X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FJalviewModel.java;fp=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FJalviewModel.java;h=2de1ebad2823e16c949c0162e8d74146d579e269;hb=3659ecfe7bb17dd25a0a6b5c94a7d9dab4525136;hp=61c767d010d07181503f6dcbc587f723e349ff11;hpb=5d49f772d8dd53aba8907f37a244b00ed8f86a87;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index 61c767d..2de1eba 100644 --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@ -1,8 +1,8 @@ // -// This file was generated by the 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 http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2022.02.07 at 04:44:47 PM GMT +// Generated on: 2023.01.31 at 04:07:08 PM GMT // @@ -24,355 +24,355 @@ import javax.xml.datatype.XMLGregorianCalendar; /** - * <p>Java class for JalviewModel complex type. + *
Java class for JalviewModel complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType name="JalviewModel"> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/> - * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/> - * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/> - * <sequence> - * <element name="JSeq" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/> - * <element name="pdbids" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <extension base="{www.jalview.org}pdbentry"> - * <sequence> - * <element name="structureState" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <simpleContent> - * <extension base="<http://www.w3.org/2001/XMLSchema>string"> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </extension> - * </simpleContent> - * </complexType> - * </element> - * </sequence> - * </extension> - * </complexContent> - * </complexType> - * </element> - * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/> - * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="secondaryStructure" maxOccurs="unbounded"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * </sequence> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * </sequence> - * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="JGroup" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/> - * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/> - * </sequence> - * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="Viewport" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/> - * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"> - * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * </extension> - * </complexContent> - * </complexType> - * </element> - * <element name="overview" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * </sequence> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> - * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="UserColours" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/> - * </sequence> - * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="tree" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence minOccurs="0"> - * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/> - * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/> - * </sequence> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /> - * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> - * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="sequencePoint" maxOccurs="unbounded"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attGroup ref="{www.jalview.org}position"/> - * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="axis" maxOccurs="3" minOccurs="3"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attGroup ref="{www.jalview.org}position"/> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="seqPointMin"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attGroup ref="{www.jalview.org}position"/> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="seqPointMax"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attGroup ref="{www.jalview.org}position"/> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="pcaData" type="{www.jalview.org}PcaDataType"/> - * </sequence> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attGroup ref="{www.jalview.org}SimilarityParams"/> - * <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> + *
+ * <complexType name="JalviewModel"> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/> + * <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/> + * <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/> + * <sequence> + * <element name="JSeq" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/> + * <element name="pdbids" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <extension base="{www.jalview.org}pdbentry"> + * <sequence> + * <element name="structureState" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <simpleContent> + * <extension base="<http://www.w3.org/2001/XMLSchema>string"> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </extension> + * </simpleContent> + * </complexType> + * </element> + * </sequence> + * </extension> + * </complexContent> + * </complexType> + * </element> + * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/> + * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="secondaryStructure" maxOccurs="unbounded"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * </sequence> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * </sequence> + * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="JGroup" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/> + * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/> + * </sequence> + * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="Viewport" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/> + * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"> + * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * </extension> + * </complexContent> + * </complexType> + * </element> + * <element name="overview" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * </sequence> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> + * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="UserColours" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/> + * </sequence> + * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="tree" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence minOccurs="0"> + * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/> + * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/> + * </sequence> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> + * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="sequencePoint" maxOccurs="unbounded"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="axis" maxOccurs="3" minOccurs="3"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="seqPointMin"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="seqPointMax"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="pcaData" type="{www.jalview.org}PcaDataType"/> + * </sequence> + * <attGroup ref="{www.jalview.org}SimilarityParams"/> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="FeatureSettings" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="setting" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/> + * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/> + * </sequence> + * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /> + * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="group" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * </sequence> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * </sequence> + * </sequence> + * </restriction> + * </complexContent> + * </complexType> + ** * */ @@ -487,20 +487,20 @@ public class JalviewModel { /** * Gets the value of the jSeq property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jSeq property.
+ * This is why there is not a set
method for the jSeq property.
*
- * <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 * {@link JalviewModel.JSeq } * @@ -516,20 +516,20 @@ public class JalviewModel { /** * Gets the value of the jGroup property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the jGroup property.
+ * This is why there is not a set
method for the jGroup property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getJGroup().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link JalviewModel.JGroup } * @@ -545,20 +545,20 @@ public class JalviewModel { /** * Gets the value of the viewport property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the viewport property.
+ * This is why there is not a set
method for the viewport property.
*
- * <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 * {@link JalviewModel.Viewport } * @@ -574,20 +574,20 @@ public class JalviewModel { /** * Gets the value of the userColours property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the userColours property.
+ * This is why there is not a set
method for the userColours property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getUserColours().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link JalviewModel.UserColours } * @@ -603,20 +603,20 @@ public class JalviewModel { /** * Gets the value of the tree property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the tree property.
+ * This is why there is not a set
method for the tree property.
*
- * <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 * {@link JalviewModel.Tree } * @@ -632,20 +632,20 @@ public class JalviewModel { /** * Gets the value of the pcaViewer property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
+ * This is why there is not a set
method for the pcaViewer property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getPcaViewer().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link JalviewModel.PcaViewer } * @@ -684,54 +684,54 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="setting" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/> - * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/> - * </sequence> - * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /> - * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /> - * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /> - * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /> - * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /> - * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="group" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * </sequence> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <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> + ** * */ @@ -750,20 +750,20 @@ public class JalviewModel { /** * Gets the value of the setting property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the setting property.
+ * This is why there is not a set
method for the setting property.
*
- * <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 * {@link JalviewModel.FeatureSettings.Setting } * @@ -779,20 +779,20 @@ public class JalviewModel { /** * Gets the value of the group property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the group property.
+ * This is why there is not a set
method for the group property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getGroup().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link JalviewModel.FeatureSettings.Group } * @@ -807,20 +807,20 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <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> + ** * */ @@ -877,34 +877,34 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
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> + *
+ * <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> + ** * */ @@ -947,20 +947,20 @@ public class JalviewModel { /** * Gets the value of the attributeName property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the attributeName property.
+ * This is why there is not a set
method for the attributeName property.
*
- * <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 } * @@ -1279,41 +1279,41 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/> - * <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/> - * </sequence> - * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <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> + ** * */ @@ -1370,20 +1370,20 @@ public class JalviewModel { /** * Gets the value of the seq property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the seq property.
+ * This is why there is not a set
method for the seq property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getSeq().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link String } * @@ -1896,80 +1896,80 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/> - * <element name="pdbids" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <extension base="{www.jalview.org}pdbentry"> - * <sequence> - * <element name="structureState" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <simpleContent> - * <extension base="<http://www.w3.org/2001/XMLSchema>string"> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </extension> - * </simpleContent> - * </complexType> - * </element> - * </sequence> - * </extension> - * </complexContent> - * </complexType> - * </element> - * <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/> - * <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="secondaryStructure" maxOccurs="unbounded"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * </sequence> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * </sequence> - * <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <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> + ** * */ @@ -2006,20 +2006,20 @@ public class JalviewModel { /** * Gets the value of the features property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the features property.
+ * This is why there is not a set
method for the features property.
*
- * <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 } * @@ -2035,20 +2035,20 @@ public class JalviewModel { /** * Gets the value of the pdbids property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the pdbids property.
+ * This is why there is not a set
method for the pdbids property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getPdbids().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link JalviewModel.JSeq.Pdbids } * @@ -2064,20 +2064,20 @@ public class JalviewModel { /** * Gets the value of the hiddenSequences property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
+ * This is why there is not a set
method for the hiddenSequences property.
*
- * <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 } * @@ -2093,20 +2093,20 @@ public class JalviewModel { /** * Gets the value of the rnaViewer property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
+ * This is why there is not a set
method for the rnaViewer property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getRnaViewer().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link JalviewModel.JSeq.RnaViewer } * @@ -2249,35 +2249,35 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
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> + *
+ * <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> + ** * */ @@ -2295,20 +2295,20 @@ public class JalviewModel { /** * Gets the value of the structureState property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the structureState property.
+ * This is why there is not a set
method for the structureState property.
*
- * <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 * {@link JalviewModel.JSeq.Pdbids.StructureState } * @@ -2323,25 +2323,25 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
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> + *
+ * <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> + ** * */ @@ -2656,37 +2656,37 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="secondaryStructure" maxOccurs="unbounded"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * </sequence> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <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> + ** * */ @@ -2718,20 +2718,20 @@ public class JalviewModel { /** * Gets the value of the secondaryStructure property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
+ * This is why there is not a set
method for the secondaryStructure property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getSecondaryStructure().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure } * @@ -2938,22 +2938,22 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
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> + *
+ * <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> + ** * */ @@ -3074,69 +3074,69 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
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="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}swingwindow"/> - * <attGroup ref="{www.jalview.org}SimilarityParams"/> - * <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> + *
+ * <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> + ** * */ @@ -3178,14 +3178,6 @@ public class JalviewModel { protected Boolean showLabels; @XmlAttribute(name = "linkToAllViews") protected Boolean linkToAllViews; - @XmlAttribute(name = "width") - protected Integer width; - @XmlAttribute(name = "height") - protected Integer height; - @XmlAttribute(name = "xpos") - protected Integer xpos; - @XmlAttribute(name = "ypos") - protected Integer ypos; @XmlAttribute(name = "includeGaps") protected Boolean includeGaps; @XmlAttribute(name = "matchGaps") @@ -3194,24 +3186,32 @@ public class JalviewModel { protected Boolean includeGappedColumns; @XmlAttribute(name = "denominateByShortestLength") protected Boolean denominateByShortestLength; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; /** * Gets the value of the sequencePoint property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
+ * This is why there is not a set
method for the sequencePoint property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getSequencePoint().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link JalviewModel.PcaViewer.SequencePoint } * @@ -3227,20 +3227,20 @@ public class JalviewModel { /** * Gets the value of the axis property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the axis property.
+ * This is why there is not a set
method for the axis property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getAxis().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link JalviewModel.PcaViewer.Axis } * @@ -3542,212 +3542,212 @@ public class JalviewModel { } /** - * Gets the value of the width property. + * Gets the value of the includeGaps property. * * @return * possible object is - * {@link Integer } + * {@link Boolean } * */ - public Integer getWidth() { - return width; + public Boolean isIncludeGaps() { + return includeGaps; } /** - * Sets the value of the width property. + * Sets the value of the includeGaps property. * * @param value * allowed object is - * {@link Integer } + * {@link Boolean } * */ - public void setWidth(Integer value) { - this.width = value; + public void setIncludeGaps(Boolean value) { + this.includeGaps = value; } /** - * Gets the value of the height property. + * Gets the value of the matchGaps property. * * @return * possible object is - * {@link Integer } + * {@link Boolean } * */ - public Integer getHeight() { - return height; + public Boolean isMatchGaps() { + return matchGaps; } /** - * Sets the value of the height property. + * Sets the value of the matchGaps property. * * @param value * allowed object is - * {@link Integer } + * {@link Boolean } * */ - public void setHeight(Integer value) { - this.height = value; + public void setMatchGaps(Boolean value) { + this.matchGaps = value; } /** - * Gets the value of the xpos property. + * Gets the value of the includeGappedColumns property. * * @return * possible object is - * {@link Integer } + * {@link Boolean } * */ - public Integer getXpos() { - return xpos; + public Boolean isIncludeGappedColumns() { + return includeGappedColumns; } /** - * Sets the value of the xpos property. + * Sets the value of the includeGappedColumns property. * * @param value * allowed object is - * {@link Integer } + * {@link Boolean } * */ - public void setXpos(Integer value) { - this.xpos = value; + public void setIncludeGappedColumns(Boolean value) { + this.includeGappedColumns = value; } /** - * Gets the value of the ypos property. + * Gets the value of the denominateByShortestLength property. * * @return * possible object is - * {@link Integer } + * {@link Boolean } * */ - public Integer getYpos() { - return ypos; + public Boolean isDenominateByShortestLength() { + return denominateByShortestLength; } /** - * Sets the value of the ypos property. + * Sets the value of the denominateByShortestLength property. * * @param value * allowed object is - * {@link Integer } + * {@link Boolean } * */ - public void setYpos(Integer value) { - this.ypos = value; + public void setDenominateByShortestLength(Boolean value) { + this.denominateByShortestLength = value; } /** - * Gets the value of the includeGaps property. + * Gets the value of the width property. * * @return * possible object is - * {@link Boolean } + * {@link Integer } * */ - public Boolean isIncludeGaps() { - return includeGaps; + public Integer getWidth() { + return width; } /** - * Sets the value of the includeGaps property. + * Sets the value of the width property. * * @param value * allowed object is - * {@link Boolean } + * {@link Integer } * */ - public void setIncludeGaps(Boolean value) { - this.includeGaps = value; + public void setWidth(Integer value) { + this.width = value; } /** - * Gets the value of the matchGaps property. + * Gets the value of the height property. * * @return * possible object is - * {@link Boolean } + * {@link Integer } * */ - public Boolean isMatchGaps() { - return matchGaps; + public Integer getHeight() { + return height; } /** - * Sets the value of the matchGaps property. + * Sets the value of the height property. * * @param value * allowed object is - * {@link Boolean } + * {@link Integer } * */ - public void setMatchGaps(Boolean value) { - this.matchGaps = value; + public void setHeight(Integer value) { + this.height = value; } /** - * Gets the value of the includeGappedColumns property. + * Gets the value of the xpos property. * * @return * possible object is - * {@link Boolean } + * {@link Integer } * */ - public Boolean isIncludeGappedColumns() { - return includeGappedColumns; + public Integer getXpos() { + return xpos; } /** - * Sets the value of the includeGappedColumns property. + * Sets the value of the xpos property. * * @param value * allowed object is - * {@link Boolean } + * {@link Integer } * */ - public void setIncludeGappedColumns(Boolean value) { - this.includeGappedColumns = value; + public void setXpos(Integer value) { + this.xpos = value; } /** - * Gets the value of the denominateByShortestLength property. + * Gets the value of the ypos property. * * @return * possible object is - * {@link Boolean } + * {@link Integer } * */ - public Boolean isDenominateByShortestLength() { - return denominateByShortestLength; + public Integer getYpos() { + return ypos; } /** - * Sets the value of the denominateByShortestLength property. + * Sets the value of the ypos property. * * @param value * allowed object is - * {@link Boolean } + * {@link Integer } * */ - public void setDenominateByShortestLength(Boolean value) { - this.denominateByShortestLength = value; + public void setYpos(Integer value) { + this.ypos = value; } /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
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}position"/> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + ** * */ @@ -3838,19 +3838,19 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
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}position"/> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + ** * */ @@ -3941,19 +3941,19 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
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}position"/> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + ** * */ @@ -4044,20 +4044,20 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
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}position"/> - * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </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> + ** * */ @@ -4176,34 +4176,34 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence minOccurs="0"> - * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/> - * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/> - * </sequence> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /> - * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> - * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence minOccurs="0"> + * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/> + * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/> + * </sequence> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> + * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * </restriction> + * </complexContent> + * </complexType> + ** * */ @@ -4668,22 +4668,22 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/> - * </sequence> - * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <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> + ** * */ @@ -4750,100 +4750,100 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <sequence> - * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/> - * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"> - * <complexType> - * <complexContent> - * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"> - * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * </extension> - * </complexContent> - * </complexType> - * </element> - * <element name="overview" minOccurs="0"> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> - * </restriction> - * </complexContent> - * </complexType> - * </element> - * </sequence> - * <attGroup ref="{www.jalview.org}swingwindow"/> - * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> - * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> - * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/> + * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"> + * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * </extension> + * </complexContent> + * </complexType> + * </element> + * <element name="overview" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * </sequence> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> + * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * </restriction> + * </complexContent> + * </complexType> + ** * */ @@ -4989,20 +4989,20 @@ public class JalviewModel { /** * Gets the value of the hiddenColumns property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
+ * This is why there is not a set
method for the hiddenColumns property.
*
- * <p>
+ *
* For example, to add a new item, do as follows: - * <pre> + *
* getHiddenColumns().add(newItem); - * </pre> + ** * - * <p> + *
* Objects of the following type(s) are allowed in the list * {@link JalviewModel.Viewport.HiddenColumns } * @@ -5018,20 +5018,20 @@ public class JalviewModel { /** * Gets the value of the calcIdParam property. * - * <p> + *
* This accessor method returns a reference to the live list,
* not a snapshot. Therefore any modification you make to the
* returned list will be present inside the JAXB object.
- * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
+ * This is why there is not a set
method for the calcIdParam property.
*
- * <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 * {@link JalviewModel.Viewport.CalcIdParam } * @@ -6250,21 +6250,21 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType> - * <complexContent> - * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"> - * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> - * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> - * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> - * </extension> - * </complexContent> - * </complexType> - * </pre> + *
+ * <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> + ** * */ @@ -6353,20 +6353,20 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
The following schema fragment specifies the expected content contained within this class. * - * <pre> - * <complexType> - * <complexContent> - * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> - * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /> - * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /> - * </restriction> - * </complexContent> - * </complexType> - * </pre> + *
+ * <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> + ** * */ @@ -6431,24 +6431,24 @@ public class JalviewModel { /** - * <p>Java class for anonymous complex type. + *
Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *
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> + *
+ * <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> + ** * */