// // 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: 2018.09.18 at 02:23:07 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>
 *                   </sequence>
 *                   <attGroup ref="{www.jalview.org}swingwindow"/>
 *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
 *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 *                   <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
 *                   <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
 *                   <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 *                   <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
 *                 </restriction>
 *               </complexContent>
 *             </complexType>
 *           </element>
 *           <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
 *             <complexType>
 *               <complexContent>
 *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 *                   <sequence>
 *                     <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
 *                   </sequence>
 *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 *                 </restriction>
 *               </complexContent>
 *             </complexType>
 *           </element>
 *           <element name="tree" maxOccurs="unbounded" minOccurs="0">
 *             <complexType>
 *               <complexContent>
 *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 *                   <sequence minOccurs="0">
 *                     <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
 *                     <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
 *                   </sequence>
 *                   <attGroup ref="{www.jalview.org}swingwindow"/>
 *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                   <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 *                   <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 *                 </restriction>
 *               </complexContent>
 *             </complexType>
 *           </element>
 *           <element name="FeatureSettings" minOccurs="0">
 *             <complexType>
 *               <complexContent>
 *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 *                   <sequence>
 *                     <element name="setting" maxOccurs="unbounded" minOccurs="0">
 *                       <complexType>
 *                         <complexContent>
 *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 *                             <sequence>
 *                               <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 *                               <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 *                             </sequence>
 *                             <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 *                             <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                             <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 *                             <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                             <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 *                             <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 *                             <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 *                             <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 *                             <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 *                             <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                             <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                           </restriction>
 *                         </complexContent>
 *                       </complexType>
 *                     </element>
 *                     <element name="group" maxOccurs="unbounded" minOccurs="0">
 *                       <complexType>
 *                         <complexContent>
 *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 *                             <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 *                           </restriction>
 *                         </complexContent>
 *                       </complexType>
 *                     </element>
 *                   </sequence>
 *                 </restriction>
 *               </complexContent>
 *             </complexType>
 *           </element>
 *         </sequence>
 *       </sequence>
 *     </restriction>
 *   </complexContent>
 * </complexType>
 *
* * */ @XmlAccessorType(XmlAccessType.FIELD) @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport", "userColours", "tree", "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 jSeq; @XmlElement(name = "JGroup") protected List jGroup; @XmlElement(name = "Viewport") protected List viewport; @XmlElement(name = "UserColours") protected List userColours; protected List tree; @XmlElement(name = "FeatureSettings") protected JalviewModel.FeatureSettings featureSettings; /** * Gets the value of the creationDate property. * * @return * possible object is * {@link XMLGregorianCalendar } * */ public XMLGregorianCalendar getCreationDate() { return creationDate; } /** * Sets the value of the creationDate property. * * @param value * allowed object is * {@link XMLGregorianCalendar } * */ public void setCreationDate(XMLGregorianCalendar value) { this.creationDate = value; } /** * Gets the value of the version property. * * @return * possible object is * {@link String } * */ public String getVersion() { return version; } /** * Sets the value of the version property. * * @param value * allowed object is * {@link String } * */ public void setVersion(String value) { this.version = value; } /** * Gets the value of the vamsasModel property. * * @return * possible object is * {@link VAMSAS } * */ public VAMSAS getVamsasModel() { return vamsasModel; } /** * Sets the value of the vamsasModel property. * * @param value * allowed object is * {@link VAMSAS } * */ public void setVamsasModel(VAMSAS value) { this.vamsasModel = value; } /** * Gets the value of the jSeq property. * *

* 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 getJSeq() { if (jSeq == null) { jSeq = new ArrayList(); } return this.jSeq; } /** * Gets the value of the jGroup property. * *

* 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 jGroup property. * *

* For example, to add a new item, do as follows: * 

     *    getJGroup().add(newItem);
     *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.JGroup } * * */ public List getJGroup() { if (jGroup == null) { jGroup = new ArrayList(); } return this.jGroup; } /** * Gets the value of the viewport property. * *

* 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 viewport property. * *

* For example, to add a new item, do as follows: * 

     *    getViewport().add(newItem);
     *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.Viewport } * * */ public List getViewport() { if (viewport == null) { viewport = new ArrayList(); } return this.viewport; } /** * Gets the value of the userColours property. * *

* 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 userColours property. * *

* For example, to add a new item, do as follows: * 

     *    getUserColours().add(newItem);
     *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.UserColours } * * */ public List getUserColours() { if (userColours == null) { userColours = new ArrayList(); } return this.userColours; } /** * Gets the value of the tree property. * *

* 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 tree property. * *

* For example, to add a new item, do as follows: * 

     *    getTree().add(newItem);
     *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.Tree } * * */ public List getTree() { if (tree == null) { tree = new ArrayList(); } return this.tree; } /** * Gets the value of the featureSettings property. * * @return * possible object is * {@link JalviewModel.FeatureSettings } * */ public JalviewModel.FeatureSettings getFeatureSettings() { return featureSettings; } /** * Sets the value of the featureSettings property. * * @param value * allowed object is * {@link JalviewModel.FeatureSettings } * */ public void setFeatureSettings(JalviewModel.FeatureSettings value) { this.featureSettings = value; } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

     * <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 List setting; @XmlElement(namespace = "www.jalview.org") protected List group; /** * Gets the value of the setting property. * *

* 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 setting property. * *

* For example, to add a new item, do as follows: * 

         *    getSetting().add(newItem);
         *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.FeatureSettings.Setting } * * */ public List getSetting() { if (setting == null) { setting = new ArrayList(); } return this.setting; } /** * Gets the value of the group property. * *

* 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 group property. * *

* For example, to add a new item, do as follows: * 

         *    getGroup().add(newItem);
         *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.FeatureSettings.Group } * * */ public List getGroup() { if (group == null) { group = new ArrayList(); } return this.group; } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

         * <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; } } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

         * <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 List attributeName; @XmlElement(namespace = "www.jalview.org") protected FeatureMatcherSet matcherSet; @XmlAttribute(name = "type", required = true) protected String type; @XmlAttribute(name = "colour", required = true) protected int colour; @XmlAttribute(name = "display", required = true) protected boolean display; @XmlAttribute(name = "order") protected Float order; @XmlAttribute(name = "mincolour") protected Integer mincolour; @XmlAttribute(name = "noValueColour") protected NoValueColour noValueColour; @XmlAttribute(name = "threshold") protected Float threshold; @XmlAttribute(name = "threshstate") protected Integer threshstate; @XmlAttribute(name = "max") protected Float max; @XmlAttribute(name = "min") protected Float min; @XmlAttribute(name = "colourByLabel") protected Boolean colourByLabel; @XmlAttribute(name = "autoScale") protected Boolean autoScale; /** * Gets the value of the attributeName property. * *

* 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 attributeName property. * *

* For example, to add a new item, do as follows: * 

             *    getAttributeName().add(newItem);
             *
* * *

* Objects of the following type(s) are allowed in the list * {@link String } * * */ public List getAttributeName() { if (attributeName == null) { attributeName = new ArrayList(); } return this.attributeName; } /** * Gets the value of the matcherSet property. * * @return * possible object is * {@link FeatureMatcherSet } * */ public FeatureMatcherSet getMatcherSet() { return matcherSet; } /** * Sets the value of the matcherSet property. * * @param value * allowed object is * {@link FeatureMatcherSet } * */ public void setMatcherSet(FeatureMatcherSet value) { this.matcherSet = 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 colour property. * */ public int getColour() { return colour; } /** * Sets the value of the colour property. * */ public void setColour(int value) { this.colour = 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; } /** * Gets the value of the order property. * * @return * possible object is * {@link Float } * */ public Float getOrder() { return order; } /** * Sets the value of the order property. * * @param value * allowed object is * {@link Float } * */ public void setOrder(Float value) { this.order = value; } /** * Gets the value of the mincolour property. * * @return * possible object is * {@link Integer } * */ public Integer getMincolour() { return mincolour; } /** * Sets the value of the mincolour property. * * @param value * allowed object is * {@link Integer } * */ public void setMincolour(Integer value) { this.mincolour = value; } /** * Gets the value of the noValueColour property. * * @return * possible object is * {@link NoValueColour } * */ public NoValueColour getNoValueColour() { if (noValueColour == null) { return NoValueColour.MIN; } else { return noValueColour; } } /** * Sets the value of the noValueColour property. * * @param value * allowed object is * {@link NoValueColour } * */ public void setNoValueColour(NoValueColour value) { this.noValueColour = 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 threshstate property. * * @return * possible object is * {@link Integer } * */ public Integer getThreshstate() { return threshstate; } /** * Sets the value of the threshstate property. * * @param value * allowed object is * {@link Integer } * */ public void setThreshstate(Integer value) { this.threshstate = value; } /** * Gets the value of the max property. * * @return * possible object is * {@link Float } * */ public Float getMax() { return max; } /** * Sets the value of the max property. * * @param value * allowed object is * {@link Float } * */ public void setMax(Float value) { this.max = value; } /** * Gets the value of the min property. * * @return * possible object is * {@link Float } * */ public Float getMin() { return min; } /** * Sets the value of the min property. * * @param value * allowed object is * {@link Float } * */ public void setMin(Float value) { this.min = value; } /** * Gets the value of the colourByLabel property. * * @return * possible object is * {@link Boolean } * */ public Boolean isColourByLabel() { return colourByLabel; } /** * Sets the value of the colourByLabel property. * * @param value * allowed object is * {@link Boolean } * */ public void setColourByLabel(Boolean value) { this.colourByLabel = value; } /** * Gets the value of the autoScale property. * * @return * possible object is * {@link Boolean } * */ public Boolean isAutoScale() { return autoScale; } /** * Sets the value of the autoScale property. * * @param value * allowed object is * {@link Boolean } * */ public void setAutoScale(Boolean value) { this.autoScale = value; } } } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

     * <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 List seq; @XmlElement(namespace = "www.jalview.org") protected AnnotationColourScheme annotationColours; @XmlAttribute(name = "start") protected Integer start; @XmlAttribute(name = "end") protected Integer end; @XmlAttribute(name = "name") protected String name; @XmlAttribute(name = "colour") protected String colour; @XmlAttribute(name = "consThreshold") protected Integer consThreshold; @XmlAttribute(name = "pidThreshold") protected Integer pidThreshold; @XmlAttribute(name = "outlineColour") protected Integer outlineColour; @XmlAttribute(name = "displayBoxes") protected Boolean displayBoxes; @XmlAttribute(name = "displayText") protected Boolean displayText; @XmlAttribute(name = "colourText") protected Boolean colourText; @XmlAttribute(name = "textCol1") protected Integer textCol1; @XmlAttribute(name = "textCol2") protected Integer textCol2; @XmlAttribute(name = "textColThreshold") protected Integer textColThreshold; @XmlAttribute(name = "showUnconserved") protected Boolean showUnconserved; @XmlAttribute(name = "ignoreGapsinConsensus") protected Boolean ignoreGapsinConsensus; @XmlAttribute(name = "showConsensusHistogram") protected Boolean showConsensusHistogram; @XmlAttribute(name = "showSequenceLogo") protected Boolean showSequenceLogo; @XmlAttribute(name = "normaliseSequenceLogo") protected Boolean normaliseSequenceLogo; @XmlAttribute(name = "id") protected String id; /** * Gets the value of the seq property. * *

* 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 seq property. * *

* For example, to add a new item, do as follows: * 

         *    getSeq().add(newItem);
         *
* * *

* Objects of the following type(s) are allowed in the list * {@link String } * * */ public List getSeq() { if (seq == null) { seq = new ArrayList(); } return this.seq; } /** * Gets the value of the annotationColours property. * * @return * possible object is * {@link AnnotationColourScheme } * */ public AnnotationColourScheme getAnnotationColours() { return annotationColours; } /** * Sets the value of the annotationColours property. * * @param value * allowed object is * {@link AnnotationColourScheme } * */ public void setAnnotationColours(AnnotationColourScheme value) { this.annotationColours = value; } /** * 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; } /** * 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 colour property. * * @return * possible object is * {@link String } * */ public String getColour() { return colour; } /** * Sets the value of the colour property. * * @param value * allowed object is * {@link String } * */ public void setColour(String value) { this.colour = value; } /** * Gets the value of the consThreshold property. * * @return * possible object is * {@link Integer } * */ public Integer getConsThreshold() { return consThreshold; } /** * Sets the value of the consThreshold property. * * @param value * allowed object is * {@link Integer } * */ public void setConsThreshold(Integer value) { this.consThreshold = value; } /** * Gets the value of the pidThreshold property. * * @return * possible object is * {@link Integer } * */ public Integer getPidThreshold() { return pidThreshold; } /** * Sets the value of the pidThreshold property. * * @param value * allowed object is * {@link Integer } * */ public void setPidThreshold(Integer value) { this.pidThreshold = value; } /** * Gets the value of the outlineColour property. * * @return * possible object is * {@link Integer } * */ public Integer getOutlineColour() { return outlineColour; } /** * Sets the value of the outlineColour property. * * @param value * allowed object is * {@link Integer } * */ public void setOutlineColour(Integer value) { this.outlineColour = value; } /** * Gets the value of the displayBoxes property. * * @return * possible object is * {@link Boolean } * */ public Boolean isDisplayBoxes() { return displayBoxes; } /** * Sets the value of the displayBoxes property. * * @param value * allowed object is * {@link Boolean } * */ public void setDisplayBoxes(Boolean value) { this.displayBoxes = value; } /** * Gets the value of the displayText property. * * @return * possible object is * {@link Boolean } * */ public Boolean isDisplayText() { return displayText; } /** * Sets the value of the displayText property. * * @param value * allowed object is * {@link Boolean } * */ public void setDisplayText(Boolean value) { this.displayText = value; } /** * Gets the value of the colourText property. * * @return * possible object is * {@link Boolean } * */ public Boolean isColourText() { return colourText; } /** * Sets the value of the colourText property. * * @param value * allowed object is * {@link Boolean } * */ public void setColourText(Boolean value) { this.colourText = value; } /** * Gets the value of the textCol1 property. * * @return * possible object is * {@link Integer } * */ public Integer getTextCol1() { return textCol1; } /** * Sets the value of the textCol1 property. * * @param value * allowed object is * {@link Integer } * */ public void setTextCol1(Integer value) { this.textCol1 = value; } /** * Gets the value of the textCol2 property. * * @return * possible object is * {@link Integer } * */ public Integer getTextCol2() { return textCol2; } /** * Sets the value of the textCol2 property. * * @param value * allowed object is * {@link Integer } * */ public void setTextCol2(Integer value) { this.textCol2 = value; } /** * Gets the value of the textColThreshold property. * * @return * possible object is * {@link Integer } * */ public Integer getTextColThreshold() { return textColThreshold; } /** * Sets the value of the textColThreshold property. * * @param value * allowed object is * {@link Integer } * */ 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; } } /** * Sets the value of the ignoreGapsinConsensus 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 } * */ public boolean isShowConsensusHistogram() { if (showConsensusHistogram == null) { return true; } else { return showConsensusHistogram; } } /** * Sets the value of the showConsensusHistogram property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowConsensusHistogram(Boolean value) { this.showConsensusHistogram = value; } /** * Gets the value of the showSequenceLogo property. * * @return * possible object is * {@link Boolean } * */ public boolean isShowSequenceLogo() { if (showSequenceLogo == null) { return false; } else { return showSequenceLogo; } } /** * Sets the value of the showSequenceLogo 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 Boolean } * */ public boolean isNormaliseSequenceLogo() { if (normaliseSequenceLogo == null) { return false; } else { return normaliseSequenceLogo; } } /** * Sets the value of the normaliseSequenceLogo property. * * @param value * allowed object is * {@link Boolean } * */ public void setNormaliseSequenceLogo(Boolean value) { this.normaliseSequenceLogo = 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; } } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

     * <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 List features; @XmlElement(namespace = "www.jalview.org") protected List pdbids; @XmlElement(namespace = "www.jalview.org", type = Integer.class) protected List hiddenSequences; @XmlElement(namespace = "www.jalview.org") protected List rnaViewer; @XmlAttribute(name = "colour") protected Integer colour; @XmlAttribute(name = "start", required = true) protected int start; @XmlAttribute(name = "end", required = true) protected int end; @XmlAttribute(name = "id", required = true) protected String id; @XmlAttribute(name = "hidden") protected Boolean hidden; @XmlAttribute(name = "viewreference") protected Boolean viewreference; /** * Gets the value of the features property. * *

* 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 features property. * *

* For example, to add a new item, do as follows: * 

         *    getFeatures().add(newItem);
         *
* * *

* Objects of the following type(s) are allowed in the list * {@link Feature } * * */ public List getFeatures() { if (features == null) { features = new ArrayList(); } return this.features; } /** * Gets the value of the pdbids property. * *

* 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 pdbids property. * *

* For example, to add a new item, do as follows: * 

         *    getPdbids().add(newItem);
         *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.JSeq.Pdbids } * * */ public List getPdbids() { if (pdbids == null) { pdbids = new ArrayList(); } return this.pdbids; } /** * Gets the value of the hiddenSequences property. * *

* 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 hiddenSequences property. * *

* For example, to add a new item, do as follows: * 

         *    getHiddenSequences().add(newItem);
         *
* * *

* Objects of the following type(s) are allowed in the list * {@link Integer } * * */ public List getHiddenSequences() { if (hiddenSequences == null) { hiddenSequences = new ArrayList(); } return this.hiddenSequences; } /** * Gets the value of the rnaViewer property. * *

* 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 rnaViewer property. * *

* For example, to add a new item, do as follows: * 

         *    getRnaViewer().add(newItem);
         *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.JSeq.RnaViewer } * * */ public List getRnaViewer() { if (rnaViewer == null) { rnaViewer = new ArrayList(); } return this.rnaViewer; } /** * Gets the value of the colour property. * * @return * possible object is * {@link Integer } * */ public Integer getColour() { return colour; } /** * Sets the value of the colour property. * * @param value * allowed object is * {@link Integer } * */ public void setColour(Integer value) { this.colour = value; } /** * Gets the value of the start property. * */ public int getStart() { return start; } /** * Sets the value of the start property. * */ public void setStart(int value) { this.start = value; } /** * Gets the value of the end property. * */ public int getEnd() { return end; } /** * Sets the value of the end property. * */ public void setEnd(int value) { this.end = 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 hidden property. * * @return * possible object is * {@link Boolean } * */ public Boolean isHidden() { return hidden; } /** * Sets the value of the hidden property. * * @param value * allowed object is * {@link Boolean } * */ public void setHidden(Boolean value) { this.hidden = value; } /** * Gets the value of the viewreference property. * * @return * possible object is * {@link Boolean } * */ public Boolean isViewreference() { return viewreference; } /** * Sets the value of the viewreference property. * * @param value * allowed object is * {@link Boolean } * */ public void setViewreference(Boolean value) { this.viewreference = value; } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

         * <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 List structureState; /** * Gets the value of the structureState property. * *

* 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 structureState property. * *

* For example, to add a new item, do as follows: * 

             *    getStructureState().add(newItem);
             *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.JSeq.Pdbids.StructureState } * * */ public List getStructureState() { if (structureState == null) { structureState = new ArrayList(); } return this.structureState; } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

             * <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; } } } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

         * <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 List secondaryStructure; @XmlAttribute(name = "title") protected String title; @XmlAttribute(name = "viewId") protected String viewId; @XmlAttribute(name = "dividerLocation") protected Integer dividerLocation; @XmlAttribute(name = "selectedRna") protected Integer selectedRna; @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 secondaryStructure property. * *

* 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 secondaryStructure property. * *

* For example, to add a new item, do as follows: * 

             *    getSecondaryStructure().add(newItem);
             *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure } * * */ public List getSecondaryStructure() { if (secondaryStructure == null) { secondaryStructure = new ArrayList(); } return this.secondaryStructure; } /** * 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 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 dividerLocation property. * * @return * possible object is * {@link Integer } * */ public Integer getDividerLocation() { return dividerLocation; } /** * Sets the value of the dividerLocation property. * * @param value * allowed object is * {@link Integer } * */ public void setDividerLocation(Integer value) { this.dividerLocation = value; } /** * Gets the value of the selectedRna property. * * @return * possible object is * {@link Integer } * */ public Integer getSelectedRna() { return selectedRna; } /** * Sets the value of the selectedRna property. * * @param value * allowed object is * {@link Integer } * */ public void setSelectedRna(Integer value) { this.selectedRna = 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; } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

             * <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; } } } } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

     * <complexType>
     *   <complexContent>
     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
     *       <sequence minOccurs="0">
     *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
     *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
     *       </sequence>
     *       <attGroup ref="{www.jalview.org}swingwindow"/>
     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
     *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
     *     </restriction>
     *   </complexContent>
     * </complexType>
     *
* * */ @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 = "id") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) @XmlID @XmlSchemaType(name = "ID") protected String id; @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 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 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; } } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

     * <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; } } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

     * <complexType>
     *   <complexContent>
     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
     *       <sequence>
     *         <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
     *         <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
     *           <complexType>
     *             <complexContent>
     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
     *                 <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
     *                 <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
     *               </restriction>
     *             </complexContent>
     *           </complexType>
     *         </element>
     *         <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
     *           <complexType>
     *             <complexContent>
     *               <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
     *                 <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
     *                 <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
     *                 <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *               </extension>
     *             </complexContent>
     *           </complexType>
     *         </element>
     *       </sequence>
     *       <attGroup ref="{www.jalview.org}swingwindow"/>
     *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
     *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
     *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
     *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
     *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
     *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
     *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
     *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
     *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
     *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
     *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
     *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
     *     </restriction>
     *   </complexContent>
     * </complexType>
     *
* * */ @XmlAccessorType(XmlAccessType.FIELD) @XmlType(name = "", propOrder = { "annotationColours", "hiddenColumns", "calcIdParam" }) public static class Viewport { @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org") protected AnnotationColourScheme annotationColours; @XmlElement(namespace = "www.jalview.org") protected List hiddenColumns; @XmlElement(namespace = "www.jalview.org") protected List calcIdParam; @XmlAttribute(name = "conservationSelected") protected Boolean conservationSelected; @XmlAttribute(name = "pidSelected") protected Boolean pidSelected; @XmlAttribute(name = "bgColour") protected String bgColour; @XmlAttribute(name = "consThreshold") protected Integer consThreshold; @XmlAttribute(name = "pidThreshold") protected Integer pidThreshold; @XmlAttribute(name = "title") protected String title; @XmlAttribute(name = "showFullId") protected Boolean showFullId; @XmlAttribute(name = "rightAlignIds") protected Boolean rightAlignIds; @XmlAttribute(name = "showText") protected Boolean showText; @XmlAttribute(name = "showColourText") protected Boolean showColourText; @XmlAttribute(name = "showUnconserved") protected Boolean showUnconserved; @XmlAttribute(name = "showBoxes") protected Boolean showBoxes; @XmlAttribute(name = "wrapAlignment") protected Boolean wrapAlignment; @XmlAttribute(name = "renderGaps") protected Boolean renderGaps; @XmlAttribute(name = "showSequenceFeatures") protected Boolean showSequenceFeatures; @XmlAttribute(name = "showNPfeatureTooltip") protected Boolean showNPfeatureTooltip; @XmlAttribute(name = "showDbRefTooltip") protected Boolean showDbRefTooltip; @XmlAttribute(name = "followHighlight") protected Boolean followHighlight; @XmlAttribute(name = "followSelection") protected Boolean followSelection; @XmlAttribute(name = "showAnnotation") protected Boolean showAnnotation; @XmlAttribute(name = "centreColumnLabels") protected Boolean centreColumnLabels; @XmlAttribute(name = "showGroupConservation") protected Boolean showGroupConservation; @XmlAttribute(name = "showGroupConsensus") protected Boolean showGroupConsensus; @XmlAttribute(name = "showConsensusHistogram") protected Boolean showConsensusHistogram; @XmlAttribute(name = "showSequenceLogo") protected Boolean showSequenceLogo; @XmlAttribute(name = "normaliseSequenceLogo") protected Boolean normaliseSequenceLogo; @XmlAttribute(name = "ignoreGapsinConsensus") protected Boolean ignoreGapsinConsensus; @XmlAttribute(name = "startRes") protected Integer startRes; @XmlAttribute(name = "startSeq") protected Integer startSeq; @XmlAttribute(name = "fontName") protected String fontName; @XmlAttribute(name = "fontSize") protected Integer fontSize; @XmlAttribute(name = "fontStyle") protected Integer fontStyle; @XmlAttribute(name = "scaleProteinAsCdna") protected Boolean scaleProteinAsCdna; @XmlAttribute(name = "viewName") protected String viewName; @XmlAttribute(name = "sequenceSetId") protected String sequenceSetId; @XmlAttribute(name = "gatheredViews") protected Boolean gatheredViews; @XmlAttribute(name = "textCol1") protected Integer textCol1; @XmlAttribute(name = "textCol2") protected Integer textCol2; @XmlAttribute(name = "textColThreshold") protected Integer textColThreshold; @XmlAttribute(name = "id") @XmlJavaTypeAdapter(CollapsedStringAdapter.class) @XmlID @XmlSchemaType(name = "ID") protected String id; @XmlAttribute(name = "complementId") protected String complementId; @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 annotationColours property. * * @return * possible object is * {@link AnnotationColourScheme } * */ public AnnotationColourScheme getAnnotationColours() { return annotationColours; } /** * Sets the value of the annotationColours property. * * @param value * allowed object is * {@link AnnotationColourScheme } * */ public void setAnnotationColours(AnnotationColourScheme value) { this.annotationColours = value; } /** * Gets the value of the hiddenColumns property. * *

* 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 hiddenColumns property. * *

* For example, to add a new item, do as follows: * 

         *    getHiddenColumns().add(newItem);
         *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.Viewport.HiddenColumns } * * */ public List getHiddenColumns() { if (hiddenColumns == null) { hiddenColumns = new ArrayList(); } return this.hiddenColumns; } /** * Gets the value of the calcIdParam property. * *

* 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 calcIdParam property. * *

* For example, to add a new item, do as follows: * 

         *    getCalcIdParam().add(newItem);
         *
* * *

* Objects of the following type(s) are allowed in the list * {@link JalviewModel.Viewport.CalcIdParam } * * */ public List getCalcIdParam() { if (calcIdParam == null) { calcIdParam = new ArrayList(); } return this.calcIdParam; } /** * Gets the value of the conservationSelected property. * * @return * possible object is * {@link Boolean } * */ public Boolean isConservationSelected() { return conservationSelected; } /** * Sets the value of the conservationSelected property. * * @param value * allowed object is * {@link Boolean } * */ public void setConservationSelected(Boolean value) { this.conservationSelected = value; } /** * Gets the value of the pidSelected property. * * @return * possible object is * {@link Boolean } * */ public Boolean isPidSelected() { return pidSelected; } /** * Sets the value of the pidSelected property. * * @param value * allowed object is * {@link Boolean } * */ public void setPidSelected(Boolean value) { this.pidSelected = value; } /** * Gets the value of the bgColour property. * * @return * possible object is * {@link String } * */ public String getBgColour() { return bgColour; } /** * Sets the value of the bgColour property. * * @param value * allowed object is * {@link String } * */ public void setBgColour(String value) { this.bgColour = value; } /** * Gets the value of the consThreshold property. * * @return * possible object is * {@link Integer } * */ public Integer getConsThreshold() { return consThreshold; } /** * Sets the value of the consThreshold property. * * @param value * allowed object is * {@link Integer } * */ public void setConsThreshold(Integer value) { this.consThreshold = value; } /** * Gets the value of the pidThreshold property. * * @return * possible object is * {@link Integer } * */ public Integer getPidThreshold() { return pidThreshold; } /** * Sets the value of the pidThreshold property. * * @param value * allowed object is * {@link Integer } * */ public void setPidThreshold(Integer value) { this.pidThreshold = 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 showFullId property. * * @return * possible object is * {@link Boolean } * */ public Boolean isShowFullId() { return showFullId; } /** * Sets the value of the showFullId property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowFullId(Boolean value) { this.showFullId = value; } /** * Gets the value of the rightAlignIds property. * * @return * possible object is * {@link Boolean } * */ public Boolean isRightAlignIds() { return rightAlignIds; } /** * Sets the value of the rightAlignIds property. * * @param value * allowed object is * {@link Boolean } * */ public void setRightAlignIds(Boolean value) { this.rightAlignIds = value; } /** * Gets the value of the showText property. * * @return * possible object is * {@link Boolean } * */ public Boolean isShowText() { return showText; } /** * Sets the value of the showText property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowText(Boolean value) { this.showText = value; } /** * Gets the value of the showColourText property. * * @return * possible object is * {@link Boolean } * */ public Boolean isShowColourText() { return showColourText; } /** * Sets the value of the showColourText property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowColourText(Boolean value) { this.showColourText = value; } /** * Gets the value of the showUnconserved property. * * @return * possible object is * {@link Boolean } * */ public boolean isShowUnconserved() { if (showUnconserved == null) { return false; } else { 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 showBoxes property. * * @return * possible object is * {@link Boolean } * */ public Boolean isShowBoxes() { return showBoxes; } /** * Sets the value of the showBoxes property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowBoxes(Boolean value) { this.showBoxes = value; } /** * Gets the value of the wrapAlignment property. * * @return * possible object is * {@link Boolean } * */ public Boolean isWrapAlignment() { return wrapAlignment; } /** * Sets the value of the wrapAlignment property. * * @param value * allowed object is * {@link Boolean } * */ public void setWrapAlignment(Boolean value) { this.wrapAlignment = value; } /** * Gets the value of the renderGaps property. * * @return * possible object is * {@link Boolean } * */ public Boolean isRenderGaps() { return renderGaps; } /** * Sets the value of the renderGaps property. * * @param value * allowed object is * {@link Boolean } * */ public void setRenderGaps(Boolean value) { this.renderGaps = value; } /** * Gets the value of the showSequenceFeatures property. * * @return * possible object is * {@link Boolean } * */ public Boolean isShowSequenceFeatures() { return showSequenceFeatures; } /** * Sets the value of the showSequenceFeatures property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowSequenceFeatures(Boolean value) { this.showSequenceFeatures = value; } /** * Gets the value of the showNPfeatureTooltip property. * * @return * possible object is * {@link Boolean } * */ public Boolean isShowNPfeatureTooltip() { return showNPfeatureTooltip; } /** * Sets the value of the showNPfeatureTooltip property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowNPfeatureTooltip(Boolean value) { this.showNPfeatureTooltip = value; } /** * Gets the value of the showDbRefTooltip property. * * @return * possible object is * {@link Boolean } * */ public Boolean isShowDbRefTooltip() { return showDbRefTooltip; } /** * Sets the value of the showDbRefTooltip property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowDbRefTooltip(Boolean value) { this.showDbRefTooltip = value; } /** * Gets the value of the followHighlight property. * * @return * possible object is * {@link Boolean } * */ public boolean isFollowHighlight() { if (followHighlight == null) { return true; } else { return followHighlight; } } /** * Sets the value of the followHighlight property. * * @param value * allowed object is * {@link Boolean } * */ public void setFollowHighlight(Boolean value) { this.followHighlight = value; } /** * Gets the value of the followSelection property. * * @return * possible object is * {@link Boolean } * */ public boolean isFollowSelection() { if (followSelection == null) { return true; } else { return followSelection; } } /** * Sets the value of the followSelection property. * * @param value * allowed object is * {@link Boolean } * */ public void setFollowSelection(Boolean value) { this.followSelection = value; } /** * Gets the value of the showAnnotation property. * * @return * possible object is * {@link Boolean } * */ public Boolean isShowAnnotation() { return showAnnotation; } /** * Sets the value of the showAnnotation property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowAnnotation(Boolean value) { this.showAnnotation = value; } /** * Gets the value of the centreColumnLabels property. * * @return * possible object is * {@link Boolean } * */ public boolean isCentreColumnLabels() { if (centreColumnLabels == null) { return false; } else { return centreColumnLabels; } } /** * Sets the value of the centreColumnLabels property. * * @param value * allowed object is * {@link Boolean } * */ public void setCentreColumnLabels(Boolean value) { this.centreColumnLabels = value; } /** * Gets the value of the showGroupConservation property. * * @return * possible object is * {@link Boolean } * */ public boolean isShowGroupConservation() { if (showGroupConservation == null) { return false; } else { return showGroupConservation; } } /** * Sets the value of the showGroupConservation property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowGroupConservation(Boolean value) { this.showGroupConservation = value; } /** * Gets the value of the showGroupConsensus property. * * @return * possible object is * {@link Boolean } * */ public boolean isShowGroupConsensus() { if (showGroupConsensus == null) { return false; } else { return showGroupConsensus; } } /** * Sets the value of the showGroupConsensus property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowGroupConsensus(Boolean value) { this.showGroupConsensus = value; } /** * Gets the value of the showConsensusHistogram property. * * @return * possible object is * {@link Boolean } * */ public boolean isShowConsensusHistogram() { if (showConsensusHistogram == null) { return true; } else { return showConsensusHistogram; } } /** * Sets the value of the showConsensusHistogram property. * * @param value * allowed object is * {@link Boolean } * */ public void setShowConsensusHistogram(Boolean value) { this.showConsensusHistogram = value; } /** * Gets the value of the showSequenceLogo property. * * @return * possible object is * {@link Boolean } * */ public boolean isShowSequenceLogo() { if (showSequenceLogo == null) { return false; } else { return showSequenceLogo; } } /** * Sets the value of the showSequenceLogo 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 Boolean } * */ public boolean isNormaliseSequenceLogo() { if (normaliseSequenceLogo == null) { return false; } else { return normaliseSequenceLogo; } } /** * Sets the value of the normaliseSequenceLogo property. * * @param value * allowed object is * {@link Boolean } * */ public void setNormaliseSequenceLogo(Boolean value) { this.normaliseSequenceLogo = 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; } } /** * Sets the value of the ignoreGapsinConsensus property. * * @param value * allowed object is * {@link Boolean } * */ public void setIgnoreGapsinConsensus(Boolean value) { this.ignoreGapsinConsensus = value; } /** * Gets the value of the startRes property. * * @return * possible object is * {@link Integer } * */ public Integer getStartRes() { return startRes; } /** * Sets the value of the startRes property. * * @param value * allowed object is * {@link Integer } * */ public void setStartRes(Integer value) { this.startRes = value; } /** * Gets the value of the startSeq property. * * @return * possible object is * {@link Integer } * */ public Integer getStartSeq() { return startSeq; } /** * Sets the value of the startSeq property. * * @param value * allowed object is * {@link Integer } * */ public void setStartSeq(Integer value) { this.startSeq = 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 scaleProteinAsCdna property. * * @return * possible object is * {@link Boolean } * */ public boolean isScaleProteinAsCdna() { if (scaleProteinAsCdna == null) { return true; } else { return scaleProteinAsCdna; } } /** * Sets the value of the scaleProteinAsCdna property. * * @param value * allowed object is * {@link Boolean } * */ public void setScaleProteinAsCdna(Boolean value) { this.scaleProteinAsCdna = value; } /** * Gets the value of the viewName property. * * @return * possible object is * {@link String } * */ public String getViewName() { return viewName; } /** * Sets the value of the viewName property. * * @param value * allowed object is * {@link String } * */ public void setViewName(String value) { this.viewName = value; } /** * Gets the value of the sequenceSetId property. * * @return * possible object is * {@link String } * */ public String getSequenceSetId() { return sequenceSetId; } /** * Sets the value of the sequenceSetId property. * * @param value * allowed object is * {@link String } * */ public void setSequenceSetId(String value) { this.sequenceSetId = value; } /** * Gets the value of the gatheredViews property. * * @return * possible object is * {@link Boolean } * */ public Boolean isGatheredViews() { return gatheredViews; } /** * Sets the value of the gatheredViews property. * * @param value * allowed object is * {@link Boolean } * */ public void setGatheredViews(Boolean value) { this.gatheredViews = value; } /** * Gets the value of the textCol1 property. * * @return * possible object is * {@link Integer } * */ public Integer getTextCol1() { return textCol1; } /** * Sets the value of the textCol1 property. * * @param value * allowed object is * {@link Integer } * */ public void setTextCol1(Integer value) { this.textCol1 = value; } /** * Gets the value of the textCol2 property. * * @return * possible object is * {@link Integer } * */ public Integer getTextCol2() { return textCol2; } /** * Sets the value of the textCol2 property. * * @param value * allowed object is * {@link Integer } * */ public void setTextCol2(Integer value) { this.textCol2 = value; } /** * Gets the value of the textColThreshold property. * * @return * possible object is * {@link Integer } * */ public Integer getTextColThreshold() { return textColThreshold; } /** * Sets the value of the textColThreshold property. * * @param value * allowed object is * {@link Integer } * */ public void setTextColThreshold(Integer value) { this.textColThreshold = 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 complementId property. * * @return * possible object is * {@link String } * */ public String getComplementId() { return complementId; } /** * Sets the value of the complementId property. * * @param value * allowed object is * {@link String } * */ public void setComplementId(String value) { this.complementId = 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; } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

         * <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; } } /** *

Java class for anonymous complex type. * *

The following schema fragment specifies the expected content contained within this class. * * 

         * <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; } } } }