//
-// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
-// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
+// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
+// See https://eclipse-ee4j.github.io/jaxb-ri
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2018.09.28 at 12:18:54 PM BST
+// Generated on: 2023.11.01 at 07:03:09 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>
- * <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>
- * </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" />
- * </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" />
- * </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>
+ * <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="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="charHeight" 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="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&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="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&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}SimilarityParams"/&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="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>
*
*
*/
"viewport",
"userColours",
"tree",
+ "pcaViewer",
"featureSettings"
})
public class JalviewModel {
@XmlElement(name = "UserColours")
protected List<JalviewModel.UserColours> userColours;
protected List<JalviewModel.Tree> tree;
+ @XmlElement(name = "PcaViewer")
+ protected List<JalviewModel.PcaViewer> pcaViewer;
@XmlElement(name = "FeatureSettings")
protected JalviewModel.FeatureSettings featureSettings;
/**
* 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>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getPcaViewer().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer> getPcaViewer() {
+ if (pcaViewer == null) {
+ pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
+ }
+ return this.pcaViewer;
+ }
+
+ /**
* Gets the value of the featureSettings property.
*
* @return
/**
- * <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>
- * <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>
+ * <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>
*
*
*/
/**
* 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>
- * <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>
+ * <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>
*
*
*/
/**
- * <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>
- * <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>
+ * <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>
*
*
*/
/**
* 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>
- * <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>
+ * <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>
*
*
*/
/**
* 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>
- * <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>
+ * <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>
*
*
*/
/**
* 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>
- * <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>
+ * <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>
*
*
*/
/**
* 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>
- * <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>
+ * <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>
*
*
*/
/**
- * <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>
- * <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>
+ * <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>
*
*
*/
/**
* 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>
- * <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>
+ * <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>
*
*
*/
/**
- * <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>
- * <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" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <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}SimilarityParams"/&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="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>
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
@XmlType(name = "", propOrder = {
- "title",
- "newick"
+ "sequencePoint",
+ "axis",
+ "seqPointMin",
+ "seqPointMax",
+ "pcaData"
})
- public static class Tree {
+ public static class PcaViewer {
- @XmlElement(namespace = "www.jalview.org")
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected List<JalviewModel.PcaViewer.Axis> axis;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected PcaDataType pcaData;
+ @XmlAttribute(name = "title")
protected String title;
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
+ @XmlAttribute(name = "scoreModelName")
+ protected String scoreModelName;
+ @XmlAttribute(name = "xDim")
+ protected Integer xDim;
+ @XmlAttribute(name = "yDim")
+ protected Integer yDim;
+ @XmlAttribute(name = "zDim")
+ protected Integer zDim;
+ @XmlAttribute(name = "bgColour")
+ protected Integer bgColour;
+ @XmlAttribute(name = "scaleFactor")
+ protected Float scaleFactor;
+ @XmlAttribute(name = "showLabels")
+ protected Boolean showLabels;
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+ @XmlAttribute(name = "includeGaps")
+ protected Boolean includeGaps;
+ @XmlAttribute(name = "matchGaps")
+ protected Boolean matchGaps;
+ @XmlAttribute(name = "includeGappedColumns")
+ protected Boolean includeGappedColumns;
+ @XmlAttribute(name = "denominateByShortestLength")
+ protected Boolean denominateByShortestLength;
@XmlAttribute(name = "width")
protected Integer width;
@XmlAttribute(name = "height")
protected Integer ypos;
/**
+ * Gets the value of the sequencePoint property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getSequencePoint().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.SequencePoint }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
+ if (sequencePoint == null) {
+ sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
+ }
+ return this.sequencePoint;
+ }
+
+ /**
+ * Gets the value of the axis property.
+ *
+ * <p>
+ * This accessor method returns a reference to the live list,
+ * not a snapshot. Therefore any modification you make to the
+ * returned list will be present inside the JAXB object.
+ * This is why there is not a <CODE>set</CODE> method for the axis property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
+ * <pre>
+ * getAxis().add(newItem);
+ * </pre>
+ *
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.Axis }
+ *
+ *
+ */
+ public List<JalviewModel.PcaViewer.Axis> getAxis() {
+ if (axis == null) {
+ axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
+ }
+ return this.axis;
+ }
+
+ /**
+ * Gets the value of the seqPointMin property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
+ return seqPointMin;
+ }
+
+ /**
+ * Sets the value of the seqPointMin property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModel.PcaViewer.SeqPointMin }
+ *
+ */
+ public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
+ this.seqPointMin = value;
+ }
+
+ /**
+ * Gets the value of the seqPointMax property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
+ return seqPointMax;
+ }
+
+ /**
+ * Sets the value of the seqPointMax property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModel.PcaViewer.SeqPointMax }
+ *
+ */
+ public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
+ this.seqPointMax = value;
+ }
+
+ /**
+ * Gets the value of the pcaData property.
+ *
+ * @return
+ * possible object is
+ * {@link PcaDataType }
+ *
+ */
+ public PcaDataType getPcaData() {
+ return pcaData;
+ }
+
+ /**
+ * Sets the value of the pcaData property.
+ *
+ * @param value
+ * allowed object is
+ * {@link PcaDataType }
+ *
+ */
+ public void setPcaData(PcaDataType value) {
+ this.pcaData = value;
+ }
+
+ /**
* Gets the value of the title property.
*
* @return
}
/**
- * Gets the value of the newick property.
+ * Gets the value of the scoreModelName property.
*
* @return
* possible object is
* {@link String }
*
*/
- public String getNewick() {
- return newick;
+ public String getScoreModelName() {
+ return scoreModelName;
}
/**
- * Sets the value of the newick property.
+ * Sets the value of the scoreModelName property.
*
* @param value
* allowed object is
* {@link String }
*
*/
- public void setNewick(String value) {
- this.newick = value;
+ public void setScoreModelName(String value) {
+ this.scoreModelName = value;
}
/**
- * Gets the value of the fontName property.
+ * Gets the value of the xDim property.
*
* @return
* possible object is
- * {@link String }
+ * {@link Integer }
*
*/
- public String getFontName() {
- return fontName;
+ public Integer getXDim() {
+ return xDim;
}
/**
- * Sets the value of the fontName property.
+ * Sets the value of the xDim property.
*
* @param value
* allowed object is
- * {@link String }
+ * {@link Integer }
*
*/
- public void setFontName(String value) {
- this.fontName = value;
+ public void setXDim(Integer value) {
+ this.xDim = value;
}
/**
- * Gets the value of the fontSize property.
+ * Gets the value of the yDim property.
*
* @return
* possible object is
* {@link Integer }
*
*/
- public Integer getFontSize() {
- return fontSize;
+ public Integer getYDim() {
+ return yDim;
}
/**
- * Sets the value of the fontSize property.
+ * Sets the value of the yDim property.
*
* @param value
* allowed object is
* {@link Integer }
*
*/
- public void setFontSize(Integer value) {
- this.fontSize = value;
+ public void setYDim(Integer value) {
+ this.yDim = value;
}
/**
- * Gets the value of the fontStyle property.
+ * Gets the value of the zDim property.
*
* @return
* possible object is
* {@link Integer }
*
*/
- public Integer getFontStyle() {
- return fontStyle;
+ public Integer getZDim() {
+ return zDim;
}
/**
- * Sets the value of the fontStyle property.
+ * Sets the value of the zDim property.
*
* @param value
* allowed object is
* {@link Integer }
*
*/
- public void setFontStyle(Integer value) {
- this.fontStyle = value;
+ public void setZDim(Integer value) {
+ this.zDim = value;
}
/**
- * Gets the value of the threshold property.
+ * Gets the value of the bgColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getBgColour() {
+ return bgColour;
+ }
+
+ /**
+ * Sets the value of the bgColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setBgColour(Integer value) {
+ this.bgColour = value;
+ }
+
+ /**
+ * Gets the value of the scaleFactor property.
*
* @return
* possible object is
* {@link Float }
*
*/
- public Float getThreshold() {
- return threshold;
+ public Float getScaleFactor() {
+ return scaleFactor;
}
/**
- * Sets the value of the threshold property.
+ * Sets the value of the scaleFactor property.
*
* @param value
* allowed object is
* {@link Float }
*
*/
- public void setThreshold(Float value) {
- this.threshold = value;
+ public void setScaleFactor(Float value) {
+ this.scaleFactor = value;
}
/**
- * Gets the value of the showBootstrap property.
+ * Gets the value of the showLabels property.
*
* @return
* possible object is
* {@link Boolean }
*
*/
- public Boolean isShowBootstrap() {
- return showBootstrap;
+ public Boolean isShowLabels() {
+ return showLabels;
}
/**
- * Sets the value of the showBootstrap property.
+ * Sets the value of the showLabels property.
*
* @param value
* allowed object is
* {@link Boolean }
*
*/
- public void setShowBootstrap(Boolean value) {
- this.showBootstrap = value;
+ public void setShowLabels(Boolean value) {
+ this.showLabels = value;
}
/**
- * Gets the value of the showDistances property.
+ * Gets the value of the linkToAllViews property.
*
* @return
* possible object is
* {@link Boolean }
*
*/
- public Boolean isShowDistances() {
- return showDistances;
+ public Boolean isLinkToAllViews() {
+ return linkToAllViews;
}
/**
- * Sets the value of the showDistances property.
+ * Sets the value of the linkToAllViews property.
*
* @param value
* allowed object is
* {@link Boolean }
*
*/
- public void setShowDistances(Boolean value) {
- this.showDistances = value;
+ public void setLinkToAllViews(Boolean value) {
+ this.linkToAllViews = value;
}
/**
- * Gets the value of the markUnlinked property.
+ * Gets the value of the includeGaps property.
*
* @return
* possible object is
* {@link Boolean }
*
*/
- public Boolean isMarkUnlinked() {
- return markUnlinked;
+ public Boolean isIncludeGaps() {
+ return includeGaps;
}
/**
- * Sets the value of the markUnlinked property.
+ * Sets the value of the includeGaps property.
*
* @param value
* allowed object is
* {@link Boolean }
*
*/
- public void setMarkUnlinked(Boolean value) {
- this.markUnlinked = value;
+ public void setIncludeGaps(Boolean value) {
+ this.includeGaps = value;
}
/**
- * Gets the value of the fitToWindow property.
+ * Gets the value of the matchGaps property.
*
* @return
* possible object is
* {@link Boolean }
*
*/
- public Boolean isFitToWindow() {
- return fitToWindow;
+ public Boolean isMatchGaps() {
+ return matchGaps;
}
/**
- * Sets the value of the fitToWindow property.
+ * Sets the value of the matchGaps property.
*
* @param value
* allowed object is
* {@link Boolean }
*
*/
- public void setFitToWindow(Boolean value) {
- this.fitToWindow = value;
+ public void setMatchGaps(Boolean value) {
+ this.matchGaps = value;
}
/**
- * Gets the value of the currentTree property.
+ * Gets the value of the includeGappedColumns property.
*
* @return
* possible object is
* {@link Boolean }
*
*/
- public Boolean isCurrentTree() {
- return currentTree;
+ public Boolean isIncludeGappedColumns() {
+ return includeGappedColumns;
}
/**
- * Sets the value of the currentTree property.
+ * Sets the value of the includeGappedColumns property.
*
* @param value
* allowed object is
* {@link Boolean }
*
*/
- public void setCurrentTree(Boolean value) {
- this.currentTree = value;
+ public void setIncludeGappedColumns(Boolean value) {
+ this.includeGappedColumns = value;
}
/**
- * Gets the value of the id property.
+ * Gets the value of the denominateByShortestLength property.
*
* @return
* possible object is
- * {@link String }
+ * {@link Boolean }
*
*/
- public String getId() {
- return id;
+ public Boolean isDenominateByShortestLength() {
+ return denominateByShortestLength;
}
/**
- * Sets the value of the id property.
+ * Sets the value of the denominateByShortestLength property.
*
* @param value
* allowed object is
- * {@link String }
+ * {@link Boolean }
*
*/
- public void setId(String value) {
- this.id = value;
+ public void setDenominateByShortestLength(Boolean value) {
+ this.denominateByShortestLength = value;
}
/**
this.ypos = value;
}
- }
-
-
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <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>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "userColourScheme"
- })
- public static class UserColours {
-
- @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
- protected JalviewUserColours userColourScheme;
- @XmlAttribute(name = "id")
- protected String id;
/**
- * Gets the value of the userColourScheme property.
+ * <p>Java class for anonymous complex type.
+ *
+ * <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>
+ *
*
- * @return
- * possible object is
- * {@link JalviewUserColours }
- *
*/
- public JalviewUserColours getUserColourScheme() {
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Axis {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <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>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMax {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <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>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMin {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <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>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequencePoint {
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getSequenceRef() {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setSequenceRef(String value) {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getXPos() {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setXPos(Float value) {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getYPos() {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setYPos(Float value) {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getZPos() {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setZPos(Float value) {
+ this.zPos = value;
+ }
+
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <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="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
+ * &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&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>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "title",
+ "newick"
+ })
+ public static class Tree {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+ @XmlAttribute(name = "columnWise")
+ protected Boolean columnWise;
+ @XmlAttribute(name = "columnReference")
+ protected String columnReference;
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getNewick() {
+ return newick;
+ }
+
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setNewick(String value) {
+ this.newick = value;
+ }
+
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getFontName() {
+ return fontName;
+ }
+
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setFontName(String value) {
+ this.fontName = value;
+ }
+
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontSize() {
+ return fontSize;
+ }
+
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value) {
+ this.fontSize = value;
+ }
+
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getFontStyle() {
+ return fontStyle;
+ }
+
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value) {
+ this.fontStyle = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return
+ * possible object is
+ * {@link Float }
+ *
+ */
+ public Float getThreshold() {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Float }
+ *
+ */
+ public void setThreshold(Float value) {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap() {
+ return showBootstrap;
+ }
+
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value) {
+ this.showBootstrap = value;
+ }
+
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances() {
+ return showDistances;
+ }
+
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value) {
+ this.showDistances = value;
+ }
+
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked() {
+ return markUnlinked;
+ }
+
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value) {
+ this.markUnlinked = value;
+ }
+
+ /**
+ * Gets the value of the fitToWindow property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow() {
+ return fitToWindow;
+ }
+
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value) {
+ this.fitToWindow = value;
+ }
+
+ /**
+ * Gets the value of the currentTree property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree() {
+ return currentTree;
+ }
+
+ /**
+ * Sets the value of the currentTree property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setCurrentTree(Boolean value) {
+ this.currentTree = value;
+ }
+
+ /**
+ * Gets the value of the columnWise property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isColumnWise() {
+ if (columnWise == null) {
+ return false;
+ } else {
+ return columnWise;
+ }
+ }
+
+ /**
+ * Sets the value of the columnWise property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setColumnWise(Boolean value) {
+ this.columnWise = value;
+ }
+
+ /**
+ * Gets the value of the columnReference property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getColumnReference() {
+ return columnReference;
+ }
+
+ /**
+ * Sets the value of the columnReference property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setColumnReference(String value) {
+ this.columnReference = value;
+ }
+
+ /**
+ * Gets the value of the id property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getId() {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setId(String value) {
+ this.id = value;
+ }
+
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isLinkToAllViews() {
+ if (linkToAllViews == null) {
+ return false;
+ } else {
+ return linkToAllViews;
+ }
+ }
+
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value) {
+ this.linkToAllViews = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ }
+
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * <pre>
+ * &lt;complexType&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>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = {
+ "userColourScheme"
+ })
+ public static class UserColours {
+
+ @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
+ protected JalviewUserColours userColourScheme;
+ @XmlAttribute(name = "id")
+ protected String id;
+
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme() {
return userColourScheme;
}
/**
- * <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>
- * <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>
- * </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" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
+ * <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="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="charHeight" 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="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
+ * &lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&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>
*
*
*/
@XmlType(name = "", propOrder = {
"annotationColours",
"hiddenColumns",
- "calcIdParam"
+ "calcIdParam",
+ "overview"
})
public static class Viewport {
protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
@XmlElement(namespace = "www.jalview.org")
protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
+ @XmlElement(namespace = "www.jalview.org")
+ protected JalviewModel.Viewport.Overview overview;
@XmlAttribute(name = "conservationSelected")
protected Boolean conservationSelected;
@XmlAttribute(name = "pidSelected")
protected Integer startRes;
@XmlAttribute(name = "startSeq")
protected Integer startSeq;
+ @XmlAttribute(name = "charWidth")
+ protected Integer charWidth;
+ @XmlAttribute(name = "charHeight")
+ protected Integer charHeight;
@XmlAttribute(name = "fontName")
protected String fontName;
@XmlAttribute(name = "fontSize")
protected Integer fontSize;
@XmlAttribute(name = "fontStyle")
protected Integer fontStyle;
+ @XmlAttribute(name = "idWidth")
+ protected Integer idWidth;
+ @XmlAttribute(name = "idWidthManuallyAdjusted")
+ protected Boolean idWidthManuallyAdjusted;
@XmlAttribute(name = "scaleProteinAsCdna")
protected Boolean scaleProteinAsCdna;
@XmlAttribute(name = "viewName")
protected String id;
@XmlAttribute(name = "complementId")
protected String complementId;
+ @XmlAttribute(name = "showComplementFeatures")
+ protected Boolean showComplementFeatures;
+ @XmlAttribute(name = "showComplementFeaturesOnTop")
+ protected Boolean showComplementFeaturesOnTop;
@XmlAttribute(name = "width")
protected Integer width;
@XmlAttribute(name = "height")
/**
* 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 }
*
}
/**
+ * Gets the value of the overview property.
+ *
+ * @return
+ * possible object is
+ * {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public JalviewModel.Viewport.Overview getOverview() {
+ return overview;
+ }
+
+ /**
+ * Sets the value of the overview property.
+ *
+ * @param value
+ * allowed object is
+ * {@link JalviewModel.Viewport.Overview }
+ *
+ */
+ public void setOverview(JalviewModel.Viewport.Overview value) {
+ this.overview = value;
+ }
+
+ /**
* Gets the value of the conservationSelected property.
*
* @return
}
/**
+ * Gets the value of the charWidth property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getCharWidth() {
+ return charWidth;
+ }
+
+ /**
+ * Sets the value of the charWidth property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setCharWidth(Integer value) {
+ this.charWidth = value;
+ }
+
+ /**
+ * Gets the value of the charHeight property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getCharHeight() {
+ return charHeight;
+ }
+
+ /**
+ * Sets the value of the charHeight property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setCharHeight(Integer value) {
+ this.charHeight = value;
+ }
+
+ /**
* Gets the value of the fontName property.
*
* @return
}
/**
+ * Gets the value of the idWidth property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getIdWidth() {
+ return idWidth;
+ }
+
+ /**
+ * Sets the value of the idWidth property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setIdWidth(Integer value) {
+ this.idWidth = value;
+ }
+
+ /**
+ * Gets the value of the idWidthManuallyAdjusted property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isIdWidthManuallyAdjusted() {
+ return idWidthManuallyAdjusted;
+ }
+
+ /**
+ * Sets the value of the idWidthManuallyAdjusted property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setIdWidthManuallyAdjusted(Boolean value) {
+ this.idWidthManuallyAdjusted = value;
+ }
+
+ /**
* Gets the value of the scaleProteinAsCdna property.
*
* @return
}
/**
+ * Gets the value of the showComplementFeatures property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeatures() {
+ if (showComplementFeatures == null) {
+ return false;
+ } else {
+ return showComplementFeatures;
+ }
+ }
+
+ /**
+ * Sets the value of the showComplementFeatures property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowComplementFeatures(Boolean value) {
+ this.showComplementFeatures = value;
+ }
+
+ /**
+ * Gets the value of the showComplementFeaturesOnTop property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public boolean isShowComplementFeaturesOnTop() {
+ if (showComplementFeaturesOnTop == null) {
+ return false;
+ } else {
+ return showComplementFeaturesOnTop;
+ }
+ }
+
+ /**
+ * Sets the value of the showComplementFeaturesOnTop property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowComplementFeaturesOnTop(Boolean value) {
+ this.showComplementFeaturesOnTop = value;
+ }
+
+ /**
* Gets the value of the width property.
*
* @return
/**
- * <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>
- * <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>
+ * <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>
*
*
*/
/**
- * <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>
- * <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>
+ * <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>
*
*
*/
}
+
+ /**
+ * <p>Java class for anonymous complex type.
+ *
+ * <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>
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Overview {
+
+ @XmlAttribute(name = "showHidden")
+ protected Boolean showHidden;
+ @XmlAttribute(name = "residueColour")
+ protected Integer residueColour;
+ @XmlAttribute(name = "gapColour")
+ protected Integer gapColour;
+ @XmlAttribute(name = "hiddenColour")
+ protected Integer hiddenColour;
+ @XmlAttribute(name = "title")
+ protected String title;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+ @XmlAttribute(name = "height")
+ protected Integer height;
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the showHidden property.
+ *
+ * @return
+ * possible object is
+ * {@link Boolean }
+ *
+ */
+ public Boolean isShowHidden() {
+ return showHidden;
+ }
+
+ /**
+ * Sets the value of the showHidden property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Boolean }
+ *
+ */
+ public void setShowHidden(Boolean value) {
+ this.showHidden = value;
+ }
+
+ /**
+ * Gets the value of the residueColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getResidueColour() {
+ return residueColour;
+ }
+
+ /**
+ * Sets the value of the residueColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setResidueColour(Integer value) {
+ this.residueColour = value;
+ }
+
+ /**
+ * Gets the value of the gapColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getGapColour() {
+ return gapColour;
+ }
+
+ /**
+ * Sets the value of the gapColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setGapColour(Integer value) {
+ this.gapColour = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColour property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHiddenColour() {
+ return hiddenColour;
+ }
+
+ /**
+ * Sets the value of the hiddenColour property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHiddenColour(Integer value) {
+ this.hiddenColour = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return
+ * possible object is
+ * {@link String }
+ *
+ */
+ public String getTitle() {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is
+ * {@link String }
+ *
+ */
+ public void setTitle(String value) {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getWidth() {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setWidth(Integer value) {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getHeight() {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setHeight(Integer value) {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getXpos() {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setXpos(Integer value) {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return
+ * possible object is
+ * {@link Integer }
+ *
+ */
+ public Integer getYpos() {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is
+ * {@link Integer }
+ *
+ */
+ public void setYpos(Integer value) {
+ this.ypos = value;
+ }
+
+ }
+
}
}