//
-// This file was generated by the Eclipse Implementation of JAXB, v2.3.3
-// See https://eclipse-ee4j.github.io/jaxb-ri
+// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
+// See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.05.13 at 06:58:41 PM BST
//
package jalview.xml.binding.jalview;
import javax.xml.datatype.XMLGregorianCalendar;
/**
- * <p>Java class for JalviewModel complex type.
+ * <p>
+ * Java class for JalviewModel complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained within
+ * this class.
*
- * <pre> &lt;complexType name="JalviewModel"&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="creationDate"
- * type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt; &lt;element
- * name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;element name="vamsasModel"
- * type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
- * &lt;sequence&gt; &lt;element name="JSeq" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="features"
- * type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
- * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
- * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;simpleContent&gt; &lt;extension
- * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="colourwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/extension&gt; &lt;/simpleContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/extension&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="hiddenSequences"
- * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="rnaViewer" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="secondaryStructure"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="hidden"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="seq"
- * type="{http://www.w3.org/2001/XMLSchema}string"
- * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="start"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="displayBoxes"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="showUnconserved"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&gt; &lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="AnnotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt; &lt;extension
- * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="autoUpdate" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
- * name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="pidSelected"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="showBoxes"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="renderGaps"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="showNPfeatureTooltip"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="followHighlight"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="showGroupConservation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&gt; &lt;attribute name="viewName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="gatheredViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textCol2"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; &lt;attribute
- * name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showComplementFeatures"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="UserColourScheme"
- * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence minOccurs="0"&gt; &lt;element name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
- * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="fontName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showBootstrap"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="markUnlinked"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="sequencePoint"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;attribute name="sequenceRef"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attGroup ref="{www.jalview.org}position"/&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="seqPointMax"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="pcaData"
- * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; &lt;attGroup
- * ref="{www.jalview.org}SimilarityParams"/&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="scoreModelName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="zDim"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="scaleFactor"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="FeatureSettings" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="setting" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; &lt;attribute
- * name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
- * default="Min" /&gt; &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;/sequence&gt; &lt;/sequence&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType name="JalviewModel">
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
+ * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
+ * <sequence>
+ * <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="overview" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="tree" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequencePoint" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="axis" maxOccurs="3" minOccurs="3">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMin">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMax">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="FeatureSettings" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the jSeq property.
*
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the jSeq property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the jSeq property.
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getJSeq().add(newItem); </pre>
+ * <p>
+ * For example, to add a new item, do as follows:
*
+ * <pre>
+ * getJSeq().add(newItem);
+ * </pre>
*
- * <p> Objects of the following type(s) are allowed in the list
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq }
*
*
/**
* Gets the value of the jGroup property.
*
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the jGroup property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the jGroup property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getJGroup().add(newItem); </pre>
+ * <pre>
+ * getJGroup().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JGroup }
*
*
/**
* Gets the value of the viewport property.
*
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the viewport property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the viewport property.
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getViewport().add(newItem); </pre>
+ * <p>
+ * For example, to add a new item, do as follows:
*
+ * <pre>
+ * getViewport().add(newItem);
+ * </pre>
*
- * <p> Objects of the following type(s) are allowed in the list
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport }
*
*
/**
* Gets the value of the userColours property.
*
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the userColours property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the userColours property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getUserColours().add(newItem); </pre>
+ * <pre>
+ * getUserColours().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.UserColours }
*
*
/**
* Gets the value of the tree property.
*
- * <p> This accessor method returns a reference to the live list, not a
- * snapshot. Therefore any modification you make to the returned list will be
- * present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the tree property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a snapshot.
+ * Therefore any modification you make to the returned list will be present
+ * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
+ * for the tree property.
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getTree().add(newItem); </pre>
+ * <p>
+ * For example, to add a new item, do as follows:
*
+ * <pre>
+ * getTree().add(newItem);
+ * </pre>
*
- * <p> Objects of the following type(s) are allowed in the list
+ *
+ * <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>
+ * 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:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getPcaViewer().add(newItem); </pre>
+ * <pre>
+ * getPcaViewer().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer }
*
*
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="setting"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="noValueColour"
- * type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
- * &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float"
- * /&gt; &lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="group" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="setting" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="group" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the setting property.
*
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
+ * <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.
+ * <CODE>set</CODE> method for the setting property.
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getSetting().add(newItem); </pre>
+ * <p>
+ * For example, to add a new item, do as follows:
*
+ * <pre>
+ * getSetting().add(newItem);
+ * </pre>
*
- * <p> Objects of the following type(s) are allowed in the list
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.FeatureSettings.Setting }
*
*
/**
* Gets the value of the group property.
*
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
+ * <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.
+ * <CODE>set</CODE> method for the group property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getGroup().add(newItem); </pre>
+ * <pre>
+ * getGroup().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.FeatureSettings.Group }
*
*
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="name" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="attributeName"
- * type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2"
- * minOccurs="0"/&gt; &lt;element name="matcherSet"
- * type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="type" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="colour" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="display" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="order"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="mincolour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="noValueColour" type="{www.jalview.org/colours}NoValueColour"
- * default="Min" /&gt; &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="threshstate"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="min"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="colourByLabel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="autoScale"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <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="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
+ * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the attributeName property.
*
- * <p> This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the returned
- * list will be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the attributeName property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the attributeName property.
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getAttributeName().add(newItem); </pre>
+ * <p>
+ * For example, to add a new item, do as follows:
*
+ * <pre>
+ * getAttributeName().add(newItem);
+ * </pre>
*
- * <p> Objects of the following type(s) are allowed in the list
- * {@link String }
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String
+ * }
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="seq"
- * type="{http://www.w3.org/2001/XMLSchema}string"
- * maxOccurs="unbounded"/&gt; &lt;element name="annotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="start"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="name"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="consThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="outlineColour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="displayText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="colourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="ignoreGapsinConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
+ * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * </sequence>
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the seq property.
*
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
+ * <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.
+ * <CODE>set</CODE> method for the seq property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getSeq().add(newItem); </pre>
+ * <pre>
+ * getSeq().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
- * {@link String }
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link String }
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="features"
- * type="{www.jalview.org}feature" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="pdbids" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;extension
- * base="{www.jalview.org}pdbentry"&gt; &lt;sequence&gt;
- * &lt;element name="structureState" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;simpleContent&gt; &lt;extension
- * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&gt; &lt;attribute name="colourwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="colourByJmol"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="type"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt; &lt;/simpleContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;/extension&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="hiddenSequences"
- * type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded"
- * minOccurs="0"/&gt; &lt;element name="rnaViewer"
- * maxOccurs="unbounded" minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="secondaryStructure"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attribute name="colour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="end" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="hidden"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewreference"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org}pdbentry">
+ * <sequence>
+ * <element name="structureState" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <simpleContent>
+ * <extension base="<http://www.w3.org/2001/XMLSchema>string">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </extension>
+ * </simpleContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
+ * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the features property.
*
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
+ * <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.
+ * <CODE>set</CODE> method for the features property.
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getFeatures().add(newItem); </pre>
+ * <p>
+ * For example, to add a new item, do as follows:
*
+ * <pre>
+ * getFeatures().add(newItem);
+ * </pre>
*
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Feature }
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Feature }
*
*
*/
/**
* Gets the value of the pdbids property.
*
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
+ * <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.
+ * <CODE>set</CODE> method for the pdbids property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getPdbids().add(newItem); </pre>
+ * <pre>
+ * getPdbids().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.Pdbids }
*
*
/**
* Gets the value of the hiddenSequences property.
*
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
+ * <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.
+ * <CODE>set</CODE> method for the hiddenSequences property.
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getHiddenSequences().add(newItem); </pre>
+ * <p>
+ * For example, to add a new item, do as follows:
*
+ * <pre>
+ * getHiddenSequences().add(newItem);
+ * </pre>
*
- * <p> Objects of the following type(s) are allowed in the list
- * {@link Integer }
+ *
+ * <p>
+ * Objects of the following type(s) are allowed in the list {@link Integer }
*
*
*/
/**
* Gets the value of the rnaViewer property.
*
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
+ * <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.
+ * <CODE>set</CODE> method for the rnaViewer property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getRnaViewer().add(newItem); </pre>
+ * <pre>
+ * getRnaViewer().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.JSeq.RnaViewer }
*
*
}
/**
- * <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;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>
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <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>
*
*
*/
/**
* Gets the value of the structureState property.
*
- * <p> This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the returned
- * list will be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the structureState property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the structureState property.
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getStructureState().add(newItem); </pre>
+ * <p>
+ * For example, to add a new item, do as follows:
*
+ * <pre>
+ * getStructureState().add(newItem);
+ * </pre>
*
- * <p> Objects of the following type(s) are allowed in the list
+ *
+ * <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>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;simpleContent&gt;
- * &lt;extension
- * base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attribute name="visible"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="alignwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
- * /&gt; &lt;attribute name="colourwithAlignPanel"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
- * /&gt; &lt;attribute name="colourByJmol"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true"
- * /&gt; &lt;attribute name="type"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/extension&gt; &lt;/simpleContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <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>
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="secondaryStructure"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="viewId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="dividerLocation"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="secondaryStructure" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
/**
* Gets the value of the secondaryStructure property.
*
- * <p> This accessor method returns a reference to the live list,
- * not a snapshot. Therefore any modification you make to the returned
- * list will be present inside the JAXB object. This is why there is not a
- * <CODE>set</CODE> method for the secondaryStructure
- * property.
+ * <p>
+ * This accessor method returns a reference to the live list, not a
+ * snapshot. Therefore any modification you make to the returned list will
+ * be present inside the JAXB object. This is why there is not a
+ * <CODE>set</CODE> method for the secondaryStructure property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getSecondaryStructure().add(newItem); </pre>
+ * <pre>
+ * getSecondaryStructure().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
+ * <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>The following schema fragment specifies the expected content
- * contained within this class.
- *
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="annotationId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="gapped"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="viewerState"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <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">
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="sequencePoint"
- * maxOccurs="unbounded"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;attribute
- * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="axis" maxOccurs="3" minOccurs="3"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="seqPointMin"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="seqPointMax"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt;
- * &lt;/element&gt; &lt;element name="pcaData"
- * type="{www.jalview.org}PcaDataType"/&gt; &lt;/sequence&gt;
- * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
- * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
- * &lt;attribute name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="xDim"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;attribute name="bgColour"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
- * &lt;attribute name="showLabels"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="sequencePoint" maxOccurs="unbounded">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="axis" maxOccurs="3" minOccurs="3">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMin">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="seqPointMax">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}SimilarityParams"/>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlAttribute(name = "linkToAllViews")
protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
-
- @XmlAttribute(name = "height")
- protected Integer height;
-
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
-
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
@XmlAttribute(name = "includeGaps")
protected Boolean includeGaps;
@XmlAttribute(name = "denominateByShortestLength")
protected Boolean denominateByShortestLength;
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
/**
* Gets the value of the sequencePoint property.
*
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
+ * <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.
+ * <CODE>set</CODE> method for the sequencePoint property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getSequencePoint().add(newItem); </pre>
+ * <pre>
+ * getSequencePoint().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer.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
+ * <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.
+ * <CODE>set</CODE> method for the axis property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getAxis().add(newItem); </pre>
+ * <pre>
+ * getAxis().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.PcaViewer.Axis }
*
*
}
/**
- * Gets the value of the width property.
+ * Gets the value of the includeGaps property.
*
- * @return possible object is {@link Integer }
+ * @return possible object is {@link Boolean }
*
*/
- public Integer getWidth()
+ public Boolean isIncludeGaps()
{
- return width;
+ return includeGaps;
}
/**
- * Sets the value of the width property.
+ * Sets the value of the includeGaps property.
*
* @param value
- * allowed object is {@link Integer }
+ * allowed object is {@link Boolean }
*
*/
- public void setWidth(Integer value)
+ public void setIncludeGaps(Boolean value)
{
- this.width = value;
+ this.includeGaps = value;
}
/**
- * Gets the value of the height property.
+ * Gets the value of the matchGaps property.
*
- * @return possible object is {@link Integer }
+ * @return possible object is {@link Boolean }
*
*/
- public Integer getHeight()
+ public Boolean isMatchGaps()
{
- return height;
+ return matchGaps;
}
/**
- * Sets the value of the height property.
+ * Sets the value of the matchGaps property.
*
* @param value
- * allowed object is {@link Integer }
+ * allowed object is {@link Boolean }
*
*/
- public void setHeight(Integer value)
+ public void setMatchGaps(Boolean value)
{
- this.height = value;
+ this.matchGaps = value;
}
/**
- * Gets the value of the xpos property.
+ * Gets the value of the includeGappedColumns property.
*
- * @return possible object is {@link Integer }
+ * @return possible object is {@link Boolean }
*
*/
- public Integer getXpos()
+ public Boolean isIncludeGappedColumns()
{
- return xpos;
+ return includeGappedColumns;
}
/**
- * Sets the value of the xpos property.
+ * Sets the value of the includeGappedColumns property.
*
* @param value
- * allowed object is {@link Integer }
+ * allowed object is {@link Boolean }
*
*/
- public void setXpos(Integer value)
+ public void setIncludeGappedColumns(Boolean value)
{
- this.xpos = value;
+ this.includeGappedColumns = value;
}
/**
- * Gets the value of the ypos property.
+ * Gets the value of the denominateByShortestLength property.
*
- * @return possible object is {@link Integer }
+ * @return possible object is {@link Boolean }
*
*/
- public Integer getYpos()
+ public Boolean isDenominateByShortestLength()
{
- return ypos;
+ return denominateByShortestLength;
}
/**
- * Sets the value of the ypos property.
+ * Sets the value of the denominateByShortestLength property.
*
* @param value
- * allowed object is {@link Integer }
+ * allowed object is {@link Boolean }
*
*/
- public void setYpos(Integer value)
+ public void setDenominateByShortestLength(Boolean value)
{
- this.ypos = value;
+ this.denominateByShortestLength = value;
}
/**
- * Gets the value of the includeGaps property.
+ * Gets the value of the width property.
*
- * @return possible object is {@link Boolean }
+ * @return possible object is {@link Integer }
*
*/
- public Boolean isIncludeGaps()
+ public Integer getWidth()
{
- return includeGaps;
+ return width;
}
/**
- * Sets the value of the includeGaps property.
+ * Sets the value of the width property.
*
* @param value
- * allowed object is {@link Boolean }
+ * allowed object is {@link Integer }
*
*/
- public void setIncludeGaps(Boolean value)
+ public void setWidth(Integer value)
{
- this.includeGaps = value;
+ this.width = value;
}
/**
- * Gets the value of the matchGaps property.
+ * Gets the value of the height property.
*
- * @return possible object is {@link Boolean }
+ * @return possible object is {@link Integer }
*
*/
- public Boolean isMatchGaps()
+ public Integer getHeight()
{
- return matchGaps;
+ return height;
}
/**
- * Sets the value of the matchGaps property.
+ * Sets the value of the height property.
*
* @param value
- * allowed object is {@link Boolean }
+ * allowed object is {@link Integer }
*
*/
- public void setMatchGaps(Boolean value)
+ public void setHeight(Integer value)
{
- this.matchGaps = value;
+ this.height = value;
}
/**
- * Gets the value of the includeGappedColumns property.
+ * Gets the value of the xpos property.
*
- * @return possible object is {@link Boolean }
+ * @return possible object is {@link Integer }
*
*/
- public Boolean isIncludeGappedColumns()
+ public Integer getXpos()
{
- return includeGappedColumns;
+ return xpos;
}
/**
- * Sets the value of the includeGappedColumns property.
+ * Sets the value of the xpos property.
*
* @param value
- * allowed object is {@link Boolean }
+ * allowed object is {@link Integer }
*
*/
- public void setIncludeGappedColumns(Boolean value)
+ public void setXpos(Integer value)
{
- this.includeGappedColumns = value;
+ this.xpos = value;
}
/**
- * Gets the value of the denominateByShortestLength property.
+ * Gets the value of the ypos property.
*
- * @return possible object is {@link Boolean }
+ * @return possible object is {@link Integer }
*
*/
- public Boolean isDenominateByShortestLength()
+ public Integer getYpos()
{
- return denominateByShortestLength;
+ return ypos;
}
/**
- * Sets the value of the denominateByShortestLength property.
+ * Sets the value of the ypos property.
*
* @param value
- * allowed object is {@link Boolean }
+ * allowed object is {@link Integer }
*
*/
- public void setDenominateByShortestLength(Boolean value)
+ public void setYpos(Integer value)
{
- this.denominateByShortestLength = value;
+ this.ypos = value;
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;/restriction&gt;
- * &lt;/complexContent&gt; &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attGroup
- * ref="{www.jalview.org}position"/&gt; &lt;attribute
- * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;sequence
- * minOccurs="0"&gt; &lt;element name="title"
- * type="{http://www.w3.org/2001/XMLSchema}string"/&gt; &lt;element
- * name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
- * name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="fontSize"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="threshold"
- * type="{http://www.w3.org/2001/XMLSchema}float" /&gt; &lt;attribute
- * name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * /&gt; &lt;attribute name="showDistances"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="markUnlinked"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="fitToWindow"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="currentTree"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID"
- * /&gt; &lt;attribute name="linkToAllViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@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
}
/**
+ * 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 }
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="UserColourScheme"
- * type="{www.jalview.org/colours}JalviewUserColours"/&gt;
- * &lt;/sequence&gt; &lt;attribute name="id"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
+ * </sequence>
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;sequence&gt; &lt;element name="AnnotationColours"
- * type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
- * &lt;element name="hiddenColumns" maxOccurs="unbounded"
- * minOccurs="0"&gt; &lt;complexType&gt;
- * &lt;complexContent&gt; &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; &lt;attribute
- * name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int"
- * /&gt; &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt; &lt;element
- * name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
- * &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;extension
- * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="false" /&gt; &lt;attribute name="autoUpdate"
- * use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; &lt;/element&gt;
- * &lt;/sequence&gt; &lt;attGroup
- * ref="{www.jalview.org}swingwindow"/&gt; &lt;attribute
- * name="conservationSelected"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="pidSelected"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="bgColour"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="pidThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="showFullId"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="rightAlignIds"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showColourText"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showUnconserved"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showBoxes"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="wrapAlignment"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="renderGaps"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showSequenceFeatures"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showNPfeatureTooltip"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="showDbRefTooltip"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="followHighlight"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="followSelection"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showAnnotation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="centreColumnLabels"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConservation"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showGroupConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showConsensusHistogram"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="showSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="normaliseSequenceLogo"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="ignoreGapsinConsensus"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
- * &lt;attribute name="startRes"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="fontStyle"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean"
- * default="true" /&gt; &lt;attribute name="viewName"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string"
- * /&gt; &lt;attribute name="gatheredViews"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;attribute name="textCol1"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;attribute name="textColThreshold"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
- * &lt;attribute name="complementId"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute
- * name="showComplementFeatures"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;attribute name="showComplementFeaturesOnTop"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="overview" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
@XmlType(
name = "",
propOrder =
- { "annotationColours", "hiddenColumns", "calcIdParam" })
+ { "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
public static class Viewport
{
@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 = "startSeq")
protected Integer startSeq;
+ @XmlAttribute(name = "charWidth")
+ protected Integer charWidth;
+
+ @XmlAttribute(name = "charHeight")
+ protected Integer charHeight;
+
@XmlAttribute(name = "fontName")
protected String fontName;
/**
* Gets the value of the hiddenColumns property.
*
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
+ * <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.
+ * <CODE>set</CODE> method for the hiddenColumns property.
+ *
+ * <p>
+ * For example, to add a new item, do as follows:
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getHiddenColumns().add(newItem); </pre>
+ * <pre>
+ * getHiddenColumns().add(newItem);
+ * </pre>
*
*
- * <p> Objects of the following type(s) are allowed in the list
+ * <p>
+ * Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport.HiddenColumns }
*
*
/**
* Gets the value of the calcIdParam property.
*
- * <p> This accessor method returns a reference to the live list, not
- * a snapshot. Therefore any modification you make to the returned list will
+ * <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.
+ * <CODE>set</CODE> method for the calcIdParam property.
*
- * <p> For example, to add a new item, do as follows: <pre>
- * getCalcIdParam().add(newItem); </pre>
+ * <p>
+ * For example, to add a new item, do as follows:
*
+ * <pre>
+ * getCalcIdParam().add(newItem);
+ * </pre>
*
- * <p> Objects of the following type(s) are allowed in the list
+ *
+ * <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 possible object is {@link Boolean }
}
/**
+ * 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 possible object is {@link String }
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;extension
- * base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
- * &lt;attribute name="calcId" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
- * &lt;attribute name="needsUpdate"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false"
- * /&gt; &lt;attribute name="autoUpdate" use="required"
- * type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
- * &lt;/extension&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
}
/**
- * <p>Java class for anonymous complex type.
+ * <p>
+ * Java class for anonymous complex type.
*
- * <p>The following schema fragment specifies the expected content
- * contained within this class.
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
*
- * <pre> &lt;complexType&gt; &lt;complexContent&gt;
- * &lt;restriction
- * base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
- * &lt;attribute name="start"
- * type="{http://www.w3.org/2001/XMLSchema}int" /&gt; &lt;attribute
- * name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
- * &lt;/restriction&gt; &lt;/complexContent&gt;
- * &lt;/complexType&gt; </pre>
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
*
*
*/
}
+ /**
+ * <p>
+ * Java class for anonymous complex type.
+ *
+ * <p>
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * <pre>
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </pre>
+ *
+ *
+ */
+ @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;
+ }
+
+ }
+
}
}
git://source.jalview.org / jalview.git / blobdiff