gets the value of the needsUpdate property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public boolean isNeedsUpdate()
-      {
-        if (needsUpdate == null)
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+         *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     </extension>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class CalcIdParam
+            extends WebServiceParameterSet
         {
-          return false;
+
+            @XmlAttribute(name = "calcId", required = true)
+            protected String calcId;
+            @XmlAttribute(name = "needsUpdate")
+            protected Boolean needsUpdate;
+            @XmlAttribute(name = "autoUpdate", required = true)
+            protected boolean autoUpdate;
+
+            /**
+             * Gets the value of the calcId property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getCalcId() {
+                return calcId;
+            }
+
+            /**
+             * Sets the value of the calcId property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setCalcId(String value) {
+                this.calcId = value;
+            }
+
+            /**
+             * Gets the value of the needsUpdate property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public boolean isNeedsUpdate() {
+                if (needsUpdate == null) {
+                    return false;
+                } else {
+                    return needsUpdate;
+                }
+            }
+
+            /**
+             * Sets the value of the needsUpdate property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setNeedsUpdate(Boolean value) {
+                this.needsUpdate = value;
+            }
+
+            /**
+             * Gets the value of the autoUpdate property.
+             * 
+             */
+            public boolean isAutoUpdate() {
+                return autoUpdate;
+            }
+
+            /**
+             * Sets the value of the autoUpdate property.
+             * 
+             */
+            public void setAutoUpdate(boolean value) {
+                this.autoUpdate = value;
+            }
+
         }
-        else
-        {
-          return needsUpdate;
-        }
-      }
-
-      /**
-       * Sets the value of the needsUpdate property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setNeedsUpdate(Boolean value)
-      {
-        this.needsUpdate = value;
-      }
-
-      /**
-       * Gets the value of the autoUpdate property.
-       * 
-       */
-      public boolean isAutoUpdate()
-      {
-        return autoUpdate;
-      }
-
-      /**
-       * Sets the value of the autoUpdate property.
-       * 
-       */
-      public void setAutoUpdate(boolean value)
-      {
-        this.autoUpdate = value;
-      }
 
-    }
 
-    /**
-     * 

-     * Java class for anonymous complex type.
-     * 
-     * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class HiddenColumns
-    {
-
-      @XmlAttribute(name = "start")
-      protected Integer start;
-
-      @XmlAttribute(name = "end")
-      protected Integer end;
-
-      /**
-       * Gets the value of the start property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getStart()
-      {
-        return start;
-      }
-
-      /**
-       * Sets the value of the start property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setStart(Integer value)
-      {
-        this.start = value;
-      }
-
-      /**
-       * Gets the value of the end property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getEnd()
-      {
-        return end;
-      }
-
-      /**
-       * Sets the value of the end property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setEnd(Integer value)
-      {
-        this.end = value;
-      }
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class HiddenColumns {
+
+            @XmlAttribute(name = "start")
+            protected Integer start;
+            @XmlAttribute(name = "end")
+            protected Integer end;
+
+            /**
+             * Gets the value of the start property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getStart() {
+                return start;
+            }
+
+            /**
+             * Sets the value of the start property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setStart(Integer value) {
+                this.start = value;
+            }
+
+            /**
+             * Gets the value of the end property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getEnd() {
+                return end;
+            }
+
+            /**
+             * Sets the value of the end property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setEnd(Integer value) {
+                this.end = value;
+            }
 
-    }
+        }
 
-    /**
-     * 

-     * Java class for anonymous complex type.
-     * 
-     * 

-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * 
-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     * 

-     * 
-     * 
-     */
-    @XmlAccessorType(XmlAccessType.FIELD)
-    @XmlType(name = "")
-    public static class Overview
-    {
-
-      @XmlAttribute(name = "showHidden")
-      protected Boolean showHidden;
-
-      @XmlAttribute(name = "residueColour")
-      protected Integer residueColour;
-
-      @XmlAttribute(name = "gapColour")
-      protected Integer gapColour;
-
-      @XmlAttribute(name = "hiddenColour")
-      protected Integer hiddenColour;
-
-      @XmlAttribute(name = "title")
-      protected String title;
-
-      @XmlAttribute(name = "width")
-      protected Integer width;
-
-      @XmlAttribute(name = "height")
-      protected Integer height;
-
-      @XmlAttribute(name = "xpos")
-      protected Integer xpos;
-
-      @XmlAttribute(name = "ypos")
-      protected Integer ypos;
-
-      /**
-       * Gets the value of the showHidden property.
-       * 
-       * @return possible object is {@link Boolean }
-       * 
-       */
-      public Boolean isShowHidden()
-      {
-        return showHidden;
-      }
-
-      /**
-       * Sets the value of the showHidden property.
-       * 
-       * @param value
-       *          allowed object is {@link Boolean }
-       * 
-       */
-      public void setShowHidden(Boolean value)
-      {
-        this.showHidden = value;
-      }
-
-      /**
-       * Gets the value of the residueColour property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getResidueColour()
-      {
-        return residueColour;
-      }
-
-      /**
-       * Sets the value of the residueColour property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setResidueColour(Integer value)
-      {
-        this.residueColour = value;
-      }
-
-      /**
-       * Gets the value of the gapColour property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getGapColour()
-      {
-        return gapColour;
-      }
-
-      /**
-       * Sets the value of the gapColour property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setGapColour(Integer value)
-      {
-        this.gapColour = value;
-      }
-
-      /**
-       * Gets the value of the hiddenColour property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getHiddenColour()
-      {
-        return hiddenColour;
-      }
-
-      /**
-       * Sets the value of the hiddenColour property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setHiddenColour(Integer value)
-      {
-        this.hiddenColour = value;
-      }
-
-      /**
-       * Gets the value of the title property.
-       * 
-       * @return possible object is {@link String }
-       * 
-       */
-      public String getTitle()
-      {
-        return title;
-      }
-
-      /**
-       * Sets the value of the title property.
-       * 
-       * @param value
-       *          allowed object is {@link String }
-       * 
-       */
-      public void setTitle(String value)
-      {
-        this.title = value;
-      }
-
-      /**
-       * Gets the value of the width property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getWidth()
-      {
-        return width;
-      }
-
-      /**
-       * Sets the value of the width property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setWidth(Integer value)
-      {
-        this.width = value;
-      }
-
-      /**
-       * Gets the value of the height property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getHeight()
-      {
-        return height;
-      }
-
-      /**
-       * Sets the value of the height property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setHeight(Integer value)
-      {
-        this.height = value;
-      }
-
-      /**
-       * Gets the value of the xpos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getXpos()
-      {
-        return xpos;
-      }
-
-      /**
-       * Sets the value of the xpos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setXpos(Integer value)
-      {
-        this.xpos = value;
-      }
-
-      /**
-       * Gets the value of the ypos property.
-       * 
-       * @return possible object is {@link Integer }
-       * 
-       */
-      public Integer getYpos()
-      {
-        return ypos;
-      }
-
-      /**
-       * Sets the value of the ypos property.
-       * 
-       * @param value
-       *          allowed object is {@link Integer }
-       * 
-       */
-      public void setYpos(Integer value)
-      {
-        this.ypos = value;
-      }
 
-    }
+        /**
+         * 
Java class for anonymous complex type.
+         * 
+         * 
The following schema fragment specifies the expected content contained within this class.
+         * 
+         * 
+         * <complexType>
+         *   <complexContent>
+         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       <attGroup ref="{www.jalview.org}swingwindow"/>
+         *       <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *     </restriction>
+         *   </complexContent>
+         * </complexType>
+         * 

+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "")
+        public static class Overview {
+
+            @XmlAttribute(name = "showHidden")
+            protected Boolean showHidden;
+            @XmlAttribute(name = "residueColour")
+            protected Integer residueColour;
+            @XmlAttribute(name = "gapColour")
+            protected Integer gapColour;
+            @XmlAttribute(name = "hiddenColour")
+            protected Integer hiddenColour;
+            @XmlAttribute(name = "title")
+            protected String title;
+            @XmlAttribute(name = "width")
+            protected Integer width;
+            @XmlAttribute(name = "height")
+            protected Integer height;
+            @XmlAttribute(name = "xpos")
+            protected Integer xpos;
+            @XmlAttribute(name = "ypos")
+            protected Integer ypos;
+
+            /**
+             * Gets the value of the showHidden property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Boolean }
+             *     
+             */
+            public Boolean isShowHidden() {
+                return showHidden;
+            }
+
+            /**
+             * Sets the value of the showHidden property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Boolean }
+             *     
+             */
+            public void setShowHidden(Boolean value) {
+                this.showHidden = value;
+            }
+
+            /**
+             * Gets the value of the residueColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getResidueColour() {
+                return residueColour;
+            }
+
+            /**
+             * Sets the value of the residueColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setResidueColour(Integer value) {
+                this.residueColour = value;
+            }
+
+            /**
+             * Gets the value of the gapColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getGapColour() {
+                return gapColour;
+            }
+
+            /**
+             * Sets the value of the gapColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setGapColour(Integer value) {
+                this.gapColour = value;
+            }
+
+            /**
+             * Gets the value of the hiddenColour property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getHiddenColour() {
+                return hiddenColour;
+            }
+
+            /**
+             * Sets the value of the hiddenColour property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setHiddenColour(Integer value) {
+                this.hiddenColour = value;
+            }
+
+            /**
+             * Gets the value of the title property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link String }
+             *     
+             */
+            public String getTitle() {
+                return title;
+            }
+
+            /**
+             * Sets the value of the title property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link String }
+             *     
+             */
+            public void setTitle(String value) {
+                this.title = value;
+            }
+
+            /**
+             * Gets the value of the width property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getWidth() {
+                return width;
+            }
+
+            /**
+             * Sets the value of the width property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setWidth(Integer value) {
+                this.width = value;
+            }
+
+            /**
+             * Gets the value of the height property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getHeight() {
+                return height;
+            }
+
+            /**
+             * Sets the value of the height property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setHeight(Integer value) {
+                this.height = value;
+            }
+
+            /**
+             * Gets the value of the xpos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getXpos() {
+                return xpos;
+            }
+
+            /**
+             * Sets the value of the xpos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setXpos(Integer value) {
+                this.xpos = value;
+            }
+
+            /**
+             * Gets the value of the ypos property.
+             * 
+             * @return
+             *     possible object is
+             *     {@link Integer }
+             *     
+             */
+            public Integer getYpos() {
+                return ypos;
+            }
+
+            /**
+             * Sets the value of the ypos property.
+             * 
+             * @param value
+             *     allowed object is
+             *     {@link Integer }
+             *     
+             */
+            public void setYpos(Integer value) {
+                this.ypos = value;
+            }
+
+        }
 
-  }
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java
index e4b160f..481a7b7 100644
--- a/src/jalview/xml/binding/jalview/JalviewUserColours.java
+++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for JalviewUserColours complex type.
+ * 
Java class for JalviewUserColours complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="JalviewUserColours">
@@ -72,556 +71,542 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "JalviewUserColours",
-  namespace = "www.jalview.org/colours",
-  propOrder =
-  { "version", "colour", "filter" })
-public class JalviewUserColours
-{
-
-  @XmlElement(name = "Version", namespace = "")
-  protected String version;
-
-  @XmlElement(namespace = "")
-  protected List colour;
-
-  @XmlElement(namespace = "")
-  protected List filter;
-
-  @XmlAttribute(name = "schemeName")
-  protected String schemeName;
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the colour property.
-   * 
-   * 

-   * 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 set method
-   * for the colour property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getColour().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewUserColours.Colour }
-   * 
-   * 
-   */
-  public List getColour()
-  {
-    if (colour == null)
-    {
-      colour = new ArrayList();
-    }
-    return this.colour;
-  }
-
-  /**
-   * Gets the value of the filter property.
-   * 
-   * 

-   * 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 set method
-   * for the filter property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getFilter().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link JalviewUserColours.Filter }
-   * 
-   * 
-   */
-  public List getFilter()
-  {
-    if (filter == null)
-    {
-      filter = new ArrayList();
-    }
-    return this.filter;
-  }
-
-  /**
-   * Gets the value of the schemeName property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSchemeName()
-  {
-    return schemeName;
-  }
-
-  /**
-   * Sets the value of the schemeName property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSchemeName(String value)
-  {
-    this.schemeName = value;
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-   *       </sequence>
-   *       <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-   *       <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
-   *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "attributeName" })
-  public static class Colour
-  {
-
+@XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
+    "version",
+    "colour",
+    "filter"
+})
+public class JalviewUserColours {
+
+    @XmlElement(name = "Version", namespace = "")
+    protected String version;
     @XmlElement(namespace = "")
-    protected List attributeName;
-
-    @XmlAttribute(name = "Name")
-    protected String name;
-
-    @XmlAttribute(name = "RGB", required = true)
-    protected String rgb;
-
-    @XmlAttribute(name = "minRGB")
-    protected String minRGB;
-
-    @XmlAttribute(name = "noValueColour")
-    protected NoValueColour noValueColour;
-
-    @XmlAttribute(name = "threshType")
-    protected ThresholdType threshType;
-
-    @XmlAttribute(name = "threshold")
-    protected Float threshold;
-
-    @XmlAttribute(name = "max")
-    protected Float max;
-
-    @XmlAttribute(name = "min")
-    protected Float min;
-
-    @XmlAttribute(name = "colourByLabel")
-    protected Boolean colourByLabel;
-
-    @XmlAttribute(name = "autoScale")
-    protected Boolean autoScale;
-
-    /**
-     * Gets the value of the attributeName property.
-     * 
-     * 

-     * 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
-     * set method for the attributeName property.
-     * 
-     * 

-     * For example, to add a new item, do as follows:
-     * 
-     * 
-     * getAttributeName().add(newItem);
-     * 

-     * 
-     * 
-     * 

-     * Objects of the following type(s) are allowed in the list {@link String }
-     * 
-     * 
-     */
-    public List getAttributeName()
-    {
-      if (attributeName == null)
-      {
-        attributeName = new ArrayList();
-      }
-      return this.attributeName;
-    }
-
-    /**
-     * Gets the value of the name property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getName()
-    {
-      return name;
-    }
-
-    /**
-     * Sets the value of the name property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setName(String value)
-    {
-      this.name = value;
-    }
-
-    /**
-     * Gets the value of the rgb property.
-     * 
-     * @return possible object is {@link String }
-     * 
-     */
-    public String getRGB()
-    {
-      return rgb;
-    }
-
-    /**
-     * Sets the value of the rgb property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setRGB(String value)
-    {
-      this.rgb = value;
-    }
+    protected List colour;
+    @XmlElement(namespace = "")
+    protected List filter;
+    @XmlAttribute(name = "schemeName")
+    protected String schemeName;
 
     /**
-     * Gets the value of the minRGB property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the version property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getMinRGB()
-    {
-      return minRGB;
+    public String getVersion() {
+        return version;
     }
 
     /**
-     * Sets the value of the minRGB property.
+     * Sets the value of the version property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setMinRGB(String value)
-    {
-      this.minRGB = value;
-    }
-
-    /**
-     * Gets the value of the noValueColour property.
-     * 
-     * @return possible object is {@link NoValueColour }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public NoValueColour getNoValueColour()
-    {
-      if (noValueColour == null)
-      {
-        return NoValueColour.MIN;
-      }
-      else
-      {
-        return noValueColour;
-      }
+    public void setVersion(String value) {
+        this.version = value;
     }
 
     /**
-     * Sets the value of the noValueColour property.
-     * 
-     * @param value
-     *          allowed object is {@link NoValueColour }
+     * Gets the value of the colour property.
      * 
-     */
-    public void setNoValueColour(NoValueColour value)
-    {
-      this.noValueColour = value;
-    }
-
-    /**
-     * Gets the value of the threshType property.
-     * 
-     * @return possible object is {@link ThresholdType }
+     * 

+     * 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 set method for the colour property.
      * 
-     */
-    public ThresholdType getThreshType()
-    {
-      return threshType;
-    }
-
-    /**
-     * Sets the value of the threshType property.
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getColour().add(newItem);
+     * 

      * 
-     * @param value
-     *          allowed object is {@link ThresholdType }
      * 
-     */
-    public void setThreshType(ThresholdType value)
-    {
-      this.threshType = value;
-    }
-
-    /**
-     * Gets the value of the threshold property.
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewUserColours.Colour }
      * 
-     * @return possible object is {@link Float }
      * 
      */
-    public Float getThreshold()
-    {
-      return threshold;
+    public List getColour() {
+        if (colour == null) {
+            colour = new ArrayList();
+        }
+        return this.colour;
     }
 
     /**
-     * Sets the value of the threshold property.
+     * Gets the value of the filter property.
      * 
-     * @param value
-     *          allowed object is {@link Float }
+     * 

+     * 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 set method for the filter property.
      * 
-     */
-    public void setThreshold(Float value)
-    {
-      this.threshold = value;
-    }
-
-    /**
-     * Gets the value of the max property.
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getFilter().add(newItem);
+     * 

      * 
-     * @return possible object is {@link Float }
      * 
-     */
-    public Float getMax()
-    {
-      return max;
-    }
-
-    /**
-     * Sets the value of the max property.
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewUserColours.Filter }
      * 
-     * @param value
-     *          allowed object is {@link Float }
      * 
      */
-    public void setMax(Float value)
-    {
-      this.max = value;
+    public List getFilter() {
+        if (filter == null) {
+            filter = new ArrayList();
+        }
+        return this.filter;
     }
 
     /**
-     * Gets the value of the min property.
-     * 
-     * @return possible object is {@link Float }
+     * Gets the value of the schemeName property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public Float getMin()
-    {
-      return min;
+    public String getSchemeName() {
+        return schemeName;
     }
 
     /**
-     * Sets the value of the min property.
+     * Sets the value of the schemeName property.
      * 
      * @param value
-     *          allowed object is {@link Float }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setMin(Float value)
-    {
-      this.min = value;
+    public void setSchemeName(String value) {
+        this.schemeName = value;
     }
 
-    /**
-     * Gets the value of the colourByLabel property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public Boolean isColourByLabel()
-    {
-      return colourByLabel;
-    }
 
     /**
-     * Sets the value of the colourByLabel property.
+     * 
Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setColourByLabel(Boolean value)
-    {
-      this.colourByLabel = value;
-    }
-
-    /**
-     * Gets the value of the autoScale property.
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *       <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

      * 
-     * @return possible object is {@link Boolean }
      * 
      */
-    public Boolean isAutoScale()
-    {
-      return autoScale;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "attributeName"
+    })
+    public static class Colour {
+
+        @XmlElement(namespace = "")
+        protected List attributeName;
+        @XmlAttribute(name = "Name")
+        protected String name;
+        @XmlAttribute(name = "RGB", required = true)
+        protected String rgb;
+        @XmlAttribute(name = "minRGB")
+        protected String minRGB;
+        @XmlAttribute(name = "noValueColour")
+        protected NoValueColour noValueColour;
+        @XmlAttribute(name = "threshType")
+        protected ThresholdType threshType;
+        @XmlAttribute(name = "threshold")
+        protected Float threshold;
+        @XmlAttribute(name = "max")
+        protected Float max;
+        @XmlAttribute(name = "min")
+        protected Float min;
+        @XmlAttribute(name = "colourByLabel")
+        protected Boolean colourByLabel;
+        @XmlAttribute(name = "autoScale")
+        protected Boolean autoScale;
+
+        /**
+         * Gets the value of the attributeName property.
+         * 
+         * 

+         * 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 set method for the attributeName property.
+         * 
+         * 

+         * For example, to add a new item, do as follows:
+         * 
+         *    getAttributeName().add(newItem);
+         * 

+         * 
+         * 
+         * 

+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List getAttributeName() {
+            if (attributeName == null) {
+                attributeName = new ArrayList();
+            }
+            return this.attributeName;
+        }
+
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
+
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
+
+        /**
+         * Gets the value of the rgb property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getRGB() {
+            return rgb;
+        }
+
+        /**
+         * Sets the value of the rgb property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setRGB(String value) {
+            this.rgb = value;
+        }
+
+        /**
+         * Gets the value of the minRGB property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getMinRGB() {
+            return minRGB;
+        }
+
+        /**
+         * Sets the value of the minRGB property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setMinRGB(String value) {
+            this.minRGB = value;
+        }
+
+        /**
+         * Gets the value of the noValueColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link NoValueColour }
+         *     
+         */
+        public NoValueColour getNoValueColour() {
+            if (noValueColour == null) {
+                return NoValueColour.MIN;
+            } else {
+                return noValueColour;
+            }
+        }
+
+        /**
+         * Sets the value of the noValueColour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link NoValueColour }
+         *     
+         */
+        public void setNoValueColour(NoValueColour value) {
+            this.noValueColour = value;
+        }
+
+        /**
+         * Gets the value of the threshType property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link ThresholdType }
+         *     
+         */
+        public ThresholdType getThreshType() {
+            return threshType;
+        }
+
+        /**
+         * Sets the value of the threshType property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link ThresholdType }
+         *     
+         */
+        public void setThreshType(ThresholdType value) {
+            this.threshType = value;
+        }
+
+        /**
+         * Gets the value of the threshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getThreshold() {
+            return threshold;
+        }
+
+        /**
+         * Sets the value of the threshold property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setThreshold(Float value) {
+            this.threshold = value;
+        }
+
+        /**
+         * Gets the value of the max property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getMax() {
+            return max;
+        }
+
+        /**
+         * Sets the value of the max property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setMax(Float value) {
+            this.max = value;
+        }
+
+        /**
+         * Gets the value of the min property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Float }
+         *     
+         */
+        public Float getMin() {
+            return min;
+        }
+
+        /**
+         * Sets the value of the min property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Float }
+         *     
+         */
+        public void setMin(Float value) {
+            this.min = value;
+        }
+
+        /**
+         * Gets the value of the colourByLabel property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isColourByLabel() {
+            return colourByLabel;
+        }
+
+        /**
+         * Sets the value of the colourByLabel property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setColourByLabel(Boolean value) {
+            this.colourByLabel = value;
+        }
+
+        /**
+         * Gets the value of the autoScale property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isAutoScale() {
+            return autoScale;
+        }
+
+        /**
+         * Sets the value of the autoScale property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setAutoScale(Boolean value) {
+            this.autoScale = value;
+        }
 
-    /**
-     * Sets the value of the autoScale property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setAutoScale(Boolean value)
-    {
-      this.autoScale = value;
     }
 
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
-   *       </sequence>
-   *       <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "matcherSet" })
-  public static class Filter
-  {
-
-    @XmlElement(namespace = "", required = true)
-    protected FeatureMatcherSet matcherSet;
-
-    @XmlAttribute(name = "featureType", required = true)
-    protected String featureType;
-
-    /**
-     * Gets the value of the matcherSet property.
-     * 
-     * @return possible object is {@link FeatureMatcherSet }
-     * 
-     */
-    public FeatureMatcherSet getMatcherSet()
-    {
-      return matcherSet;
-    }
 
     /**
-     * Sets the value of the matcherSet property.
+     * 
Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link FeatureMatcherSet }
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setMatcherSet(FeatureMatcherSet value)
-    {
-      this.matcherSet = value;
-    }
-
-    /**
-     * Gets the value of the featureType property.
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+     *       </sequence>
+     *       <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getFeatureType()
-    {
-      return featureType;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "matcherSet"
+    })
+    public static class Filter {
+
+        @XmlElement(namespace = "", required = true)
+        protected FeatureMatcherSet matcherSet;
+        @XmlAttribute(name = "featureType", required = true)
+        protected String featureType;
+
+        /**
+         * Gets the value of the matcherSet property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link FeatureMatcherSet }
+         *     
+         */
+        public FeatureMatcherSet getMatcherSet() {
+            return matcherSet;
+        }
+
+        /**
+         * Sets the value of the matcherSet property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link FeatureMatcherSet }
+         *     
+         */
+        public void setMatcherSet(FeatureMatcherSet value) {
+            this.matcherSet = value;
+        }
+
+        /**
+         * Gets the value of the featureType property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getFeatureType() {
+            return featureType;
+        }
+
+        /**
+         * Sets the value of the featureType property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setFeatureType(String value) {
+            this.featureType = value;
+        }
 
-    /**
-     * Sets the value of the featureType property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
-     * 
-     */
-    public void setFeatureType(String value)
-    {
-      this.featureType = value;
     }
 
-  }
-
 }
diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java
index 1f16680..498e6e2 100644
--- a/src/jalview/xml/binding/jalview/MapListType.java
+++ b/src/jalview/xml/binding/jalview/MapListType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.math.BigInteger;
@@ -17,17 +18,15 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * 
- * This effectively represents a java.util.MapList object
+ * 				This effectively represents a java.util.MapList object
+ * 			
  * 
+ * 
Java class for mapListType complex type.
  * 
- * 

- * Java class for mapListType complex type.
- * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="mapListType">
@@ -65,271 +64,252 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "mapListType", propOrder = { "mapListFrom", "mapListTo" })
-@XmlSeeAlso({ Mapping.class })
-public class MapListType
-{
-
-  protected List mapListFrom;
-
-  protected List mapListTo;
-
-  @XmlAttribute(name = "mapFromUnit", required = true)
-  @XmlSchemaType(name = "positiveInteger")
-  protected BigInteger mapFromUnit;
-
-  @XmlAttribute(name = "mapToUnit", required = true)
-  @XmlSchemaType(name = "positiveInteger")
-  protected BigInteger mapToUnit;
-
-  /**
-   * Gets the value of the mapListFrom property.
-   * 
-   * 

-   * 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 set method
-   * for the mapListFrom property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getMapListFrom().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link MapListType.MapListFrom }
-   * 
-   * 
-   */
-  public List getMapListFrom()
-  {
-    if (mapListFrom == null)
-    {
-      mapListFrom = new ArrayList();
-    }
-    return this.mapListFrom;
-  }
-
-  /**
-   * Gets the value of the mapListTo property.
-   * 
-   * 

-   * 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 set method
-   * for the mapListTo property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getMapListTo().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link MapListType.MapListTo }
-   * 
-   * 
-   */
-  public List getMapListTo()
-  {
-    if (mapListTo == null)
-    {
-      mapListTo = new ArrayList();
-    }
-    return this.mapListTo;
-  }
-
-  /**
-   * Gets the value of the mapFromUnit property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getMapFromUnit()
-  {
-    return mapFromUnit;
-  }
-
-  /**
-   * Sets the value of the mapFromUnit property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setMapFromUnit(BigInteger value)
-  {
-    this.mapFromUnit = value;
-  }
+@XmlType(name = "mapListType", propOrder = {
+    "mapListFrom",
+    "mapListTo"
+})
+@XmlSeeAlso({
+    Mapping.class
+})
+public class MapListType {
 
-  /**
-   * Gets the value of the mapToUnit property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getMapToUnit()
-  {
-    return mapToUnit;
-  }
-
-  /**
-   * Sets the value of the mapToUnit property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setMapToUnit(BigInteger value)
-  {
-    this.mapToUnit = value;
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class MapListFrom
-  {
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
+    protected List mapListFrom;
+    protected List mapListTo;
+    @XmlAttribute(name = "mapFromUnit", required = true)
+    @XmlSchemaType(name = "positiveInteger")
+    protected BigInteger mapFromUnit;
+    @XmlAttribute(name = "mapToUnit", required = true)
+    @XmlSchemaType(name = "positiveInteger")
+    protected BigInteger mapToUnit;
 
     /**
-     * Gets the value of the start property.
+     * Gets the value of the mapListFrom property.
+     * 
+     * 

+     * 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 set method for the mapListFrom property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getMapListFrom().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link MapListType.MapListFrom }
+     * 
      * 
      */
-    public int getStart()
-    {
-      return start;
+    public List getMapListFrom() {
+        if (mapListFrom == null) {
+            mapListFrom = new ArrayList();
+        }
+        return this.mapListFrom;
     }
 
     /**
-     * Sets the value of the start property.
+     * Gets the value of the mapListTo property.
+     * 
+     * 

+     * 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 set method for the mapListTo property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getMapListTo().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link MapListType.MapListTo }
+     * 
      * 
      */
-    public void setStart(int value)
-    {
-      this.start = value;
+    public List getMapListTo() {
+        if (mapListTo == null) {
+            mapListTo = new ArrayList();
+        }
+        return this.mapListTo;
     }
 
     /**
-     * Gets the value of the end property.
+     * Gets the value of the mapFromUnit property.
      * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
      */
-    public int getEnd()
-    {
-      return end;
+    public BigInteger getMapFromUnit() {
+        return mapFromUnit;
     }
 
     /**
-     * Sets the value of the end property.
+     * Sets the value of the mapFromUnit property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
      */
-    public void setEnd(int value)
-    {
-      this.end = value;
+    public void setMapFromUnit(BigInteger value) {
+        this.mapFromUnit = value;
     }
 
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class MapListTo
-  {
-
-    @XmlAttribute(name = "start", required = true)
-    protected int start;
-
-    @XmlAttribute(name = "end", required = true)
-    protected int end;
-
     /**
-     * Gets the value of the start property.
+     * Gets the value of the mapToUnit property.
      * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
      */
-    public int getStart()
-    {
-      return start;
+    public BigInteger getMapToUnit() {
+        return mapToUnit;
     }
 
     /**
-     * Sets the value of the start property.
+     * Sets the value of the mapToUnit property.
      * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
      */
-    public void setStart(int value)
-    {
-      this.start = value;
+    public void setMapToUnit(BigInteger value) {
+        this.mapToUnit = value;
     }
 
+
     /**
-     * Gets the value of the end property.
+     * 
Java class for anonymous complex type.
+     * 
+     * 
The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
      * 
      */
-    public int getEnd()
-    {
-      return end;
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class MapListFrom {
+
+        @XmlAttribute(name = "start", required = true)
+        protected int start;
+        @XmlAttribute(name = "end", required = true)
+        protected int end;
+
+        /**
+         * Gets the value of the start property.
+         * 
+         */
+        public int getStart() {
+            return start;
+        }
+
+        /**
+         * Sets the value of the start property.
+         * 
+         */
+        public void setStart(int value) {
+            this.start = value;
+        }
+
+        /**
+         * Gets the value of the end property.
+         * 
+         */
+        public int getEnd() {
+            return end;
+        }
+
+        /**
+         * Sets the value of the end property.
+         * 
+         */
+        public void setEnd(int value) {
+            this.end = value;
+        }
+
     }
 
+
     /**
-     * Sets the value of the end property.
+     * 
Java class for anonymous complex type.
+     * 
+     * 
The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
      * 
      */
-    public void setEnd(int value)
-    {
-      this.end = value;
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class MapListTo {
 
-  }
+        @XmlAttribute(name = "start", required = true)
+        protected int start;
+        @XmlAttribute(name = "end", required = true)
+        protected int end;
+
+        /**
+         * Gets the value of the start property.
+         * 
+         */
+        public int getStart() {
+            return start;
+        }
+
+        /**
+         * Sets the value of the start property.
+         * 
+         */
+        public void setStart(int value) {
+            this.start = value;
+        }
+
+        /**
+         * Gets the value of the end property.
+         * 
+         */
+        public int getEnd() {
+            return end;
+        }
+
+        /**
+         * Sets the value of the end property.
+         * 
+         */
+        public void setEnd(int value) {
+            this.end = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/MapOnAMatrixType.java b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java
new file mode 100644
index 0000000..91ac690
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/MapOnAMatrixType.java
@@ -0,0 +1,156 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See http://java.sun.com/xml/jaxb 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.util.ArrayList;
+import java.util.List;
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * 
Java class for MapOnAMatrixType complex type.
+ * 
+ * 
The following schema fragment specifies the expected content contained within this class.
+ * 
+ * 
+ * <complexType name="MapOnAMatrixType">
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="property" type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="mapping" type="{www.vamsas.ac.uk/jalview/version2}mapListType" minOccurs="0"/>
+ *       </sequence>
+ *       <attribute name="matrix" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ * 

+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "MapOnAMatrixType", propOrder = {
+    "property",
+    "mapping"
+})
+public class MapOnAMatrixType {
+
+    protected List property;
+    protected MapListType mapping;
+    @XmlAttribute(name = "matrix", required = true)
+    protected String matrix;
+    @XmlAttribute(name = "id")
+    protected String id;
+
+    /**
+     * Gets the value of the property property.
+     * 
+     * 

+     * 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 set method for the property property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getProperty().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link Property }
+     * 
+     * 
+     */
+    public List getProperty() {
+        if (property == null) {
+            property = new ArrayList();
+        }
+        return this.property;
+    }
+
+    /**
+     * Gets the value of the mapping property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link MapListType }
+     *     
+     */
+    public MapListType getMapping() {
+        return mapping;
+    }
+
+    /**
+     * Sets the value of the mapping property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link MapListType }
+     *     
+     */
+    public void setMapping(MapListType value) {
+        this.mapping = value;
+    }
+
+    /**
+     * Gets the value of the matrix property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getMatrix() {
+        return matrix;
+    }
+
+    /**
+     * Sets the value of the matrix property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setMatrix(String value) {
+        this.matrix = value;
+    }
+
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
+
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java
index 69bf01d..a3ce15f 100644
--- a/src/jalview/xml/binding/jalview/Mapping.java
+++ b/src/jalview/xml/binding/jalview/Mapping.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -14,19 +15,17 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * 
- * Represent the jalview.datamodel.Mapping object - it also provides a way of
- * storing sequences that are mapped 'to' without adding them to the sequence
- * set (which will mean they are then added to the alignment too).
- * 
+ * 					Represent the jalview.datamodel.Mapping object - it also provides
+ * 					a way of storing sequences that are mapped 'to' without adding them
+ * 					to the sequence set (which will mean they are then added to the alignment too).
+ * 				
  * 
- * 

- * Java class for anonymous complex type.
+ * 
Java class for anonymous complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType>
@@ -52,86 +51,91 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "sequence", "dseqFor" })
+@XmlType(name = "", propOrder = {
+    "sequence",
+    "dseqFor"
+})
 @XmlRootElement(name = "Mapping")
-public class Mapping extends MapListType
+public class Mapping
+    extends MapListType
 {
 
-  @XmlElement(name = "Sequence")
-  protected Sequence sequence;
-
-  protected String dseqFor;
-
-  @XmlAttribute(name = "mappingType")
-  protected String mappingType;
+    @XmlElement(name = "Sequence")
+    protected Sequence sequence;
+    protected String dseqFor;
+    @XmlAttribute(name = "mappingType")
+    protected String mappingType;
 
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link Sequence }
-   * 
-   */
-  public Sequence getSequence()
-  {
-    return sequence;
-  }
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Sequence }
+     *     
+     */
+    public Sequence getSequence() {
+        return sequence;
+    }
 
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link Sequence }
-   * 
-   */
-  public void setSequence(Sequence value)
-  {
-    this.sequence = value;
-  }
+    /**
+     * Sets the value of the sequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Sequence }
+     *     
+     */
+    public void setSequence(Sequence value) {
+        this.sequence = value;
+    }
 
-  /**
-   * Gets the value of the dseqFor property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDseqFor()
-  {
-    return dseqFor;
-  }
+    /**
+     * Gets the value of the dseqFor property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDseqFor() {
+        return dseqFor;
+    }
 
-  /**
-   * Sets the value of the dseqFor property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDseqFor(String value)
-  {
-    this.dseqFor = value;
-  }
+    /**
+     * Sets the value of the dseqFor property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDseqFor(String value) {
+        this.dseqFor = value;
+    }
 
-  /**
-   * Gets the value of the mappingType property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getMappingType()
-  {
-    return mappingType;
-  }
+    /**
+     * Gets the value of the mappingType property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getMappingType() {
+        return mappingType;
+    }
 
-  /**
-   * Sets the value of the mappingType property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setMappingType(String value)
-  {
-    this.mappingType = value;
-  }
+    /**
+     * Sets the value of the mappingType property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setMappingType(String value) {
+        this.mappingType = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/MatrixType.java b/src/jalview/xml/binding/jalview/MatrixType.java
index c405597..973456e 100644
--- a/src/jalview/xml/binding/jalview/MatrixType.java
+++ b/src/jalview/xml/binding/jalview/MatrixType.java
@@ -2,7 +2,7 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
 
@@ -19,12 +19,9 @@ import javax.xml.bind.annotation.XmlType;
 
 
 /**
- * 

- * Java class for MatrixType complex type.
+ * 
Java class for MatrixType complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="MatrixType">
@@ -42,7 +39,7 @@ import javax.xml.bind.annotation.XmlType;
  *       <attribute name="cols" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
  *       <attribute name="treeMethod" type="{http://www.w3.org/2001/XMLSchema}string" />
  *       <attribute name="cutHeight" type="{http://www.w3.org/2001/XMLSchema}double" />
- *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
  *     </restriction>
  *   </complexContent>
  * </complexType>
@@ -51,317 +48,311 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "MatrixType",
-  propOrder =
-  { "elements", "groups", "newick", "property", "mapping" })
-public class MatrixType
-{
-
-  @XmlElement(required = true)
-  protected String elements;
-
-  protected List groups;
-
-  protected List newick;
-
-  protected List property;
-
-  protected MapListType mapping;
-
-  @XmlAttribute(name = "type", required = true)
-  protected String type;
-
-  @XmlAttribute(name = "rows", required = true)
-  protected BigInteger rows;
-
-  @XmlAttribute(name = "cols", required = true)
-  protected BigInteger cols;
-
-  @XmlAttribute(name = "treeMethod")
-  protected String treeMethod;
-
-  @XmlAttribute(name = "cutHeight")
-  protected Double cutHeight;
-
-  @XmlAttribute(name = "id")
-  protected String id;
-
-  /**
-   * Gets the value of the elements property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getElements()
-  {
-    return elements;
-  }
+@XmlType(name = "MatrixType", propOrder = {
+    "elements",
+    "groups",
+    "newick",
+    "property",
+    "mapping"
+})
+public class MatrixType {
+
+    @XmlElement(required = true)
+    protected String elements;
+    protected List groups;
+    protected List newick;
+    protected List property;
+    protected MapListType mapping;
+    @XmlAttribute(name = "type", required = true)
+    protected String type;
+    @XmlAttribute(name = "rows", required = true)
+    protected BigInteger rows;
+    @XmlAttribute(name = "cols", required = true)
+    protected BigInteger cols;
+    @XmlAttribute(name = "treeMethod")
+    protected String treeMethod;
+    @XmlAttribute(name = "cutHeight")
+    protected Double cutHeight;
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
+
+    /**
+     * Gets the value of the elements property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getElements() {
+        return elements;
+    }
 
-  /**
-   * Sets the value of the elements property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setElements(String value)
-  {
-    this.elements = value;
-  }
+    /**
+     * Sets the value of the elements property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setElements(String value) {
+        this.elements = value;
+    }
 
-  /**
-   * Gets the value of the groups property.
-   * 
-   * 

-   * 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 set method
-   * for the groups property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getGroups().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getGroups()
-  {
-    if (groups == null)
-    {
-      groups = new ArrayList();
+    /**
+     * Gets the value of the groups property.
+     * 
+     * 

+     * 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 set method for the groups property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getGroups().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getGroups() {
+        if (groups == null) {
+            groups = new ArrayList();
+        }
+        return this.groups;
     }
-    return this.groups;
-  }
 
-  /**
-   * Gets the value of the newick property.
-   * 
-   * 

-   * 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 set method
-   * for the newick property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getNewick().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getNewick()
-  {
-    if (newick == null)
-    {
-      newick = new ArrayList();
+    /**
+     * Gets the value of the newick property.
+     * 
+     * 

+     * 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 set method for the newick property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getNewick().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getNewick() {
+        if (newick == null) {
+            newick = new ArrayList();
+        }
+        return this.newick;
     }
-    return this.newick;
-  }
 
-  /**
-   * Gets the value of the property property.
-   * 
-   * 

-   * 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 set method
-   * for the property property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getProperty().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link Property }
-   * 
-   * 
-   */
-  public List getProperty()
-  {
-    if (property == null)
-    {
-      property = new ArrayList();
+    /**
+     * Gets the value of the property property.
+     * 
+     * 

+     * 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 set method for the property property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getProperty().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link Property }
+     * 
+     * 
+     */
+    public List getProperty() {
+        if (property == null) {
+            property = new ArrayList();
+        }
+        return this.property;
     }
-    return this.property;
-  }
 
-  /**
-   * Gets the value of the mapping property.
-   * 
-   * @return possible object is {@link MapListType }
-   * 
-   */
-  public MapListType getMapping()
-  {
-    return mapping;
-  }
+    /**
+     * Gets the value of the mapping property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link MapListType }
+     *     
+     */
+    public MapListType getMapping() {
+        return mapping;
+    }
 
-  /**
-   * Sets the value of the mapping property.
-   * 
-   * @param value
-   *          allowed object is {@link MapListType }
-   * 
-   */
-  public void setMapping(MapListType value)
-  {
-    this.mapping = value;
-  }
+    /**
+     * Sets the value of the mapping property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link MapListType }
+     *     
+     */
+    public void setMapping(MapListType value) {
+        this.mapping = value;
+    }
 
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
+    /**
+     * Gets the value of the type property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getType() {
+        return type;
+    }
 
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
+    /**
+     * Sets the value of the type property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
 
-  /**
-   * Gets the value of the rows property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getRows()
-  {
-    return rows;
-  }
+    /**
+     * Gets the value of the rows property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getRows() {
+        return rows;
+    }
 
-  /**
-   * Sets the value of the rows property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setRows(BigInteger value)
-  {
-    this.rows = value;
-  }
+    /**
+     * Sets the value of the rows property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setRows(BigInteger value) {
+        this.rows = value;
+    }
 
-  /**
-   * Gets the value of the cols property.
-   * 
-   * @return possible object is {@link BigInteger }
-   * 
-   */
-  public BigInteger getCols()
-  {
-    return cols;
-  }
+    /**
+     * Gets the value of the cols property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link BigInteger }
+     *     
+     */
+    public BigInteger getCols() {
+        return cols;
+    }
 
-  /**
-   * Sets the value of the cols property.
-   * 
-   * @param value
-   *          allowed object is {@link BigInteger }
-   * 
-   */
-  public void setCols(BigInteger value)
-  {
-    this.cols = value;
-  }
+    /**
+     * Sets the value of the cols property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link BigInteger }
+     *     
+     */
+    public void setCols(BigInteger value) {
+        this.cols = value;
+    }
 
-  /**
-   * Gets the value of the treeMethod property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getTreeMethod()
-  {
-    return treeMethod;
-  }
+    /**
+     * Gets the value of the treeMethod property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getTreeMethod() {
+        return treeMethod;
+    }
 
-  /**
-   * Sets the value of the treeMethod property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setTreeMethod(String value)
-  {
-    this.treeMethod = value;
-  }
+    /**
+     * Sets the value of the treeMethod property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setTreeMethod(String value) {
+        this.treeMethod = value;
+    }
 
-  /**
-   * Gets the value of the cutHeight property.
-   * 
-   * @return possible object is {@link Double }
-   * 
-   */
-  public Double getCutHeight()
-  {
-    return cutHeight;
-  }
+    /**
+     * Gets the value of the cutHeight property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link Double }
+     *     
+     */
+    public Double getCutHeight() {
+        return cutHeight;
+    }
 
-  /**
-   * Sets the value of the cutHeight property.
-   * 
-   * @param value
-   *          allowed object is {@link Double }
-   * 
-   */
-  public void setCutHeight(Double value)
-  {
-    this.cutHeight = value;
-  }
+    /**
+     * Sets the value of the cutHeight property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link Double }
+     *     
+     */
+    public void setCutHeight(Double value) {
+        this.cutHeight = value;
+    }
 
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
 
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java
index eeeed22..3bede57 100644
--- a/src/jalview/xml/binding/jalview/NoValueColour.java
+++ b/src/jalview/xml/binding/jalview/NoValueColour.java
@@ -2,24 +2,22 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlEnumValue;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for NoValueColour.
+ * 
Java class for NoValueColour.
  * 
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 

- * The following schema fragment specifies the expected content contained within
- * this class.
- * 

- * 
  * 
  * <simpleType name="NoValueColour">
  *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
@@ -33,36 +31,31 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "NoValueColour", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum NoValueColour
-{
-
-  @XmlEnumValue("None")
-  NONE("None"), @XmlEnumValue("Min")
-  MIN("Min"), @XmlEnumValue("Max")
-  MAX("Max");
-
-  private final String value;
-
-  NoValueColour(String v)
-  {
-    value = v;
-  }
+public enum NoValueColour {
+
+    @XmlEnumValue("None")
+    NONE("None"),
+    @XmlEnumValue("Min")
+    MIN("Min"),
+    @XmlEnumValue("Max")
+    MAX("Max");
+    private final String value;
+
+    NoValueColour(String v) {
+        value = v;
+    }
 
-  public String value()
-  {
-    return value;
-  }
+    public String value() {
+        return value;
+    }
 
-  public static NoValueColour fromValue(String v)
-  {
-    for (NoValueColour c : NoValueColour.values())
-    {
-      if (c.value.equals(v))
-      {
-        return c;
-      }
+    public static NoValueColour fromValue(String v) {
+        for (NoValueColour c: NoValueColour.values()) {
+            if (c.value.equals(v)) {
+                return c;
+            }
+        }
+        throw new IllegalArgumentException(v);
     }
-    throw new IllegalArgumentException(v);
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
index 993adae7..4cb7753 100644
--- a/src/jalview/xml/binding/jalview/ObjectFactory.java
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.JAXBElement;
@@ -12,567 +13,500 @@ import javax.xml.bind.annotation.XmlElementDecl;
 import javax.xml.bind.annotation.XmlRegistry;
 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.
- * 

- * 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 and classes representing the binding
- * of schema type definitions, element declarations and model groups. Factory
- * methods for each of these are provided in this class.
+ * This object contains factory methods for each 
+ * Java content interface and Java element interface 
+ * generated in the jalview.xml.binding.jalview package. 
+ * 
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 
+ * and classes representing the binding of schema 
+ * type definitions, element declarations and model 
+ * groups.  Factory methods for each of these are 
+ * provided in this class.
  * 
  */
 @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");
-
-  /**
-   * Create a new ObjectFactory that can be used to create new instances of
-   * schema derived classes for package: jalview.xml.binding.jalview
-   * 
-   */
-  public ObjectFactory()
-  {
-  }
-
-  /**
-   * Create an instance of {@link AlcodonFrame }
-   * 
-   */
-  public AlcodonFrame createAlcodonFrame()
-  {
-    return new AlcodonFrame();
-  }
-
-  /**
-   * Create an instance of {@link MapListType }
-   * 
-   */
-  public MapListType createMapListType()
-  {
-    return new MapListType();
-  }
-
-  /**
-   * Create an instance of {@link Sequence }
-   * 
-   */
-  public Sequence createSequence()
-  {
-    return new Sequence();
-  }
-
-  /**
-   * Create an instance of {@link Annotation }
-   * 
-   */
-  public Annotation createAnnotation()
-  {
-    return new Annotation();
-  }
-
-  /**
-   * Create an instance of {@link SequenceSet }
-   * 
-   */
-  public SequenceSet createSequenceSet()
-  {
-    return new SequenceSet();
-  }
-
-  /**
-   * Create an instance of {@link FeatureMatcherSet }
-   * 
-   */
-  public FeatureMatcherSet createFeatureMatcherSet()
-  {
-    return new FeatureMatcherSet();
-  }
-
-  /**
-   * Create an instance of {@link JalviewUserColours }
-   * 
-   */
-  public JalviewUserColours createJalviewUserColours()
-  {
-    return new JalviewUserColours();
-  }
-
-  /**
-   * Create an instance of {@link Pdbentry }
-   * 
-   */
-  public Pdbentry createPdbentry()
-  {
-    return new Pdbentry();
-  }
-
-  /**
-   * Create an instance of {@link Feature }
-   * 
-   */
-  public Feature createFeature()
-  {
-    return new Feature();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel }
-   * 
-   */
-  public JalviewModel createJalviewModel()
-  {
-    return new JalviewModel();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.FeatureSettings }
-   * 
-   */
-  public JalviewModel.FeatureSettings createJalviewModelFeatureSettings()
-  {
-    return new JalviewModel.FeatureSettings();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer }
-   * 
-   */
-  public JalviewModel.PcaViewer createJalviewModelPcaViewer()
-  {
-    return new JalviewModel.PcaViewer();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Viewport }
-   * 
-   */
-  public JalviewModel.Viewport createJalviewModelViewport()
-  {
-    return new JalviewModel.Viewport();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq }
-   * 
-   */
-  public JalviewModel.JSeq createJalviewModelJSeq()
-  {
-    return new JalviewModel.JSeq();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
-   * 
-   */
-  public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer()
-  {
-    return new JalviewModel.JSeq.RnaViewer();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq.Pdbids }
-   * 
-   */
-  public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids()
-  {
-    return new JalviewModel.JSeq.Pdbids();
-  }
-
-  /**
-   * Create an instance of {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix createDoubleMatrix()
-  {
-    return new DoubleMatrix();
-  }
-
-  /**
-   * Create an instance of {@link AnnotationColourScheme }
-   * 
-   */
-  public AnnotationColourScheme createAnnotationColourScheme()
-  {
-    return new AnnotationColourScheme();
-  }
-
-  /**
-   * Create an instance of {@link PcaDataType }
-   * 
-   */
-  public PcaDataType createPcaDataType()
-  {
-    return new PcaDataType();
-  }
-
-  /**
-   * Create an instance of {@link DoubleVector }
-   * 
-   */
-  public DoubleVector createDoubleVector()
-  {
-    return new DoubleVector();
-  }
-
-  /**
-   * 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 Mapping }
-   * 
-   */
-  public Mapping createMapping()
-  {
-    return new Mapping();
-  }
-
-  /**
-   * Create an instance of {@link MapListType.MapListFrom }
-   * 
-   */
-  public MapListType.MapListFrom createMapListTypeMapListFrom()
-  {
-    return new MapListType.MapListFrom();
-  }
-
-  /**
-   * Create an instance of {@link MapListType.MapListTo }
-   * 
-   */
-  public MapListType.MapListTo createMapListTypeMapListTo()
-  {
-    return new MapListType.MapListTo();
-  }
-
-  /**
-   * Create an instance of {@link SequenceType }
-   * 
-   */
-  public SequenceType createSequenceType()
-  {
-    return new SequenceType();
-  }
-
-  /**
-   * Create an instance of {@link Sequence.DBRef }
-   * 
-   */
-  public Sequence.DBRef createSequenceDBRef()
-  {
-    return new Sequence.DBRef();
-  }
-
-  /**
-   * Create an instance of {@link Annotation.ThresholdLine }
-   * 
-   */
-  public Annotation.ThresholdLine createAnnotationThresholdLine()
-  {
-    return new Annotation.ThresholdLine();
-  }
-
-  /**
-   * Create an instance of {@link MatrixType }
-   * 
-   */
-  public MatrixType createMatrixType()
-  {
-    return new MatrixType();
-  }
-
-  /**
-   * Create an instance of {@link jalview.xml.binding.jalview.Property }
-   * 
-   */
-  public jalview.xml.binding.jalview.Property createProperty()
-  {
-    return new jalview.xml.binding.jalview.Property();
-  }
-
-  /**
-   * Create an instance of {@link SequenceSet.SequenceSetProperties }
-   * 
-   */
-  public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties()
-  {
-    return new SequenceSet.SequenceSetProperties();
-  }
-
-  /**
-   * Create an instance of {@link VAMSAS }
-   * 
-   */
-  public VAMSAS createVAMSAS()
-  {
-    return new VAMSAS();
-  }
-
-  /**
-   * Create an instance of {@link FeatureMatcher }
-   * 
-   */
-  public FeatureMatcher createFeatureMatcher()
-  {
-    return new FeatureMatcher();
-  }
-
-  /**
-   * Create an instance of {@link WebServiceParameterSet }
-   * 
-   */
-  public WebServiceParameterSet createWebServiceParameterSet()
-  {
-    return new WebServiceParameterSet();
-  }
-
-  /**
-   * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
-   * 
-   */
-  public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher()
-  {
-    return new FeatureMatcherSet.CompoundMatcher();
-  }
-
-  /**
-   * Create an instance of {@link JalviewUserColours.Colour }
-   * 
-   */
-  public JalviewUserColours.Colour createJalviewUserColoursColour()
-  {
-    return new JalviewUserColours.Colour();
-  }
-
-  /**
-   * Create an instance of {@link JalviewUserColours.Filter }
-   * 
-   */
-  public JalviewUserColours.Filter createJalviewUserColoursFilter()
-  {
-    return new JalviewUserColours.Filter();
-  }
-
-  /**
-   * Create an instance of {@link Pdbentry.Property }
-   * 
-   */
-  public Pdbentry.Property createPdbentryProperty()
-  {
-    return new Pdbentry.Property();
-  }
-
-  /**
-   * Create an instance of {@link Feature.OtherData }
-   * 
-   */
-  public Feature.OtherData createFeatureOtherData()
-  {
-    return new Feature.OtherData();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JGroup }
-   * 
-   */
-  public JalviewModel.JGroup createJalviewModelJGroup()
-  {
-    return new JalviewModel.JGroup();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.UserColours }
-   * 
-   */
-  public JalviewModel.UserColours createJalviewModelUserColours()
-  {
-    return new JalviewModel.UserColours();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Tree }
-   * 
-   */
-  public JalviewModel.Tree createJalviewModelTree()
-  {
-    return new JalviewModel.Tree();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
-   * 
-   */
-  public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting()
-  {
-    return new JalviewModel.FeatureSettings.Setting();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.FeatureSettings.Group }
-   * 
-   */
-  public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup()
-  {
-    return new JalviewModel.FeatureSettings.Group();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
-   * 
-   */
-  public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint()
-  {
-    return new JalviewModel.PcaViewer.SequencePoint();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.Axis }
-   * 
-   */
-  public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis()
-  {
-    return new JalviewModel.PcaViewer.Axis();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
-   * 
-   */
-  public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin()
-  {
-    return new JalviewModel.PcaViewer.SeqPointMin();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
-   * 
-   */
-  public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax()
-  {
-    return new JalviewModel.PcaViewer.SeqPointMax();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
-   * 
-   */
-  public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns()
-  {
-    return new JalviewModel.Viewport.HiddenColumns();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
-   * 
-   */
-  public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam()
-  {
-    return new JalviewModel.Viewport.CalcIdParam();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.Viewport.Overview }
-   * 
-   */
-  public JalviewModel.Viewport.Overview createJalviewModelViewportOverview()
-  {
-    return new JalviewModel.Viewport.Overview();
-  }
-
-  /**
-   * Create an instance of
-   * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
-   * 
-   */
-  public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure()
-  {
-    return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
-  }
-
-  /**
-   * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
-   * 
-   */
-  public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState()
-  {
-    return new JalviewModel.JSeq.Pdbids.StructureState();
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement
-   * }{@code <}{@link WebServiceParameterSet }{@code >}}
-   * 
-   */
-  @XmlElementDecl(
-    namespace = "www.jalview.org/xml/wsparamset",
-    name = "WebServiceParameterSet")
-  public JAXBElement createWebServiceParameterSet(
-          WebServiceParameterSet value)
-  {
-    return new JAXBElement(
-            _WebServiceParameterSet_QNAME, WebServiceParameterSet.class,
-            null, value);
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel
-   * }{@code >}}
-   * 
-   */
-  @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
-  public JAXBElement createJalviewModel(JalviewModel value)
-  {
-    return new JAXBElement(_JalviewModel_QNAME,
-            JalviewModel.class, null, value);
-  }
-
-  /**
-   * Create an instance of {@link JAXBElement
-   * }{@code <}{@link JalviewUserColours }{@code >}}
-   * 
-   */
-  @XmlElementDecl(
-    namespace = "www.jalview.org/colours",
-    name = "JalviewUserColours")
-  public JAXBElement createJalviewUserColours(
-          JalviewUserColours value)
-  {
-    return new JAXBElement(_JalviewUserColours_QNAME,
-            JalviewUserColours.class, null, value);
-  }
+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");
+
+    /**
+     * Create a new ObjectFactory that can be used to create new instances of schema derived classes for package: jalview.xml.binding.jalview
+     * 
+     */
+    public ObjectFactory() {
+    }
+
+    /**
+     * Create an instance of {@link AlcodonFrame }
+     * 
+     */
+    public AlcodonFrame createAlcodonFrame() {
+        return new AlcodonFrame();
+    }
+
+    /**
+     * Create an instance of {@link MapListType }
+     * 
+     */
+    public MapListType createMapListType() {
+        return new MapListType();
+    }
+
+    /**
+     * Create an instance of {@link Sequence }
+     * 
+     */
+    public Sequence createSequence() {
+        return new Sequence();
+    }
+
+    /**
+     * Create an instance of {@link Annotation }
+     * 
+     */
+    public Annotation createAnnotation() {
+        return new Annotation();
+    }
+
+    /**
+     * Create an instance of {@link SequenceSet }
+     * 
+     */
+    public SequenceSet createSequenceSet() {
+        return new SequenceSet();
+    }
+
+    /**
+     * Create an instance of {@link FeatureMatcherSet }
+     * 
+     */
+    public FeatureMatcherSet createFeatureMatcherSet() {
+        return new FeatureMatcherSet();
+    }
+
+    /**
+     * Create an instance of {@link JalviewUserColours }
+     * 
+     */
+    public JalviewUserColours createJalviewUserColours() {
+        return new JalviewUserColours();
+    }
+
+    /**
+     * Create an instance of {@link Pdbentry }
+     * 
+     */
+    public Pdbentry createPdbentry() {
+        return new Pdbentry();
+    }
+
+    /**
+     * Create an instance of {@link Feature }
+     * 
+     */
+    public Feature createFeature() {
+        return new Feature();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel }
+     * 
+     */
+    public JalviewModel createJalviewModel() {
+        return new JalviewModel();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.FeatureSettings }
+     * 
+     */
+    public JalviewModel.FeatureSettings createJalviewModelFeatureSettings() {
+        return new JalviewModel.FeatureSettings();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer }
+     * 
+     */
+    public JalviewModel.PcaViewer createJalviewModelPcaViewer() {
+        return new JalviewModel.PcaViewer();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport }
+     * 
+     */
+    public JalviewModel.Viewport createJalviewModelViewport() {
+        return new JalviewModel.Viewport();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq }
+     * 
+     */
+    public JalviewModel.JSeq createJalviewModelJSeq() {
+        return new JalviewModel.JSeq();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.RnaViewer }
+     * 
+     */
+    public JalviewModel.JSeq.RnaViewer createJalviewModelJSeqRnaViewer() {
+        return new JalviewModel.JSeq.RnaViewer();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.Pdbids }
+     * 
+     */
+    public JalviewModel.JSeq.Pdbids createJalviewModelJSeqPdbids() {
+        return new JalviewModel.JSeq.Pdbids();
+    }
+
+    /**
+     * Create an instance of {@link DoubleMatrix }
+     * 
+     */
+    public DoubleMatrix createDoubleMatrix() {
+        return new DoubleMatrix();
+    }
+
+    /**
+     * Create an instance of {@link AnnotationColourScheme }
+     * 
+     */
+    public AnnotationColourScheme createAnnotationColourScheme() {
+        return new AnnotationColourScheme();
+    }
+
+    /**
+     * Create an instance of {@link PcaDataType }
+     * 
+     */
+    public PcaDataType createPcaDataType() {
+        return new PcaDataType();
+    }
+
+    /**
+     * Create an instance of {@link DoubleVector }
+     * 
+     */
+    public DoubleVector createDoubleVector() {
+        return new DoubleVector();
+    }
+
+    /**
+     * 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 Mapping }
+     * 
+     */
+    public Mapping createMapping() {
+        return new Mapping();
+    }
+
+    /**
+     * Create an instance of {@link MapListType.MapListFrom }
+     * 
+     */
+    public MapListType.MapListFrom createMapListTypeMapListFrom() {
+        return new MapListType.MapListFrom();
+    }
+
+    /**
+     * Create an instance of {@link MapListType.MapListTo }
+     * 
+     */
+    public MapListType.MapListTo createMapListTypeMapListTo() {
+        return new MapListType.MapListTo();
+    }
+
+    /**
+     * Create an instance of {@link SequenceType }
+     * 
+     */
+    public SequenceType createSequenceType() {
+        return new SequenceType();
+    }
+
+    /**
+     * Create an instance of {@link Sequence.DBRef }
+     * 
+     */
+    public Sequence.DBRef createSequenceDBRef() {
+        return new Sequence.DBRef();
+    }
+
+    /**
+     * Create an instance of {@link Annotation.ThresholdLine }
+     * 
+     */
+    public Annotation.ThresholdLine createAnnotationThresholdLine() {
+        return new Annotation.ThresholdLine();
+    }
+
+    /**
+     * Create an instance of {@link MatrixType }
+     * 
+     */
+    public MatrixType createMatrixType() {
+        return new MatrixType();
+    }
+
+    /**
+     * Create an instance of {@link jalview.xml.binding.jalview.Property }
+     * 
+     */
+    public jalview.xml.binding.jalview.Property createProperty() {
+        return new jalview.xml.binding.jalview.Property();
+    }
+
+    /**
+     * Create an instance of {@link SequenceSet.SequenceSetProperties }
+     * 
+     */
+    public SequenceSet.SequenceSetProperties createSequenceSetSequenceSetProperties() {
+        return new SequenceSet.SequenceSetProperties();
+    }
+
+    /**
+     * Create an instance of {@link MapOnAMatrixType }
+     * 
+     */
+    public MapOnAMatrixType createMapOnAMatrixType() {
+        return new MapOnAMatrixType();
+    }
+
+    /**
+     * Create an instance of {@link VAMSAS }
+     * 
+     */
+    public VAMSAS createVAMSAS() {
+        return new VAMSAS();
+    }
+
+    /**
+     * Create an instance of {@link FeatureMatcher }
+     * 
+     */
+    public FeatureMatcher createFeatureMatcher() {
+        return new FeatureMatcher();
+    }
+
+    /**
+     * Create an instance of {@link WebServiceParameterSet }
+     * 
+     */
+    public WebServiceParameterSet createWebServiceParameterSet() {
+        return new WebServiceParameterSet();
+    }
+
+    /**
+     * Create an instance of {@link FeatureMatcherSet.CompoundMatcher }
+     * 
+     */
+    public FeatureMatcherSet.CompoundMatcher createFeatureMatcherSetCompoundMatcher() {
+        return new FeatureMatcherSet.CompoundMatcher();
+    }
+
+    /**
+     * Create an instance of {@link JalviewUserColours.Colour }
+     * 
+     */
+    public JalviewUserColours.Colour createJalviewUserColoursColour() {
+        return new JalviewUserColours.Colour();
+    }
+
+    /**
+     * Create an instance of {@link JalviewUserColours.Filter }
+     * 
+     */
+    public JalviewUserColours.Filter createJalviewUserColoursFilter() {
+        return new JalviewUserColours.Filter();
+    }
+
+    /**
+     * Create an instance of {@link Pdbentry.Property }
+     * 
+     */
+    public Pdbentry.Property createPdbentryProperty() {
+        return new Pdbentry.Property();
+    }
+
+    /**
+     * Create an instance of {@link Feature.OtherData }
+     * 
+     */
+    public Feature.OtherData createFeatureOtherData() {
+        return new Feature.OtherData();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JGroup }
+     * 
+     */
+    public JalviewModel.JGroup createJalviewModelJGroup() {
+        return new JalviewModel.JGroup();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.UserColours }
+     * 
+     */
+    public JalviewModel.UserColours createJalviewModelUserColours() {
+        return new JalviewModel.UserColours();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Tree }
+     * 
+     */
+    public JalviewModel.Tree createJalviewModelTree() {
+        return new JalviewModel.Tree();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.FeatureSettings.Setting }
+     * 
+     */
+    public JalviewModel.FeatureSettings.Setting createJalviewModelFeatureSettingsSetting() {
+        return new JalviewModel.FeatureSettings.Setting();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.FeatureSettings.Group }
+     * 
+     */
+    public JalviewModel.FeatureSettings.Group createJalviewModelFeatureSettingsGroup() {
+        return new JalviewModel.FeatureSettings.Group();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.SequencePoint }
+     * 
+     */
+    public JalviewModel.PcaViewer.SequencePoint createJalviewModelPcaViewerSequencePoint() {
+        return new JalviewModel.PcaViewer.SequencePoint();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.Axis }
+     * 
+     */
+    public JalviewModel.PcaViewer.Axis createJalviewModelPcaViewerAxis() {
+        return new JalviewModel.PcaViewer.Axis();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMin }
+     * 
+     */
+    public JalviewModel.PcaViewer.SeqPointMin createJalviewModelPcaViewerSeqPointMin() {
+        return new JalviewModel.PcaViewer.SeqPointMin();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.PcaViewer.SeqPointMax }
+     * 
+     */
+    public JalviewModel.PcaViewer.SeqPointMax createJalviewModelPcaViewerSeqPointMax() {
+        return new JalviewModel.PcaViewer.SeqPointMax();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport.HiddenColumns }
+     * 
+     */
+    public JalviewModel.Viewport.HiddenColumns createJalviewModelViewportHiddenColumns() {
+        return new JalviewModel.Viewport.HiddenColumns();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport.CalcIdParam }
+     * 
+     */
+    public JalviewModel.Viewport.CalcIdParam createJalviewModelViewportCalcIdParam() {
+        return new JalviewModel.Viewport.CalcIdParam();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.Viewport.Overview }
+     * 
+     */
+    public JalviewModel.Viewport.Overview createJalviewModelViewportOverview() {
+        return new JalviewModel.Viewport.Overview();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+     * 
+     */
+    public JalviewModel.JSeq.RnaViewer.SecondaryStructure createJalviewModelJSeqRnaViewerSecondaryStructure() {
+        return new JalviewModel.JSeq.RnaViewer.SecondaryStructure();
+    }
+
+    /**
+     * Create an instance of {@link JalviewModel.JSeq.Pdbids.StructureState }
+     * 
+     */
+    public JalviewModel.JSeq.Pdbids.StructureState createJalviewModelJSeqPdbidsStructureState() {
+        return new JalviewModel.JSeq.Pdbids.StructureState();
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link WebServiceParameterSet }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "www.jalview.org/xml/wsparamset", name = "WebServiceParameterSet")
+    public JAXBElement createWebServiceParameterSet(WebServiceParameterSet value) {
+        return new JAXBElement(_WebServiceParameterSet_QNAME, WebServiceParameterSet.class, null, value);
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewModel }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+    public JAXBElement createJalviewModel(JalviewModel value) {
+        return new JAXBElement(_JalviewModel_QNAME, JalviewModel.class, null, value);
+    }
+
+    /**
+     * Create an instance of {@link JAXBElement }{@code <}{@link JalviewUserColours }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "www.jalview.org/colours", name = "JalviewUserColours")
+    public JAXBElement createJalviewUserColours(JalviewUserColours value) {
+        return new JAXBElement(_JalviewUserColours_QNAME, JalviewUserColours.class, null, value);
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/PcaDataType.java b/src/jalview/xml/binding/jalview/PcaDataType.java
index 2ff7a55..b7e2881 100644
--- a/src/jalview/xml/binding/jalview/PcaDataType.java
+++ b/src/jalview/xml/binding/jalview/PcaDataType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,17 +13,15 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
  * 
- * The results of a PCA calculation
- * 
+ * 				The results of a PCA calculation
+ * 			
  * 
- * 

- * Java class for PcaDataType complex type.
+ * 
Java class for PcaDataType complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="PcaDataType">
@@ -41,90 +40,90 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "PcaDataType",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "pairwiseMatrix", "tridiagonalMatrix", "eigenMatrix" })
-public class PcaDataType
-{
-
-  @XmlElement(required = true)
-  protected DoubleMatrix pairwiseMatrix;
-
-  @XmlElement(required = true)
-  protected DoubleMatrix tridiagonalMatrix;
+@XmlType(name = "PcaDataType", namespace = "www.jalview.org", propOrder = {
+    "pairwiseMatrix",
+    "tridiagonalMatrix",
+    "eigenMatrix"
+})
+public class PcaDataType {
 
-  @XmlElement(required = true)
-  protected DoubleMatrix eigenMatrix;
+    @XmlElement(required = true)
+    protected DoubleMatrix pairwiseMatrix;
+    @XmlElement(required = true)
+    protected DoubleMatrix tridiagonalMatrix;
+    @XmlElement(required = true)
+    protected DoubleMatrix eigenMatrix;
 
-  /**
-   * Gets the value of the pairwiseMatrix property.
-   * 
-   * @return possible object is {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix getPairwiseMatrix()
-  {
-    return pairwiseMatrix;
-  }
+    /**
+     * Gets the value of the pairwiseMatrix property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public DoubleMatrix getPairwiseMatrix() {
+        return pairwiseMatrix;
+    }
 
-  /**
-   * Sets the value of the pairwiseMatrix property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleMatrix }
-   * 
-   */
-  public void setPairwiseMatrix(DoubleMatrix value)
-  {
-    this.pairwiseMatrix = value;
-  }
+    /**
+     * Sets the value of the pairwiseMatrix property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public void setPairwiseMatrix(DoubleMatrix value) {
+        this.pairwiseMatrix = value;
+    }
 
-  /**
-   * Gets the value of the tridiagonalMatrix property.
-   * 
-   * @return possible object is {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix getTridiagonalMatrix()
-  {
-    return tridiagonalMatrix;
-  }
+    /**
+     * Gets the value of the tridiagonalMatrix property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public DoubleMatrix getTridiagonalMatrix() {
+        return tridiagonalMatrix;
+    }
 
-  /**
-   * Sets the value of the tridiagonalMatrix property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleMatrix }
-   * 
-   */
-  public void setTridiagonalMatrix(DoubleMatrix value)
-  {
-    this.tridiagonalMatrix = value;
-  }
+    /**
+     * Sets the value of the tridiagonalMatrix property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public void setTridiagonalMatrix(DoubleMatrix value) {
+        this.tridiagonalMatrix = value;
+    }
 
-  /**
-   * Gets the value of the eigenMatrix property.
-   * 
-   * @return possible object is {@link DoubleMatrix }
-   * 
-   */
-  public DoubleMatrix getEigenMatrix()
-  {
-    return eigenMatrix;
-  }
+    /**
+     * Gets the value of the eigenMatrix property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public DoubleMatrix getEigenMatrix() {
+        return eigenMatrix;
+    }
 
-  /**
-   * Sets the value of the eigenMatrix property.
-   * 
-   * @param value
-   *          allowed object is {@link DoubleMatrix }
-   * 
-   */
-  public void setEigenMatrix(DoubleMatrix value)
-  {
-    this.eigenMatrix = value;
-  }
+    /**
+     * Sets the value of the eigenMatrix property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link DoubleMatrix }
+     *     
+     */
+    public void setEigenMatrix(DoubleMatrix value) {
+        this.eigenMatrix = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java
index f0fd2f3..19c44fb 100644
--- a/src/jalview/xml/binding/jalview/Pdbentry.java
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -15,13 +16,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for pdbentry complex type.
+ * 
Java class for pdbentry complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="pdbentry">
@@ -50,205 +49,199 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "pdbentry",
-  namespace = "www.jalview.org",
-  propOrder =
-  { "property" })
-@XmlSeeAlso({ jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class })
-public class Pdbentry
-{
-
-  protected List property;
-
-  @XmlAttribute(name = "id", required = true)
-  protected String id;
-
-  @XmlAttribute(name = "type")
-  protected String type;
-
-  @XmlAttribute(name = "file")
-  protected String file;
-
-  /**
-   * Gets the value of the property property.
-   * 
-   * 

-   * 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 set method
-   * for the property property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getProperty().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link Pdbentry.Property }
-   * 
-   * 
-   */
-  public List getProperty()
-  {
-    if (property == null)
-    {
-      property = new ArrayList();
-    }
-    return this.property;
-  }
-
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
-
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
-
-  /**
-   * Gets the value of the type property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getType()
-  {
-    return type;
-  }
-
-  /**
-   * Sets the value of the type property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setType(String value)
-  {
-    this.type = value;
-  }
-
-  /**
-   * Gets the value of the file property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getFile()
-  {
-    return file;
-  }
-
-  /**
-   * Sets the value of the file property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setFile(String value)
-  {
-    this.file = value;
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class Property
-  {
-
-    @XmlAttribute(name = "name", required = true)
-    protected String name;
-
-    @XmlAttribute(name = "value", required = true)
-    protected String value;
+@XmlType(name = "pdbentry", namespace = "www.jalview.org", propOrder = {
+    "property"
+})
+@XmlSeeAlso({
+    jalview.xml.binding.jalview.JalviewModel.JSeq.Pdbids.class
+})
+public class Pdbentry {
+
+    protected List property;
+    @XmlAttribute(name = "id", required = true)
+    protected String id;
+    @XmlAttribute(name = "type")
+    protected String type;
+    @XmlAttribute(name = "file")
+    protected String file;
 
     /**
-     * Gets the value of the name property.
+     * Gets the value of the property property.
+     * 
+     * 

+     * 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 set method for the property property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getProperty().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link Pdbentry.Property }
+     * 
      * 
-     * @return possible object is {@link String }
+     */
+    public List getProperty() {
+        if (property == null) {
+            property = new ArrayList();
+        }
+        return this.property;
+    }
+
+    /**
+     * Gets the value of the id property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getName()
-    {
-      return name;
+    public String getId() {
+        return id;
     }
 
     /**
-     * Sets the value of the name property.
+     * Sets the value of the id property.
      * 
      * @param value
-     *          allowed object is {@link String }
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
+    /**
+     * Gets the value of the type property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setName(String value)
-    {
-      this.name = value;
+    public String getType() {
+        return type;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the type property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setType(String value) {
+        this.type = value;
+    }
+
+    /**
+     * Gets the value of the file property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public String getFile() {
+        return file;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the file property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public void setFile(String value) {
+        this.file = value;
     }
 
-  }
+
+    /**
+     * 
Java class for anonymous complex type.
+     * 
+     * 
The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Property {
+
+        @XmlAttribute(name = "name", required = true)
+        protected String name;
+        @XmlAttribute(name = "value", required = true)
+        protected String value;
+
+        /**
+         * Gets the value of the name property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getName() {
+            return name;
+        }
+
+        /**
+         * Sets the value of the name property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setName(String value) {
+            this.name = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Property.java b/src/jalview/xml/binding/jalview/Property.java
index b70e665..d171a73 100644
--- a/src/jalview/xml/binding/jalview/Property.java
+++ b/src/jalview/xml/binding/jalview/Property.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -12,13 +13,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for property complex type.
+ * 
Java class for property complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="property">
@@ -35,59 +34,59 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlAccessorType(XmlAccessType.FIELD)
 @XmlType(name = "property")
-public class Property
-{
-
-  @XmlAttribute(name = "name")
-  protected String name;
+public class Property {
 
-  @XmlAttribute(name = "value")
-  protected String value;
+    @XmlAttribute(name = "name")
+    protected String name;
+    @XmlAttribute(name = "value")
+    protected String value;
 
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
 
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
 
-  /**
-   * Gets the value of the value property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getValue()
-  {
-    return value;
-  }
+    /**
+     * Gets the value of the value property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getValue() {
+        return value;
+    }
 
-  /**
-   * Sets the value of the value property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setValue(String value)
-  {
-    this.value = value;
-  }
+    /**
+     * Sets the value of the value property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setValue(String value) {
+        this.value = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
index a5923e1..98390ef 100644
--- a/src/jalview/xml/binding/jalview/Sequence.java
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,13 +17,11 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for anonymous complex type.
+ * 
Java class for anonymous complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType>
@@ -56,300 +55,294 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "dbRef" })
+@XmlType(name = "", propOrder = {
+    "dbRef"
+})
 @XmlRootElement(name = "Sequence")
-public class Sequence extends SequenceType
+public class Sequence
+    extends SequenceType
 {
 
-  @XmlElement(name = "DBRef")
-  protected List dbRef;
-
-  @XmlAttribute(name = "dsseqid")
-  protected String dsseqid;
-
-  @XmlAttribute(name = "biotype")
-  protected String biotype;
-
-  /**
-   * Gets the value of the dbRef property.
-   * 
-   * 

-   * 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 set method
-   * for the dbRef property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getDBRef().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link Sequence.DBRef }
-   * 
-   * 
-   */
-  public List getDBRef()
-  {
-    if (dbRef == null)
-    {
-      dbRef = new ArrayList();
-    }
-    return this.dbRef;
-  }
-
-  /**
-   * Gets the value of the dsseqid property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDsseqid()
-  {
-    return dsseqid;
-  }
-
-  /**
-   * Sets the value of the dsseqid property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDsseqid(String value)
-  {
-    this.dsseqid = value;
-  }
-
-  /**
-   * Gets the value of the biotype property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getBiotype()
-  {
-    return biotype;
-  }
-
-  /**
-   * Sets the value of the biotype property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setBiotype(String value)
-  {
-    this.biotype = value;
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
-   *       </sequence>
-   *       <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "", propOrder = { "mapping" })
-  public static class DBRef
-  {
-
-    @XmlElement(name = "Mapping")
-    protected Mapping mapping;
-
-    @XmlAttribute(name = "source")
-    protected String source;
-
-    @XmlAttribute(name = "version")
-    protected String version;
-
-    @XmlAttribute(name = "accessionId")
-    protected String accessionId;
-
-    @XmlAttribute(name = "locus")
-    protected Boolean locus;
-
-    @XmlAttribute(name = "canonical")
-    protected Boolean canonical;
+    @XmlElement(name = "DBRef")
+    protected List dbRef;
+    @XmlAttribute(name = "dsseqid")
+    protected String dsseqid;
+    @XmlAttribute(name = "biotype")
+    protected String biotype;
 
     /**
-     * Gets the value of the mapping property.
+     * Gets the value of the dbRef property.
      * 
-     * @return possible object is {@link Mapping }
+     * 

+     * 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 set method for the dbRef property.
      * 
-     */
-    public Mapping getMapping()
-    {
-      return mapping;
-    }
-
-    /**
-     * Sets the value of the mapping property.
-     * 
-     * @param value
-     *          allowed object is {@link Mapping }
-     * 
-     */
-    public void setMapping(Mapping value)
-    {
-      this.mapping = value;
-    }
-
-    /**
-     * Gets the value of the source property.
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getDBRef().add(newItem);
+     * 

      * 
-     * @return possible object is {@link String }
      * 
-     */
-    public String getSource()
-    {
-      return source;
-    }
-
-    /**
-     * Sets the value of the source property.
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link Sequence.DBRef }
      * 
-     * @param value
-     *          allowed object is {@link String }
      * 
      */
-    public void setSource(String value)
-    {
-      this.source = value;
+    public List getDBRef() {
+        if (dbRef == null) {
+            dbRef = new ArrayList();
+        }
+        return this.dbRef;
     }
 
     /**
-     * Gets the value of the version property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the dsseqid property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getVersion()
-    {
-      return version;
+    public String getDsseqid() {
+        return dsseqid;
     }
 
     /**
-     * Sets the value of the version property.
+     * Sets the value of the dsseqid property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setVersion(String value)
-    {
-      this.version = value;
+    public void setDsseqid(String value) {
+        this.dsseqid = value;
     }
 
     /**
-     * Gets the value of the accessionId property.
-     * 
-     * @return possible object is {@link String }
+     * Gets the value of the biotype property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getAccessionId()
-    {
-      return accessionId;
+    public String getBiotype() {
+        return biotype;
     }
 
     /**
-     * Sets the value of the accessionId property.
+     * Sets the value of the biotype property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setAccessionId(String value)
-    {
-      this.accessionId = value;
+    public void setBiotype(String value) {
+        this.biotype = value;
     }
 
-    /**
-     * Gets the value of the locus property.
-     * 
-     * @return possible object is {@link Boolean }
-     * 
-     */
-    public boolean isLocus()
-    {
-      if (locus == null)
-      {
-        return false;
-      }
-      else
-      {
-        return locus;
-      }
-    }
 
     /**
-     * Sets the value of the locus property.
+     * 
Java class for anonymous complex type.
      * 
-     * @param value
-     *          allowed object is {@link Boolean }
+     * 
The following schema fragment specifies the expected content contained within this class.
      * 
-     */
-    public void setLocus(Boolean value)
-    {
-      this.locus = value;
-    }
-
-    /**
-     * Gets the value of the canonical property.
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <sequence>
+     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+     *       </sequence>
+     *       <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       <attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

      * 
-     * @return possible object is {@link Boolean }
      * 
      */
-    public boolean isCanonical()
-    {
-      if (canonical == null)
-      {
-        return false;
-      }
-      else
-      {
-        return canonical;
-      }
-    }
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "mapping"
+    })
+    public static class DBRef {
+
+        @XmlElement(name = "Mapping")
+        protected Mapping mapping;
+        @XmlAttribute(name = "source")
+        protected String source;
+        @XmlAttribute(name = "version")
+        protected String version;
+        @XmlAttribute(name = "accessionId")
+        protected String accessionId;
+        @XmlAttribute(name = "locus")
+        protected Boolean locus;
+        @XmlAttribute(name = "canonical")
+        protected Boolean canonical;
+
+        /**
+         * Gets the value of the mapping property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Mapping }
+         *     
+         */
+        public Mapping getMapping() {
+            return mapping;
+        }
+
+        /**
+         * Sets the value of the mapping property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Mapping }
+         *     
+         */
+        public void setMapping(Mapping value) {
+            this.mapping = value;
+        }
+
+        /**
+         * Gets the value of the source property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getSource() {
+            return source;
+        }
+
+        /**
+         * Sets the value of the source property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setSource(String value) {
+            this.source = value;
+        }
+
+        /**
+         * Gets the value of the version property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getVersion() {
+            return version;
+        }
+
+        /**
+         * Sets the value of the version property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setVersion(String value) {
+            this.version = value;
+        }
+
+        /**
+         * Gets the value of the accessionId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getAccessionId() {
+            return accessionId;
+        }
+
+        /**
+         * Sets the value of the accessionId property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setAccessionId(String value) {
+            this.accessionId = value;
+        }
+
+        /**
+         * Gets the value of the locus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isLocus() {
+            if (locus == null) {
+                return false;
+            } else {
+                return locus;
+            }
+        }
+
+        /**
+         * Sets the value of the locus property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setLocus(Boolean value) {
+            this.locus = value;
+        }
+
+        /**
+         * Gets the value of the canonical property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isCanonical() {
+            if (canonical == null) {
+                return false;
+            } else {
+                return canonical;
+            }
+        }
+
+        /**
+         * Sets the value of the canonical property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCanonical(Boolean value) {
+            this.canonical = value;
+        }
 
-    /**
-     * Sets the value of the canonical property.
-     * 
-     * @param value
-     *          allowed object is {@link Boolean }
-     * 
-     */
-    public void setCanonical(Boolean value)
-    {
-      this.canonical = value;
     }
 
-  }
-
 }
diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
index f08b225..8322ca7 100644
--- a/src/jalview/xml/binding/jalview/SequenceSet.java
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -16,13 +17,11 @@ import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlRootElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for anonymous complex type.
+ * 
Java class for anonymous complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType>
@@ -42,6 +41,7 @@ import javax.xml.bind.annotation.XmlType;
  *           </complexType>
  *         </element>
  *         <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
+ *         <element name="Matrices" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/>
  *       </sequence>
  *       <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
  *       <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
@@ -53,282 +53,299 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "",
-  propOrder =
-  { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame" })
+@XmlType(name = "", propOrder = {
+    "sequence",
+    "annotation",
+    "sequenceSetProperties",
+    "alcodonFrame",
+    "matrices"
+})
 @XmlRootElement(name = "SequenceSet")
-public class SequenceSet
-{
-
-  @XmlElement(name = "Sequence")
-  protected List sequence;
-
-  @XmlElement(name = "Annotation")
-  protected List annotation;
-
-  protected List sequenceSetProperties;
+public class SequenceSet {
 
-  @XmlElement(name = "AlcodonFrame")
-  protected List alcodonFrame;
+    @XmlElement(name = "Sequence")
+    protected List sequence;
+    @XmlElement(name = "Annotation")
+    protected List annotation;
+    protected List sequenceSetProperties;
+    @XmlElement(name = "AlcodonFrame")
+    protected List alcodonFrame;
+    @XmlElement(name = "Matrices")
+    protected List matrices;
+    @XmlAttribute(name = "gapChar", required = true)
+    protected String gapChar;
+    @XmlAttribute(name = "datasetId")
+    protected String datasetId;
 
-  @XmlAttribute(name = "gapChar", required = true)
-  protected String gapChar;
-
-  @XmlAttribute(name = "datasetId")
-  protected String datasetId;
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * 

-   * 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 set method
-   * for the sequence property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getSequence().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link Sequence }
-   * 
-   * 
-   */
-  public List getSequence()
-  {
-    if (sequence == null)
-    {
-      sequence = new ArrayList();
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * 

+     * 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 set method for the sequence property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getSequence().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link Sequence }
+     * 
+     * 
+     */
+    public List getSequence() {
+        if (sequence == null) {
+            sequence = new ArrayList();
+        }
+        return this.sequence;
     }
-    return this.sequence;
-  }
 
-  /**
-   * Gets the value of the annotation property.
-   * 
-   * 

-   * 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 set method
-   * for the annotation property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getAnnotation().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link Annotation
-   * }
-   * 
-   * 
-   */
-  public List getAnnotation()
-  {
-    if (annotation == null)
-    {
-      annotation = new ArrayList();
+    /**
+     * Gets the value of the annotation property.
+     * 
+     * 

+     * 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 set method for the annotation property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getAnnotation().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link Annotation }
+     * 
+     * 
+     */
+    public List getAnnotation() {
+        if (annotation == null) {
+            annotation = new ArrayList();
+        }
+        return this.annotation;
     }
-    return this.annotation;
-  }
 
-  /**
-   * Gets the value of the sequenceSetProperties property.
-   * 
-   * 

-   * 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 set method
-   * for the sequenceSetProperties property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getSequenceSetProperties().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link SequenceSet.SequenceSetProperties }
-   * 
-   * 
-   */
-  public List getSequenceSetProperties()
-  {
-    if (sequenceSetProperties == null)
-    {
-      sequenceSetProperties = new ArrayList();
+    /**
+     * Gets the value of the sequenceSetProperties property.
+     * 
+     * 

+     * 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 set method for the sequenceSetProperties property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getSequenceSetProperties().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link SequenceSet.SequenceSetProperties }
+     * 
+     * 
+     */
+    public List getSequenceSetProperties() {
+        if (sequenceSetProperties == null) {
+            sequenceSetProperties = new ArrayList();
+        }
+        return this.sequenceSetProperties;
     }
-    return this.sequenceSetProperties;
-  }
 
-  /**
-   * Gets the value of the alcodonFrame property.
-   * 
-   * 

-   * 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 set method
-   * for the alcodonFrame property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getAlcodonFrame().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list
-   * {@link AlcodonFrame }
-   * 
-   * 
-   */
-  public List getAlcodonFrame()
-  {
-    if (alcodonFrame == null)
-    {
-      alcodonFrame = new ArrayList();
+    /**
+     * Gets the value of the alcodonFrame property.
+     * 
+     * 

+     * 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 set method for the alcodonFrame property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getAlcodonFrame().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame }
+     * 
+     * 
+     */
+    public List getAlcodonFrame() {
+        if (alcodonFrame == null) {
+            alcodonFrame = new ArrayList();
+        }
+        return this.alcodonFrame;
     }
-    return this.alcodonFrame;
-  }
-
-  /**
-   * Gets the value of the gapChar property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getGapChar()
-  {
-    return gapChar;
-  }
-
-  /**
-   * Sets the value of the gapChar property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setGapChar(String value)
-  {
-    this.gapChar = value;
-  }
-
-  /**
-   * Gets the value of the datasetId property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDatasetId()
-  {
-    return datasetId;
-  }
-
-  /**
-   * Sets the value of the datasetId property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDatasetId(String value)
-  {
-    this.datasetId = value;
-  }
-
-  /**
-   * 

-   * Java class for anonymous complex type.
-   * 
-   * 

-   * The following schema fragment specifies the expected content contained
-   * within this class.
-   * 
-   * 
-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   * 

-   * 
-   * 
-   */
-  @XmlAccessorType(XmlAccessType.FIELD)
-  @XmlType(name = "")
-  public static class SequenceSetProperties
-  {
-
-    @XmlAttribute(name = "key")
-    protected String key;
-
-    @XmlAttribute(name = "value")
-    protected String value;
 
     /**
-     * Gets the value of the key property.
+     * Gets the value of the matrices property.
+     * 
+     * 

+     * 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 set method for the matrices property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getMatrices().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link MatrixType }
      * 
-     * @return possible object is {@link String }
      * 
      */
-    public String getKey()
-    {
-      return key;
+    public List getMatrices() {
+        if (matrices == null) {
+            matrices = new ArrayList();
+        }
+        return this.matrices;
     }
 
     /**
-     * Sets the value of the key property.
-     * 
-     * @param value
-     *          allowed object is {@link String }
+     * Gets the value of the gapChar property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public void setKey(String value)
-    {
-      this.key = value;
+    public String getGapChar() {
+        return gapChar;
     }
 
     /**
-     * Gets the value of the value property.
+     * Sets the value of the gapChar property.
      * 
-     * @return possible object is {@link String }
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setGapChar(String value) {
+        this.gapChar = value;
+    }
+
+    /**
+     * Gets the value of the datasetId property.
      * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
      */
-    public String getValue()
-    {
-      return value;
+    public String getDatasetId() {
+        return datasetId;
     }
 
     /**
-     * Sets the value of the value property.
+     * Sets the value of the datasetId property.
      * 
      * @param value
-     *          allowed object is {@link String }
-     * 
+     *     allowed object is
+     *     {@link String }
+     *     
      */
-    public void setValue(String value)
-    {
-      this.value = value;
+    public void setDatasetId(String value) {
+        this.datasetId = value;
     }
 
-  }
+
+    /**
+     * 
Java class for anonymous complex type.
+     * 
+     * 
The following schema fragment specifies the expected content contained within this class.
+     * 
+     * 
+     * <complexType>
+     *   <complexContent>
+     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     </restriction>
+     *   </complexContent>
+     * </complexType>
+     * 

+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class SequenceSetProperties {
+
+        @XmlAttribute(name = "key")
+        protected String key;
+        @XmlAttribute(name = "value")
+        protected String value;
+
+        /**
+         * Gets the value of the key property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getKey() {
+            return key;
+        }
+
+        /**
+         * Sets the value of the key property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setKey(String value) {
+            this.key = value;
+        }
+
+        /**
+         * Gets the value of the value property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getValue() {
+            return value;
+        }
+
+        /**
+         * Sets the value of the value property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setValue(String value) {
+            this.value = value;
+        }
+
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/SequenceType.java b/src/jalview/xml/binding/jalview/SequenceType.java
index 44e606d..ca7e899 100644
--- a/src/jalview/xml/binding/jalview/SequenceType.java
+++ b/src/jalview/xml/binding/jalview/SequenceType.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlAccessType;
@@ -13,13 +14,11 @@ import javax.xml.bind.annotation.XmlAttribute;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for SequenceType complex type.
+ * 
Java class for SequenceType complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="SequenceType">
@@ -39,111 +38,116 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "SequenceType", propOrder = { "sequence", "name" })
-@XmlSeeAlso({ Sequence.class })
-public class SequenceType
-{
-
-  protected String sequence;
-
-  protected String name;
-
-  @XmlAttribute(name = "id")
-  protected String id;
-
-  @XmlAttribute(name = "description")
-  protected String description;
-
-  /**
-   * Gets the value of the sequence property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getSequence()
-  {
-    return sequence;
-  }
-
-  /**
-   * Sets the value of the sequence property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setSequence(String value)
-  {
-    this.sequence = value;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
-
-  /**
-   * Gets the value of the id property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getId()
-  {
-    return id;
-  }
-
-  /**
-   * Sets the value of the id property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setId(String value)
-  {
-    this.id = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
+@XmlType(name = "SequenceType", propOrder = {
+    "sequence",
+    "name"
+})
+@XmlSeeAlso({
+    Sequence.class
+})
+public class SequenceType {
+
+    protected String sequence;
+    protected String name;
+    @XmlAttribute(name = "id")
+    protected String id;
+    @XmlAttribute(name = "description")
+    protected String description;
+
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getSequence() {
+        return sequence;
+    }
+
+    /**
+     * Sets the value of the sequence property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setSequence(String value) {
+        this.sequence = value;
+    }
+
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
+    }
+
+    /**
+     * Gets the value of the id property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getId() {
+        return id;
+    }
+
+    /**
+     * Sets the value of the id property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setId(String value) {
+        this.id = value;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
+
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java
index ad0ea1e..42cf56a 100644
--- a/src/jalview/xml/binding/jalview/ThresholdType.java
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -2,23 +2,21 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import javax.xml.bind.annotation.XmlEnum;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for ThresholdType.
+ * 
Java class for ThresholdType.
  * 
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 

- * The following schema fragment specifies the expected content contained within
- * this class.
- * 

- * 
  * 
  * <simpleType name="ThresholdType">
  *   <restriction base="{http://www.w3.org/2001/XMLSchema}string">
@@ -32,19 +30,18 @@ import javax.xml.bind.annotation.XmlType;
  */
 @XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
 @XmlEnum
-public enum ThresholdType
-{
+public enum ThresholdType {
 
-  NONE, ABOVE, BELOW;
+    NONE,
+    ABOVE,
+    BELOW;
 
-  public String value()
-  {
-    return name();
-  }
+    public String value() {
+        return name();
+    }
 
-  public static ThresholdType fromValue(String v)
-  {
-    return valueOf(v);
-  }
+    public static ThresholdType fromValue(String v) {
+        return valueOf(v);
+    }
 
 }
diff --git a/src/jalview/xml/binding/jalview/VAMSAS.java b/src/jalview/xml/binding/jalview/VAMSAS.java
index 099af84..84fe566 100644
--- a/src/jalview/xml/binding/jalview/VAMSAS.java
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -14,13 +15,11 @@ import javax.xml.bind.annotation.XmlAccessorType;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for VAMSAS complex type.
+ * 
Java class for VAMSAS complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="VAMSAS">
@@ -38,77 +37,73 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "VAMSAS", propOrder = { "tree", "sequenceSet" })
-public class VAMSAS
-{
-
-  @XmlElement(name = "Tree")
-  protected List tree;
+@XmlType(name = "VAMSAS", propOrder = {
+    "tree",
+    "sequenceSet"
+})
+public class VAMSAS {
 
-  @XmlElement(name = "SequenceSet")
-  protected List sequenceSet;
+    @XmlElement(name = "Tree")
+    protected List tree;
+    @XmlElement(name = "SequenceSet")
+    protected List sequenceSet;
 
-  /**
-   * Gets the value of the tree property.
-   * 
-   * 

-   * 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 set method
-   * for the tree property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getTree().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getTree()
-  {
-    if (tree == null)
-    {
-      tree = new ArrayList();
+    /**
+     * Gets the value of the tree property.
+     * 
+     * 

+     * 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 set method for the tree property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getTree().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getTree() {
+        if (tree == null) {
+            tree = new ArrayList();
+        }
+        return this.tree;
     }
-    return this.tree;
-  }
 
-  /**
-   * Gets the value of the sequenceSet property.
-   * 
-   * 

-   * 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 set method
-   * for the sequenceSet property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getSequenceSet().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link SequenceSet
-   * }
-   * 
-   * 
-   */
-  public List getSequenceSet()
-  {
-    if (sequenceSet == null)
-    {
-      sequenceSet = new ArrayList();
+    /**
+     * Gets the value of the sequenceSet property.
+     * 
+     * 

+     * 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 set method for the sequenceSet property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getSequenceSet().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link SequenceSet }
+     * 
+     * 
+     */
+    public List getSequenceSet() {
+        if (sequenceSet == null) {
+            sequenceSet = new ArrayList();
+        }
+        return this.sequenceSet;
     }
-    return this.sequenceSet;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
index 4374c83..0c61ab1 100644
--- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
+++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
@@ -2,9 +2,10 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
+
 package jalview.xml.binding.jalview;
 
 import java.util.ArrayList;
@@ -17,13 +18,11 @@ import javax.xml.bind.annotation.XmlSchemaType;
 import javax.xml.bind.annotation.XmlSeeAlso;
 import javax.xml.bind.annotation.XmlType;
 
+
 /**
- * 

- * Java class for WebServiceParameterSet complex type.
+ * 
Java class for WebServiceParameterSet complex type.
  * 
- * 

- * The following schema fragment specifies the expected content contained within
- * this class.
+ * 
The following schema fragment specifies the expected content contained within this class.
  * 
  * 
  * <complexType name="WebServiceParameterSet">
@@ -44,153 +43,152 @@ import javax.xml.bind.annotation.XmlType;
  * 
  */
 @XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(
-  name = "WebServiceParameterSet",
-  namespace = "www.jalview.org/xml/wsparamset",
-  propOrder =
-  { "version", "description", "serviceURL", "parameters" })
+@XmlType(name = "WebServiceParameterSet", namespace = "www.jalview.org/xml/wsparamset", propOrder = {
+    "version",
+    "description",
+    "serviceURL",
+    "parameters"
+})
 @XmlSeeAlso({
-    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class })
-public class WebServiceParameterSet
-{
-
-  @XmlElement(name = "Version", namespace = "")
-  protected String version;
-
-  @XmlElement(namespace = "")
-  protected String description;
-
-  @XmlElement(namespace = "", required = true)
-  @XmlSchemaType(name = "anyURI")
-  protected List serviceURL;
-
-  @XmlElement(namespace = "", required = true)
-  protected String parameters;
-
-  @XmlAttribute(name = "name", required = true)
-  protected String name;
-
-  /**
-   * Gets the value of the version property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getVersion()
-  {
-    return version;
-  }
-
-  /**
-   * Sets the value of the version property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setVersion(String value)
-  {
-    this.version = value;
-  }
-
-  /**
-   * Gets the value of the description property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getDescription()
-  {
-    return description;
-  }
-
-  /**
-   * Sets the value of the description property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setDescription(String value)
-  {
-    this.description = value;
-  }
-
-  /**
-   * Gets the value of the serviceURL property.
-   * 
-   * 

-   * 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 set method
-   * for the serviceURL property.
-   * 
-   * 

-   * For example, to add a new item, do as follows:
-   * 
-   * 
-   * getServiceURL().add(newItem);
-   * 

-   * 
-   * 
-   * 

-   * Objects of the following type(s) are allowed in the list {@link String }
-   * 
-   * 
-   */
-  public List getServiceURL()
-  {
-    if (serviceURL == null)
-    {
-      serviceURL = new ArrayList();
+    jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam.class
+})
+public class WebServiceParameterSet {
+
+    @XmlElement(name = "Version", namespace = "")
+    protected String version;
+    @XmlElement(namespace = "")
+    protected String description;
+    @XmlElement(namespace = "", required = true)
+    @XmlSchemaType(name = "anyURI")
+    protected List serviceURL;
+    @XmlElement(namespace = "", required = true)
+    protected String parameters;
+    @XmlAttribute(name = "name", required = true)
+    protected String name;
+
+    /**
+     * Gets the value of the version property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getVersion() {
+        return version;
+    }
+
+    /**
+     * Sets the value of the version property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setVersion(String value) {
+        this.version = value;
+    }
+
+    /**
+     * Gets the value of the description property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDescription() {
+        return description;
+    }
+
+    /**
+     * Sets the value of the description property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDescription(String value) {
+        this.description = value;
+    }
+
+    /**
+     * Gets the value of the serviceURL property.
+     * 
+     * 

+     * 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 set method for the serviceURL property.
+     * 
+     * 

+     * For example, to add a new item, do as follows:
+     * 
+     *    getServiceURL().add(newItem);
+     * 

+     * 
+     * 
+     * 

+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List getServiceURL() {
+        if (serviceURL == null) {
+            serviceURL = new ArrayList();
+        }
+        return this.serviceURL;
+    }
+
+    /**
+     * Gets the value of the parameters property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getParameters() {
+        return parameters;
+    }
+
+    /**
+     * Sets the value of the parameters property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setParameters(String value) {
+        this.parameters = value;
+    }
+
+    /**
+     * Gets the value of the name property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getName() {
+        return name;
+    }
+
+    /**
+     * Sets the value of the name property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setName(String value) {
+        this.name = value;
     }
-    return this.serviceURL;
-  }
-
-  /**
-   * Gets the value of the parameters property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getParameters()
-  {
-    return parameters;
-  }
-
-  /**
-   * Sets the value of the parameters property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setParameters(String value)
-  {
-    this.parameters = value;
-  }
-
-  /**
-   * Gets the value of the name property.
-   * 
-   * @return possible object is {@link String }
-   * 
-   */
-  public String getName()
-  {
-    return name;
-  }
-
-  /**
-   * Sets the value of the name property.
-   * 
-   * @param value
-   *          allowed object is {@link String }
-   * 
-   */
-  public void setName(String value)
-  {
-    this.name = value;
-  }
 
 }
diff --git a/src/jalview/xml/binding/jalview/package-info.java b/src/jalview/xml/binding/jalview/package-info.java
index 65d49d5..d2c51bc 100644
--- a/src/jalview/xml/binding/jalview/package-info.java
+++ b/src/jalview/xml/binding/jalview/package-info.java
@@ -2,10 +2,8 @@
 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
 // See http://java.sun.com/xml/jaxb 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2023.05.13 at 06:58:41 PM BST 
+// Generated on: 2023.07.18 at 05:07:54 PM BST 
 //
 
-@javax.xml.bind.annotation.XmlSchema(
-  namespace = "www.vamsas.ac.uk/jalview/version2",
-  elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
 package jalview.xml.binding.jalview;
-- 
1.7.10.2