From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Tue, 18 Sep 2018 15:01:52 +0000 (+0100)
Subject: JAL-3063 JAXB binding classes generated by xjc from jalview.xsd
X-Git-Tag: Release_2_11_1_0~78^2~31
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=85ed72a5a52344d202f671eb6892dc74656c29ea;p=jalview.git

JAL-3063 JAXB binding classes generated by xjc from jalview.xsd
---

diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java
new file mode 100644
index 0000000..f4e7d84
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java
@@ -0,0 +1,326 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 PM BST 
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.math.BigInteger;
+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.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="alcodon" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *         &lt;element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;sequence>
+ *                   &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+ *                 &lt;/sequence>
+ *                 &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+    "alcodon",
+    "alcodMap"
+})
+@XmlRootElement(name = "AlcodonFrame")
+public class AlcodonFrame {
+
+    protected List<AlcodonFrame.Alcodon> alcodon;
+    protected List<AlcodonFrame.AlcodMap> alcodMap;
+
+    /**
+     * Gets the value of the alcodon property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the alcodon property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAlcodon().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame.Alcodon }
+     * 
+     * 
+     */
+    public List<AlcodonFrame.Alcodon> getAlcodon() {
+        if (alcodon == null) {
+            alcodon = new ArrayList<AlcodonFrame.Alcodon>();
+        }
+        return this.alcodon;
+    }
+
+    /**
+     * Gets the value of the alcodMap property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAlcodMap().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame.AlcodMap }
+     * 
+     * 
+     */
+    public List<AlcodonFrame.AlcodMap> getAlcodMap() {
+        if (alcodMap == null) {
+            alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
+        }
+        return this.alcodMap;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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;
+
+        /**
+         * 
+         * 										a Mapping entry and an associated protein sequence
+         * 									
+         * 
+         * @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 dnasq property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getDnasq() {
+            return dnasq;
+        }
+
+        /**
+         * Sets the value of the dnasq property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setDnasq(String value) {
+            this.dnasq = value;
+        }
+
+    }
+
+
+    /**
+     * 
+     * 								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).
+     * 							
+     * 
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *       &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Alcodon {
+
+        @XmlAttribute(name = "pos1")
+        protected BigInteger pos1;
+        @XmlAttribute(name = "pos2")
+        protected BigInteger pos2;
+        @XmlAttribute(name = "pos3")
+        protected BigInteger pos3;
+
+        /**
+         * Gets the value of the pos1 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos1() {
+            return pos1;
+        }
+
+        /**
+         * Sets the value of the pos1 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos1(BigInteger value) {
+            this.pos1 = value;
+        }
+
+        /**
+         * Gets the value of the pos2 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos2() {
+            return pos2;
+        }
+
+        /**
+         * Sets the value of the pos2 property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link BigInteger }
+         *     
+         */
+        public void setPos2(BigInteger value) {
+            this.pos2 = value;
+        }
+
+        /**
+         * Gets the value of the pos3 property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link BigInteger }
+         *     
+         */
+        public BigInteger getPos3() {
+            return pos3;
+        }
+
+        /**
+         * 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
new file mode 100644
index 0000000..22f6674
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/Annotation.java
@@ -0,0 +1,857 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="thresholdLine" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *         &lt;element name="property" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *       &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
+ *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *       &lt;attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *       &lt;attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+    "annotationElement",
+    "label",
+    "description",
+    "thresholdLine",
+    "property"
+})
+@XmlRootElement(name = "Annotation")
+public class Annotation {
+
+    protected List<AnnotationElement> annotationElement;
+    @XmlElement(required = true)
+    protected String label;
+    protected String description;
+    protected Annotation.ThresholdLine thresholdLine;
+    protected List<Annotation.Property> 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.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAnnotationElement().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link AnnotationElement }
+     * 
+     * 
+     */
+    public List<AnnotationElement> getAnnotationElement() {
+        if (annotationElement == null) {
+            annotationElement = new ArrayList<AnnotationElement>();
+        }
+        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 property property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the property property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getProperty().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Annotation.Property }
+     * 
+     * 
+     */
+    public List<Annotation.Property> getProperty() {
+        if (property == null) {
+            property = new ArrayList<Annotation.Property>();
+        }
+        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;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "")
+    public static class Property {
+
+        @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;
+        }
+
+        /**
+         * 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;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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
new file mode 100644
index 0000000..bcf3302
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java
@@ -0,0 +1,254 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 PM BST 
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for AnnotationColourScheme complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="AnnotationColourScheme">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;attribute name="aboveThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="annotation" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="minColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="maxColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="colourScheme" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *       &lt;attribute name="perSequence" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *       &lt;attribute name="predefinedColours" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@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;
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/AnnotationElement.java b/src/jalview/xml/binding/jalview/AnnotationElement.java
new file mode 100644
index 0000000..dcee889
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/AnnotationElement.java
@@ -0,0 +1,203 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 PM BST 
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="displayCharacter" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="secondaryStructure" minOccurs="0">
+ *           &lt;simpleType>
+ *             &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *               &lt;length value="1"/>
+ *             &lt;/restriction>
+ *           &lt;/simpleType>
+ *         &lt;/element>
+ *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}float" minOccurs="0"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="position" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@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;
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/Feature.java b/src/jalview/xml/binding/jalview/Feature.java
new file mode 100644
index 0000000..1040636
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/Feature.java
@@ -0,0 +1,363 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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;
+
+
+/**
+ * <p>Java class for feature complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="feature">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="otherData" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="status" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="featureGroup" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "feature", namespace = "www.jalview.org", propOrder = {
+    "otherData"
+})
+public class Feature {
+
+    protected List<Feature.OtherData> 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.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the otherData property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getOtherData().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Feature.OtherData }
+     * 
+     * 
+     */
+    public List<Feature.OtherData> getOtherData() {
+        if (otherData == null) {
+            otherData = new ArrayList<Feature.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;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="key2" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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
new file mode 100644
index 0000000..3f3d812
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java
@@ -0,0 +1,160 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for FeatureMatcher complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="FeatureMatcher">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *         &lt;element name="condition" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="by" type="{www.jalview.org/colours}FilterBy" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "FeatureMatcher", namespace = "www.jalview.org/colours", propOrder = {
+    "attributeName",
+    "condition",
+    "value"
+})
+public class FeatureMatcher {
+
+    @XmlElement(namespace = "")
+    protected List<String> attributeName;
+    @XmlElement(namespace = "", required = true)
+    protected String condition;
+    @XmlElement(namespace = "", required = true)
+    protected String value;
+    @XmlAttribute(name = "by")
+    protected FilterBy by;
+
+    /**
+     * Gets the value of the attributeName property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAttributeName().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List<String> getAttributeName() {
+        if (attributeName == null) {
+            attributeName = new ArrayList<String>();
+        }
+        return this.attributeName;
+    }
+
+    /**
+     * 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;
+    }
+
+    /**
+     * 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 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;
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
new file mode 100644
index 0000000..f33d379
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java
@@ -0,0 +1,192 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * A feature match condition, which may be simple or compound
+ * 
+ * <p>Java class for FeatureMatcherSet complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="FeatureMatcherSet">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;choice>
+ *         &lt;element name="matchCondition" type="{www.jalview.org/colours}FeatureMatcher"/>
+ *         &lt;element name="compoundMatcher">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;sequence>
+ *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+ *                 &lt;/sequence>
+ *                 &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/choice>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@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;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" maxOccurs="2" minOccurs="2"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="and" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "matcherSet"
+    })
+    public static class CompoundMatcher {
+
+        @XmlElement(namespace = "", required = true)
+        protected List<FeatureMatcherSet> matcherSet;
+        @XmlAttribute(name = "and", required = true)
+        protected boolean and;
+
+        /**
+         * Gets the value of the matcherSet property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the matcherSet property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getMatcherSet().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link FeatureMatcherSet }
+         * 
+         * 
+         */
+        public List<FeatureMatcherSet> getMatcherSet() {
+            if (matcherSet == null) {
+                matcherSet = new ArrayList<FeatureMatcherSet>();
+            }
+            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
new file mode 100644
index 0000000..7877175
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/FilterBy.java
@@ -0,0 +1,61 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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;
+
+
+/**
+ * <p>Java class for FilterBy.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * &lt;simpleType name="FilterBy">
+ *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     &lt;enumeration value="byLabel"/>
+ *     &lt;enumeration value="byScore"/>
+ *     &lt;enumeration value="byAttribute"/>
+ *   &lt;/restriction>
+ * &lt;/simpleType>
+ * </pre>
+ * 
+ */
+@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 String value() {
+        return value;
+    }
+
+    public static FilterBy fromValue(String v) {
+        for (FilterBy c: FilterBy.values()) {
+            if (c.value.equals(v)) {
+                return c;
+            }
+        }
+        throw new IllegalArgumentException(v);
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
new file mode 100644
index 0000000..9cc7d80
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -0,0 +1,5090 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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.XmlElement;
+import javax.xml.bind.annotation.XmlID;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
+import javax.xml.datatype.XMLGregorianCalendar;
+
+
+/**
+ * <p>Java class for JalviewModel complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="JalviewModel">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ *         &lt;sequence>
+ *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;extension base="{www.jalview.org}pdbentry">
+ *                             &lt;sequence>
+ *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ *                                 &lt;complexType>
+ *                                   &lt;simpleContent>
+ *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+ *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     &lt;/extension>
+ *                                   &lt;/simpleContent>
+ *                                 &lt;/complexType>
+ *                               &lt;/element>
+ *                             &lt;/sequence>
+ *                           &lt;/extension>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;sequence>
+ *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
+ *                                 &lt;complexType>
+ *                                   &lt;complexContent>
+ *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     &lt;/restriction>
+ *                                   &lt;/complexContent>
+ *                                 &lt;/complexType>
+ *                               &lt;/element>
+ *                             &lt;/sequence>
+ *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                   &lt;/sequence>
+ *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                   &lt;/sequence>
+ *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           &lt;/extension>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                   &lt;/sequence>
+ *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ *                   &lt;/sequence>
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence minOccurs="0">
+ *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                   &lt;/sequence>
+ *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="FeatureSettings" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;sequence>
+ *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ *                             &lt;/sequence>
+ *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                   &lt;/sequence>
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *         &lt;/sequence>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
+    "creationDate",
+    "version",
+    "vamsasModel",
+    "jSeq",
+    "jGroup",
+    "viewport",
+    "userColours",
+    "tree",
+    "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<JalviewModel.JSeq> jSeq;
+    @XmlElement(name = "JGroup")
+    protected List<JalviewModel.JGroup> jGroup;
+    @XmlElement(name = "Viewport")
+    protected List<JalviewModel.Viewport> viewport;
+    @XmlElement(name = "UserColours")
+    protected List<JalviewModel.UserColours> userColours;
+    protected List<JalviewModel.Tree> tree;
+    @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.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getJSeq().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.JSeq }
+     * 
+     * 
+     */
+    public List<JalviewModel.JSeq> getJSeq() {
+        if (jSeq == null) {
+            jSeq = new ArrayList<JalviewModel.JSeq>();
+        }
+        return this.jSeq;
+    }
+
+    /**
+     * Gets the value of the jGroup property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getJGroup().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.JGroup }
+     * 
+     * 
+     */
+    public List<JalviewModel.JGroup> getJGroup() {
+        if (jGroup == null) {
+            jGroup = new ArrayList<JalviewModel.JGroup>();
+        }
+        return this.jGroup;
+    }
+
+    /**
+     * Gets the value of the viewport property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the viewport property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getViewport().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.Viewport }
+     * 
+     * 
+     */
+    public List<JalviewModel.Viewport> getViewport() {
+        if (viewport == null) {
+            viewport = new ArrayList<JalviewModel.Viewport>();
+        }
+        return this.viewport;
+    }
+
+    /**
+     * Gets the value of the userColours property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the userColours property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getUserColours().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.UserColours }
+     * 
+     * 
+     */
+    public List<JalviewModel.UserColours> getUserColours() {
+        if (userColours == null) {
+            userColours = new ArrayList<JalviewModel.UserColours>();
+        }
+        return this.userColours;
+    }
+
+    /**
+     * Gets the value of the tree property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the tree property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getTree().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModel.Tree }
+     * 
+     * 
+     */
+    public List<JalviewModel.Tree> getTree() {
+        if (tree == null) {
+            tree = new ArrayList<JalviewModel.Tree>();
+        }
+        return this.tree;
+    }
+
+    /**
+     * 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;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;sequence>
+     *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *                 &lt;/sequence>
+     *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "setting",
+        "group"
+    })
+    public static class FeatureSettings {
+
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.FeatureSettings.Setting> setting;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.FeatureSettings.Group> group;
+
+        /**
+         * Gets the value of the setting property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the setting property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getSetting().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.FeatureSettings.Setting }
+         * 
+         * 
+         */
+        public List<JalviewModel.FeatureSettings.Setting> getSetting() {
+            if (setting == null) {
+                setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
+            }
+            return this.setting;
+        }
+
+        /**
+         * Gets the value of the group property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the group property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getGroup().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.FeatureSettings.Group }
+         * 
+         * 
+         */
+        public List<JalviewModel.FeatureSettings.Group> getGroup() {
+            if (group == null) {
+                group = new ArrayList<JalviewModel.FeatureSettings.Group>();
+            }
+            return this.group;
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @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;
+            }
+
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;sequence>
+         *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+         *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+         *       &lt;/sequence>
+         *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+         *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "attributeName",
+            "matcherSet"
+        })
+        public static class Setting {
+
+            @XmlElement(namespace = "www.jalview.org")
+            protected List<String> 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.
+             * 
+             * <p>
+             * This accessor method returns a reference to the live list,
+             * not a snapshot. Therefore any modification you make to the
+             * returned list will be present inside the JAXB object.
+             * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+             * 
+             * <p>
+             * For example, to add a new item, do as follows:
+             * <pre>
+             *    getAttributeName().add(newItem);
+             * </pre>
+             * 
+             * 
+             * <p>
+             * Objects of the following type(s) are allowed in the list
+             * {@link String }
+             * 
+             * 
+             */
+            public List<String> getAttributeName() {
+                if (attributeName == null) {
+                    attributeName = new ArrayList<String>();
+                }
+                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;
+            }
+
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+     *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "seq",
+        "annotationColours"
+    })
+    public static class JGroup {
+
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List<String> 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.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the seq property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getSeq().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List<String> getSeq() {
+            if (seq == null) {
+                seq = new ArrayList<String>();
+            }
+            return this.seq;
+        }
+
+        /**
+         * 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 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;
+        }
+
+        /**
+         * 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 colour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getColour() {
+            return colour;
+        }
+
+        /**
+         * Sets the value of the colour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setColour(String value) {
+            this.colour = value;
+        }
+
+        /**
+         * Gets the value of the consThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getConsThreshold() {
+            return consThreshold;
+        }
+
+        /**
+         * 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 pidThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getPidThreshold() {
+            return pidThreshold;
+        }
+
+        /**
+         * 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 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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.
+         * 
+         * @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;
+        }
+
+        /**
+         * 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;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;extension base="{www.jalview.org}pdbentry">
+     *                 &lt;sequence>
+     *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *                     &lt;complexType>
+     *                       &lt;simpleContent>
+     *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+     *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         &lt;/extension>
+     *                       &lt;/simpleContent>
+     *                     &lt;/complexType>
+     *                   &lt;/element>
+     *                 &lt;/sequence>
+     *               &lt;/extension>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;sequence>
+     *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
+     *                     &lt;complexType>
+     *                       &lt;complexContent>
+     *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         &lt;/restriction>
+     *                       &lt;/complexContent>
+     *                     &lt;/complexType>
+     *                   &lt;/element>
+     *                 &lt;/sequence>
+     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "features",
+        "pdbids",
+        "hiddenSequences",
+        "rnaViewer"
+    })
+    public static class JSeq {
+
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<Feature> features;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.JSeq.Pdbids> pdbids;
+        @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+        protected List<Integer> hiddenSequences;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.JSeq.RnaViewer> 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.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the features property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getFeatures().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Feature }
+         * 
+         * 
+         */
+        public List<Feature> getFeatures() {
+            if (features == null) {
+                features = new ArrayList<Feature>();
+            }
+            return this.features;
+        }
+
+        /**
+         * Gets the value of the pdbids property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getPdbids().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.JSeq.Pdbids }
+         * 
+         * 
+         */
+        public List<JalviewModel.JSeq.Pdbids> getPdbids() {
+            if (pdbids == null) {
+                pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
+            }
+            return this.pdbids;
+        }
+
+        /**
+         * Gets the value of the hiddenSequences property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getHiddenSequences().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List<Integer> getHiddenSequences() {
+            if (hiddenSequences == null) {
+                hiddenSequences = new ArrayList<Integer>();
+            }
+            return this.hiddenSequences;
+        }
+
+        /**
+         * Gets the value of the rnaViewer property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getRnaViewer().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.JSeq.RnaViewer }
+         * 
+         * 
+         */
+        public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
+            if (rnaViewer == null) {
+                rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
+            }
+            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;
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;extension base="{www.jalview.org}pdbentry">
+         *       &lt;sequence>
+         *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+         *           &lt;complexType>
+         *             &lt;simpleContent>
+         *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+         *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+         *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               &lt;/extension>
+         *             &lt;/simpleContent>
+         *           &lt;/complexType>
+         *         &lt;/element>
+         *       &lt;/sequence>
+         *     &lt;/extension>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "structureState"
+        })
+        public static class Pdbids
+            extends Pdbentry
+        {
+
+            @XmlElement(namespace = "www.jalview.org")
+            protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
+
+            /**
+             * Gets the value of the structureState property.
+             * 
+             * <p>
+             * This accessor method returns a reference to the live list,
+             * not a snapshot. Therefore any modification you make to the
+             * returned list will be present inside the JAXB object.
+             * This is why there is not a <CODE>set</CODE> method for the structureState property.
+             * 
+             * <p>
+             * For example, to add a new item, do as follows:
+             * <pre>
+             *    getStructureState().add(newItem);
+             * </pre>
+             * 
+             * 
+             * <p>
+             * Objects of the following type(s) are allowed in the list
+             * {@link JalviewModel.JSeq.Pdbids.StructureState }
+             * 
+             * 
+             */
+            public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
+                if (structureState == null) {
+                    structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
+                }
+                return this.structureState;
+            }
+
+
+            /**
+             * <p>Java class for anonymous complex type.
+             * 
+             * <p>The following schema fragment specifies the expected content contained within this class.
+             * 
+             * <pre>
+             * &lt;complexType>
+             *   &lt;simpleContent>
+             *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+             *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+             *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+             *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     &lt;/extension>
+             *   &lt;/simpleContent>
+             * &lt;/complexType>
+             * </pre>
+             * 
+             * 
+             */
+            @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;
+                }
+
+            }
+
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;sequence>
+         *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
+         *           &lt;complexType>
+         *             &lt;complexContent>
+         *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               &lt;/restriction>
+         *             &lt;/complexContent>
+         *           &lt;/complexType>
+         *         &lt;/element>
+         *       &lt;/sequence>
+         *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+         *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "secondaryStructure"
+        })
+        public static class RnaViewer {
+
+            @XmlElement(namespace = "www.jalview.org", required = true)
+            protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> 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.
+             * 
+             * <p>
+             * This accessor method returns a reference to the live list,
+             * not a snapshot. Therefore any modification you make to the
+             * returned list will be present inside the JAXB object.
+             * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+             * 
+             * <p>
+             * For example, to add a new item, do as follows:
+             * <pre>
+             *    getSecondaryStructure().add(newItem);
+             * </pre>
+             * 
+             * 
+             * <p>
+             * Objects of the following type(s) are allowed in the list
+             * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+             * 
+             * 
+             */
+            public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
+                if (secondaryStructure == null) {
+                    secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
+                }
+                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;
+            }
+
+
+            /**
+             * <p>Java class for anonymous complex type.
+             * 
+             * <p>The following schema fragment specifies the expected content contained within this class.
+             * 
+             * <pre>
+             * &lt;complexType>
+             *   &lt;complexContent>
+             *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     &lt;/restriction>
+             *   &lt;/complexContent>
+             * &lt;/complexType>
+             * </pre>
+             * 
+             * 
+             */
+            @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;
+                }
+
+            }
+
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence minOccurs="0">
+     *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *       &lt;/sequence>
+     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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 = "id")
+        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+        @XmlID
+        @XmlSchemaType(name = "ID")
+        protected String id;
+        @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;
+        }
+
+        /**
+         * 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 newick property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getNewick() {
+            return newick;
+        }
+
+        /**
+         * Sets the value of the newick property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setNewick(String value) {
+            this.newick = value;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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 showBootstrap property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowBootstrap() {
+            return showBootstrap;
+        }
+
+        /**
+         * Sets the value of the showBootstrap property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowBootstrap(Boolean value) {
+            this.showBootstrap = value;
+        }
+
+        /**
+         * Gets the value of the showDistances property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowDistances() {
+            return showDistances;
+        }
+
+        /**
+         * Sets the value of the showDistances property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowDistances(Boolean value) {
+            this.showDistances = value;
+        }
+
+        /**
+         * Gets the value of the markUnlinked property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isMarkUnlinked() {
+            return markUnlinked;
+        }
+
+        /**
+         * Sets the value of the markUnlinked property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setMarkUnlinked(Boolean value) {
+            this.markUnlinked = value;
+        }
+
+        /**
+         * Gets the value of the fitToWindow property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isFitToWindow() {
+            return fitToWindow;
+        }
+
+        /**
+         * Sets the value of the fitToWindow property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFitToWindow(Boolean value) {
+            this.fitToWindow = value;
+        }
+
+        /**
+         * Gets the value of the currentTree property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isCurrentTree() {
+            return currentTree;
+        }
+
+        /**
+         * Sets the value of the currentTree property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCurrentTree(Boolean value) {
+            this.currentTree = 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 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;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               &lt;/extension>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "annotationColours",
+        "hiddenColumns",
+        "calcIdParam"
+    })
+    public static class Viewport {
+
+        @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+        protected AnnotationColourScheme annotationColours;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
+        @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 = "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 = "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 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.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getHiddenColumns().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.Viewport.HiddenColumns }
+         * 
+         * 
+         */
+        public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
+            if (hiddenColumns == null) {
+                hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
+            }
+            return this.hiddenColumns;
+        }
+
+        /**
+         * Gets the value of the calcIdParam property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getCalcIdParam().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModel.Viewport.CalcIdParam }
+         * 
+         * 
+         */
+        public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
+            if (calcIdParam == null) {
+                calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
+            }
+            return this.calcIdParam;
+        }
+
+        /**
+         * Gets the value of the conservationSelected property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isConservationSelected() {
+            return conservationSelected;
+        }
+
+        /**
+         * 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 bgColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getBgColour() {
+            return bgColour;
+        }
+
+        /**
+         * 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 consThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getConsThreshold() {
+            return consThreshold;
+        }
+
+        /**
+         * 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 pidThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getPidThreshold() {
+            return pidThreshold;
+        }
+
+        /**
+         * 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 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 showFullId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowFullId() {
+            return showFullId;
+        }
+
+        /**
+         * 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 rightAlignIds property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isRightAlignIds() {
+            return rightAlignIds;
+        }
+
+        /**
+         * 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 showText property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowText() {
+            return showText;
+        }
+
+        /**
+         * 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 showColourText property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowColourText() {
+            return showColourText;
+        }
+
+        /**
+         * 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 showUnconserved property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowUnconserved() {
+            if (showUnconserved == null) {
+                return false;
+            } else {
+                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 showBoxes property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowBoxes() {
+            return showBoxes;
+        }
+
+        /**
+         * 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 wrapAlignment property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isWrapAlignment() {
+            return wrapAlignment;
+        }
+
+        /**
+         * 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 renderGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isRenderGaps() {
+            return renderGaps;
+        }
+
+        /**
+         * 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 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;
+        }
+
+        /**
+         * Gets the value of the showNPfeatureTooltip property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowNPfeatureTooltip() {
+            return showNPfeatureTooltip;
+        }
+
+        /**
+         * 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 showDbRefTooltip property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowDbRefTooltip() {
+            return showDbRefTooltip;
+        }
+
+        /**
+         * 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 followHighlight property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isFollowHighlight() {
+            if (followHighlight == null) {
+                return true;
+            } else {
+                return followHighlight;
+            }
+        }
+
+        /**
+         * 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 followSelection property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isFollowSelection() {
+            if (followSelection == null) {
+                return true;
+            } else {
+                return followSelection;
+            }
+        }
+
+        /**
+         * 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 showAnnotation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowAnnotation() {
+            return showAnnotation;
+        }
+
+        /**
+         * 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 centreColumnLabels property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isCentreColumnLabels() {
+            if (centreColumnLabels == null) {
+                return false;
+            } else {
+                return centreColumnLabels;
+            }
+        }
+
+        /**
+         * 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 showGroupConservation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowGroupConservation() {
+            if (showGroupConservation == null) {
+                return false;
+            } else {
+                return showGroupConservation;
+            }
+        }
+
+        /**
+         * 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 showGroupConsensus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowGroupConsensus() {
+            if (showGroupConsensus == null) {
+                return false;
+            } else {
+                return showGroupConsensus;
+            }
+        }
+
+        /**
+         * 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 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 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 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;
+        }
+
+        /**
+         * 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 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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 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 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;
+        }
+
+        /**
+         * 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;
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+         *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     &lt;/extension>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @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) {
+                    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;
+            }
+
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @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;
+            }
+
+        }
+
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/JalviewModelType.java b/src/jalview/xml/binding/jalview/JalviewModelType.java
new file mode 100644
index 0000000..f084bc3
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/JalviewModelType.java
@@ -0,0 +1,5090 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 01:33:02 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.XmlElement;
+import javax.xml.bind.annotation.XmlID;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlType;
+import javax.xml.bind.annotation.XmlValue;
+import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
+import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
+import javax.xml.datatype.XMLGregorianCalendar;
+
+
+/**
+ * <p>Java class for JalviewModelType complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="JalviewModelType">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ *         &lt;sequence>
+ *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;extension base="{www.jalview.org}pdbentry">
+ *                             &lt;sequence>
+ *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ *                                 &lt;complexType>
+ *                                   &lt;simpleContent>
+ *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+ *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     &lt;/extension>
+ *                                   &lt;/simpleContent>
+ *                                 &lt;/complexType>
+ *                               &lt;/element>
+ *                             &lt;/sequence>
+ *                           &lt;/extension>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;sequence>
+ *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
+ *                                 &lt;complexType>
+ *                                   &lt;complexContent>
+ *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                                     &lt;/restriction>
+ *                                   &lt;/complexContent>
+ *                                 &lt;/complexType>
+ *                               &lt;/element>
+ *                             &lt;/sequence>
+ *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                   &lt;/sequence>
+ *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                   &lt;/sequence>
+ *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           &lt;/extension>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                   &lt;/sequence>
+ *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ *                   &lt;/sequence>
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence minOccurs="0">
+ *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *                   &lt;/sequence>
+ *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+ *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *           &lt;element name="FeatureSettings" minOccurs="0">
+ *             &lt;complexType>
+ *               &lt;complexContent>
+ *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                   &lt;sequence>
+ *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;sequence>
+ *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ *                             &lt;/sequence>
+ *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
+ *                       &lt;complexType>
+ *                         &lt;complexContent>
+ *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                           &lt;/restriction>
+ *                         &lt;/complexContent>
+ *                       &lt;/complexType>
+ *                     &lt;/element>
+ *                   &lt;/sequence>
+ *                 &lt;/restriction>
+ *               &lt;/complexContent>
+ *             &lt;/complexType>
+ *           &lt;/element>
+ *         &lt;/sequence>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "JalviewModelType", namespace = "www.jalview.org", propOrder = {
+    "creationDate",
+    "version",
+    "vamsasModel",
+    "jSeq",
+    "jGroup",
+    "viewport",
+    "userColours",
+    "tree",
+    "featureSettings"
+})
+public class JalviewModelType {
+
+    @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<JalviewModelType.JSeq> jSeq;
+    @XmlElement(name = "JGroup")
+    protected List<JalviewModelType.JGroup> jGroup;
+    @XmlElement(name = "Viewport")
+    protected List<JalviewModelType.Viewport> viewport;
+    @XmlElement(name = "UserColours")
+    protected List<JalviewModelType.UserColours> userColours;
+    protected List<JalviewModelType.Tree> tree;
+    @XmlElement(name = "FeatureSettings")
+    protected JalviewModelType.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.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getJSeq().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModelType.JSeq }
+     * 
+     * 
+     */
+    public List<JalviewModelType.JSeq> getJSeq() {
+        if (jSeq == null) {
+            jSeq = new ArrayList<JalviewModelType.JSeq>();
+        }
+        return this.jSeq;
+    }
+
+    /**
+     * Gets the value of the jGroup property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getJGroup().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModelType.JGroup }
+     * 
+     * 
+     */
+    public List<JalviewModelType.JGroup> getJGroup() {
+        if (jGroup == null) {
+            jGroup = new ArrayList<JalviewModelType.JGroup>();
+        }
+        return this.jGroup;
+    }
+
+    /**
+     * Gets the value of the viewport property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the viewport property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getViewport().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModelType.Viewport }
+     * 
+     * 
+     */
+    public List<JalviewModelType.Viewport> getViewport() {
+        if (viewport == null) {
+            viewport = new ArrayList<JalviewModelType.Viewport>();
+        }
+        return this.viewport;
+    }
+
+    /**
+     * Gets the value of the userColours property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the userColours property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getUserColours().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModelType.UserColours }
+     * 
+     * 
+     */
+    public List<JalviewModelType.UserColours> getUserColours() {
+        if (userColours == null) {
+            userColours = new ArrayList<JalviewModelType.UserColours>();
+        }
+        return this.userColours;
+    }
+
+    /**
+     * Gets the value of the tree property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the tree property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getTree().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewModelType.Tree }
+     * 
+     * 
+     */
+    public List<JalviewModelType.Tree> getTree() {
+        if (tree == null) {
+            tree = new ArrayList<JalviewModelType.Tree>();
+        }
+        return this.tree;
+    }
+
+    /**
+     * Gets the value of the featureSettings property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link JalviewModelType.FeatureSettings }
+     *     
+     */
+    public JalviewModelType.FeatureSettings getFeatureSettings() {
+        return featureSettings;
+    }
+
+    /**
+     * Sets the value of the featureSettings property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link JalviewModelType.FeatureSettings }
+     *     
+     */
+    public void setFeatureSettings(JalviewModelType.FeatureSettings value) {
+        this.featureSettings = value;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;sequence>
+     *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+     *                 &lt;/sequence>
+     *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "setting",
+        "group"
+    })
+    public static class FeatureSettings {
+
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModelType.FeatureSettings.Setting> setting;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModelType.FeatureSettings.Group> group;
+
+        /**
+         * Gets the value of the setting property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the setting property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getSetting().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModelType.FeatureSettings.Setting }
+         * 
+         * 
+         */
+        public List<JalviewModelType.FeatureSettings.Setting> getSetting() {
+            if (setting == null) {
+                setting = new ArrayList<JalviewModelType.FeatureSettings.Setting>();
+            }
+            return this.setting;
+        }
+
+        /**
+         * Gets the value of the group property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the group property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getGroup().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModelType.FeatureSettings.Group }
+         * 
+         * 
+         */
+        public List<JalviewModelType.FeatureSettings.Group> getGroup() {
+            if (group == null) {
+                group = new ArrayList<JalviewModelType.FeatureSettings.Group>();
+            }
+            return this.group;
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @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;
+            }
+
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;sequence>
+         *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+         *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+         *       &lt;/sequence>
+         *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+         *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+         *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "attributeName",
+            "matcherSet"
+        })
+        public static class Setting {
+
+            @XmlElement(namespace = "www.jalview.org")
+            protected List<String> 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.
+             * 
+             * <p>
+             * This accessor method returns a reference to the live list,
+             * not a snapshot. Therefore any modification you make to the
+             * returned list will be present inside the JAXB object.
+             * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+             * 
+             * <p>
+             * For example, to add a new item, do as follows:
+             * <pre>
+             *    getAttributeName().add(newItem);
+             * </pre>
+             * 
+             * 
+             * <p>
+             * Objects of the following type(s) are allowed in the list
+             * {@link String }
+             * 
+             * 
+             */
+            public List<String> getAttributeName() {
+                if (attributeName == null) {
+                    attributeName = new ArrayList<String>();
+                }
+                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;
+            }
+
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+     *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "seq",
+        "annotationColours"
+    })
+    public static class JGroup {
+
+        @XmlElement(namespace = "www.jalview.org", required = true)
+        protected List<String> 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.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the seq property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getSeq().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List<String> getSeq() {
+            if (seq == null) {
+                seq = new ArrayList<String>();
+            }
+            return this.seq;
+        }
+
+        /**
+         * 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 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;
+        }
+
+        /**
+         * 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 colour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getColour() {
+            return colour;
+        }
+
+        /**
+         * Sets the value of the colour property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setColour(String value) {
+            this.colour = value;
+        }
+
+        /**
+         * Gets the value of the consThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getConsThreshold() {
+            return consThreshold;
+        }
+
+        /**
+         * 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 pidThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getPidThreshold() {
+            return pidThreshold;
+        }
+
+        /**
+         * 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 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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.
+         * 
+         * @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;
+        }
+
+        /**
+         * 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;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;extension base="{www.jalview.org}pdbentry">
+     *                 &lt;sequence>
+     *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+     *                     &lt;complexType>
+     *                       &lt;simpleContent>
+     *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+     *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         &lt;/extension>
+     *                       &lt;/simpleContent>
+     *                     &lt;/complexType>
+     *                   &lt;/element>
+     *                 &lt;/sequence>
+     *               &lt;/extension>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+     *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;sequence>
+     *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
+     *                     &lt;complexType>
+     *                       &lt;complexContent>
+     *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                         &lt;/restriction>
+     *                       &lt;/complexContent>
+     *                     &lt;/complexType>
+     *                   &lt;/element>
+     *                 &lt;/sequence>
+     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "features",
+        "pdbids",
+        "hiddenSequences",
+        "rnaViewer"
+    })
+    public static class JSeq {
+
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<Feature> features;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModelType.JSeq.Pdbids> pdbids;
+        @XmlElement(namespace = "www.jalview.org", type = Integer.class)
+        protected List<Integer> hiddenSequences;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModelType.JSeq.RnaViewer> 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.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the features property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getFeatures().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Feature }
+         * 
+         * 
+         */
+        public List<Feature> getFeatures() {
+            if (features == null) {
+                features = new ArrayList<Feature>();
+            }
+            return this.features;
+        }
+
+        /**
+         * Gets the value of the pdbids property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getPdbids().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModelType.JSeq.Pdbids }
+         * 
+         * 
+         */
+        public List<JalviewModelType.JSeq.Pdbids> getPdbids() {
+            if (pdbids == null) {
+                pdbids = new ArrayList<JalviewModelType.JSeq.Pdbids>();
+            }
+            return this.pdbids;
+        }
+
+        /**
+         * Gets the value of the hiddenSequences property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getHiddenSequences().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link Integer }
+         * 
+         * 
+         */
+        public List<Integer> getHiddenSequences() {
+            if (hiddenSequences == null) {
+                hiddenSequences = new ArrayList<Integer>();
+            }
+            return this.hiddenSequences;
+        }
+
+        /**
+         * Gets the value of the rnaViewer property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getRnaViewer().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModelType.JSeq.RnaViewer }
+         * 
+         * 
+         */
+        public List<JalviewModelType.JSeq.RnaViewer> getRnaViewer() {
+            if (rnaViewer == null) {
+                rnaViewer = new ArrayList<JalviewModelType.JSeq.RnaViewer>();
+            }
+            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;
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;extension base="{www.jalview.org}pdbentry">
+         *       &lt;sequence>
+         *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
+         *           &lt;complexType>
+         *             &lt;simpleContent>
+         *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+         *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+         *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+         *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               &lt;/extension>
+         *             &lt;/simpleContent>
+         *           &lt;/complexType>
+         *         &lt;/element>
+         *       &lt;/sequence>
+         *     &lt;/extension>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "structureState"
+        })
+        public static class Pdbids
+            extends Pdbentry
+        {
+
+            @XmlElement(namespace = "www.jalview.org")
+            protected List<JalviewModelType.JSeq.Pdbids.StructureState> structureState;
+
+            /**
+             * Gets the value of the structureState property.
+             * 
+             * <p>
+             * This accessor method returns a reference to the live list,
+             * not a snapshot. Therefore any modification you make to the
+             * returned list will be present inside the JAXB object.
+             * This is why there is not a <CODE>set</CODE> method for the structureState property.
+             * 
+             * <p>
+             * For example, to add a new item, do as follows:
+             * <pre>
+             *    getStructureState().add(newItem);
+             * </pre>
+             * 
+             * 
+             * <p>
+             * Objects of the following type(s) are allowed in the list
+             * {@link JalviewModelType.JSeq.Pdbids.StructureState }
+             * 
+             * 
+             */
+            public List<JalviewModelType.JSeq.Pdbids.StructureState> getStructureState() {
+                if (structureState == null) {
+                    structureState = new ArrayList<JalviewModelType.JSeq.Pdbids.StructureState>();
+                }
+                return this.structureState;
+            }
+
+
+            /**
+             * <p>Java class for anonymous complex type.
+             * 
+             * <p>The following schema fragment specifies the expected content contained within this class.
+             * 
+             * <pre>
+             * &lt;complexType>
+             *   &lt;simpleContent>
+             *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
+             *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+             *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+             *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+             *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     &lt;/extension>
+             *   &lt;/simpleContent>
+             * &lt;/complexType>
+             * </pre>
+             * 
+             * 
+             */
+            @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;
+                }
+
+            }
+
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;sequence>
+         *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
+         *           &lt;complexType>
+         *             &lt;complexContent>
+         *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *               &lt;/restriction>
+         *             &lt;/complexContent>
+         *           &lt;/complexType>
+         *         &lt;/element>
+         *       &lt;/sequence>
+         *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+         *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @XmlAccessorType(XmlAccessType.FIELD)
+        @XmlType(name = "", propOrder = {
+            "secondaryStructure"
+        })
+        public static class RnaViewer {
+
+            @XmlElement(namespace = "www.jalview.org", required = true)
+            protected List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> 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.
+             * 
+             * <p>
+             * This accessor method returns a reference to the live list,
+             * not a snapshot. Therefore any modification you make to the
+             * returned list will be present inside the JAXB object.
+             * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+             * 
+             * <p>
+             * For example, to add a new item, do as follows:
+             * <pre>
+             *    getSecondaryStructure().add(newItem);
+             * </pre>
+             * 
+             * 
+             * <p>
+             * Objects of the following type(s) are allowed in the list
+             * {@link JalviewModelType.JSeq.RnaViewer.SecondaryStructure }
+             * 
+             * 
+             */
+            public List<JalviewModelType.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
+                if (secondaryStructure == null) {
+                    secondaryStructure = new ArrayList<JalviewModelType.JSeq.RnaViewer.SecondaryStructure>();
+                }
+                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;
+            }
+
+
+            /**
+             * <p>Java class for anonymous complex type.
+             * 
+             * <p>The following schema fragment specifies the expected content contained within this class.
+             * 
+             * <pre>
+             * &lt;complexType>
+             *   &lt;complexContent>
+             *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+             *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+             *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+             *     &lt;/restriction>
+             *   &lt;/complexContent>
+             * &lt;/complexType>
+             * </pre>
+             * 
+             * 
+             */
+            @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;
+                }
+
+            }
+
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence minOccurs="0">
+     *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+     *       &lt;/sequence>
+     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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 = "id")
+        @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+        @XmlID
+        @XmlSchemaType(name = "ID")
+        protected String id;
+        @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;
+        }
+
+        /**
+         * 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 newick property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getNewick() {
+            return newick;
+        }
+
+        /**
+         * Sets the value of the newick property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link String }
+         *     
+         */
+        public void setNewick(String value) {
+            this.newick = value;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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 showBootstrap property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowBootstrap() {
+            return showBootstrap;
+        }
+
+        /**
+         * Sets the value of the showBootstrap property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowBootstrap(Boolean value) {
+            this.showBootstrap = value;
+        }
+
+        /**
+         * Gets the value of the showDistances property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowDistances() {
+            return showDistances;
+        }
+
+        /**
+         * Sets the value of the showDistances property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setShowDistances(Boolean value) {
+            this.showDistances = value;
+        }
+
+        /**
+         * Gets the value of the markUnlinked property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isMarkUnlinked() {
+            return markUnlinked;
+        }
+
+        /**
+         * Sets the value of the markUnlinked property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setMarkUnlinked(Boolean value) {
+            this.markUnlinked = value;
+        }
+
+        /**
+         * Gets the value of the fitToWindow property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isFitToWindow() {
+            return fitToWindow;
+        }
+
+        /**
+         * Sets the value of the fitToWindow property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setFitToWindow(Boolean value) {
+            this.fitToWindow = value;
+        }
+
+        /**
+         * Gets the value of the currentTree property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isCurrentTree() {
+            return currentTree;
+        }
+
+        /**
+         * Sets the value of the currentTree property.
+         * 
+         * @param value
+         *     allowed object is
+         *     {@link Boolean }
+         *     
+         */
+        public void setCurrentTree(Boolean value) {
+            this.currentTree = 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 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;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+     *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *               &lt;/restriction>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+     *           &lt;complexType>
+     *             &lt;complexContent>
+     *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+     *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *               &lt;/extension>
+     *             &lt;/complexContent>
+     *           &lt;/complexType>
+     *         &lt;/element>
+     *       &lt;/sequence>
+     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
+     *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+     *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+     *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "annotationColours",
+        "hiddenColumns",
+        "calcIdParam"
+    })
+    public static class Viewport {
+
+        @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+        protected AnnotationColourScheme annotationColours;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModelType.Viewport.HiddenColumns> hiddenColumns;
+        @XmlElement(namespace = "www.jalview.org")
+        protected List<JalviewModelType.Viewport.CalcIdParam> calcIdParam;
+        @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 = "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 = "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 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.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getHiddenColumns().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModelType.Viewport.HiddenColumns }
+         * 
+         * 
+         */
+        public List<JalviewModelType.Viewport.HiddenColumns> getHiddenColumns() {
+            if (hiddenColumns == null) {
+                hiddenColumns = new ArrayList<JalviewModelType.Viewport.HiddenColumns>();
+            }
+            return this.hiddenColumns;
+        }
+
+        /**
+         * Gets the value of the calcIdParam property.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getCalcIdParam().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link JalviewModelType.Viewport.CalcIdParam }
+         * 
+         * 
+         */
+        public List<JalviewModelType.Viewport.CalcIdParam> getCalcIdParam() {
+            if (calcIdParam == null) {
+                calcIdParam = new ArrayList<JalviewModelType.Viewport.CalcIdParam>();
+            }
+            return this.calcIdParam;
+        }
+
+        /**
+         * Gets the value of the conservationSelected property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isConservationSelected() {
+            return conservationSelected;
+        }
+
+        /**
+         * 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 bgColour property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link String }
+         *     
+         */
+        public String getBgColour() {
+            return bgColour;
+        }
+
+        /**
+         * 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 consThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getConsThreshold() {
+            return consThreshold;
+        }
+
+        /**
+         * 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 pidThreshold property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Integer }
+         *     
+         */
+        public Integer getPidThreshold() {
+            return pidThreshold;
+        }
+
+        /**
+         * 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 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 showFullId property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowFullId() {
+            return showFullId;
+        }
+
+        /**
+         * 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 rightAlignIds property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isRightAlignIds() {
+            return rightAlignIds;
+        }
+
+        /**
+         * 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 showText property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowText() {
+            return showText;
+        }
+
+        /**
+         * 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 showColourText property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowColourText() {
+            return showColourText;
+        }
+
+        /**
+         * 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 showUnconserved property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowUnconserved() {
+            if (showUnconserved == null) {
+                return false;
+            } else {
+                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 showBoxes property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowBoxes() {
+            return showBoxes;
+        }
+
+        /**
+         * 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 wrapAlignment property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isWrapAlignment() {
+            return wrapAlignment;
+        }
+
+        /**
+         * 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 renderGaps property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isRenderGaps() {
+            return renderGaps;
+        }
+
+        /**
+         * 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 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;
+        }
+
+        /**
+         * Gets the value of the showNPfeatureTooltip property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowNPfeatureTooltip() {
+            return showNPfeatureTooltip;
+        }
+
+        /**
+         * 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 showDbRefTooltip property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowDbRefTooltip() {
+            return showDbRefTooltip;
+        }
+
+        /**
+         * 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 followHighlight property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isFollowHighlight() {
+            if (followHighlight == null) {
+                return true;
+            } else {
+                return followHighlight;
+            }
+        }
+
+        /**
+         * 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 followSelection property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isFollowSelection() {
+            if (followSelection == null) {
+                return true;
+            } else {
+                return followSelection;
+            }
+        }
+
+        /**
+         * 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 showAnnotation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public Boolean isShowAnnotation() {
+            return showAnnotation;
+        }
+
+        /**
+         * 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 centreColumnLabels property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isCentreColumnLabels() {
+            if (centreColumnLabels == null) {
+                return false;
+            } else {
+                return centreColumnLabels;
+            }
+        }
+
+        /**
+         * 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 showGroupConservation property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowGroupConservation() {
+            if (showGroupConservation == null) {
+                return false;
+            } else {
+                return showGroupConservation;
+            }
+        }
+
+        /**
+         * 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 showGroupConsensus property.
+         * 
+         * @return
+         *     possible object is
+         *     {@link Boolean }
+         *     
+         */
+        public boolean isShowGroupConsensus() {
+            if (showGroupConsensus == null) {
+                return false;
+            } else {
+                return showGroupConsensus;
+            }
+        }
+
+        /**
+         * 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 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 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 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;
+        }
+
+        /**
+         * 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 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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;
+        }
+
+        /**
+         * 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 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 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;
+        }
+
+        /**
+         * 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;
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+         *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+         *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+         *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+         *     &lt;/extension>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @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) {
+                    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;
+            }
+
+        }
+
+
+        /**
+         * <p>Java class for anonymous complex type.
+         * 
+         * <p>The following schema fragment specifies the expected content contained within this class.
+         * 
+         * <pre>
+         * &lt;complexType>
+         *   &lt;complexContent>
+         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+         *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+         *     &lt;/restriction>
+         *   &lt;/complexContent>
+         * &lt;/complexType>
+         * </pre>
+         * 
+         * 
+         */
+        @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;
+            }
+
+        }
+
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/JalviewUserColours.java b/src/jalview/xml/binding/jalview/JalviewUserColours.java
new file mode 100644
index 0000000..b6f6b83
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java
@@ -0,0 +1,612 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for JalviewUserColours complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="JalviewUserColours">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="colour" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;sequence>
+ *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ *                 &lt;/sequence>
+ *                 &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ *                 &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+ *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *         &lt;element name="filter" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;sequence>
+ *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+ *                 &lt;/sequence>
+ *                 &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@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<JalviewUserColours.Colour> colour;
+    @XmlElement(namespace = "")
+    protected List<JalviewUserColours.Filter> 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.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the colour property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getColour().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewUserColours.Colour }
+     * 
+     * 
+     */
+    public List<JalviewUserColours.Colour> getColour() {
+        if (colour == null) {
+            colour = new ArrayList<JalviewUserColours.Colour>();
+        }
+        return this.colour;
+    }
+
+    /**
+     * Gets the value of the filter property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the filter property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getFilter().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link JalviewUserColours.Filter }
+     * 
+     * 
+     */
+    public List<JalviewUserColours.Filter> getFilter() {
+        if (filter == null) {
+            filter = new ArrayList<JalviewUserColours.Filter>();
+        }
+        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;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+     *       &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
+     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+     *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @XmlAccessorType(XmlAccessType.FIELD)
+    @XmlType(name = "", propOrder = {
+        "attributeName"
+    })
+    public static class Colour {
+
+        @XmlElement(namespace = "")
+        protected List<String> 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.
+         * 
+         * <p>
+         * This accessor method returns a reference to the live list,
+         * not a snapshot. Therefore any modification you make to the
+         * returned list will be present inside the JAXB object.
+         * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+         * 
+         * <p>
+         * For example, to add a new item, do as follows:
+         * <pre>
+         *    getAttributeName().add(newItem);
+         * </pre>
+         * 
+         * 
+         * <p>
+         * Objects of the following type(s) are allowed in the list
+         * {@link String }
+         * 
+         * 
+         */
+        public List<String> getAttributeName() {
+            if (attributeName == null) {
+                attributeName = new ArrayList<String>();
+            }
+            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;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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;
+        }
+
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/MapListType.java b/src/jalview/xml/binding/jalview/MapListType.java
new file mode 100644
index 0000000..8e5f553
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/MapListType.java
@@ -0,0 +1,315 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 PM BST 
+//
+
+
+package jalview.xml.binding.jalview;
+
+import java.math.BigInteger;
+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.XmlSchemaType;
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * 
+ * 				This effectively represents a java.util.MapList object
+ * 			
+ * 
+ * <p>Java class for mapListType complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="mapListType">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="mapListFrom" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                 &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *         &lt;element name="mapListTo" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *                 &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="mapFromUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ *       &lt;attribute name="mapToUnit" use="required" type="{http://www.w3.org/2001/XMLSchema}positiveInteger" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "mapListType", propOrder = {
+    "mapListFrom",
+    "mapListTo"
+})
+@XmlSeeAlso({
+    Mapping.class
+})
+public class MapListType {
+
+    protected List<MapListType.MapListFrom> mapListFrom;
+    protected List<MapListType.MapListTo> 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.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the mapListFrom property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getMapListFrom().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link MapListType.MapListFrom }
+     * 
+     * 
+     */
+    public List<MapListType.MapListFrom> getMapListFrom() {
+        if (mapListFrom == null) {
+            mapListFrom = new ArrayList<MapListType.MapListFrom>();
+        }
+        return this.mapListFrom;
+    }
+
+    /**
+     * Gets the value of the mapListTo property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the mapListTo property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getMapListTo().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link MapListType.MapListTo }
+     * 
+     * 
+     */
+    public List<MapListType.MapListTo> getMapListTo() {
+        if (mapListTo == null) {
+            mapListTo = new ArrayList<MapListType.MapListTo>();
+        }
+        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;
+    }
+
+    /**
+     * 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;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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;
+        }
+
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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/Mapping.java b/src/jalview/xml/binding/jalview/Mapping.java
new file mode 100644
index 0000000..da64ed2
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/Mapping.java
@@ -0,0 +1,113 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 PM BST 
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+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).
+ * 				
+ * 
+ * <p>Java class for anonymous complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;extension base="{www.vamsas.ac.uk/jalview/version2}mapListType">
+ *       &lt;sequence>
+ *         &lt;choice minOccurs="0">
+ *           &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence"/>
+ *           &lt;element name="dseqFor">
+ *             &lt;simpleType>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *               &lt;/restriction>
+ *             &lt;/simpleType>
+ *           &lt;/element>
+ *         &lt;/choice>
+ *       &lt;/sequence>
+ *     &lt;/extension>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+    "sequence",
+    "dseqFor"
+})
+@XmlRootElement(name = "Mapping")
+public class Mapping
+    extends MapListType
+{
+
+    @XmlElement(name = "Sequence")
+    protected Sequence sequence;
+    protected String dseqFor;
+
+    /**
+     * 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;
+    }
+
+    /**
+     * 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;
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/NoValueColour.java b/src/jalview/xml/binding/jalview/NoValueColour.java
new file mode 100644
index 0000000..9bce64b
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/NoValueColour.java
@@ -0,0 +1,61 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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;
+
+
+/**
+ * <p>Java class for NoValueColour.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * &lt;simpleType name="NoValueColour">
+ *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     &lt;enumeration value="None"/>
+ *     &lt;enumeration value="Min"/>
+ *     &lt;enumeration value="Max"/>
+ *   &lt;/restriction>
+ * &lt;/simpleType>
+ * </pre>
+ * 
+ */
+@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 String value() {
+        return value;
+    }
+
+    public static NoValueColour fromValue(String v) {
+        for (NoValueColour c: NoValueColour.values()) {
+            if (c.value.equals(v)) {
+                return c;
+            }
+        }
+        throw new IllegalArgumentException(v);
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/ObjectFactory.java b/src/jalview/xml/binding/jalview/ObjectFactory.java
new file mode 100644
index 0000000..3b9cae3
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/ObjectFactory.java
@@ -0,0 +1,404 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 PM BST 
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.JAXBElement;
+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. 
+ * <p>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 _JalviewModel_QNAME = new QName("www.jalview.org", "JalviewModel");
+
+    /**
+     * 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.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 AnnotationColourScheme }
+     * 
+     */
+    public AnnotationColourScheme createAnnotationColourScheme() {
+        return new AnnotationColourScheme();
+    }
+
+    /**
+     * 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 Annotation.Property }
+     * 
+     */
+    public Annotation.Property createAnnotationProperty() {
+        return new Annotation.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.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.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 JalviewModel }{@code >}}
+     * 
+     */
+    @XmlElementDecl(namespace = "www.jalview.org", name = "JalviewModel")
+    public JAXBElement<JalviewModel> createJalviewModel(JalviewModel value) {
+        return new JAXBElement<JalviewModel>(_JalviewModel_QNAME, JalviewModel.class, null, value);
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/Pdbentry.java b/src/jalview/xml/binding/jalview/Pdbentry.java
new file mode 100644
index 0000000..acb0f78
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/Pdbentry.java
@@ -0,0 +1,247 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for pdbentry complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="pdbentry">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence maxOccurs="unbounded" minOccurs="0">
+ *         &lt;element name="property" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="file" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@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<Pdbentry.Property> 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.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the property property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getProperty().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Pdbentry.Property }
+     * 
+     * 
+     */
+    public List<Pdbentry.Property> getProperty() {
+        if (property == null) {
+            property = new ArrayList<Pdbentry.Property>();
+        }
+        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;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java
new file mode 100644
index 0000000..d5e1d33
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/Sequence.java
@@ -0,0 +1,257 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
+ *       &lt;sequence>
+ *         &lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;sequence>
+ *                   &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+ *                 &lt;/sequence>
+ *                 &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *       &lt;/sequence>
+ *       &lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/extension>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+    "dbRef"
+})
+@XmlRootElement(name = "Sequence")
+public class Sequence
+    extends SequenceType
+{
+
+    @XmlElement(name = "DBRef")
+    protected List<Sequence.DBRef> dbRef;
+    @XmlAttribute(name = "dsseqid")
+    protected String dsseqid;
+
+    /**
+     * Gets the value of the dbRef property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the dbRef property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getDBRef().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Sequence.DBRef }
+     * 
+     * 
+     */
+    public List<Sequence.DBRef> getDBRef() {
+        if (dbRef == null) {
+            dbRef = new ArrayList<Sequence.DBRef>();
+        }
+        return this.dbRef;
+    }
+
+    /**
+     * Gets the value of the dsseqid property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDsseqid() {
+        return dsseqid;
+    }
+
+    /**
+     * Sets the value of the dsseqid property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDsseqid(String value) {
+        this.dsseqid = value;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;sequence>
+     *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
+     *       &lt;/sequence>
+     *       &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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;
+
+        /**
+         * 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;
+        }
+
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java
new file mode 100644
index 0000000..1ac96eb
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/SequenceSet.java
@@ -0,0 +1,318 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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.XmlElement;
+import javax.xml.bind.annotation.XmlRootElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for anonymous complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType>
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
+ *           &lt;complexType>
+ *             &lt;complexContent>
+ *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *                 &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               &lt;/restriction>
+ *             &lt;/complexContent>
+ *           &lt;/complexType>
+ *         &lt;/element>
+ *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "", propOrder = {
+    "sequence",
+    "annotation",
+    "sequenceSetProperties",
+    "alcodonFrame"
+})
+@XmlRootElement(name = "SequenceSet")
+public class SequenceSet {
+
+    @XmlElement(name = "Sequence")
+    protected List<Sequence> sequence;
+    @XmlElement(name = "Annotation")
+    protected List<Annotation> annotation;
+    protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
+    @XmlElement(name = "AlcodonFrame")
+    protected List<AlcodonFrame> alcodonFrame;
+    @XmlAttribute(name = "gapChar", required = true)
+    protected String gapChar;
+    @XmlAttribute(name = "datasetId")
+    protected String datasetId;
+
+    /**
+     * Gets the value of the sequence property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the sequence property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getSequence().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Sequence }
+     * 
+     * 
+     */
+    public List<Sequence> getSequence() {
+        if (sequence == null) {
+            sequence = new ArrayList<Sequence>();
+        }
+        return this.sequence;
+    }
+
+    /**
+     * Gets the value of the annotation property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the annotation property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAnnotation().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link Annotation }
+     * 
+     * 
+     */
+    public List<Annotation> getAnnotation() {
+        if (annotation == null) {
+            annotation = new ArrayList<Annotation>();
+        }
+        return this.annotation;
+    }
+
+    /**
+     * Gets the value of the sequenceSetProperties property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getSequenceSetProperties().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link SequenceSet.SequenceSetProperties }
+     * 
+     * 
+     */
+    public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() {
+        if (sequenceSetProperties == null) {
+            sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
+        }
+        return this.sequenceSetProperties;
+    }
+
+    /**
+     * Gets the value of the alcodonFrame property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getAlcodonFrame().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link AlcodonFrame }
+     * 
+     * 
+     */
+    public List<AlcodonFrame> getAlcodonFrame() {
+        if (alcodonFrame == null) {
+            alcodonFrame = new ArrayList<AlcodonFrame>();
+        }
+        return this.alcodonFrame;
+    }
+
+    /**
+     * Gets the value of the gapChar property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getGapChar() {
+        return gapChar;
+    }
+
+    /**
+     * Sets the value of the gapChar property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setGapChar(String value) {
+        this.gapChar = value;
+    }
+
+    /**
+     * Gets the value of the datasetId property.
+     * 
+     * @return
+     *     possible object is
+     *     {@link String }
+     *     
+     */
+    public String getDatasetId() {
+        return datasetId;
+    }
+
+    /**
+     * Sets the value of the datasetId property.
+     * 
+     * @param value
+     *     allowed object is
+     *     {@link String }
+     *     
+     */
+    public void setDatasetId(String value) {
+        this.datasetId = value;
+    }
+
+
+    /**
+     * <p>Java class for anonymous complex type.
+     * 
+     * <p>The following schema fragment specifies the expected content contained within this class.
+     * 
+     * <pre>
+     * &lt;complexType>
+     *   &lt;complexContent>
+     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+     *       &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *       &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
+     *     &lt;/restriction>
+     *   &lt;/complexContent>
+     * &lt;/complexType>
+     * </pre>
+     * 
+     * 
+     */
+    @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
new file mode 100644
index 0000000..d59b714
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/SequenceType.java
@@ -0,0 +1,153 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 PM BST 
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlAccessType;
+import javax.xml.bind.annotation.XmlAccessorType;
+import javax.xml.bind.annotation.XmlAttribute;
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for SequenceType complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="SequenceType">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *       &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@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;
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/ThresholdType.java b/src/jalview/xml/binding/jalview/ThresholdType.java
new file mode 100644
index 0000000..a987524
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/ThresholdType.java
@@ -0,0 +1,47 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 PM BST 
+//
+
+
+package jalview.xml.binding.jalview;
+
+import javax.xml.bind.annotation.XmlEnum;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for ThresholdType.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>
+ * <pre>
+ * &lt;simpleType name="ThresholdType">
+ *   &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string">
+ *     &lt;enumeration value="NONE"/>
+ *     &lt;enumeration value="ABOVE"/>
+ *     &lt;enumeration value="BELOW"/>
+ *   &lt;/restriction>
+ * &lt;/simpleType>
+ * </pre>
+ * 
+ */
+@XmlType(name = "ThresholdType", namespace = "www.jalview.org/colours")
+@XmlEnum
+public enum ThresholdType {
+
+    NONE,
+    ABOVE,
+    BELOW;
+
+    public String value() {
+        return name();
+    }
+
+    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
new file mode 100644
index 0000000..bcefa96
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/VAMSAS.java
@@ -0,0 +1,109 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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.XmlElement;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for VAMSAS complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="VAMSAS">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
+ *         &lt;element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
+ *       &lt;/sequence>
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@XmlType(name = "VAMSAS", propOrder = {
+    "tree",
+    "sequenceSet"
+})
+public class VAMSAS {
+
+    @XmlElement(name = "Tree")
+    protected List<String> tree;
+    @XmlElement(name = "SequenceSet")
+    protected List<SequenceSet> sequenceSet;
+
+    /**
+     * Gets the value of the tree property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the tree property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getTree().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List<String> getTree() {
+        if (tree == null) {
+            tree = new ArrayList<String>();
+        }
+        return this.tree;
+    }
+
+    /**
+     * Gets the value of the sequenceSet property.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the sequenceSet property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getSequenceSet().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link SequenceSet }
+     * 
+     * 
+     */
+    public List<SequenceSet> getSequenceSet() {
+        if (sequenceSet == null) {
+            sequenceSet = new ArrayList<SequenceSet>();
+        }
+        return this.sequenceSet;
+    }
+
+}
diff --git a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
new file mode 100644
index 0000000..8bd69a1
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java
@@ -0,0 +1,194 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 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.XmlElement;
+import javax.xml.bind.annotation.XmlSchemaType;
+import javax.xml.bind.annotation.XmlSeeAlso;
+import javax.xml.bind.annotation.XmlType;
+
+
+/**
+ * <p>Java class for WebServiceParameterSet complex type.
+ * 
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ * 
+ * <pre>
+ * &lt;complexType name="WebServiceParameterSet">
+ *   &lt;complexContent>
+ *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       &lt;sequence>
+ *         &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
+ *         &lt;element name="serviceURL" type="{http://www.w3.org/2001/XMLSchema}anyURI" maxOccurs="unbounded"/>
+ *         &lt;element name="parameters" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ *       &lt;/sequence>
+ *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *     &lt;/restriction>
+ *   &lt;/complexContent>
+ * &lt;/complexType>
+ * </pre>
+ * 
+ * 
+ */
+@XmlAccessorType(XmlAccessType.FIELD)
+@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<String> 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.
+     * 
+     * <p>
+     * This accessor method returns a reference to the live list,
+     * not a snapshot. Therefore any modification you make to the
+     * returned list will be present inside the JAXB object.
+     * This is why there is not a <CODE>set</CODE> method for the serviceURL property.
+     * 
+     * <p>
+     * For example, to add a new item, do as follows:
+     * <pre>
+     *    getServiceURL().add(newItem);
+     * </pre>
+     * 
+     * 
+     * <p>
+     * Objects of the following type(s) are allowed in the list
+     * {@link String }
+     * 
+     * 
+     */
+    public List<String> getServiceURL() {
+        if (serviceURL == null) {
+            serviceURL = new ArrayList<String>();
+        }
+        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
new file mode 100644
index 0000000..de1dd05
--- /dev/null
+++ b/src/jalview/xml/binding/jalview/package-info.java
@@ -0,0 +1,9 @@
+//
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// Any modifications to this file will be lost upon recompilation of the source schema. 
+// Generated on: 2018.09.18 at 02:23:07 PM BST 
+//
+
+@javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)
+package jalview.xml.binding.jalview;