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JAL-4366 avoid corrupting map when no complete mapping available for chain to sequence
[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 b77d98d..18a2571 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: 2023.03.17 at 05:31:44 PM GMT 
+// Generated on: 2023.11.01 at 07:03:09 PM GMT 
 //
 
 package jalview.xml.binding.jalview;
@@ -22,362 +22,367 @@ import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
 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;element name="overview" minOccurs="0">
- *                       &lt;complexType>
- *                         &lt;complexContent>
- *                           &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                             &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             &lt;attribute name="title" 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="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="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   &lt;attribute name="charHeight" 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="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   &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}SimilarityParams"/>
- *                   &lt;attGroup ref="{www.jalview.org}swingwindow"/>
- *                   &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;element
+ * name="overview" 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;attGroup
+ * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
+ * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
+ * &amp;lt;attribute name="residueColour"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
+ * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ * &amp;lt;attribute name="hiddenColour"
+ * 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;/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="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="charWidth"
+ * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
+ * name="charHeight" 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="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+ * &amp;lt;attribute name="idWidthManuallyAdjusted"
+ * type="{http://www.w3.org/2001/XMLSchema}boolean" /&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="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean"
+ * default="false" /&amp;gt; &amp;lt;attribute name="columnReference"
+ * type="{http://www.w3.org/2001/XMLSchema}string" /&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}SimilarityParams"/&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="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;
  * 
  * 
  */
@@ -493,22 +498,16 @@ public class JalviewModel
   /**
    * Gets the value of the jSeq property.
    * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the jSeq property.
+   * &lt;p&gt; This accessor method returns a reference to the live list, not a
+   * snapshot. Therefore any modification you make to the returned list will be
+   * present inside the JAXB object. This is why there is not a
+   * &lt;CODE&gt;set&lt;/CODE&gt; method for the jSeq property.
    * 
-   * <p>
-   * For example, to add a new item, do as follows:
+   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+   * getJSeq().add(newItem); &lt;/pre&gt;
    * 
-   * <pre>
-   * getJSeq().add(newItem);
-   * </pre>
    * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
+   * &lt;p&gt; Objects of the following type(s) are allowed in the list
    * {@link JalviewModel.JSeq }
    * 
    * 
@@ -525,22 +524,16 @@ public class JalviewModel
   /**
    * Gets the value of the jGroup property.
    * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the jGroup property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
+   * &lt;p&gt; This accessor method returns a reference to the live list, not a
+   * snapshot. Therefore any modification you make to the returned list will be
+   * present inside the JAXB object. This is why there is not a
+   * &lt;CODE&gt;set&lt;/CODE&gt; method for the jGroup property.
    * 
-   * <pre>
-   * getJGroup().add(newItem);
-   * </pre>
+   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+   * getJGroup().add(newItem); &lt;/pre&gt;
    * 
    * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
+   * &lt;p&gt; Objects of the following type(s) are allowed in the list
    * {@link JalviewModel.JGroup }
    * 
    * 
@@ -557,22 +550,16 @@ public class JalviewModel
   /**
    * Gets the value of the viewport property.
    * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the viewport property.
+   * &lt;p&gt; This accessor method returns a reference to the live list, not a
+   * snapshot. Therefore any modification you make to the returned list will be
+   * present inside the JAXB object. This is why there is not a
+   * &lt;CODE&gt;set&lt;/CODE&gt; method for the viewport property.
    * 
-   * <p>
-   * For example, to add a new item, do as follows:
+   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+   * getViewport().add(newItem); &lt;/pre&gt;
    * 
-   * <pre>
-   * getViewport().add(newItem);
-   * </pre>
    * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
+   * &lt;p&gt; Objects of the following type(s) are allowed in the list
    * {@link JalviewModel.Viewport }
    * 
    * 
@@ -589,22 +576,16 @@ public class JalviewModel
   /**
    * Gets the value of the userColours property.
    * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the userColours property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
+   * &lt;p&gt; This accessor method returns a reference to the live list, not a
+   * snapshot. Therefore any modification you make to the returned list will be
+   * present inside the JAXB object. This is why there is not a
+   * &lt;CODE&gt;set&lt;/CODE&gt; method for the userColours property.
    * 
-   * <pre>
-   * getUserColours().add(newItem);
-   * </pre>
+   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+   * getUserColours().add(newItem); &lt;/pre&gt;
    * 
    * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
+   * &lt;p&gt; Objects of the following type(s) are allowed in the list
    * {@link JalviewModel.UserColours }
    * 
    * 
@@ -621,22 +602,16 @@ public class JalviewModel
   /**
    * Gets the value of the tree property.
    * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the tree property.
+   * &lt;p&gt; This accessor method returns a reference to the live list, not a
+   * snapshot. Therefore any modification you make to the returned list will be
+   * present inside the JAXB object. This is why there is not a
+   * &lt;CODE&gt;set&lt;/CODE&gt; method for the tree property.
    * 
-   * <p>
-   * For example, to add a new item, do as follows:
+   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+   * getTree().add(newItem); &lt;/pre&gt;
    * 
-   * <pre>
-   * getTree().add(newItem);
-   * </pre>
    * 
-   * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
+   * &lt;p&gt; Objects of the following type(s) are allowed in the list
    * {@link JalviewModel.Tree }
    * 
    * 
@@ -653,22 +628,16 @@ public class JalviewModel
   /**
    * Gets the value of the pcaViewer property.
    * 
-   * <p>
-   * This accessor method returns a reference to the live list, not a snapshot.
-   * Therefore any modification you make to the returned list will be present
-   * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
-   * for the pcaViewer property.
-   * 
-   * <p>
-   * For example, to add a new item, do as follows:
+   * &lt;p&gt; This accessor method returns a reference to the live list, not a
+   * snapshot. Therefore any modification you make to the returned list will be
+   * present inside the JAXB object. This is why there is not a
+   * &lt;CODE&gt;set&lt;/CODE&gt; method for the pcaViewer property.
    * 
-   * <pre>
-   * getPcaViewer().add(newItem);
-   * </pre>
+   * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+   * getPcaViewer().add(newItem); &lt;/pre&gt;
    * 
    * 
-   * <p>
-   * Objects of the following type(s) are allowed in the list
+   * &lt;p&gt; Objects of the following type(s) are allowed in the list
    * {@link JalviewModel.PcaViewer }
    * 
    * 
@@ -706,57 +675,54 @@ 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;
    * 
    * 
    */
@@ -774,22 +740,16 @@ public class JalviewModel
     /**
      * Gets the value of the setting property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the setting property.
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getSetting().add(newItem); &lt;/pre&gt;
      * 
-     * <pre>
-     * getSetting().add(newItem);
-     * </pre>
      * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.FeatureSettings.Setting }
      * 
      * 
@@ -806,22 +766,16 @@ public class JalviewModel
     /**
      * Gets the value of the group property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the group property.
      * 
-     * <pre>
-     * getGroup().add(newItem);
-     * </pre>
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getGroup().add(newItem); &lt;/pre&gt;
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.FeatureSettings.Group }
      * 
      * 
@@ -836,23 +790,20 @@ 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;
      * 
      * 
      */
@@ -911,37 +862,42 @@ public class JalviewModel
     }
 
     /**
-     * <p>
-     * Java class for anonymous complex type.
-     * 
-     * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       &lt;sequence>
-     *         &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *         &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-     *       &lt;/sequence>
-     *       &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *       &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     &lt;/restriction>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &lt;p&gt;Java class for anonymous complex type.
+     * 
+     * &lt;p&gt;The following schema fragment specifies the expected content
+     * contained within this class.
+     * 
+     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
+     * &amp;lt;restriction
+     * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+     * &amp;lt;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;
      * 
      * 
      */
@@ -995,23 +951,17 @@ public class JalviewModel
       /**
        * Gets the value of the attributeName property.
        * 
-       * <p>
-       * This accessor method returns a reference to the live list, not a
-       * snapshot. Therefore any modification you make to the returned list will
-       * be present inside the JAXB object. This is why there is not a
-       * <CODE>set</CODE> method for the attributeName property.
+       * &lt;p&gt; This accessor method returns a reference to the live list,
+       * not a snapshot. Therefore any modification you make to the returned
+       * list will be present inside the JAXB object. This is why there is not a
+       * &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
        * 
-       * <p>
-       * For example, to add a new item, do as follows:
+       * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+       * getAttributeName().add(newItem); &lt;/pre&gt;
        * 
-       * <pre>
-       * getAttributeName().add(newItem);
-       * </pre>
        * 
-       * 
-       * <p>
-       * Objects of the following type(s) are allowed in the list {@link String
-       * }
+       * &lt;p&gt; Objects of the following type(s) are allowed in the list
+       * {@link String }
        * 
        * 
        */
@@ -1325,44 +1275,51 @@ 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;
    * 
    * 
    */
@@ -1437,22 +1394,17 @@ public class JalviewModel
     /**
      * Gets the value of the seq property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the seq property.
      * 
-     * <pre>
-     * getSeq().add(newItem);
-     * </pre>
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getSeq().add(newItem); &lt;/pre&gt;
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link String }
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
+     * {@link String }
      * 
      * 
      */
@@ -1956,83 +1908,79 @@ 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;
    * 
    * 
    */
@@ -2077,22 +2025,17 @@ public class JalviewModel
     /**
      * Gets the value of the features property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the features property.
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getFeatures().add(newItem); &lt;/pre&gt;
      * 
-     * <pre>
-     * getFeatures().add(newItem);
-     * </pre>
      * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link Feature }
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
+     * {@link Feature }
      * 
      * 
      */
@@ -2108,22 +2051,16 @@ public class JalviewModel
     /**
      * Gets the value of the pdbids property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the pdbids property.
      * 
-     * <pre>
-     * getPdbids().add(newItem);
-     * </pre>
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getPdbids().add(newItem); &lt;/pre&gt;
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.JSeq.Pdbids }
      * 
      * 
@@ -2140,22 +2077,17 @@ public class JalviewModel
     /**
      * Gets the value of the hiddenSequences property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenSequences property.
      * 
-     * <pre>
-     * getHiddenSequences().add(newItem);
-     * </pre>
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getHiddenSequences().add(newItem); &lt;/pre&gt;
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list {@link Integer }
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
+     * {@link Integer }
      * 
      * 
      */
@@ -2171,22 +2103,16 @@ public class JalviewModel
     /**
      * Gets the value of the rnaViewer property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the rnaViewer property.
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getRnaViewer().add(newItem); &lt;/pre&gt;
      * 
-     * <pre>
-     * getRnaViewer().add(newItem);
-     * </pre>
      * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.JSeq.RnaViewer }
      * 
      * 
@@ -2329,38 +2255,34 @@ public class JalviewModel
     }
 
     /**
-     * <p>
-     * Java class for anonymous complex type.
-     * 
-     * <p>
-     * The following schema fragment specifies the expected content contained
-     * within this class.
-     * 
-     * <pre>
-     * &lt;complexType>
-     *   &lt;complexContent>
-     *     &lt;extension base="{www.jalview.org}pdbentry">
-     *       &lt;sequence>
-     *         &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0">
-     *           &lt;complexType>
-     *             &lt;simpleContent>
-     *               &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-     *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                 &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                 &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               &lt;/extension>
-     *             &lt;/simpleContent>
-     *           &lt;/complexType>
-     *         &lt;/element>
-     *       &lt;/sequence>
-     *     &lt;/extension>
-     *   &lt;/complexContent>
-     * &lt;/complexType>
-     * </pre>
+     * &lt;p&gt;Java class for anonymous complex type.
+     * 
+     * &lt;p&gt;The following schema fragment specifies the expected content
+     * contained within this class.
+     * 
+     * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
+     * &amp;lt;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;
      * 
      * 
      */
@@ -2375,22 +2297,16 @@ public class JalviewModel
       /**
        * Gets the value of the structureState property.
        * 
-       * <p>
-       * This accessor method returns a reference to the live list, not a
-       * snapshot. Therefore any modification you make to the returned list will
-       * be present inside the JAXB object. This is why there is not a
-       * <CODE>set</CODE> method for the structureState property.
-       * 
-       * <p>
-       * For example, to add a new item, do as follows:
+       * &lt;p&gt; This accessor method returns a reference to the live list,
+       * not a snapshot. Therefore any modification you make to the returned
+       * list will be present inside the JAXB object. This is why there is not a
+       * &lt;CODE&gt;set&lt;/CODE&gt; method for the structureState property.
        * 
-       * <pre>
-       * getStructureState().add(newItem);
-       * </pre>
+       * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+       * getStructureState().add(newItem); &lt;/pre&gt;
        * 
        * 
-       * <p>
-       * Objects of the following type(s) are allowed in the list
+       * &lt;p&gt; Objects of the following type(s) are allowed in the list
        * {@link JalviewModel.JSeq.Pdbids.StructureState }
        * 
        * 
@@ -2405,28 +2321,29 @@ public class JalviewModel
       }
 
       /**
-       * <p>
-       * Java class for anonymous complex type.
-       * 
-       * <p>
-       * The following schema fragment specifies the expected content contained
-       * within this class.
-       * 
-       * <pre>
-       * &lt;complexType>
-       *   &lt;simpleContent>
-       *     &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema>string">
-       *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-       *       &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-       *       &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-       *       &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-       *       &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-       *       &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *     &lt;/extension>
-       *   &lt;/simpleContent>
-       * &lt;/complexType>
-       * </pre>
+       * &lt;p&gt;Java class for anonymous complex type.
+       * 
+       * &lt;p&gt;The following schema fragment specifies the expected content
+       * contained within this class.
+       * 
+       * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;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;
        * 
        * 
        */
@@ -2747,40 +2664,38 @@ 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;
      * 
      * 
      */
@@ -2819,22 +2734,17 @@ public class JalviewModel
       /**
        * Gets the value of the secondaryStructure property.
        * 
-       * <p>
-       * This accessor method returns a reference to the live list, not a
-       * snapshot. Therefore any modification you make to the returned list will
-       * be present inside the JAXB object. This is why there is not a
-       * <CODE>set</CODE> method for the secondaryStructure property.
+       * &lt;p&gt; This accessor method returns a reference to the live list,
+       * not a snapshot. Therefore any modification you make to the returned
+       * list will be present inside the JAXB object. This is why there is not a
+       * &lt;CODE&gt;set&lt;/CODE&gt; method for the secondaryStructure
+       * property.
        * 
-       * <p>
-       * For example, to add a new item, do as follows:
+       * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+       * getSecondaryStructure().add(newItem); &lt;/pre&gt;
        * 
-       * <pre>
-       * getSecondaryStructure().add(newItem);
-       * </pre>
        * 
-       * 
-       * <p>
-       * Objects of the following type(s) are allowed in the list
+       * &lt;p&gt; Objects of the following type(s) are allowed in the list
        * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
        * 
        * 
@@ -3033,25 +2943,24 @@ public class JalviewModel
       }
 
       /**
-       * <p>
-       * Java class for anonymous complex type.
-       * 
-       * <p>
-       * The following schema fragment specifies the expected content contained
-       * within this class.
-       * 
-       * <pre>
-       * &lt;complexType>
-       *   &lt;complexContent>
-       *     &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-       *       &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-       *       &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *     &lt;/restriction>
-       *   &lt;/complexContent>
-       * &lt;/complexType>
-       * </pre>
+       * &lt;p&gt;Java class for anonymous complex type.
+       * 
+       * &lt;p&gt;The following schema fragment specifies the expected content
+       * contained within this class.
+       * 
+       * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
+       * &amp;lt;restriction
+       * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
+       * &amp;lt;attribute name="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;
        * 
        * 
        */
@@ -3171,72 +3080,59 @@ 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}SimilarityParams"/>
-   *       &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-   *       &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}SimilarityParams"/&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="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;
    * 
    * 
    */
@@ -3317,22 +3213,16 @@ public class JalviewModel
     /**
      * Gets the value of the sequencePoint property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the sequencePoint property.
      * 
-     * <pre>
-     * getSequencePoint().add(newItem);
-     * </pre>
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getSequencePoint().add(newItem); &lt;/pre&gt;
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.PcaViewer.SequencePoint }
      * 
      * 
@@ -3349,22 +3239,16 @@ public class JalviewModel
     /**
      * Gets the value of the axis property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the axis property.
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getAxis().add(newItem); &lt;/pre&gt;
      * 
-     * <pre>
-     * getAxis().add(newItem);
-     * </pre>
      * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.PcaViewer.Axis }
      * 
      * 
@@ -3839,22 +3723,16 @@ 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;
      * 
      * 
      */
@@ -3944,22 +3822,16 @@ 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;
      * 
      * 
      */
@@ -4049,22 +3921,16 @@ 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;
      * 
      * 
      */
@@ -4154,23 +4020,18 @@ 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;
      * 
      * 
      */
@@ -4288,39 +4149,43 @@ 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="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       &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="columnWise"
+   * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&amp;gt;
+   * &amp;lt;attribute name="columnReference"
+   * type="{http://www.w3.org/2001/XMLSchema}string" /&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;
    * 
    * 
    */
@@ -4843,25 +4708,20 @@ 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;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;
    * 
    * 
    */
@@ -4928,105 +4788,137 @@ 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;element name="overview" minOccurs="0">
-   *           &lt;complexType>
-   *             &lt;complexContent>
-   *               &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 &lt;attGroup ref="{www.jalview.org}swingwindow"/>
-   *                 &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                 &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 &lt;attribute name="title" 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="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="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       &lt;attribute name="charHeight" 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;element
+   * name="overview" 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;attGroup
+   * ref="{www.jalview.org}swingwindow"/&amp;gt; &amp;lt;attribute
+   * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean"
+   * /&amp;gt; &amp;lt;attribute name="residueColour"
+   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
+   * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+   * &amp;lt;attribute name="hiddenColour"
+   * 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;/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="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="charWidth"
+   * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
+   * name="charHeight" 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="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+   * &amp;lt;attribute name="idWidthManuallyAdjusted"
+   * type="{http://www.w3.org/2001/XMLSchema}boolean" /&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;
    * 
    * 
    */
@@ -5152,6 +5044,12 @@ public class JalviewModel
     @XmlAttribute(name = "fontStyle")
     protected Integer fontStyle;
 
+    @XmlAttribute(name = "idWidth")
+    protected Integer idWidth;
+
+    @XmlAttribute(name = "idWidthManuallyAdjusted")
+    protected Boolean idWidthManuallyAdjusted;
+
     @XmlAttribute(name = "scaleProteinAsCdna")
     protected Boolean scaleProteinAsCdna;
 
@@ -5226,22 +5124,16 @@ public class JalviewModel
     /**
      * Gets the value of the hiddenColumns property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
-     * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the hiddenColumns property.
      * 
-     * <pre>
-     * getHiddenColumns().add(newItem);
-     * </pre>
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getHiddenColumns().add(newItem); &lt;/pre&gt;
      * 
      * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.Viewport.HiddenColumns }
      * 
      * 
@@ -5258,22 +5150,16 @@ public class JalviewModel
     /**
      * Gets the value of the calcIdParam property.
      * 
-     * <p>
-     * This accessor method returns a reference to the live list, not a
-     * snapshot. Therefore any modification you make to the returned list will
+     * &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.
+     * &lt;CODE&gt;set&lt;/CODE&gt; method for the calcIdParam property.
      * 
-     * <p>
-     * For example, to add a new item, do as follows:
+     * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
+     * getCalcIdParam().add(newItem); &lt;/pre&gt;
      * 
-     * <pre>
-     * getCalcIdParam().add(newItem);
-     * </pre>
      * 
-     * 
-     * <p>
-     * Objects of the following type(s) are allowed in the list
+     * &lt;p&gt; Objects of the following type(s) are allowed in the list
      * {@link JalviewModel.Viewport.CalcIdParam }
      * 
      * 
@@ -6163,6 +6049,52 @@ public class JalviewModel
     }
 
     /**
+     * Gets the value of the idWidth property.
+     * 
+     * @return possible object is {@link Integer }
+     * 
+     */
+    public Integer getIdWidth()
+    {
+      return idWidth;
+    }
+
+    /**
+     * Sets the value of the idWidth property.
+     * 
+     * @param value
+     *          allowed object is {@link Integer }
+     * 
+     */
+    public void setIdWidth(Integer value)
+    {
+      this.idWidth = value;
+    }
+
+    /**
+     * Gets the value of the idWidthManuallyAdjusted property.
+     * 
+     * @return possible object is {@link Boolean }
+     * 
+     */
+    public Boolean isIdWidthManuallyAdjusted()
+    {
+      return idWidthManuallyAdjusted;
+    }
+
+    /**
+     * Sets the value of the idWidthManuallyAdjusted property.
+     * 
+     * @param value
+     *          allowed object is {@link Boolean }
+     * 
+     */
+    public void setIdWidthManuallyAdjusted(Boolean value)
+    {
+      this.idWidthManuallyAdjusted = value;
+    }
+
+    /**
      * Gets the value of the scaleProteinAsCdna property.
      * 
      * @return possible object is {@link Boolean }
@@ -6529,24 +6461,22 @@ 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;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;
      * 
      * 
      */
@@ -6638,23 +6568,19 @@ 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;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;
      * 
      * 
      */
@@ -6718,27 +6644,24 @@ 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}swingwindow"/>
-     *       &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       &lt;attribute name="title" 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}swingwindow"/&amp;gt; &amp;lt;attribute
+     * name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean"
+     * /&amp;gt; &amp;lt;attribute name="residueColour"
+     * type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt; &amp;lt;attribute
+     * name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
+     * &amp;lt;attribute name="hiddenColour"
+     * 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;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
+     * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
      * 
      * 
      */