X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FJalviewModel.java;h=94f9373cbc152b08dd69ce52a007d537b143d801;hb=7b5d11bce39b76612773aa4d606ffbe55bb86a02;hp=61c767d010d07181503f6dcbc587f723e349ff11;hpb=7b32d373b60d0af55481cfd6d377b2cc1ec035c0;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/JalviewModel.java b/src/jalview/xml/binding/jalview/JalviewModel.java index 61c767d..94f9373 100644 --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@ -1,11 +1,10 @@ // -// 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: 2023.05.13 at 06:58:41 PM BST // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -22,6677 +21,6968 @@ import javax.xml.bind.annotation.adapters.CollapsedStringAdapter; import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; 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="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /> + * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> + * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="UserColours" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/> + * </sequence> + * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="tree" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence minOccurs="0"> + * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/> + * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/> + * </sequence> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /> + * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="sequencePoint" maxOccurs="unbounded"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="axis" maxOccurs="3" minOccurs="3"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="seqPointMin"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="seqPointMax"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attGroup ref="{www.jalview.org}position"/> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="pcaData" type="{www.jalview.org}PcaDataType"/> + * </sequence> + * <attGroup ref="{www.jalview.org}SimilarityParams"/> + * <attGroup ref="{www.jalview.org}swingwindow"/> + * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="FeatureSettings" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="setting" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <sequence> + * <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/> + * <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/> + * </sequence> + * <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /> + * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /> + * <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /> + * <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * <element name="group" maxOccurs="unbounded" minOccurs="0"> + * <complexType> + * <complexContent> + * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> + * <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> + * <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * </sequence> + * </restriction> + * </complexContent> + * </complexType> + * </element> + * </sequence> + * </sequence> + * </restriction> + * </complexContent> + * </complexType> + ** * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = { - "creationDate", - "version", - "vamsasModel", - "jSeq", - "jGroup", - "viewport", - "userColours", - "tree", - "pcaViewer", - "featureSettings" -}) -public class JalviewModel { - - @XmlElement(required = true) - @XmlSchemaType(name = "dateTime") - protected XMLGregorianCalendar creationDate; - @XmlElement(required = true) - protected String version; - @XmlElement(required = true) - protected VAMSAS vamsasModel; - @XmlElement(name = "JSeq") - protected List
+ * 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 set
method
+ * for the jSeq property.
+ *
+ *
+ * For example, to add a new item, do as follows: + * + *
+ * getJSeq().add(newItem); + *+ * + * + *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq }
+ *
+ *
+ */
+ public List
+ * 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
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JGroup }
+ *
+ *
+ */
+ public List
+ * 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
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport }
+ *
+ *
+ */
+ public List
+ * 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
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.UserColours }
+ *
+ *
+ */
+ public List
+ * 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
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Tree }
+ *
+ *
+ */
+ public List
+ * 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
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer }
+ *
+ *
+ */
+ public List
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Setting }
+ *
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getVersion() {
- return version;
+ public List
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.FeatureSettings.Group }
+ *
*
- * @param value
- * allowed object is
- * {@link String }
- *
*/
- public void setVersion(String value) {
- this.version = value;
+ public List
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list {@link String
+ * }
+ *
+ *
+ */
+ public List
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * 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
+ *
* For example, to add a new item, do as follows:
- * <pre>
- * getJSeq().add(newItem);
- * </pre>
*
+ *
+ * Objects of the following type(s) are allowed in the list {@link String }
*
*
*/
- public List
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list {@link Feature }
+ *
+ *
+ */
+ public List
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids }
+ *
+ *
+ */
+ public List
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list {@link Integer }
+ *
+ *
+ */
+ public List
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer }
+ *
+ *
+ */
+ public List
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.Pdbids.StructureState }
+ *
+ *
+ */
+ public List
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
+ *
+ *
+ */
+ public List
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.SequencePoint }
*
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "features",
- "pdbids",
- "hiddenSequences",
- "rnaViewer"
- })
- public static class JSeq {
-
- @XmlElement(namespace = "www.jalview.org")
- protected List
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.PcaViewer.Axis }
+ *
+ *
+ */
+ public List
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * 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
+ *
+ * For example, to add a new item, do as follows:
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.HiddenColumns }
*
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "userColourScheme"
- })
- public static class UserColours {
-
- @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
- protected JalviewUserColours userColourScheme;
- @XmlAttribute(name = "id")
- protected String id;
-
- /**
- * Gets the value of the userColourScheme property.
- *
- * @return
- * possible object is
- * {@link JalviewUserColours }
- *
- */
- public JalviewUserColours getUserColourScheme() {
- return userColourScheme;
- }
-
- /**
- * Sets the value of the userColourScheme property.
- *
- * @param value
- * allowed object is
- * {@link JalviewUserColours }
- *
- */
- public void setUserColourScheme(JalviewUserColours value) {
- this.userColourScheme = value;
- }
-
- /**
- * Gets the value of the id property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getId() {
- return id;
- }
-
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
-
+ public List
+ * 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
+ *
+ * For example, to add a new item, do as follows:
+ *
+ *
+ * Objects of the following type(s) are allowed in the list
+ * {@link JalviewModel.Viewport.CalcIdParam }
*
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "annotationColours",
- "hiddenColumns",
- "calcIdParam",
- "overview"
- })
- public static class Viewport {
-
- @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
- protected AnnotationColourScheme annotationColours;
- @XmlElement(namespace = "www.jalview.org")
- protected List
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ *
+ * Java class for anonymous complex type.
+ *
+ *
+ * The following schema fragment specifies the expected content contained
+ * within this class.
+ *
+ * set
method
+ * for the jGroup property.
+ *
+ *
+ * getJGroup().add(newItem);
+ *
+ *
+ *
+ * set
method
+ * for the viewport property.
+ *
+ *
+ * getViewport().add(newItem);
+ *
+ *
+ *
+ * set
method
+ * for the userColours property.
+ *
+ *
+ * getUserColours().add(newItem);
+ *
+ *
+ *
+ * set
method
+ * for the tree property.
+ *
+ *
+ * getTree().add(newItem);
+ *
+ *
+ *
+ * set
method
+ * for the pcaViewer property.
+ *
+ *
+ * getPcaViewer().add(newItem);
+ *
+ *
+ *
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "setting", "group" })
+ public static class FeatureSettings
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected Listset
method for the setting property.
+ *
+ *
+ * getSetting().add(newItem);
+ *
+ *
+ *
+ * set
method for the group property.
+ *
+ *
+ * getGroup().add(newItem);
+ *
+ *
+ *
+ *
+ * <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>
+ *
+ *
*
- * @return
- * possible object is
- * {@link VAMSAS }
- *
*/
- public VAMSAS getVamsasModel() {
- return vamsasModel;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Group
+ {
+
+ @XmlAttribute(name = "name", required = true)
+ protected String name;
+
+ @XmlAttribute(name = "display", required = true)
+ protected boolean display;
+
+ /**
+ * Gets the value of the name property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getName()
+ {
+ return name;
+ }
+
+ /**
+ * Sets the value of the name property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setName(String value)
+ {
+ this.name = value;
+ }
+
+ /**
+ * Gets the value of the display property.
+ *
+ */
+ public boolean isDisplay()
+ {
+ return display;
+ }
+
+ /**
+ * Sets the value of the display property.
+ *
+ */
+ public void setDisplay(boolean value)
+ {
+ this.display = value;
+ }
+
}
/**
- * Sets the value of the vamsasModel property.
+ *
+ * <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>
+ *
+ *
*
- * @param value
- * allowed object is
- * {@link VAMSAS }
- *
*/
- public void setVamsasModel(VAMSAS value) {
- this.vamsasModel = value;
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "attributeName", "matcherSet" })
+ public static class Setting
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected Listset
method for the attributeName property.
+ *
+ *
+ * getAttributeName().add(newItem);
+ *
+ *
+ *
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "seq", "annotationColours" })
+ public static class JGroup
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected Listset
method for the seq property.
*
- * <p>
+ *
+ * getSeq().add(newItem);
+ *
*
- * <p>
- * Objects of the following type(s) are allowed in the list
- * {@link JalviewModel.JSeq }
+ *
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "features", "pdbids", "hiddenSequences", "rnaViewer" })
+ public static class JSeq
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected Listset
method for the features property.
+ *
+ *
+ * getFeatures().add(newItem);
+ *
+ *
+ *
+ * set
method for the pdbids property.
+ *
+ *
+ * getPdbids().add(newItem);
+ *
+ *
+ *
+ * set
method for the hiddenSequences property.
+ *
+ *
+ * getHiddenSequences().add(newItem);
+ *
+ *
+ *
+ * set
method for the rnaViewer property.
+ *
+ *
+ * getRnaViewer().add(newItem);
+ *
+ *
+ *
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "structureState" })
+ public static class Pdbids extends Pdbentry
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected Listset
method for the structureState property.
+ *
+ *
+ * getStructureState().add(newItem);
+ *
+ *
+ *
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "value" })
+ public static class StructureState
+ {
+
+ @XmlValue
+ protected String value;
+
+ @XmlAttribute(name = "visible")
+ protected Boolean visible;
+
+ @XmlAttribute(name = "viewId")
+ protected String viewId;
+
+ @XmlAttribute(name = "alignwithAlignPanel")
+ protected Boolean alignwithAlignPanel;
+
+ @XmlAttribute(name = "colourwithAlignPanel")
+ protected Boolean colourwithAlignPanel;
+
+ @XmlAttribute(name = "colourByJmol")
+ protected Boolean colourByJmol;
+
+ @XmlAttribute(name = "type")
+ protected String type;
+
+ @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 start property.
+ * Gets the value of the value property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getStart() {
- return start;
+ public String getValue()
+ {
+ return value;
}
/**
- * Sets the value of the start property.
+ * Sets the value of the value property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setStart(Integer value) {
- this.start = value;
+ public void setValue(String value)
+ {
+ this.value = value;
}
/**
- * Gets the value of the end property.
+ * Gets the value of the visible property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getEnd() {
- return end;
+ public Boolean isVisible()
+ {
+ return visible;
}
/**
- * Sets the value of the end property.
+ * Sets the value of the visible property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setEnd(Integer value) {
- this.end = value;
+ public void setVisible(Boolean value)
+ {
+ this.visible = value;
}
/**
- * Gets the value of the name property.
+ * Gets the value of the viewId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getName() {
- return name;
+ public String getViewId()
+ {
+ return viewId;
}
/**
- * Sets the value of the name property.
+ * Sets the value of the viewId property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setName(String value) {
- this.name = value;
+ public void setViewId(String value)
+ {
+ this.viewId = value;
}
/**
- * Gets the value of the colour property.
+ * Gets the value of the alignwithAlignPanel property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getColour() {
- return colour;
+ public boolean isAlignwithAlignPanel()
+ {
+ if (alignwithAlignPanel == null)
+ {
+ return true;
+ }
+ else
+ {
+ return alignwithAlignPanel;
+ }
}
/**
- * Sets the value of the colour property.
+ * Sets the value of the alignwithAlignPanel property.
*
* @param value
- * allowed object is
- * {@link String }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setColour(String value) {
- this.colour = value;
+ public void setAlignwithAlignPanel(Boolean value)
+ {
+ this.alignwithAlignPanel = value;
}
/**
- * Gets the value of the consThreshold property.
+ * Gets the value of the colourwithAlignPanel property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getConsThreshold() {
- return consThreshold;
+ public boolean isColourwithAlignPanel()
+ {
+ if (colourwithAlignPanel == null)
+ {
+ return false;
+ }
+ else
+ {
+ return colourwithAlignPanel;
+ }
}
/**
- * Sets the value of the consThreshold property.
+ * Sets the value of the colourwithAlignPanel property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setConsThreshold(Integer value) {
- this.consThreshold = value;
+ public void setColourwithAlignPanel(Boolean value)
+ {
+ this.colourwithAlignPanel = value;
}
/**
- * Gets the value of the pidThreshold property.
+ * Gets the value of the colourByJmol property.
+ *
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getPidThreshold() {
- return pidThreshold;
+ public boolean isColourByJmol()
+ {
+ if (colourByJmol == null)
+ {
+ return true;
+ }
+ else
+ {
+ return colourByJmol;
+ }
}
/**
- * Sets the value of the pidThreshold property.
+ * Sets the value of the colourByJmol property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Boolean }
+ *
*/
- public void setPidThreshold(Integer value) {
- this.pidThreshold = value;
+ public void setColourByJmol(Boolean value)
+ {
+ this.colourByJmol = value;
}
/**
- * Gets the value of the outlineColour property.
+ * Gets the value of the type property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getOutlineColour() {
- return outlineColour;
+ public String getType()
+ {
+ return type;
}
/**
- * Sets the value of the outlineColour property.
+ * Sets the value of the type property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setOutlineColour(Integer value) {
- this.outlineColour = value;
+ public void setType(String value)
+ {
+ this.type = value;
}
/**
- * Gets the value of the displayBoxes property.
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isDisplayBoxes() {
- return displayBoxes;
+ public Integer getWidth()
+ {
+ return width;
}
/**
- * Sets the value of the displayBoxes property.
+ * Sets the value of the width property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setDisplayBoxes(Boolean value) {
- this.displayBoxes = value;
+ public void setWidth(Integer value)
+ {
+ this.width = value;
}
/**
- * Gets the value of the displayText property.
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isDisplayText() {
- return displayText;
+ public Integer getHeight()
+ {
+ return height;
}
/**
- * Sets the value of the displayText property.
+ * Sets the value of the height property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setDisplayText(Boolean value) {
- this.displayText = value;
+ public void setHeight(Integer value)
+ {
+ this.height = value;
}
/**
- * Gets the value of the colourText property.
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public Boolean isColourText() {
- return colourText;
+ public Integer getXpos()
+ {
+ return xpos;
}
/**
- * Sets the value of the colourText property.
+ * Sets the value of the xpos property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setColourText(Boolean value) {
- this.colourText = value;
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
}
/**
- * Gets the value of the textCol1 property.
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextCol1() {
- return textCol1;
+ public Integer getYpos()
+ {
+ return ypos;
}
/**
- * Sets the value of the textCol1 property.
+ * Sets the value of the ypos property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link Integer }
+ *
*/
- public void setTextCol1(Integer value) {
- this.textCol1 = value;
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
}
+ }
+
+ }
+
+ /**
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "secondaryStructure" })
+ public static class RnaViewer
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected Listset
method for the secondaryStructure property.
+ *
+ *
+ * getSecondaryStructure().add(newItem);
+ *
+ *
+ *
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SecondaryStructure
+ {
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "annotationId", required = true)
+ protected String annotationId;
+
+ @XmlAttribute(name = "gapped")
+ protected Boolean gapped;
+
+ @XmlAttribute(name = "viewerState")
+ protected String viewerState;
+
/**
- * Gets the value of the textCol2 property.
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextCol2() {
- return textCol2;
+ public String getTitle()
+ {
+ return title;
}
/**
- * Sets the value of the textCol2 property.
+ * Sets the value of the title property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setTextCol2(Integer value) {
- this.textCol2 = value;
+ public void setTitle(String value)
+ {
+ this.title = value;
}
/**
- * Gets the value of the textColThreshold property.
+ * Gets the value of the annotationId property.
+ *
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Integer }
- *
*/
- public Integer getTextColThreshold() {
- return textColThreshold;
+ public String getAnnotationId()
+ {
+ return annotationId;
}
/**
- * Sets the value of the textColThreshold property.
+ * Sets the value of the annotationId property.
*
* @param value
- * allowed object is
- * {@link Integer }
- *
+ * allowed object is {@link String }
+ *
*/
- public void setTextColThreshold(Integer value) {
- this.textColThreshold = value;
- }
-
- /**
- * Gets the value of the showUnconserved property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowUnconserved() {
- return showUnconserved;
- }
-
- /**
- * Sets the value of the showUnconserved property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowUnconserved(Boolean value) {
- this.showUnconserved = value;
- }
-
- /**
- * Gets the value of the ignoreGapsinConsensus property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public boolean isIgnoreGapsinConsensus() {
- if (ignoreGapsinConsensus == null) {
- return true;
- } else {
- return ignoreGapsinConsensus;
- }
+ public void setAnnotationId(String value)
+ {
+ this.annotationId = value;
}
/**
- * Sets the value of the ignoreGapsinConsensus property.
+ * Gets the value of the gapped property.
*
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIgnoreGapsinConsensus(Boolean value) {
- this.ignoreGapsinConsensus = value;
- }
-
- /**
- * Gets the value of the showConsensusHistogram property.
+ * @return possible object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isShowConsensusHistogram() {
- if (showConsensusHistogram == null) {
- return true;
- } else {
- return showConsensusHistogram;
- }
+ public Boolean isGapped()
+ {
+ return gapped;
}
/**
- * Sets the value of the showConsensusHistogram property.
+ * Sets the value of the gapped property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowConsensusHistogram(Boolean value) {
- this.showConsensusHistogram = value;
- }
-
- /**
- * Gets the value of the showSequenceLogo property.
+ * allowed object is {@link Boolean }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isShowSequenceLogo() {
- if (showSequenceLogo == null) {
- return false;
- } else {
- return showSequenceLogo;
- }
+ public void setGapped(Boolean value)
+ {
+ this.gapped = value;
}
/**
- * Sets the value of the showSequenceLogo property.
+ * Gets the value of the viewerState property.
*
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowSequenceLogo(Boolean value) {
- this.showSequenceLogo = value;
- }
-
- /**
- * Gets the value of the normaliseSequenceLogo property.
+ * @return possible object is {@link String }
*
- * @return
- * possible object is
- * {@link Boolean }
- *
*/
- public boolean isNormaliseSequenceLogo() {
- if (normaliseSequenceLogo == null) {
- return false;
- } else {
- return normaliseSequenceLogo;
- }
+ public String getViewerState()
+ {
+ return viewerState;
}
/**
- * Sets the value of the normaliseSequenceLogo property.
+ * Sets the value of the viewerState property.
*
* @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setNormaliseSequenceLogo(Boolean value) {
- this.normaliseSequenceLogo = value;
- }
-
- /**
- * Gets the value of the id property.
+ * allowed object is {@link String }
*
- * @return
- * possible object is
- * {@link String }
- *
*/
- public String getId() {
- return id;
+ public void setViewerState(String value)
+ {
+ this.viewerState = value;
}
- /**
- * Sets the value of the id property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setId(String value) {
- this.id = value;
- }
+ }
}
+ }
+
+ /**
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "sequencePoint", "axis", "seqPointMin", "seqPointMax", "pcaData" })
+ public static class PcaViewer
+ {
+
+ @XmlElement(namespace = "www.jalview.org", required = true)
+ protected Listset
method for the sequencePoint property.
+ *
+ *
+ * getSequencePoint().add(newItem);
+ *
+ *
+ *
+ * set
method for the axis property.
+ *
+ *
+ * getAxis().add(newItem);
+ *
+ *
+ *
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Axis
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
+ }
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
+ /**
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMax
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
+ }
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
+ /**
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}position"/>
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SeqPointMin
+ {
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
+ }
+
+ /**
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class SequencePoint
+ {
+
+ @XmlAttribute(name = "sequenceRef")
+ protected String sequenceRef;
+
+ @XmlAttribute(name = "xPos")
+ protected Float xPos;
+
+ @XmlAttribute(name = "yPos")
+ protected Float yPos;
+
+ @XmlAttribute(name = "zPos")
+ protected Float zPos;
+
+ /**
+ * Gets the value of the sequenceRef property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getSequenceRef()
+ {
+ return sequenceRef;
+ }
+
+ /**
+ * Sets the value of the sequenceRef property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setSequenceRef(String value)
+ {
+ this.sequenceRef = value;
+ }
+
+ /**
+ * Gets the value of the xPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getXPos()
+ {
+ return xPos;
+ }
+
+ /**
+ * Sets the value of the xPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setXPos(Float value)
+ {
+ this.xPos = value;
+ }
+
+ /**
+ * Gets the value of the yPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getYPos()
+ {
+ return yPos;
+ }
+
+ /**
+ * Sets the value of the yPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setYPos(Float value)
+ {
+ this.yPos = value;
+ }
+
+ /**
+ * Gets the value of the zPos property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getZPos()
+ {
+ return zPos;
+ }
+
+ /**
+ * Sets the value of the zPos property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setZPos(Float value)
+ {
+ this.zPos = value;
+ }
+
+ }
+
+ }
+
+ /**
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence minOccurs="0">
+ * <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
+ * <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "title", "newick" })
+ public static class Tree
+ {
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String title;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected String newick;
+
+ @XmlAttribute(name = "fontName")
+ protected String fontName;
+
+ @XmlAttribute(name = "fontSize")
+ protected Integer fontSize;
+
+ @XmlAttribute(name = "fontStyle")
+ protected Integer fontStyle;
+
+ @XmlAttribute(name = "threshold")
+ protected Float threshold;
+
+ @XmlAttribute(name = "showBootstrap")
+ protected Boolean showBootstrap;
+
+ @XmlAttribute(name = "showDistances")
+ protected Boolean showDistances;
+
+ @XmlAttribute(name = "markUnlinked")
+ protected Boolean markUnlinked;
+
+ @XmlAttribute(name = "fitToWindow")
+ protected Boolean fitToWindow;
+
+ @XmlAttribute(name = "currentTree")
+ protected Boolean currentTree;
+
+ @XmlAttribute(name = "columnWise")
+ protected Boolean columnWise;
+
+ @XmlAttribute(name = "columnReference")
+ protected String columnReference;
+
+ @XmlAttribute(name = "id")
+ @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
+ @XmlID
+ @XmlSchemaType(name = "ID")
+ protected String id;
+
+ @XmlAttribute(name = "linkToAllViews")
+ protected Boolean linkToAllViews;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the newick property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getNewick()
+ {
+ return newick;
+ }
+
+ /**
+ * Sets the value of the newick property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setNewick(String value)
+ {
+ this.newick = value;
+ }
+
+ /**
+ * Gets the value of the fontName property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getFontName()
+ {
+ return fontName;
+ }
+
+ /**
+ * Sets the value of the fontName property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setFontName(String value)
+ {
+ this.fontName = value;
+ }
+
+ /**
+ * Gets the value of the fontSize property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontSize()
+ {
+ return fontSize;
+ }
+
+ /**
+ * Sets the value of the fontSize property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontSize(Integer value)
+ {
+ this.fontSize = value;
+ }
+
+ /**
+ * Gets the value of the fontStyle property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getFontStyle()
+ {
+ return fontStyle;
+ }
+
+ /**
+ * Sets the value of the fontStyle property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setFontStyle(Integer value)
+ {
+ this.fontStyle = value;
+ }
+
+ /**
+ * Gets the value of the threshold property.
+ *
+ * @return possible object is {@link Float }
+ *
+ */
+ public Float getThreshold()
+ {
+ return threshold;
+ }
+
+ /**
+ * Sets the value of the threshold property.
+ *
+ * @param value
+ * allowed object is {@link Float }
+ *
+ */
+ public void setThreshold(Float value)
+ {
+ this.threshold = value;
+ }
+
+ /**
+ * Gets the value of the showBootstrap property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowBootstrap()
+ {
+ return showBootstrap;
+ }
+
+ /**
+ * Sets the value of the showBootstrap property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowBootstrap(Boolean value)
+ {
+ this.showBootstrap = value;
+ }
+
+ /**
+ * Gets the value of the showDistances property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowDistances()
+ {
+ return showDistances;
+ }
+
+ /**
+ * Sets the value of the showDistances property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowDistances(Boolean value)
+ {
+ this.showDistances = value;
+ }
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
+ /**
+ * Gets the value of the markUnlinked property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isMarkUnlinked()
+ {
+ return markUnlinked;
+ }
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
+ /**
+ * Sets the value of the markUnlinked property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setMarkUnlinked(Boolean value)
+ {
+ this.markUnlinked = value;
+ }
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ /**
+ * Gets the value of the fitToWindow property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isFitToWindow()
+ {
+ return fitToWindow;
+ }
- /**
- * Gets the value of the includeGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGaps() {
- return includeGaps;
- }
+ /**
+ * Sets the value of the fitToWindow property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setFitToWindow(Boolean value)
+ {
+ this.fitToWindow = value;
+ }
- /**
- * Sets the value of the includeGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGaps(Boolean value) {
- this.includeGaps = value;
- }
+ /**
+ * Gets the value of the currentTree property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isCurrentTree()
+ {
+ return currentTree;
+ }
- /**
- * Gets the value of the matchGaps property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isMatchGaps() {
- return matchGaps;
- }
+ /**
+ * Sets the value of the currentTree property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setCurrentTree(Boolean value)
+ {
+ this.currentTree = value;
+ }
- /**
- * Sets the value of the matchGaps property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setMatchGaps(Boolean value) {
- this.matchGaps = value;
- }
+ /**
+ * Gets the value of the columnWise property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isColumnWise()
+ {
+ if (columnWise == null)
+ {
+ return false;
+ }
+ else
+ {
+ return columnWise;
+ }
+ }
- /**
- * Gets the value of the includeGappedColumns property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isIncludeGappedColumns() {
- return includeGappedColumns;
- }
+ /**
+ * Sets the value of the columnWise property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setColumnWise(Boolean value)
+ {
+ this.columnWise = value;
+ }
- /**
- * Sets the value of the includeGappedColumns property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setIncludeGappedColumns(Boolean value) {
- this.includeGappedColumns = value;
- }
+ /**
+ * Gets the value of the columnReference property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getColumnReference()
+ {
+ return columnReference;
+ }
- /**
- * Gets the value of the denominateByShortestLength property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isDenominateByShortestLength() {
- return denominateByShortestLength;
- }
+ /**
+ * Sets the value of the columnReference property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setColumnReference(String value)
+ {
+ this.columnReference = value;
+ }
- /**
- * Sets the value of the denominateByShortestLength property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setDenominateByShortestLength(Boolean value) {
- this.denominateByShortestLength = value;
- }
+ /**
+ * Gets the value of the id property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getId()
+ {
+ return id;
+ }
+ /**
+ * Sets the value of the id property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Axis {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the linkToAllViews property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isLinkToAllViews()
+ {
+ if (linkToAllViews == null)
+ {
+ return false;
+ }
+ else
+ {
+ return linkToAllViews;
+ }
+ }
- }
+ /**
+ * Sets the value of the linkToAllViews property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setLinkToAllViews(Boolean value)
+ {
+ this.linkToAllViews = value;
+ }
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMax {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
- }
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SeqPointMin {
-
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
- }
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}position"/>
- * <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class SequencePoint {
-
- @XmlAttribute(name = "sequenceRef")
- protected String sequenceRef;
- @XmlAttribute(name = "xPos")
- protected Float xPos;
- @XmlAttribute(name = "yPos")
- protected Float yPos;
- @XmlAttribute(name = "zPos")
- protected Float zPos;
-
- /**
- * Gets the value of the sequenceRef property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getSequenceRef() {
- return sequenceRef;
- }
-
- /**
- * Sets the value of the sequenceRef property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setSequenceRef(String value) {
- this.sequenceRef = value;
- }
-
- /**
- * Gets the value of the xPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getXPos() {
- return xPos;
- }
-
- /**
- * Sets the value of the xPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setXPos(Float value) {
- this.xPos = value;
- }
-
- /**
- * Gets the value of the yPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getYPos() {
- return yPos;
- }
-
- /**
- * Sets the value of the yPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setYPos(Float value) {
- this.yPos = value;
- }
-
- /**
- * Gets the value of the zPos property.
- *
- * @return
- * possible object is
- * {@link Float }
- *
- */
- public Float getZPos() {
- return zPos;
- }
-
- /**
- * Sets the value of the zPos property.
- *
- * @param value
- * allowed object is
- * {@link Float }
- *
- */
- public void setZPos(Float value) {
- this.zPos = value;
- }
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
- }
+ }
+
+ /**
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "", propOrder = { "userColourScheme" })
+ public static class UserColours
+ {
+
+ @XmlElement(
+ name = "UserColourScheme",
+ namespace = "www.jalview.org",
+ required = true)
+ protected JalviewUserColours userColourScheme;
+
+ @XmlAttribute(name = "id")
+ protected String id;
+ /**
+ * Gets the value of the userColourScheme property.
+ *
+ * @return possible object is {@link JalviewUserColours }
+ *
+ */
+ public JalviewUserColours getUserColourScheme()
+ {
+ return userColourScheme;
}
+ /**
+ * Sets the value of the userColourScheme property.
+ *
+ * @param value
+ * allowed object is {@link JalviewUserColours }
+ *
+ */
+ public void setUserColourScheme(JalviewUserColours value)
+ {
+ this.userColourScheme = value;
+ }
/**
- * <p>Java class for anonymous complex type.
+ * Gets the value of the id property.
*
- * <p>The following schema fragment specifies the expected content contained within this class.
+ * @return possible object is {@link String }
*
- * <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>
+ */
+ public String getId()
+ {
+ return id;
+ }
+
+ /**
+ * Sets the value of the id property.
*
+ * @param value
+ * allowed object is {@link String }
*
*/
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "", propOrder = {
- "title",
- "newick"
- })
- public static class Tree {
+ public void setId(String value)
+ {
+ this.id = value;
+ }
- @XmlElement(namespace = "www.jalview.org")
- protected String title;
- @XmlElement(namespace = "www.jalview.org")
- protected String newick;
- @XmlAttribute(name = "fontName")
- protected String fontName;
- @XmlAttribute(name = "fontSize")
- protected Integer fontSize;
- @XmlAttribute(name = "fontStyle")
- protected Integer fontStyle;
- @XmlAttribute(name = "threshold")
- protected Float threshold;
- @XmlAttribute(name = "showBootstrap")
- protected Boolean showBootstrap;
- @XmlAttribute(name = "showDistances")
- protected Boolean showDistances;
- @XmlAttribute(name = "markUnlinked")
- protected Boolean markUnlinked;
- @XmlAttribute(name = "fitToWindow")
- protected Boolean fitToWindow;
- @XmlAttribute(name = "currentTree")
- protected Boolean currentTree;
- @XmlAttribute(name = "id")
- @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
- @XmlID
- @XmlSchemaType(name = "ID")
- protected String id;
- @XmlAttribute(name = "linkToAllViews")
- protected Boolean linkToAllViews;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
+ }
+
+ /**
+ *
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <sequence>
+ * <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
+ * <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
+ * <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * </extension>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * <element name="overview" minOccurs="0">
+ * <complexType>
+ * <complexContent>
+ * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ * </element>
+ * </sequence>
+ * <attGroup ref="{www.jalview.org}swingwindow"/>
+ * <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
+ * <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
+ * <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
+ * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
+ * <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
+ * <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
+ * </restriction>
+ * </complexContent>
+ * </complexType>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(
+ name = "",
+ propOrder =
+ { "annotationColours", "hiddenColumns", "calcIdParam", "overview" })
+ public static class Viewport
+ {
+
+ @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
+ protected AnnotationColourScheme annotationColours;
+
+ @XmlElement(namespace = "www.jalview.org")
+ protected Listset
method for the hiddenColumns property.
+ *
+ *
+ * getHiddenColumns().add(newItem);
+ *
*
- * <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>
+ *
+ * set
method for the calcIdParam property.
+ *
+ *
+ * getCalcIdParam().add(newItem);
+ *
+ *
+ *
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class CalcIdParam extends WebServiceParameterSet
+ {
+
+ @XmlAttribute(name = "calcId", required = true)
+ protected String calcId;
+
+ @XmlAttribute(name = "needsUpdate")
+ protected Boolean needsUpdate;
+
+ @XmlAttribute(name = "autoUpdate", required = true)
+ protected boolean autoUpdate;
+
+ /**
+ * Gets the value of the calcId property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getCalcId()
+ {
+ return calcId;
+ }
+
+ /**
+ * Sets the value of the calcId property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setCalcId(String value)
+ {
+ this.calcId = value;
+ }
+
+ /**
+ * Gets the value of the needsUpdate property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public boolean isNeedsUpdate()
+ {
+ if (needsUpdate == null)
+ {
+ return false;
}
+ else
+ {
+ return needsUpdate;
+ }
+ }
+
+ /**
+ * Sets the value of the needsUpdate property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setNeedsUpdate(Boolean value)
+ {
+ this.needsUpdate = value;
+ }
+
+ /**
+ * Gets the value of the autoUpdate property.
+ *
+ */
+ public boolean isAutoUpdate()
+ {
+ return autoUpdate;
+ }
+
+ /**
+ * Sets the value of the autoUpdate property.
+ *
+ */
+ public void setAutoUpdate(boolean value)
+ {
+ this.autoUpdate = value;
+ }
+ }
- /**
- * <p>Java class for anonymous complex type.
- *
- * <p>The following schema fragment specifies the expected content contained within this class.
- *
- * <pre>
- * <complexType>
- * <complexContent>
- * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- * <attGroup ref="{www.jalview.org}swingwindow"/>
- * <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- * <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- * <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- * </restriction>
- * </complexContent>
- * </complexType>
- * </pre>
- *
- *
- */
- @XmlAccessorType(XmlAccessType.FIELD)
- @XmlType(name = "")
- public static class Overview {
-
- @XmlAttribute(name = "showHidden")
- protected Boolean showHidden;
- @XmlAttribute(name = "residueColour")
- protected Integer residueColour;
- @XmlAttribute(name = "gapColour")
- protected Integer gapColour;
- @XmlAttribute(name = "hiddenColour")
- protected Integer hiddenColour;
- @XmlAttribute(name = "title")
- protected String title;
- @XmlAttribute(name = "width")
- protected Integer width;
- @XmlAttribute(name = "height")
- protected Integer height;
- @XmlAttribute(name = "xpos")
- protected Integer xpos;
- @XmlAttribute(name = "ypos")
- protected Integer ypos;
-
- /**
- * Gets the value of the showHidden property.
- *
- * @return
- * possible object is
- * {@link Boolean }
- *
- */
- public Boolean isShowHidden() {
- return showHidden;
- }
-
- /**
- * Sets the value of the showHidden property.
- *
- * @param value
- * allowed object is
- * {@link Boolean }
- *
- */
- public void setShowHidden(Boolean value) {
- this.showHidden = value;
- }
-
- /**
- * Gets the value of the residueColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getResidueColour() {
- return residueColour;
- }
-
- /**
- * Sets the value of the residueColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setResidueColour(Integer value) {
- this.residueColour = value;
- }
-
- /**
- * Gets the value of the gapColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getGapColour() {
- return gapColour;
- }
-
- /**
- * Sets the value of the gapColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setGapColour(Integer value) {
- this.gapColour = value;
- }
-
- /**
- * Gets the value of the hiddenColour property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHiddenColour() {
- return hiddenColour;
- }
-
- /**
- * Sets the value of the hiddenColour property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHiddenColour(Integer value) {
- this.hiddenColour = value;
- }
-
- /**
- * Gets the value of the title property.
- *
- * @return
- * possible object is
- * {@link String }
- *
- */
- public String getTitle() {
- return title;
- }
-
- /**
- * Sets the value of the title property.
- *
- * @param value
- * allowed object is
- * {@link String }
- *
- */
- public void setTitle(String value) {
- this.title = value;
- }
-
- /**
- * Gets the value of the width property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getWidth() {
- return width;
- }
-
- /**
- * Sets the value of the width property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setWidth(Integer value) {
- this.width = value;
- }
-
- /**
- * Gets the value of the height property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getHeight() {
- return height;
- }
-
- /**
- * Sets the value of the height property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setHeight(Integer value) {
- this.height = value;
- }
-
- /**
- * Gets the value of the xpos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getXpos() {
- return xpos;
- }
-
- /**
- * Sets the value of the xpos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setXpos(Integer value) {
- this.xpos = value;
- }
-
- /**
- * Gets the value of the ypos property.
- *
- * @return
- * possible object is
- * {@link Integer }
- *
- */
- public Integer getYpos() {
- return ypos;
- }
-
- /**
- * Sets the value of the ypos property.
- *
- * @param value
- * allowed object is
- * {@link Integer }
- *
- */
- public void setYpos(Integer value) {
- this.ypos = value;
- }
+ /**
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class HiddenColumns
+ {
+
+ @XmlAttribute(name = "start")
+ protected Integer start;
+
+ @XmlAttribute(name = "end")
+ protected Integer end;
+
+ /**
+ * Gets the value of the start property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getStart()
+ {
+ return start;
+ }
+
+ /**
+ * Sets the value of the start property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setStart(Integer value)
+ {
+ this.start = value;
+ }
+
+ /**
+ * Gets the value of the end property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getEnd()
+ {
+ return end;
+ }
+
+ /**
+ * Sets the value of the end property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setEnd(Integer value)
+ {
+ this.end = value;
+ }
- }
+ }
+
+ /**
+ *
+ * <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>
+ *
+ *
+ *
+ */
+ @XmlAccessorType(XmlAccessType.FIELD)
+ @XmlType(name = "")
+ public static class Overview
+ {
+
+ @XmlAttribute(name = "showHidden")
+ protected Boolean showHidden;
+
+ @XmlAttribute(name = "residueColour")
+ protected Integer residueColour;
+
+ @XmlAttribute(name = "gapColour")
+ protected Integer gapColour;
+
+ @XmlAttribute(name = "hiddenColour")
+ protected Integer hiddenColour;
+
+ @XmlAttribute(name = "title")
+ protected String title;
+
+ @XmlAttribute(name = "width")
+ protected Integer width;
+
+ @XmlAttribute(name = "height")
+ protected Integer height;
+
+ @XmlAttribute(name = "xpos")
+ protected Integer xpos;
+
+ @XmlAttribute(name = "ypos")
+ protected Integer ypos;
+
+ /**
+ * Gets the value of the showHidden property.
+ *
+ * @return possible object is {@link Boolean }
+ *
+ */
+ public Boolean isShowHidden()
+ {
+ return showHidden;
+ }
+
+ /**
+ * Sets the value of the showHidden property.
+ *
+ * @param value
+ * allowed object is {@link Boolean }
+ *
+ */
+ public void setShowHidden(Boolean value)
+ {
+ this.showHidden = value;
+ }
+
+ /**
+ * Gets the value of the residueColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getResidueColour()
+ {
+ return residueColour;
+ }
+
+ /**
+ * Sets the value of the residueColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setResidueColour(Integer value)
+ {
+ this.residueColour = value;
+ }
+
+ /**
+ * Gets the value of the gapColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getGapColour()
+ {
+ return gapColour;
+ }
+
+ /**
+ * Sets the value of the gapColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setGapColour(Integer value)
+ {
+ this.gapColour = value;
+ }
+
+ /**
+ * Gets the value of the hiddenColour property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHiddenColour()
+ {
+ return hiddenColour;
+ }
+
+ /**
+ * Sets the value of the hiddenColour property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHiddenColour(Integer value)
+ {
+ this.hiddenColour = value;
+ }
+
+ /**
+ * Gets the value of the title property.
+ *
+ * @return possible object is {@link String }
+ *
+ */
+ public String getTitle()
+ {
+ return title;
+ }
+
+ /**
+ * Sets the value of the title property.
+ *
+ * @param value
+ * allowed object is {@link String }
+ *
+ */
+ public void setTitle(String value)
+ {
+ this.title = value;
+ }
+
+ /**
+ * Gets the value of the width property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getWidth()
+ {
+ return width;
+ }
+
+ /**
+ * Sets the value of the width property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setWidth(Integer value)
+ {
+ this.width = value;
+ }
+
+ /**
+ * Gets the value of the height property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getHeight()
+ {
+ return height;
+ }
+
+ /**
+ * Sets the value of the height property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setHeight(Integer value)
+ {
+ this.height = value;
+ }
+
+ /**
+ * Gets the value of the xpos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getXpos()
+ {
+ return xpos;
+ }
+
+ /**
+ * Sets the value of the xpos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setXpos(Integer value)
+ {
+ this.xpos = value;
+ }
+
+ /**
+ * Gets the value of the ypos property.
+ *
+ * @return possible object is {@link Integer }
+ *
+ */
+ public Integer getYpos()
+ {
+ return ypos;
+ }
+
+ /**
+ * Sets the value of the ypos property.
+ *
+ * @param value
+ * allowed object is {@link Integer }
+ *
+ */
+ public void setYpos(Integer value)
+ {
+ this.ypos = value;
+ }
}
+ }
+
}