X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FJalviewModelType.java;fp=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FJalviewModelType.java;h=f084bc3f05021c6c5567ca476a553b63130affbd;hb=4d64932654de3f6ffe07db11d18f2d21f558c6e6;hp=0000000000000000000000000000000000000000;hpb=382f5ff058a4c2fed1e9874bb712b40f16ec1a4e;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/JalviewModelType.java b/src/jalview/xml/binding/jalview/JalviewModelType.java new file mode 100644 index 0000000..f084bc3 --- /dev/null +++ b/src/jalview/xml/binding/jalview/JalviewModelType.java @@ -0,0 +1,5090 @@ +// +// 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 01:33:02 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 JalviewModelType complex type. + * + *

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

+ * <complexType name="JalviewModelType">
+ *   <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 = "JalviewModelType", namespace = "www.jalview.org", propOrder = { + "creationDate", + "version", + "vamsasModel", + "jSeq", + "jGroup", + "viewport", + "userColours", + "tree", + "featureSettings" +}) +public class JalviewModelType { + + @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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.FeatureSettings } + * + */ + public JalviewModelType.FeatureSettings getFeatureSettings() { + return featureSettings; + } + + /** + * Sets the value of the featureSettings property. + * + * @param value + * allowed object is + * {@link JalviewModelType.FeatureSettings } + * + */ + public void setFeatureSettings(JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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 JalviewModelType.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; + } + + } + + } + +}