From: Jim Procter Date: Wed, 9 Jan 2019 16:23:37 +0000 (+0000) Subject: JAL-3063 remove stale JAXB binding POJO X-Git-Tag: Release_2_11_1_0~78^2~4^2 X-Git-Url: http://source.jalview.org/gitweb/?p=jalview.git;a=commitdiff_plain;h=2f0267f5df56bb5969b3946434d45110bf994ce7 JAL-3063 remove stale JAXB binding POJO --- diff --git a/src/jalview/xml/binding/jalview/JalviewModelType.java b/src/jalview/xml/binding/jalview/JalviewModelType.java deleted file mode 100644 index f084bc3..0000000 --- a/src/jalview/xml/binding/jalview/JalviewModelType.java +++ /dev/null @@ -1,5090 +0,0 @@ -// -// 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; - } - - } - - } - -}