//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2022.02.07 at 04:44:47 PM GMT
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
/**
- * <p>Java class for JalviewModel complex type.
+ * <p>Java class for JalviewModel complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType name="JalviewModel"&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
- * &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
- * &lt;sequence&gt;
- * &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org}pdbentry"&gt;
- * &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
- * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="overview" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence minOccurs="0"&gt;
- * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMax"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="FeatureSettings" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType name="JalviewModel">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ * <sequence>
+ * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="overview" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="tree" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequencePoint" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="axis" maxOccurs="3" minOccurs="3">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMin">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMax">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="FeatureSettings" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the jSeq property.
*
- * <p>
+ * <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.
+ * This is why there is not a <CODE>set</CODE> method for the jSeq property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getJSeq().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq }
*
/**
* Gets the value of the jGroup property.
*
- * <p>
+ * <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.
+ * This is why there is not a <CODE>set</CODE> method for the jGroup property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getJGroup().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JGroup }
*
/**
* Gets the value of the viewport property.
*
- * <p>
+ * <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.
+ * This is why there is not a <CODE>set</CODE> method for the viewport property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getViewport().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport }
*
/**
* Gets the value of the userColours property.
*
- * <p>
+ * <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.
+ * This is why there is not a <CODE>set</CODE> method for the userColours property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getUserColours().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.UserColours }
*
/**
* Gets the value of the tree property.
*
- * <p>
+ * <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.
+ * This is why there is not a <CODE>set</CODE> method for the tree property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getTree().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Tree }
*
/**
* Gets the value of the pcaViewer property.
*
- * <p>
+ * <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.
+ * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getPcaViewer().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the setting property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the setting property.
+ * This is why there is not a <CODE>set</CODE> method for the setting property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSetting().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.FeatureSettings.Setting }
*
/**
* Gets the value of the group property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the group property.
+ * This is why there is not a <CODE>set</CODE> method for the group property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getGroup().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.FeatureSettings.Group }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
- * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the attributeName property.
*
- * <p>
+ * <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.
+ * This is why there is not a <CODE>set</CODE> method for the attributeName property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAttributeName().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
- * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the seq property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the seq property.
+ * This is why there is not a <CODE>set</CODE> method for the seq property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSeq().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link String }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org}pdbentry"&gt;
- * &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the features property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the features property.
+ * This is why there is not a <CODE>set</CODE> method for the features property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getFeatures().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Feature }
*
/**
* Gets the value of the pdbids property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+ * This is why there is not a <CODE>set</CODE> method for the pdbids property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getPdbids().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.Pdbids }
*
/**
* Gets the value of the hiddenSequences property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getHiddenSequences().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link Integer }
*
/**
* Gets the value of the rnaViewer property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+ * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getRnaViewer().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.RnaViewer }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org}pdbentry"&gt;
- * &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the structureState property.
*
- * <p>
+ * <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.
+ * This is why there is not a <CODE>set</CODE> method for the structureState property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getStructureState().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.Pdbids.StructureState }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;simpleContent&gt;
- * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt;
- * &lt;/simpleContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the secondaryStructure property.
*
- * <p>
+ * <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.
+ * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSecondaryStructure().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="seqPointMax"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequencePoint" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="axis" maxOccurs="3" minOccurs="3">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMin">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMax">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
protected Boolean showLabels;
@XmlAttribute(name = "linkToAllViews")
protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
@XmlAttribute(name = "includeGaps")
protected Boolean includeGaps;
@XmlAttribute(name = "matchGaps")
protected Boolean includeGappedColumns;
@XmlAttribute(name = "denominateByShortestLength")
protected Boolean denominateByShortestLength;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
/**
* Gets the value of the sequencePoint property.
*
- * <p>
+ * <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 sequencePoint property.
+ * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getSequencePoint().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer.SequencePoint }
*
/**
* Gets the value of the axis property.
*
- * <p>
+ * <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 axis property.
+ * This is why there is not a <CODE>set</CODE> method for the axis property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getAxis().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer.Axis }
*
}
/**
- * Gets the value of the width property.
+ * Gets the value of the includeGaps property.
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public Integer getWidth() {
- return width;
+ public Boolean isIncludeGaps() {
+ return includeGaps;
}
/**
- * Sets the value of the width property.
+ * Sets the value of the includeGaps property.
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public void setWidth(Integer value) {
- this.width = value;
+ public void setIncludeGaps(Boolean value) {
+ this.includeGaps = value;
}
/**
- * Gets the value of the height property.
+ * Gets the value of the matchGaps property.
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public Integer getHeight() {
- return height;
+ public Boolean isMatchGaps() {
+ return matchGaps;
}
/**
- * Sets the value of the height property.
+ * Sets the value of the matchGaps property.
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public void setHeight(Integer value) {
- this.height = value;
+ public void setMatchGaps(Boolean value) {
+ this.matchGaps = value;
}
/**
- * Gets the value of the xpos property.
+ * Gets the value of the includeGappedColumns property.
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public Integer getXpos() {
- return xpos;
+ public Boolean isIncludeGappedColumns() {
+ return includeGappedColumns;
}
/**
- * Sets the value of the xpos property.
+ * Sets the value of the includeGappedColumns property.
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public void setXpos(Integer value) {
- this.xpos = value;
+ public void setIncludeGappedColumns(Boolean value) {
+ this.includeGappedColumns = value;
}
/**
- * Gets the value of the ypos property.
+ * Gets the value of the denominateByShortestLength property.
*
* @return
* possible object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public Integer getYpos() {
- return ypos;
+ public Boolean isDenominateByShortestLength() {
+ return denominateByShortestLength;
}
/**
- * Sets the value of the ypos property.
+ * Sets the value of the denominateByShortestLength property.
*
* @param value
* allowed object is
- * {@link Integer }
+ * {@link Boolean }
*
*/
- public void setYpos(Integer value) {
- this.ypos = value;
+ public void setDenominateByShortestLength(Boolean value) {
+ this.denominateByShortestLength = value;
}
/**
- * Gets the value of the includeGaps property.
+ * Gets the value of the width property.
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public Boolean isIncludeGaps() {
- return includeGaps;
+ public Integer getWidth() {
+ return width;
}
/**
- * Sets the value of the includeGaps property.
+ * Sets the value of the width property.
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public void setIncludeGaps(Boolean value) {
- this.includeGaps = value;
+ public void setWidth(Integer value) {
+ this.width = value;
}
/**
- * Gets the value of the matchGaps property.
+ * Gets the value of the height property.
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public Boolean isMatchGaps() {
- return matchGaps;
+ public Integer getHeight() {
+ return height;
}
/**
- * Sets the value of the matchGaps property.
+ * Sets the value of the height property.
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public void setMatchGaps(Boolean value) {
- this.matchGaps = value;
+ public void setHeight(Integer value) {
+ this.height = value;
}
/**
- * Gets the value of the includeGappedColumns property.
+ * Gets the value of the xpos property.
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public Boolean isIncludeGappedColumns() {
- return includeGappedColumns;
+ public Integer getXpos() {
+ return xpos;
}
/**
- * Sets the value of the includeGappedColumns property.
+ * Sets the value of the xpos property.
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public void setIncludeGappedColumns(Boolean value) {
- this.includeGappedColumns = value;
+ public void setXpos(Integer value) {
+ this.xpos = value;
}
/**
- * Gets the value of the denominateByShortestLength property.
+ * Gets the value of the ypos property.
*
* @return
* possible object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public Boolean isDenominateByShortestLength() {
- return denominateByShortestLength;
+ public Integer getYpos() {
+ return ypos;
}
/**
- * Sets the value of the denominateByShortestLength property.
+ * Sets the value of the ypos property.
*
* @param value
* allowed object is
- * {@link Boolean }
+ * {@link Integer }
*
*/
- public void setDenominateByShortestLength(Boolean value) {
- this.denominateByShortestLength = value;
+ public void setYpos(Integer value) {
+ this.ypos = value;
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence minOccurs="0"&gt;
- * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt;
- * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;element name="overview" minOccurs="0"&gt;
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * &lt;/element&gt;
- * &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="overview" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the hiddenColumns property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+ * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getHiddenColumns().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport.HiddenColumns }
*
/**
* Gets the value of the calcIdParam property.
*
- * <p>
+ * <p>
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+ * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
*
- * <p>
+ * <p>
* For example, to add a new item, do as follows:
- * <pre>
+ * <pre>
* getCalcIdParam().add(newItem);
- * </pre>
+ * </pre>
*
*
- * <p>
+ * <p>
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport.CalcIdParam }
*
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * <p>The following schema fragment specifies the expected content contained within this class.
*
- * <pre>
- * &lt;complexType&gt;
- * &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt;
- * &lt;/complexContent&gt;
- * &lt;/complexType&gt;
- * </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
git://source.jalview.org / jalview.git / blobdiff