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JAL-3863 add canonical DBRefEntry flag to Jalview project
[jalview.git] / src / jalview / xml / binding / jalview / JalviewModel.java
diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java
index 0ea2491..90819d7 100644 (file)
--- a/src/jalview/xml/binding/jalview/JalviewModel.java
+++ b/src/jalview/xml/binding/jalview/JalviewModel.java
@@ -1,8 +1,8 @@
 //
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a> 
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 
+// See https://eclipse-ee4j.github.io/jaxb-ri 
 // Any modifications to this file will be lost upon recompilation of the source schema. 
-// Generated on: 2019.06.07 at 02:21:15 PM BST 
+// Generated on: 2021.08.30 at 11:05:22 AM BST 
 //
 
 
@@ -24,341 +24,341 @@ import javax.xml.datatype.XMLGregorianCalendar;
 
 
 /**
- * <p>Java class for JalviewModel complex type.
+ * &lt;p&gt;Java class for JalviewModel complex type.
  * 
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
  * 
- * <pre>
- * &lt;complexType name="JalviewModel">
- *   &lt;complexContent>
- *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       &lt;sequence>
- *         &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
- *         &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *         &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
- *         &lt;sequence>
- *           &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- *                     &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;extension base="{www.jalview.org}pdbentry">
- *                             &lt;sequence>
- *                               &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
- *                                 &lt;complexType>
- *                                   &lt;simpleContent>
- *                                     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
- *                                       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                                       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                                       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     &lt;/extension>
- *                                   &lt;/simpleContent>
- *                                 &lt;/complexType>
- *                               &lt;/element>
- *                             &lt;/sequence>
- *                           &lt;/extension>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- *                     &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;sequence>
- *                               &lt;element name="secondaryStructure" maxOccurs="unbounded">
- *                                 &lt;complexType>
- *                                   &lt;complexContent>
- *                                     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                                       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     &lt;/restriction>
- *                                   &lt;/complexContent>
- *                                 &lt;/complexType>
- *                               &lt;/element>
- *                             &lt;/sequence>
- *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                             &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                   &lt;/sequence>
- *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- *                     &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                   &lt;/sequence>
- *                   &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                     &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- *                             &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                             &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           &lt;/extension>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                   &lt;/sequence>
- *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                   &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- *                   &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- *                   &lt;/sequence>
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="tree" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence minOccurs="0">
- *                     &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *                     &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *                   &lt;/sequence>
- *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                   &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                   &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="sequencePoint" maxOccurs="unbounded">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attGroup ref="{www.jalview.org}position"/>
- *                             &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="axis" maxOccurs="3" minOccurs="3">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attGroup ref="{www.jalview.org}position"/>
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="seqPointMin">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attGroup ref="{www.jalview.org}position"/>
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="seqPointMax">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attGroup ref="{www.jalview.org}position"/>
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
- *                   &lt;/sequence>
- *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                   &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
- *                   &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                   &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *           &lt;element name="FeatureSettings" minOccurs="0">
- *             &lt;complexType>
- *               &lt;complexContent>
- *                 &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   &lt;sequence>
- *                     &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;sequence>
- *                               &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- *                               &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- *                             &lt;/sequence>
- *                             &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- *                             &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                     &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           &lt;/restriction>
- *                         &lt;/complexContent>
- *                       &lt;/complexType>
- *                     &lt;/element>
- *                   &lt;/sequence>
- *                 &lt;/restriction>
- *               &lt;/complexContent>
- *             &lt;/complexType>
- *           &lt;/element>
- *         &lt;/sequence>
- *       &lt;/sequence>
- *     &lt;/restriction>
- *   &lt;/complexContent>
- * &lt;/complexType>
- * </pre>
+ * &lt;pre&gt;
+ * &amp;lt;complexType name="JalviewModel"&amp;gt;
+ *   &amp;lt;complexContent&amp;gt;
+ *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *       &amp;lt;sequence&amp;gt;
+ *         &amp;lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&amp;gt;
+ *         &amp;lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+ *         &amp;lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&amp;gt;
+ *         &amp;lt;sequence&amp;gt;
+ *           &amp;lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *             &amp;lt;complexType&amp;gt;
+ *               &amp;lt;complexContent&amp;gt;
+ *                 &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                   &amp;lt;sequence&amp;gt;
+ *                     &amp;lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *                     &amp;lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
+ *                             &amp;lt;sequence&amp;gt;
+ *                               &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *                                 &amp;lt;complexType&amp;gt;
+ *                                   &amp;lt;simpleContent&amp;gt;
+ *                                     &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
+ *                                       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+ *                                       &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                                       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                                       &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                                       &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                                       &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                                       &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                                     &amp;lt;/extension&amp;gt;
+ *                                   &amp;lt;/simpleContent&amp;gt;
+ *                                 &amp;lt;/complexType&amp;gt;
+ *                               &amp;lt;/element&amp;gt;
+ *                             &amp;lt;/sequence&amp;gt;
+ *                           &amp;lt;/extension&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+ *                     &amp;lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                             &amp;lt;sequence&amp;gt;
+ *                               &amp;lt;element name="secondaryStructure" maxOccurs="unbounded"&amp;gt;
+ *                                 &amp;lt;complexType&amp;gt;
+ *                                   &amp;lt;complexContent&amp;gt;
+ *                                     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                                       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                                       &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                                       &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                                       &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                                     &amp;lt;/restriction&amp;gt;
+ *                                   &amp;lt;/complexContent&amp;gt;
+ *                                 &amp;lt;/complexType&amp;gt;
+ *                               &amp;lt;/element&amp;gt;
+ *                             &amp;lt;/sequence&amp;gt;
+ *                             &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+ *                             &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                             &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                             &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                             &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                 &amp;lt;/restriction&amp;gt;
+ *               &amp;lt;/complexContent&amp;gt;
+ *             &amp;lt;/complexType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *             &amp;lt;complexType&amp;gt;
+ *               &amp;lt;complexContent&amp;gt;
+ *                 &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                   &amp;lt;sequence&amp;gt;
+ *                     &amp;lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&amp;gt;
+ *                     &amp;lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                 &amp;lt;/restriction&amp;gt;
+ *               &amp;lt;/complexContent&amp;gt;
+ *             &amp;lt;/complexType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *             &amp;lt;complexType&amp;gt;
+ *               &amp;lt;complexContent&amp;gt;
+ *                 &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                   &amp;lt;sequence&amp;gt;
+ *                     &amp;lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
+ *                     &amp;lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                             &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                             &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
+ *                             &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                             &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                             &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                           &amp;lt;/extension&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+ *                   &amp;lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+ *                   &amp;lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
+ *                   &amp;lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                   &amp;lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                 &amp;lt;/restriction&amp;gt;
+ *               &amp;lt;/complexContent&amp;gt;
+ *             &amp;lt;/complexType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *             &amp;lt;complexType&amp;gt;
+ *               &amp;lt;complexContent&amp;gt;
+ *                 &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                   &amp;lt;sequence&amp;gt;
+ *                     &amp;lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                 &amp;lt;/restriction&amp;gt;
+ *               &amp;lt;/complexContent&amp;gt;
+ *             &amp;lt;/complexType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *             &amp;lt;complexType&amp;gt;
+ *               &amp;lt;complexContent&amp;gt;
+ *                 &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                   &amp;lt;sequence minOccurs="0"&amp;gt;
+ *                     &amp;lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+ *                     &amp;lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+ *                   &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                   &amp;lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
+ *                   &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+ *                 &amp;lt;/restriction&amp;gt;
+ *               &amp;lt;/complexContent&amp;gt;
+ *             &amp;lt;/complexType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *             &amp;lt;complexType&amp;gt;
+ *               &amp;lt;complexContent&amp;gt;
+ *                 &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                   &amp;lt;sequence&amp;gt;
+ *                     &amp;lt;element name="sequencePoint" maxOccurs="unbounded"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                             &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+ *                             &amp;lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="axis" maxOccurs="3" minOccurs="3"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                             &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="seqPointMin"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                             &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="seqPointMax"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                             &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                   &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+ *                   &amp;lt;attGroup ref="{www.jalview.org}SimilarityParams"/&amp;gt;
+ *                   &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                   &amp;lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                   &amp;lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                   &amp;lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                   &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                 &amp;lt;/restriction&amp;gt;
+ *               &amp;lt;/complexContent&amp;gt;
+ *             &amp;lt;/complexType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *           &amp;lt;element name="FeatureSettings" minOccurs="0"&amp;gt;
+ *             &amp;lt;complexType&amp;gt;
+ *               &amp;lt;complexContent&amp;gt;
+ *                 &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                   &amp;lt;sequence&amp;gt;
+ *                     &amp;lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                             &amp;lt;sequence&amp;gt;
+ *                               &amp;lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
+ *                               &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
+ *                             &amp;lt;/sequence&amp;gt;
+ *                             &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                             &amp;lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                             &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                             &amp;lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                             &amp;lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                             &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
+ *                             &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                             &amp;lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ *                             &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                             &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+ *                             &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                             &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                     &amp;lt;element name="group" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+ *                       &amp;lt;complexType&amp;gt;
+ *                         &amp;lt;complexContent&amp;gt;
+ *                           &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+ *                             &amp;lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+ *                             &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ *                           &amp;lt;/restriction&amp;gt;
+ *                         &amp;lt;/complexContent&amp;gt;
+ *                       &amp;lt;/complexType&amp;gt;
+ *                     &amp;lt;/element&amp;gt;
+ *                   &amp;lt;/sequence&amp;gt;
+ *                 &amp;lt;/restriction&amp;gt;
+ *               &amp;lt;/complexContent&amp;gt;
+ *             &amp;lt;/complexType&amp;gt;
+ *           &amp;lt;/element&amp;gt;
+ *         &amp;lt;/sequence&amp;gt;
+ *       &amp;lt;/sequence&amp;gt;
+ *     &amp;lt;/restriction&amp;gt;
+ *   &amp;lt;/complexContent&amp;gt;
+ * &amp;lt;/complexType&amp;gt;
+ * &lt;/pre&gt;
  * 
  * 
  */
@@ -473,20 +473,20 @@ public class JalviewModel {
     /**
      * Gets the value of the jSeq property.
      * 
-     * <p>
+     * &lt;p&gt;
      * This accessor method returns a reference to the live list,
      * not a snapshot. Therefore any modification you make to the
      * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the jSeq property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getJSeq().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.JSeq }
      * 
@@ -502,20 +502,20 @@ public class JalviewModel {
     /**
      * Gets the value of the jGroup property.
      * 
-     * <p>
+     * &lt;p&gt;
      * This accessor method returns a reference to the live list,
      * not a snapshot. Therefore any modification you make to the
      * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the jGroup property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getJGroup().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.JGroup }
      * 
@@ -531,20 +531,20 @@ public class JalviewModel {
     /**
      * Gets the value of the viewport property.
      * 
-     * <p>
+     * &lt;p&gt;
      * This accessor method returns a reference to the live list,
      * not a snapshot. Therefore any modification you make to the
      * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the viewport property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the viewport property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getViewport().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.Viewport }
      * 
@@ -560,20 +560,20 @@ public class JalviewModel {
     /**
      * Gets the value of the userColours property.
      * 
-     * <p>
+     * &lt;p&gt;
      * This accessor method returns a reference to the live list,
      * not a snapshot. Therefore any modification you make to the
      * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the userColours property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the userColours property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getUserColours().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.UserColours }
      * 
@@ -589,20 +589,20 @@ public class JalviewModel {
     /**
      * Gets the value of the tree property.
      * 
-     * <p>
+     * &lt;p&gt;
      * This accessor method returns a reference to the live list,
      * not a snapshot. Therefore any modification you make to the
      * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the tree property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the tree property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getTree().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.Tree }
      * 
@@ -618,20 +618,20 @@ public class JalviewModel {
     /**
      * Gets the value of the pcaViewer property.
      * 
-     * <p>
+     * &lt;p&gt;
      * This accessor method returns a reference to the live list,
      * not a snapshot. Therefore any modification you make to the
      * returned list will be present inside the JAXB object.
-     * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
+     * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the pcaViewer property.
      * 
-     * <p>
+     * &lt;p&gt;
      * For example, to add a new item, do as follows:
-     * <pre>
+     * &lt;pre&gt;
      *    getPcaViewer().add(newItem);
-     * </pre>
+     * &lt;/pre&gt;
      * 
      * 
-     * <p>
+     * &lt;p&gt;
      * Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.PcaViewer }
      * 
@@ -670,54 +670,54 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="setting" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;sequence>
-     *                   &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *                   &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-     *                 &lt;/sequence>
-     *                 &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *                 &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *                 &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="group" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &lt;pre&gt;
+     * &amp;lt;complexType&amp;gt;
+     *   &amp;lt;complexContent&amp;gt;
+     *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *       &amp;lt;sequence&amp;gt;
+     *         &amp;lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *                 &amp;lt;sequence&amp;gt;
+     *                   &amp;lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
+     *                   &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
+     *                 &amp;lt;/sequence&amp;gt;
+     *                 &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                 &amp;lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *                 &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *                 &amp;lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *                 &amp;lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *                 &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
+     *                 &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *                 &amp;lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *                 &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *                 &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *                 &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *                 &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="group" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *                 &amp;lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                 &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -736,20 +736,20 @@ public class JalviewModel {
         /**
          * Gets the value of the setting property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the setting property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the setting property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getSetting().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.FeatureSettings.Setting }
          * 
@@ -765,20 +765,20 @@ public class JalviewModel {
         /**
          * Gets the value of the group property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the group property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the group property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getGroup().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.FeatureSettings.Group }
          * 
@@ -793,20 +793,20 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+         *       &amp;lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *       &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -863,34 +863,34 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;sequence>
-         *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-         *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-         *       &lt;/sequence>
-         *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-         *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-         *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+         *       &amp;lt;sequence&amp;gt;
+         *         &amp;lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
+         *         &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&amp;gt;
+         *       &amp;lt;/sequence&amp;gt;
+         *       &amp;lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *       &amp;lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *       &amp;lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *       &amp;lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+         *       &amp;lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *       &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
+         *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+         *       &amp;lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *       &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+         *       &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+         *       &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *       &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -933,20 +933,20 @@ public class JalviewModel {
             /**
              * Gets the value of the attributeName property.
              * 
-             * <p>
+             * &lt;p&gt;
              * This accessor method returns a reference to the live list,
              * not a snapshot. Therefore any modification you make to the
              * returned list will be present inside the JAXB object.
-             * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+             * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
              * 
-             * <p>
+             * &lt;p&gt;
              * For example, to add a new item, do as follows:
-             * <pre>
+             * &lt;pre&gt;
              *    getAttributeName().add(newItem);
-             * </pre>
+             * &lt;/pre&gt;
              * 
              * 
-             * <p>
+             * &lt;p&gt;
              * Objects of the following type(s) are allowed in the list
              * {@link String }
              * 
@@ -1265,41 +1265,41 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-     *         &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &lt;pre&gt;
+     * &amp;lt;complexType&amp;gt;
+     *   &amp;lt;complexContent&amp;gt;
+     *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *       &amp;lt;sequence&amp;gt;
+     *         &amp;lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&amp;gt;
+     *         &amp;lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -1356,20 +1356,20 @@ public class JalviewModel {
         /**
          * Gets the value of the seq property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the seq property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the seq property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getSeq().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link String }
          * 
@@ -1882,80 +1882,80 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;extension base="{www.jalview.org}pdbentry">
-     *                 &lt;sequence>
-     *                   &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
-     *                     &lt;complexType>
-     *                       &lt;simpleContent>
-     *                         &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-     *                           &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *                           &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                           &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                           &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                           &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                           &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         &lt;/extension>
-     *                       &lt;/simpleContent>
-     *                     &lt;/complexType>
-     *                   &lt;/element>
-     *                 &lt;/sequence>
-     *               &lt;/extension>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
-     *         &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;sequence>
-     *                   &lt;element name="secondaryStructure" maxOccurs="unbounded">
-     *                     &lt;complexType>
-     *                       &lt;complexContent>
-     *                         &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                           &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                           &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                           &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                         &lt;/restriction>
-     *                       &lt;/complexContent>
-     *                     &lt;/complexType>
-     *                   &lt;/element>
-     *                 &lt;/sequence>
-     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *       &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &lt;pre&gt;
+     * &amp;lt;complexType&amp;gt;
+     *   &amp;lt;complexContent&amp;gt;
+     *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *       &amp;lt;sequence&amp;gt;
+     *         &amp;lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+     *         &amp;lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
+     *                 &amp;lt;sequence&amp;gt;
+     *                   &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+     *                     &amp;lt;complexType&amp;gt;
+     *                       &amp;lt;simpleContent&amp;gt;
+     *                         &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
+     *                           &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+     *                           &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *                           &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                           &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *                           &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *                           &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *                           &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                         &amp;lt;/extension&amp;gt;
+     *                       &amp;lt;/simpleContent&amp;gt;
+     *                     &amp;lt;/complexType&amp;gt;
+     *                   &amp;lt;/element&amp;gt;
+     *                 &amp;lt;/sequence&amp;gt;
+     *               &amp;lt;/extension&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&amp;gt;
+     *         &amp;lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *                 &amp;lt;sequence&amp;gt;
+     *                   &amp;lt;element name="secondaryStructure" maxOccurs="unbounded"&amp;gt;
+     *                     &amp;lt;complexType&amp;gt;
+     *                       &amp;lt;complexContent&amp;gt;
+     *                         &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *                           &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                           &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                           &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *                           &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                         &amp;lt;/restriction&amp;gt;
+     *                       &amp;lt;/complexContent&amp;gt;
+     *                     &amp;lt;/complexType&amp;gt;
+     *                   &amp;lt;/element&amp;gt;
+     *                 &amp;lt;/sequence&amp;gt;
+     *                 &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+     *                 &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                 &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                 &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *                 &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -1992,20 +1992,20 @@ public class JalviewModel {
         /**
          * Gets the value of the features property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the features property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the features property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getFeatures().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link Feature }
          * 
@@ -2021,20 +2021,20 @@ public class JalviewModel {
         /**
          * Gets the value of the pdbids property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the pdbids property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getPdbids().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.JSeq.Pdbids }
          * 
@@ -2050,20 +2050,20 @@ public class JalviewModel {
         /**
          * Gets the value of the hiddenSequences property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenSequences property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getHiddenSequences().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link Integer }
          * 
@@ -2079,20 +2079,20 @@ public class JalviewModel {
         /**
          * Gets the value of the rnaViewer property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the rnaViewer property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getRnaViewer().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.JSeq.RnaViewer }
          * 
@@ -2235,35 +2235,35 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;extension base="{www.jalview.org}pdbentry">
-         *       &lt;sequence>
-         *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
-         *           &lt;complexType>
-         *             &lt;simpleContent>
-         *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-         *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-         *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-         *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-         *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *               &lt;/extension>
-         *             &lt;/simpleContent>
-         *           &lt;/complexType>
-         *         &lt;/element>
-         *       &lt;/sequence>
-         *     &lt;/extension>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;extension base="{www.jalview.org}pdbentry"&amp;gt;
+         *       &amp;lt;sequence&amp;gt;
+         *         &amp;lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+         *           &amp;lt;complexType&amp;gt;
+         *             &amp;lt;simpleContent&amp;gt;
+         *               &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
+         *                 &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+         *                 &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *                 &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *                 &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+         *                 &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+         *                 &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+         *                 &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *               &amp;lt;/extension&amp;gt;
+         *             &amp;lt;/simpleContent&amp;gt;
+         *           &amp;lt;/complexType&amp;gt;
+         *         &amp;lt;/element&amp;gt;
+         *       &amp;lt;/sequence&amp;gt;
+         *     &amp;lt;/extension&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -2281,20 +2281,20 @@ public class JalviewModel {
             /**
              * Gets the value of the structureState property.
              * 
-             * <p>
+             * &lt;p&gt;
              * This accessor method returns a reference to the live list,
              * not a snapshot. Therefore any modification you make to the
              * returned list will be present inside the JAXB object.
-             * This is why there is not a <CODE>set</CODE> method for the structureState property.
+             * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the structureState property.
              * 
-             * <p>
+             * &lt;p&gt;
              * For example, to add a new item, do as follows:
-             * <pre>
+             * &lt;pre&gt;
              *    getStructureState().add(newItem);
-             * </pre>
+             * &lt;/pre&gt;
              * 
              * 
-             * <p>
+             * &lt;p&gt;
              * Objects of the following type(s) are allowed in the list
              * {@link JalviewModel.JSeq.Pdbids.StructureState }
              * 
@@ -2309,25 +2309,25 @@ public class JalviewModel {
 
 
             /**
-             * <p>Java class for anonymous complex type.
+             * &lt;p&gt;Java class for anonymous complex type.
              * 
-             * <p>The following schema fragment specifies the expected content contained within this class.
+             * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
              * 
-             * <pre>
-             * &lt;complexType>
-             *   &lt;simpleContent>
-             *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-             *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-             *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-             *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-             *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     &lt;/extension>
-             *   &lt;/simpleContent>
-             * &lt;/complexType>
-             * </pre>
+             * &lt;pre&gt;
+             * &amp;lt;complexType&amp;gt;
+             *   &amp;lt;simpleContent&amp;gt;
+             *     &amp;lt;extension base="&amp;lt;http://www.w3.org/2001/XMLSchema&amp;gt;string"&amp;gt;
+             *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+             *       &amp;lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+             *       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+             *       &amp;lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+             *       &amp;lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+             *       &amp;lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+             *       &amp;lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+             *     &amp;lt;/extension&amp;gt;
+             *   &amp;lt;/simpleContent&amp;gt;
+             * &amp;lt;/complexType&amp;gt;
+             * &lt;/pre&gt;
              * 
              * 
              */
@@ -2642,37 +2642,37 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;sequence>
-         *         &lt;element name="secondaryStructure" maxOccurs="unbounded">
-         *           &lt;complexType>
-         *             &lt;complexContent>
-         *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *                 &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *                 &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *                 &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *               &lt;/restriction>
-         *             &lt;/complexContent>
-         *           &lt;/complexType>
-         *         &lt;/element>
-         *       &lt;/sequence>
-         *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-         *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+         *       &amp;lt;sequence&amp;gt;
+         *         &amp;lt;element name="secondaryStructure" maxOccurs="unbounded"&amp;gt;
+         *           &amp;lt;complexType&amp;gt;
+         *             &amp;lt;complexContent&amp;gt;
+         *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+         *                 &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *                 &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *                 &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *                 &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *               &amp;lt;/restriction&amp;gt;
+         *             &amp;lt;/complexContent&amp;gt;
+         *           &amp;lt;/complexType&amp;gt;
+         *         &amp;lt;/element&amp;gt;
+         *       &amp;lt;/sequence&amp;gt;
+         *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+         *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *       &amp;lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *       &amp;lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *       &amp;lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -2704,20 +2704,20 @@ public class JalviewModel {
             /**
              * Gets the value of the secondaryStructure property.
              * 
-             * <p>
+             * &lt;p&gt;
              * This accessor method returns a reference to the live list,
              * not a snapshot. Therefore any modification you make to the
              * returned list will be present inside the JAXB object.
-             * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+             * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the secondaryStructure property.
              * 
-             * <p>
+             * &lt;p&gt;
              * For example, to add a new item, do as follows:
-             * <pre>
+             * &lt;pre&gt;
              *    getSecondaryStructure().add(newItem);
-             * </pre>
+             * &lt;/pre&gt;
              * 
              * 
-             * <p>
+             * &lt;p&gt;
              * Objects of the following type(s) are allowed in the list
              * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
              * 
@@ -2924,22 +2924,22 @@ public class JalviewModel {
 
 
             /**
-             * <p>Java class for anonymous complex type.
+             * &lt;p&gt;Java class for anonymous complex type.
              * 
-             * <p>The following schema fragment specifies the expected content contained within this class.
+             * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
              * 
-             * <pre>
-             * &lt;complexType>
-             *   &lt;complexContent>
-             *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-             *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-             *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-             *     &lt;/restriction>
-             *   &lt;/complexContent>
-             * &lt;/complexType>
-             * </pre>
+             * &lt;pre&gt;
+             * &amp;lt;complexType&amp;gt;
+             *   &amp;lt;complexContent&amp;gt;
+             *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+             *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+             *       &amp;lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+             *       &amp;lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+             *       &amp;lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+             *     &amp;lt;/restriction&amp;gt;
+             *   &amp;lt;/complexContent&amp;gt;
+             * &amp;lt;/complexType&amp;gt;
+             * &lt;/pre&gt;
              * 
              * 
              */
@@ -3060,69 +3060,69 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="sequencePoint" maxOccurs="unbounded">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *                 &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="axis" maxOccurs="3" minOccurs="3">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="seqPointMin">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="seqPointMax">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attGroup ref="{www.jalview.org}position"/>
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/>
-     *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *       &lt;attGroup ref="{www.jalview.org}SimilarityParams"/>
-     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &lt;pre&gt;
+     * &amp;lt;complexType&amp;gt;
+     *   &amp;lt;complexContent&amp;gt;
+     *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *       &amp;lt;sequence&amp;gt;
+     *         &amp;lt;element name="sequencePoint" maxOccurs="unbounded"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+     *                 &amp;lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="axis" maxOccurs="3" minOccurs="3"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="seqPointMin"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="seqPointMax"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *                 &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+     *       &amp;lt;attGroup ref="{www.jalview.org}SimilarityParams"/&amp;gt;
+     *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *       &amp;lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -3184,20 +3184,20 @@ public class JalviewModel {
         /**
          * Gets the value of the sequencePoint property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the sequencePoint property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getSequencePoint().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.PcaViewer.SequencePoint }
          * 
@@ -3213,20 +3213,20 @@ public class JalviewModel {
         /**
          * Gets the value of the axis property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the axis property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the axis property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getAxis().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.PcaViewer.Axis }
          * 
@@ -3721,19 +3721,19 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+         *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -3824,19 +3824,19 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+         *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -3927,19 +3927,19 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+         *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -4030,20 +4030,20 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attGroup ref="{www.jalview.org}position"/>
-         *       &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+         *       &amp;lt;attGroup ref="{www.jalview.org}position"/&amp;gt;
+         *       &amp;lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -4162,34 +4162,34 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence minOccurs="0">
-     *         &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *         &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
-     *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-     *       &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &lt;pre&gt;
+     * &amp;lt;complexType&amp;gt;
+     *   &amp;lt;complexContent&amp;gt;
+     *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *       &amp;lt;sequence minOccurs="0"&amp;gt;
+     *         &amp;lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+     *         &amp;lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+     *       &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
+     *       &amp;lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
+     *       &amp;lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -4654,22 +4654,22 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &lt;pre&gt;
+     * &amp;lt;complexType&amp;gt;
+     *   &amp;lt;complexContent&amp;gt;
+     *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *       &amp;lt;sequence&amp;gt;
+     *         &amp;lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -4736,86 +4736,86 @@ public class JalviewModel {
 
 
     /**
-     * <p>Java class for anonymous complex type.
+     * &lt;p&gt;Java class for anonymous complex type.
      * 
-     * <p>The following schema fragment specifies the expected content contained within this class.
+     * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
      * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-     *         &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *                 &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *               &lt;/restriction>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *         &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;complexContent>
-     *               &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-     *                 &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *               &lt;/extension>
-     *             &lt;/complexContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *       &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *       &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-     *       &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &lt;pre&gt;
+     * &amp;lt;complexType&amp;gt;
+     *   &amp;lt;complexContent&amp;gt;
+     *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *       &amp;lt;sequence&amp;gt;
+     *         &amp;lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&amp;gt;
+     *         &amp;lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     *                 &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *                 &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *               &amp;lt;/restriction&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *         &amp;lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&amp;gt;
+     *           &amp;lt;complexType&amp;gt;
+     *             &amp;lt;complexContent&amp;gt;
+     *               &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
+     *                 &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *                 &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *                 &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *               &amp;lt;/extension&amp;gt;
+     *             &amp;lt;/complexContent&amp;gt;
+     *           &amp;lt;/complexType&amp;gt;
+     *         &amp;lt;/element&amp;gt;
+     *       &amp;lt;/sequence&amp;gt;
+     *       &amp;lt;attGroup ref="{www.jalview.org}swingwindow"/&amp;gt;
+     *       &amp;lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&amp;gt;
+     *       &amp;lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+     *       &amp;lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     *       &amp;lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&amp;gt;
+     *       &amp;lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+     *       &amp;lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *       &amp;lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+     *     &amp;lt;/restriction&amp;gt;
+     *   &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt;
+     * &lt;/pre&gt;
      * 
      * 
      */
@@ -4958,20 +4958,20 @@ public class JalviewModel {
         /**
          * Gets the value of the hiddenColumns property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenColumns property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getHiddenColumns().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.Viewport.HiddenColumns }
          * 
@@ -4987,20 +4987,20 @@ public class JalviewModel {
         /**
          * Gets the value of the calcIdParam property.
          * 
-         * <p>
+         * &lt;p&gt;
          * This accessor method returns a reference to the live list,
          * not a snapshot. Therefore any modification you make to the
          * returned list will be present inside the JAXB object.
-         * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+         * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the calcIdParam property.
          * 
-         * <p>
+         * &lt;p&gt;
          * For example, to add a new item, do as follows:
-         * <pre>
+         * &lt;pre&gt;
          *    getCalcIdParam().add(newItem);
-         * </pre>
+         * &lt;/pre&gt;
          * 
          * 
-         * <p>
+         * &lt;p&gt;
          * Objects of the following type(s) are allowed in the list
          * {@link JalviewModel.Viewport.CalcIdParam }
          * 
@@ -6195,21 +6195,21 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-         *       &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-         *       &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-         *       &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-         *     &lt;/extension>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&amp;gt;
+         *       &amp;lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
+         *       &amp;lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+         *       &amp;lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+         *     &amp;lt;/extension&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */
@@ -6298,20 +6298,20 @@ public class JalviewModel {
 
 
         /**
-         * <p>Java class for anonymous complex type.
+         * &lt;p&gt;Java class for anonymous complex type.
          * 
-         * <p>The following schema fragment specifies the expected content contained within this class.
+         * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
          * 
-         * <pre>
-         * &lt;complexType>
-         *   &lt;complexContent>
-         *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-         *       &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *       &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-         *     &lt;/restriction>
-         *   &lt;/complexContent>
-         * &lt;/complexType>
-         * </pre>
+         * &lt;pre&gt;
+         * &amp;lt;complexType&amp;gt;
+         *   &amp;lt;complexContent&amp;gt;
+         *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+         *       &amp;lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *       &amp;lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+         *     &amp;lt;/restriction&amp;gt;
+         *   &amp;lt;/complexContent&amp;gt;
+         * &amp;lt;/complexType&amp;gt;
+         * &lt;/pre&gt;
          * 
          * 
          */