// // 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: 2023.05.13 at 06:58:41 PM BST // package jalview.xml.binding.jalview; import java.util.ArrayList; import java.util.List; import javax.xml.bind.annotation.XmlAccessType; import javax.xml.bind.annotation.XmlAccessorType; import javax.xml.bind.annotation.XmlAttribute; import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlID; import javax.xml.bind.annotation.XmlSchemaType; import javax.xml.bind.annotation.XmlType; import javax.xml.bind.annotation.XmlValue; import javax.xml.bind.annotation.adapters.CollapsedStringAdapter; import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; import javax.xml.datatype.XMLGregorianCalendar; /** *
* Java class for JalviewModel complex type. * *
* The following schema fragment specifies the expected content contained within * this class. * *
* <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 }
*
*
*/
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 }
*
*
*/
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:
*
*
* 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 }
*
*
*/
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.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:
*
*
* Objects of the following type(s) are allowed in the list
* {@link JalviewModel.Viewport.HiddenColumns }
*
*
*/
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 }
*
*
*/
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.
*
* 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>
*
*
*
*/
@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;
}
}
/**
*
* <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>
*
*
*
*/
@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.
*
*
* getSeq().add(newItem);
*
*
*
*
* <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 value property.
*
* @return possible object is {@link String }
*
*/
public String getValue()
{
return value;
}
/**
* Sets the value of the value property.
*
* @param value
* allowed object is {@link String }
*
*/
public void setValue(String value)
{
this.value = value;
}
/**
* Gets the value of the visible property.
*
* @return possible object is {@link Boolean }
*
*/
public Boolean isVisible()
{
return visible;
}
/**
* Sets the value of the visible property.
*
* @param value
* allowed object is {@link Boolean }
*
*/
public void setVisible(Boolean value)
{
this.visible = value;
}
/**
* Gets the value of the viewId property.
*
* @return possible object is {@link String }
*
*/
public String getViewId()
{
return viewId;
}
/**
* Sets the value of the viewId property.
*
* @param value
* allowed object is {@link String }
*
*/
public void setViewId(String value)
{
this.viewId = value;
}
/**
* Gets the value of the alignwithAlignPanel property.
*
* @return possible object is {@link Boolean }
*
*/
public boolean isAlignwithAlignPanel()
{
if (alignwithAlignPanel == null)
{
return true;
}
else
{
return alignwithAlignPanel;
}
}
/**
* Sets the value of the alignwithAlignPanel property.
*
* @param value
* allowed object is {@link Boolean }
*
*/
public void setAlignwithAlignPanel(Boolean value)
{
this.alignwithAlignPanel = value;
}
/**
* Gets the value of the colourwithAlignPanel property.
*
* @return possible object is {@link Boolean }
*
*/
public boolean isColourwithAlignPanel()
{
if (colourwithAlignPanel == null)
{
return false;
}
else
{
return colourwithAlignPanel;
}
}
/**
* Sets the value of the colourwithAlignPanel property.
*
* @param value
* allowed object is {@link Boolean }
*
*/
public void setColourwithAlignPanel(Boolean value)
{
this.colourwithAlignPanel = value;
}
/**
* Gets the value of the colourByJmol property.
*
* @return possible object is {@link Boolean }
*
*/
public boolean isColourByJmol()
{
if (colourByJmol == null)
{
return true;
}
else
{
return colourByJmol;
}
}
/**
* Sets the value of the colourByJmol property.
*
* @param value
* allowed object is {@link Boolean }
*
*/
public void setColourByJmol(Boolean value)
{
this.colourByJmol = value;
}
/**
* Gets the value of the type property.
*
* @return possible object is {@link String }
*
*/
public String getType()
{
return type;
}
/**
* Sets the value of the type property.
*
* @param value
* allowed object is {@link String }
*
*/
public void setType(String value)
{
this.type = 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">
* <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 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 annotationId property.
*
* @return possible object is {@link String }
*
*/
public String getAnnotationId()
{
return annotationId;
}
/**
* Sets the value of the annotationId property.
*
* @param value
* allowed object is {@link String }
*
*/
public void setAnnotationId(String value)
{
this.annotationId = value;
}
/**
* Gets the value of the gapped property.
*
* @return possible object is {@link Boolean }
*
*/
public Boolean isGapped()
{
return gapped;
}
/**
* Sets the value of the gapped property.
*
* @param value
* allowed object is {@link Boolean }
*
*/
public void setGapped(Boolean value)
{
this.gapped = value;
}
/**
* Gets the value of the viewerState property.
*
* @return possible object is {@link String }
*
*/
public String getViewerState()
{
return viewerState;
}
/**
* Sets the value of the viewerState property.
*
* @param value
* allowed object is {@link String }
*
*/
public void setViewerState(String value)
{
this.viewerState = 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;
}
}
/**
*
* <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;
}
}
/**
*
* <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;
}
}
/**
*
* <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;
}
/**
* Gets the value of the markUnlinked property.
*
* @return possible object is {@link Boolean }
*
*/
public Boolean isMarkUnlinked()
{
return markUnlinked;
}
/**
* Sets the value of the markUnlinked property.
*
* @param value
* allowed object is {@link Boolean }
*
*/
public void setMarkUnlinked(Boolean value)
{
this.markUnlinked = value;
}
/**
* Gets the value of the fitToWindow property.
*
* @return possible object is {@link Boolean }
*
*/
public Boolean isFitToWindow()
{
return fitToWindow;
}
/**
* Sets the value of the fitToWindow property.
*
* @param value
* allowed object is {@link Boolean }
*
*/
public void setFitToWindow(Boolean value)
{
this.fitToWindow = value;
}
/**
* Gets the value of the currentTree property.
*
* @return possible object is {@link Boolean }
*
*/
public Boolean isCurrentTree()
{
return currentTree;
}
/**
* Sets the value of the currentTree property.
*
* @param value
* allowed object is {@link Boolean }
*
*/
public void setCurrentTree(Boolean value)
{
this.currentTree = value;
}
/**
* Gets the value of the columnWise property.
*
* @return possible object is {@link Boolean }
*
*/
public boolean isColumnWise()
{
if (columnWise == null)
{
return false;
}
else
{
return columnWise;
}
}
/**
* Sets the value of the columnWise property.
*
* @param value
* allowed object is {@link Boolean }
*
*/
public void setColumnWise(Boolean value)
{
this.columnWise = value;
}
/**
* Gets the value of the columnReference property.
*
* @return possible object is {@link String }
*
*/
public String getColumnReference()
{
return columnReference;
}
/**
* Sets the value of the columnReference property.
*
* @param value
* allowed object is {@link String }
*
*/
public void setColumnReference(String value)
{
this.columnReference = value;
}
/**
* Gets the value of the id property.
*
* @return possible object is {@link String }
*
*/
public String getId()
{
return id;
}
/**
* Sets the value of the id property.
*
* @param value
* allowed object is {@link String }
*
*/
public void setId(String value)
{
this.id = value;
}
/**
* Gets the value of the linkToAllViews property.
*
* @return possible object is {@link Boolean }
*
*/
public boolean isLinkToAllViews()
{
if (linkToAllViews == null)
{
return false;
}
else
{
return linkToAllViews;
}
}
/**
* Sets the value of the linkToAllViews property.
*
* @param value
* allowed object is {@link Boolean }
*
*/
public void setLinkToAllViews(Boolean value)
{
this.linkToAllViews = value;
}
/**
* Gets the value of the width property.
*
* @return possible object is {@link Integer }
*
*/
public Integer getWidth()
{
return width;
}
/**
* Sets the value of the width property.
*
* @param value
* allowed object is {@link Integer }
*
*/
public void setWidth(Integer value)
{
this.width = value;
}
/**
* Gets the value of the height property.
*
* @return possible object is {@link Integer }
*
*/
public Integer getHeight()
{
return height;
}
/**
* Sets the value of the height property.
*
* @param value
* allowed object is {@link Integer }
*
*/
public void setHeight(Integer value)
{
this.height = value;
}
/**
* Gets the value of the xpos property.
*
* @return possible object is {@link Integer }
*
*/
public Integer getXpos()
{
return xpos;
}
/**
* Sets the value of the xpos property.
*
* @param value
* allowed object is {@link Integer }
*
*/
public void setXpos(Integer value)
{
this.xpos = value;
}
/**
* Gets the value of the ypos property.
*
* @return possible object is {@link Integer }
*
*/
public Integer getYpos()
{
return ypos;
}
/**
* Sets the value of the ypos property.
*
* @param value
* allowed object is {@link Integer }
*
*/
public void setYpos(Integer value)
{
this.ypos = value;
}
}
/**
*
* <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;
}
/**
* 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;
}
}
/**
*
* <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);
*
*
*
* 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;
}
}
/**
*
* <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;
}
}
}
}