From: hansonr Date: Fri, 2 Nov 2018 01:39:39 +0000 (-0500) Subject: JAXB update site + transpiler X-Git-Tag: Develop-2_11_2_0-d20201215~24^2~68^2~430 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=962217a2b1ded38f78ff36d1875253caa04b0060;p=jalview.git JAXB update site + transpiler - ObjectFactory hack (does not actually use the methods) - removal of jalviewBH - new SwingJS-site and transpiler --- diff --git a/libjs/json-site.zip b/libjs/json-site.zip index e00b241..2e9ee54 100644 Binary files a/libjs/json-site.zip and b/libjs/json-site.zip differ diff --git a/src/jalview/xml/binding/jalviewBH/JalviewModel.java b/src/jalview/xml/binding/jalviewBH/JalviewModel.java deleted file mode 100644 index 413c3dd..0000000 --- a/src/jalview/xml/binding/jalviewBH/JalviewModel.java +++ /dev/null @@ -1,5241 +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 04:36:20 PM BST -// - -package jalview.xml.binding.jalviewBH; - -import jalview.schemabinding.version2.AnnotationColourScheme; -import jalview.schemabinding.version2.WebServiceParameterSet; - -import java.util.ArrayList; -import java.util.List; - -import javax.xml.bind.annotation.XmlAccessType; -import javax.xml.bind.annotation.XmlAccessorType; -import javax.xml.bind.annotation.XmlAttribute; -import javax.xml.bind.annotation.XmlElement; -import javax.xml.bind.annotation.XmlID; -import javax.xml.bind.annotation.XmlSchemaType; -import javax.xml.bind.annotation.XmlType; -import javax.xml.bind.annotation.XmlValue; -import javax.xml.bind.annotation.adapters.CollapsedStringAdapter; -import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter; -import javax.xml.datatype.XMLGregorianCalendar; - -/** - *

- * Java class for JalviewModel complex type. - * - *

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

- * <complexType name="JalviewModel">
- *   <complexContent>
- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       <sequence>
- *         <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
- *         <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *         <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
- *         <sequence>
- *           <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
- *                     <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <extension base="{www.jalview.org}pdbentry">
- *                             <sequence>
- *                               <element name="structureState" maxOccurs="unbounded" minOccurs="0">
- *                                 <complexType>
- *                                   <simpleContent>
- *                                     <extension base="<http://www.w3.org/2001/XMLSchema>string">
- *                                       <attGroup ref="{www.jalview.org}swingwindow"/>
- *                                       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                                       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                                       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     </extension>
- *                                   </simpleContent>
- *                                 </complexType>
- *                               </element>
- *                             </sequence>
- *                           </extension>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                     <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
- *                     <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             <sequence>
- *                               <element name="secondaryStructure" maxOccurs="unbounded">
- *                                 <complexType>
- *                                   <complexContent>
- *                                     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                                       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                                       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                                     </restriction>
- *                                   </complexContent>
- *                                 </complexType>
- *                               </element>
- *                             </sequence>
- *                             <attGroup ref="{www.jalview.org}swingwindow"/>
- *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           </restriction>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                   </sequence>
- *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
- *                     <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                   </sequence>
- *                   <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
- *                     <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                           </restriction>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                     <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
- *                             <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                             <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           </extension>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                   </sequence>
- *                   <attGroup ref="{www.jalview.org}swingwindow"/>
- *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
- *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
- *                   <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- *                   <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
- *                   </sequence>
- *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="tree" maxOccurs="unbounded" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence minOccurs="0">
- *                     <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *                     <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
- *                   </sequence>
- *                   <attGroup ref="{www.jalview.org}swingwindow"/>
- *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                   <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                   <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *           <element name="FeatureSettings" minOccurs="0">
- *             <complexType>
- *               <complexContent>
- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                   <sequence>
- *                     <element name="setting" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             <sequence>
- *                               <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
- *                               <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
- *                             </sequence>
- *                             <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
- *                             <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
- *                             <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
- *                             <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                             <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           </restriction>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                     <element name="group" maxOccurs="unbounded" minOccurs="0">
- *                       <complexType>
- *                         <complexContent>
- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                             <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
- *                           </restriction>
- *                         </complexContent>
- *                       </complexType>
- *                     </element>
- *                   </sequence>
- *                 </restriction>
- *               </complexContent>
- *             </complexType>
- *           </element>
- *         </sequence>
- *       </sequence>
- *     </restriction>
- *   </complexContent>
- * </complexType>
- *
- * - * - */ -@XmlAccessorType(XmlAccessType.FIELD) -@XmlType( - name = "JalviewModel", - namespace = "www.jalview.org", - propOrder = - { "creationDate", "version", "vamsasModel", "jSeq", "jGroup", "viewport", - "userColours", "tree", "featureSettings" }) -public class JalviewModel -{ - - @XmlElement(required = true) - @XmlSchemaType(name = "dateTime") - protected XMLGregorianCalendar creationDate; - - @XmlElement(required = true) - protected String version; - - @XmlElement(required = true) - protected VAMSAS vamsasModel; - - @XmlElement(name = "JSeq") - protected List jSeq; - - @XmlElement(name = "JGroup") - protected List jGroup; - - @XmlElement(name = "Viewport") - protected List viewport; - - @XmlElement(name = "UserColours") - protected List userColours; - - protected List tree; - - - @XmlElement(nillable=true) - protected String bhTest = "bhtest"; - - @XmlElement(name = "FeatureSettings") - protected JalviewModel.FeatureSettings featureSettings; - - /** - * Gets the value of the creationDate property. - * - * @return possible object is {@link XMLGregorianCalendar } - * - */ - public XMLGregorianCalendar getCreationDate() - { - return creationDate; - } - - /** - * Sets the value of the creationDate property. - * - * @param value - * allowed object is {@link XMLGregorianCalendar } - * - */ - public void setCreationDate(XMLGregorianCalendar value) - { - this.creationDate = value; - } - - /** - * Gets the value of the version property. - * - * @return possible object is {@link String } - * - */ - public String getVersion() - { - return version; - } - - /** - * Sets the value of the version property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setVersion(String value) - { - this.version = value; - } - - /** - * Gets the value of the vamsasModel property. - * - * @return possible object is {@link VAMSAS } - * - */ - public VAMSAS getVamsasModel() - { - return vamsasModel; - } - - /** - * Sets the value of the vamsasModel property. - * - * @param value - * allowed object is {@link VAMSAS } - * - */ - public void setVamsasModel(VAMSAS value) - { - this.vamsasModel = value; - } - - /** - * Gets the value of the jSeq property. - * - *

- * This accessor method returns a reference to the live list, not a snapshot. - * Therefore any modification you make to the returned list will be present - * inside the JAXB object. This is why there is not a set method - * for the jSeq property. - * - *

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

-   * getJSeq().add(newItem);
-   *
- * - * - *

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

- * This accessor method returns a reference to the live list, not a snapshot. - * Therefore any modification you make to the returned list will be present - * inside the JAXB object. This is why there is not a set method - * for the jGroup property. - * - *

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

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

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

- * This accessor method returns a reference to the live list, not a snapshot. - * Therefore any modification you make to the returned list will be present - * inside the JAXB object. This is why there is not a set method - * for the viewport property. - * - *

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

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

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

- * This accessor method returns a reference to the live list, not a snapshot. - * Therefore any modification you make to the returned list will be present - * inside the JAXB object. This is why there is not a set method - * for the userColours property. - * - *

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

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

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

- * This accessor method returns a reference to the live list, not a snapshot. - * Therefore any modification you make to the returned list will be present - * inside the JAXB object. This is why there is not a set method - * for the tree property. - * - *

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

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

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

- * Java class for anonymous complex type. - * - *

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

-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="setting" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <sequence>
-   *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-   *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-   *                 </sequence>
-   *                 <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                 <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-   *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="group" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { "setting", "group" }) - public static class FeatureSettings - { - - @XmlElement(namespace = "www.jalview.org") - protected List setting; - - @XmlElement(namespace = "www.jalview.org") - protected List group; - - /** - * Gets the value of the setting property. - * - *

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the setting property. - * - *

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

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

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

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the group property. - * - *

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

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

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

- * Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Group - { - - @XmlAttribute(name = "name", required = true) - protected String name; - - @XmlAttribute(name = "display", required = true) - protected boolean display; - - /** - * Gets the value of the name property. - * - * @return possible object is {@link String } - * - */ - public String getName() - { - return name; - } - - /** - * Sets the value of the name property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setName(String value) - { - this.name = value; - } - - /** - * Gets the value of the display property. - * - */ - public boolean isDisplay() - { - return display; - } - - /** - * Sets the value of the display property. - * - */ - public void setDisplay(boolean value) - { - this.display = value; - } - - } - - /** - *

- * Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
-     *         <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
-     *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
-     *       <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *       <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { "attributeName", "matcherSet" }) - public static class Setting - { - - @XmlElement(namespace = "www.jalview.org") - protected List attributeName; - - @XmlElement(namespace = "www.jalview.org") - protected Object/*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 Object/*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 Object/*FeatureMatcherSet*/ getMatcherSet() - { - return matcherSet; - } - - /** - * Sets the value of the matcherSet property. - * - * @param value - * allowed object is {@link FeatureMatcherSet } - * - */ - public void setMatcherSet(Object/*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 Object/*NoValueColour*/ getNoValueColour() - { - if (noValueColour == null) - { - return null/* NoValueColour */;// NoValueColour.MIN; - } - else - { - return noValueColour; - } - } - - /** - * Sets the value of the noValueColour property. - * - * @param value - * allowed object is {@link NoValueColour } - * - */ - public void setNoValueColour(Object/*NoValueColour*/ value) - { - this.noValueColour = value; - } - - /** - * Gets the value of the threshold property. - * - * @return possible object is {@link Float } - * - */ - public Float getThreshold() - { - return threshold; - } - - /** - * Sets the value of the threshold property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setThreshold(Float value) - { - this.threshold = value; - } - - /** - * Gets the value of the threshstate property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getThreshstate() - { - return threshstate; - } - - /** - * Sets the value of the threshstate property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setThreshstate(Integer value) - { - this.threshstate = value; - } - - /** - * Gets the value of the max property. - * - * @return possible object is {@link Float } - * - */ - public Float getMax() - { - return max; - } - - /** - * Sets the value of the max property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setMax(Float value) - { - this.max = value; - } - - /** - * Gets the value of the min property. - * - * @return possible object is {@link Float } - * - */ - public Float getMin() - { - return min; - } - - /** - * Sets the value of the min property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setMin(Float value) - { - this.min = value; - } - - /** - * Gets the value of the colourByLabel property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isColourByLabel() - { - return colourByLabel; - } - - /** - * Sets the value of the colourByLabel property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setColourByLabel(Boolean value) - { - this.colourByLabel = value; - } - - /** - * Gets the value of the autoScale property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isAutoScale() - { - return autoScale; - } - - /** - * Sets the value of the autoScale property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setAutoScale(Boolean value) - { - this.autoScale = value; - } - - } - - } - - /** - *

- * Java class for anonymous complex type. - * - *

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

-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-   *         <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
-   *       </sequence>
-   *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { "seq", "annotationColours" }) - public static class JGroup - { - - @XmlElement(namespace = "www.jalview.org", required = true) - protected List seq; - - @XmlElement(namespace = "www.jalview.org") - protected AnnotationColourScheme annotationColours; - - @XmlAttribute(name = "start") - protected Integer start; - - @XmlAttribute(name = "end") - protected Integer end; - - @XmlAttribute(name = "name") - protected String name; - - @XmlAttribute(name = "colour") - protected String colour; - - @XmlAttribute(name = "consThreshold") - protected Integer consThreshold; - - @XmlAttribute(name = "pidThreshold") - protected Integer pidThreshold; - - @XmlAttribute(name = "outlineColour") - protected Integer outlineColour; - - @XmlAttribute(name = "displayBoxes") - protected Boolean displayBoxes; - - @XmlAttribute(name = "displayText") - protected Boolean displayText; - - @XmlAttribute(name = "colourText") - protected Boolean colourText; - - @XmlAttribute(name = "textCol1") - protected Integer textCol1; - - @XmlAttribute(name = "textCol2") - protected Integer textCol2; - - @XmlAttribute(name = "textColThreshold") - protected Integer textColThreshold; - - @XmlAttribute(name = "showUnconserved") - protected Boolean showUnconserved; - - @XmlAttribute(name = "ignoreGapsinConsensus") - protected Boolean ignoreGapsinConsensus; - - @XmlAttribute(name = "showConsensusHistogram") - protected Boolean showConsensusHistogram; - - @XmlAttribute(name = "showSequenceLogo") - protected Boolean showSequenceLogo; - - @XmlAttribute(name = "normaliseSequenceLogo") - protected Boolean normaliseSequenceLogo; - - @XmlAttribute(name = "id") - protected String id; - - /** - * Gets the value of the seq property. - * - *

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the seq property. - * - *

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

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

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

- * Java class for anonymous complex type. - * - *

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

-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <extension base="{www.jalview.org}pdbentry">
-   *                 <sequence>
-   *                   <element name="structureState" maxOccurs="unbounded" minOccurs="0">
-   *                     <complexType>
-   *                       <simpleContent>
-   *                         <extension base="<http://www.w3.org/2001/XMLSchema>string">
-   *                           <attGroup ref="{www.jalview.org}swingwindow"/>
-   *                           <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                           <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *                           <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-   *                           <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-   *                           <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                         </extension>
-   *                       </simpleContent>
-   *                     </complexType>
-   *                   </element>
-   *                 </sequence>
-   *               </extension>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *         <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
-   *         <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
-   *           <complexType>
-   *             <complexContent>
-   *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                 <sequence>
-   *                   <element name="secondaryStructure" maxOccurs="unbounded">
-   *                     <complexType>
-   *                       <complexContent>
-   *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *                           <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                           <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *                           <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                         </restriction>
-   *                       </complexContent>
-   *                     </complexType>
-   *                   </element>
-   *                 </sequence>
-   *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-   *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *                 <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *                 <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *               </restriction>
-   *             </complexContent>
-   *           </complexType>
-   *         </element>
-   *       </sequence>
-   *       <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType( - name = "", - propOrder = - { "features", "pdbids", "hiddenSequences", "rnaViewer" }) - public static class JSeq - { - - @XmlElement(namespace = "www.jalview.org") - protected List features; - - @XmlElement(namespace = "www.jalview.org") - protected List pdbids; - - @XmlElement(namespace = "www.jalview.org", type = Integer.class) - protected List hiddenSequences; - - @XmlElement(namespace = "www.jalview.org") - protected List rnaViewer; - - @XmlAttribute(name = "colour") - protected Integer colour; - - @XmlAttribute(name = "start", required = true) - protected int start; - - @XmlAttribute(name = "end", required = true) - protected int end; - - @XmlAttribute(name = "id", required = true) - protected String id; - - @XmlAttribute(name = "hidden") - protected Boolean hidden; - - @XmlAttribute(name = "viewreference") - protected Boolean viewreference; - - /** - * Gets the value of the features property. - * - *

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the features property. - * - *

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

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

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

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the pdbids property. - * - *

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

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

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

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the hiddenSequences property. - * - *

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

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

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

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the rnaViewer property. - * - *

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

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

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

- * Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <extension base="{www.jalview.org}pdbentry">
-     *       <sequence>
-     *         <element name="structureState" maxOccurs="unbounded" minOccurs="0">
-     *           <complexType>
-     *             <simpleContent>
-     *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
-     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
-     *                 <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                 <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *                 <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-     *                 <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </extension>
-     *             </simpleContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *     </extension>
-     *   </complexContent>
-     * </complexType>
-     *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { "structureState" }) - public static class Pdbids //extends Pdbentry - { - - @XmlElement(namespace = "www.jalview.org") - protected List structureState; - - /** - * Gets the value of the structureState property. - * - *

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the structureState property. - * - *

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

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

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

- * Java class for anonymous complex type. - * - *

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

-       * <complexType>
-       *   <simpleContent>
-       *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-       *       <attGroup ref="{www.jalview.org}swingwindow"/>
-       *       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-       *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-       *       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-       *       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
-       *       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *     </extension>
-       *   </simpleContent>
-       * </complexType>
-       *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { "value" }) - public static class StructureState - { - - @XmlValue - protected String value; - - @XmlAttribute(name = "visible") - protected Boolean visible; - - @XmlAttribute(name = "viewId") - protected String viewId; - - @XmlAttribute(name = "alignwithAlignPanel") - protected Boolean alignwithAlignPanel; - - @XmlAttribute(name = "colourwithAlignPanel") - protected Boolean colourwithAlignPanel; - - @XmlAttribute(name = "colourByJmol") - protected Boolean colourByJmol; - - @XmlAttribute(name = "type") - protected String type; - - @XmlAttribute(name = "width") - protected Integer width; - - @XmlAttribute(name = "height") - protected Integer height; - - @XmlAttribute(name = "xpos") - protected Integer xpos; - - @XmlAttribute(name = "ypos") - protected Integer ypos; - - /** - * Gets the value of the value property. - * - * @return possible object is {@link String } - * - */ - public String getValue() - { - return value; - } - - /** - * Sets the value of the value property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setValue(String value) - { - this.value = value; - } - - /** - * Gets the value of the visible property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isVisible() - { - return visible; - } - - /** - * Sets the value of the visible property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setVisible(Boolean value) - { - this.visible = value; - } - - /** - * Gets the value of the viewId property. - * - * @return possible object is {@link String } - * - */ - public String getViewId() - { - return viewId; - } - - /** - * Sets the value of the viewId property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setViewId(String value) - { - this.viewId = value; - } - - /** - * Gets the value of the alignwithAlignPanel property. - * - * @return possible object is {@link Boolean } - * - */ - public boolean isAlignwithAlignPanel() - { - if (alignwithAlignPanel == null) - { - return true; - } - else - { - return alignwithAlignPanel; - } - } - - /** - * Sets the value of the alignwithAlignPanel property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setAlignwithAlignPanel(Boolean value) - { - this.alignwithAlignPanel = value; - } - - /** - * Gets the value of the colourwithAlignPanel property. - * - * @return possible object is {@link Boolean } - * - */ - public boolean isColourwithAlignPanel() - { - if (colourwithAlignPanel == null) - { - return false; - } - else - { - return colourwithAlignPanel; - } - } - - /** - * Sets the value of the colourwithAlignPanel property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setColourwithAlignPanel(Boolean value) - { - this.colourwithAlignPanel = value; - } - - /** - * Gets the value of the colourByJmol property. - * - * @return possible object is {@link Boolean } - * - */ - public boolean isColourByJmol() - { - if (colourByJmol == null) - { - return true; - } - else - { - return colourByJmol; - } - } - - /** - * Sets the value of the colourByJmol property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setColourByJmol(Boolean value) - { - this.colourByJmol = value; - } - - /** - * Gets the value of the type property. - * - * @return possible object is {@link String } - * - */ - public String getType() - { - return type; - } - - /** - * Sets the value of the type property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setType(String value) - { - this.type = value; - } - - /** - * Gets the value of the width property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getWidth() - { - return width; - } - - /** - * Sets the value of the width property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setWidth(Integer value) - { - this.width = value; - } - - /** - * Gets the value of the height property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getHeight() - { - return height; - } - - /** - * Sets the value of the height property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setHeight(Integer value) - { - this.height = value; - } - - /** - * Gets the value of the xpos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getXpos() - { - return xpos; - } - - /** - * Sets the value of the xpos property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setXpos(Integer value) - { - this.xpos = value; - } - - /** - * Gets the value of the ypos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getYpos() - { - return ypos; - } - - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setYpos(Integer value) - { - this.ypos = value; - } - - } - - } - - /** - *

- * Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element name="secondaryStructure" maxOccurs="unbounded">
-     *           <complexType>
-     *             <complexContent>
-     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *                 <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *                 <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *               </restriction>
-     *             </complexContent>
-     *           </complexType>
-     *         </element>
-     *       </sequence>
-     *       <attGroup ref="{www.jalview.org}swingwindow"/>
-     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { "secondaryStructure" }) - public static class RnaViewer - { - - @XmlElement(namespace = "www.jalview.org", required = true) - protected List secondaryStructure; - - @XmlAttribute(name = "title") - protected String title; - - @XmlAttribute(name = "viewId") - protected String viewId; - - @XmlAttribute(name = "dividerLocation") - protected Integer dividerLocation; - - @XmlAttribute(name = "selectedRna") - protected Integer selectedRna; - - @XmlAttribute(name = "width") - protected Integer width; - - @XmlAttribute(name = "height") - protected Integer height; - - @XmlAttribute(name = "xpos") - protected Integer xpos; - - @XmlAttribute(name = "ypos") - protected Integer ypos; - - /** - * Gets the value of the secondaryStructure property. - * - *

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the secondaryStructure property. - * - *

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

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

- * Objects of the following type(s) are allowed in the list - * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure } - * - * - */ - public List getSecondaryStructure() - { - if (secondaryStructure == null) - { - secondaryStructure = new ArrayList(); - } - return this.secondaryStructure; - } - - /** - * Gets the value of the title property. - * - * @return possible object is {@link String } - * - */ - public String getTitle() - { - return title; - } - - /** - * Sets the value of the title property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setTitle(String value) - { - this.title = value; - } - - /** - * Gets the value of the viewId property. - * - * @return possible object is {@link String } - * - */ - public String getViewId() - { - return viewId; - } - - /** - * Sets the value of the viewId property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setViewId(String value) - { - this.viewId = value; - } - - /** - * Gets the value of the dividerLocation property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getDividerLocation() - { - return dividerLocation; - } - - /** - * Sets the value of the dividerLocation property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setDividerLocation(Integer value) - { - this.dividerLocation = value; - } - - /** - * Gets the value of the selectedRna property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getSelectedRna() - { - return selectedRna; - } - - /** - * Sets the value of the selectedRna property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setSelectedRna(Integer value) - { - this.selectedRna = value; - } - - /** - * Gets the value of the width property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getWidth() - { - return width; - } - - /** - * Sets the value of the width property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setWidth(Integer value) - { - this.width = value; - } - - /** - * Gets the value of the height property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getHeight() - { - return height; - } - - /** - * Sets the value of the height property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setHeight(Integer value) - { - this.height = value; - } - - /** - * Gets the value of the xpos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getXpos() - { - return xpos; - } - - /** - * Sets the value of the xpos property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setXpos(Integer value) - { - this.xpos = value; - } - - /** - * Gets the value of the ypos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getYpos() - { - return ypos; - } - - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setYpos(Integer value) - { - this.ypos = value; - } - - /** - *

- * Java class for anonymous complex type. - * - *

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

-       * <complexType>
-       *   <complexContent>
-       *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-       *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-       *       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
-       *     </restriction>
-       *   </complexContent>
-       * </complexType>
-       *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class SecondaryStructure - { - - @XmlAttribute(name = "title") - protected String title; - - @XmlAttribute(name = "annotationId", required = true) - protected String annotationId; - - @XmlAttribute(name = "gapped") - protected Boolean gapped; - - @XmlAttribute(name = "viewerState") - protected String viewerState; - - /** - * Gets the value of the title property. - * - * @return possible object is {@link String } - * - */ - public String getTitle() - { - return title; - } - - /** - * Sets the value of the title property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setTitle(String value) - { - this.title = value; - } - - /** - * Gets the value of the annotationId property. - * - * @return possible object is {@link String } - * - */ - public String getAnnotationId() - { - return annotationId; - } - - /** - * Sets the value of the annotationId property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setAnnotationId(String value) - { - this.annotationId = value; - } - - /** - * Gets the value of the gapped property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isGapped() - { - return gapped; - } - - /** - * Sets the value of the gapped property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setGapped(Boolean value) - { - this.gapped = value; - } - - /** - * Gets the value of the viewerState property. - * - * @return possible object is {@link String } - * - */ - public String getViewerState() - { - return viewerState; - } - - /** - * Sets the value of the viewerState property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setViewerState(String value) - { - this.viewerState = value; - } - - } - - } - - } - - /** - *

- * Java class for anonymous complex type. - * - *

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

-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence minOccurs="0">
-   *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *         <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
-   *       </sequence>
-   *       <attGroup ref="{www.jalview.org}swingwindow"/>
-   *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
-   *       <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
-   *       <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { "title", "newick" }) - public static class Tree - { - - @XmlElement(namespace = "www.jalview.org") - protected String title; - - @XmlElement(namespace = "www.jalview.org") - protected String newick; - - @XmlAttribute(name = "fontName") - protected String fontName; - - @XmlAttribute(name = "fontSize") - protected Integer fontSize; - - @XmlAttribute(name = "fontStyle") - protected Integer fontStyle; - - @XmlAttribute(name = "threshold") - protected Float threshold; - - @XmlAttribute(name = "showBootstrap") - protected Boolean showBootstrap; - - @XmlAttribute(name = "showDistances") - protected Boolean showDistances; - - @XmlAttribute(name = "markUnlinked") - protected Boolean markUnlinked; - - @XmlAttribute(name = "fitToWindow") - protected Boolean fitToWindow; - - @XmlAttribute(name = "currentTree") - protected Boolean currentTree; - - @XmlAttribute(name = "id") - @XmlJavaTypeAdapter(CollapsedStringAdapter.class) - @XmlID - @XmlSchemaType(name = "ID") - protected String id; - - @XmlAttribute(name = "width") - protected Integer width; - - @XmlAttribute(name = "height") - protected Integer height; - - @XmlAttribute(name = "xpos") - protected Integer xpos; - - @XmlAttribute(name = "ypos") - protected Integer ypos; - - /** - * Gets the value of the title property. - * - * @return possible object is {@link String } - * - */ - public String getTitle() - { - return title; - } - - /** - * Sets the value of the title property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setTitle(String value) - { - this.title = value; - } - - /** - * Gets the value of the newick property. - * - * @return possible object is {@link String } - * - */ - public String getNewick() - { - return newick; - } - - /** - * Sets the value of the newick property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setNewick(String value) - { - this.newick = value; - } - - /** - * Gets the value of the fontName property. - * - * @return possible object is {@link String } - * - */ - public String getFontName() - { - return fontName; - } - - /** - * Sets the value of the fontName property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setFontName(String value) - { - this.fontName = value; - } - - /** - * Gets the value of the fontSize property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getFontSize() - { - return fontSize; - } - - /** - * Sets the value of the fontSize property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setFontSize(Integer value) - { - this.fontSize = value; - } - - /** - * Gets the value of the fontStyle property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getFontStyle() - { - return fontStyle; - } - - /** - * Sets the value of the fontStyle property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setFontStyle(Integer value) - { - this.fontStyle = value; - } - - /** - * Gets the value of the threshold property. - * - * @return possible object is {@link Float } - * - */ - public Float getThreshold() - { - return threshold; - } - - /** - * Sets the value of the threshold property. - * - * @param value - * allowed object is {@link Float } - * - */ - public void setThreshold(Float value) - { - this.threshold = value; - } - - /** - * Gets the value of the showBootstrap property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowBootstrap() - { - return showBootstrap; - } - - /** - * Sets the value of the showBootstrap property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setShowBootstrap(Boolean value) - { - this.showBootstrap = value; - } - - /** - * Gets the value of the showDistances property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isShowDistances() - { - return showDistances; - } - - /** - * Sets the value of the showDistances property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setShowDistances(Boolean value) - { - this.showDistances = value; - } - - /** - * Gets the value of the markUnlinked property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isMarkUnlinked() - { - return markUnlinked; - } - - /** - * Sets the value of the markUnlinked property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setMarkUnlinked(Boolean value) - { - this.markUnlinked = value; - } - - /** - * Gets the value of the fitToWindow property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isFitToWindow() - { - return fitToWindow; - } - - /** - * Sets the value of the fitToWindow property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setFitToWindow(Boolean value) - { - this.fitToWindow = value; - } - - /** - * Gets the value of the currentTree property. - * - * @return possible object is {@link Boolean } - * - */ - public Boolean isCurrentTree() - { - return currentTree; - } - - /** - * Sets the value of the currentTree property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setCurrentTree(Boolean value) - { - this.currentTree = value; - } - - /** - * Gets the value of the id property. - * - * @return possible object is {@link String } - * - */ - public String getId() - { - return id; - } - - /** - * Sets the value of the id property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setId(String value) - { - this.id = value; - } - - /** - * Gets the value of the width property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getWidth() - { - return width; - } - - /** - * Sets the value of the width property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setWidth(Integer value) - { - this.width = value; - } - - /** - * Gets the value of the height property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getHeight() - { - return height; - } - - /** - * Sets the value of the height property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setHeight(Integer value) - { - this.height = value; - } - - /** - * Gets the value of the xpos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getXpos() - { - return xpos; - } - - /** - * Sets the value of the xpos property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setXpos(Integer value) - { - this.xpos = value; - } - - /** - * Gets the value of the ypos property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getYpos() - { - return ypos; - } - - /** - * Sets the value of the ypos property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setYpos(Integer value) - { - this.ypos = value; - } - - } - - /** - *

- * Java class for anonymous complex type. - * - *

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

-   * <complexType>
-   *   <complexContent>
-   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-   *       <sequence>
-   *         <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
-   *       </sequence>
-   *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-   *     </restriction>
-   *   </complexContent>
-   * </complexType>
-   *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { "userColourScheme" }) - public static class UserColours - { - - @XmlElement( - name = "UserColourScheme", - namespace = "www.jalview.org", - required = true) - protected Object/*JalviewUserColours*/ userColourScheme; - - @XmlAttribute(name = "id") - protected String id; - - /** - * Gets the value of the userColourScheme property. - * - * @return possible object is {@link JalviewUserColours } - * - */ - public Object/*JalviewUserColours*/ getUserColourScheme() - { - return userColourScheme; - } - - /** - * Sets the value of the userColourScheme property. - * - * @param value - * allowed object is {@link JalviewUserColours } - * - */ - public void setUserColourScheme(Object/*JalviewUserColours*/ value) - { - this.userColourScheme = value; - } - - /** - * Gets the value of the id property. - * - * @return possible object is {@link String } - * - */ - public String getId() - { - return id; - } - - /** - * Sets the value of the id property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setId(String value) - { - this.id = value; - } - - } - - /** - *

- * Java class for anonymous complex type. - * - *

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

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

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the hiddenColumns property. - * - *

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

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

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

- * This accessor method returns a reference to the live list, not a - * snapshot. Therefore any modification you make to the returned list will - * be present inside the JAXB object. This is why there is not a - * set method for the calcIdParam property. - * - *

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

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

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

- * Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
-     *       <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-     *       <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-     *     </extension>
-     *   </complexContent>
-     * </complexType>
-     *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class CalcIdParam extends WebServiceParameterSet - { - - @XmlAttribute(name = "calcId", required = true) - protected String calcId; - - @XmlAttribute(name = "needsUpdate") - protected Boolean needsUpdate; - - @XmlAttribute(name = "autoUpdate", required = true) - protected boolean autoUpdate; - - /** - * Gets the value of the calcId property. - * - * @return possible object is {@link String } - * - */ - public String getCalcId() - { - return calcId; - } - - /** - * Sets the value of the calcId property. - * - * @param value - * allowed object is {@link String } - * - */ - public void setCalcId(String value) - { - this.calcId = value; - } - - /** - * Gets the value of the needsUpdate property. - * - * @return possible object is {@link Boolean } - * - */ - public boolean isNeedsUpdate() - { - if (needsUpdate == null) - { - return false; - } - else - { - return needsUpdate; - } - } - - /** - * Sets the value of the needsUpdate property. - * - * @param value - * allowed object is {@link Boolean } - * - */ - public void setNeedsUpdate(Boolean value) - { - this.needsUpdate = value; - } - - /** - * Gets the value of the autoUpdate property. - * - */ - public boolean isAutoUpdate() - { - return autoUpdate; - } - - /** - * Sets the value of the autoUpdate property. - * - */ - public void setAutoUpdate(boolean value) - { - this.autoUpdate = value; - } - - } - - /** - *

- * Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *       <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class HiddenColumns - { - - @XmlAttribute(name = "start") - protected Integer start; - - @XmlAttribute(name = "end") - protected Integer end; - - /** - * Gets the value of the start property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getStart() - { - return start; - } - - /** - * Sets the value of the start property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setStart(Integer value) - { - this.start = value; - } - - /** - * Gets the value of the end property. - * - * @return possible object is {@link Integer } - * - */ - public Integer getEnd() - { - return end; - } - - /** - * Sets the value of the end property. - * - * @param value - * allowed object is {@link Integer } - * - */ - public void setEnd(Integer value) - { - this.end = value; - } - - } - - } - -} diff --git a/src/jalview/xml/binding/jalviewBH/SequenceSet.java b/src/jalview/xml/binding/jalviewBH/SequenceSet.java deleted file mode 100644 index d78c585..0000000 --- a/src/jalview/xml/binding/jalviewBH/SequenceSet.java +++ /dev/null @@ -1,324 +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 04:36:20 PM BST -// - - -package jalview.xml.binding.jalviewBH; - -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.XmlRootElement; -import javax.xml.bind.annotation.XmlType; - - -/** - *

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 ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
- *         <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
- *         <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
- *           <complexType>
- *             <complexContent>
- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- *               </restriction>
- *             </complexContent>
- *           </complexType>
- *         </element>
- *         <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
- *       </sequence>
- *       <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     </restriction>
- *   </complexContent>
- * </complexType>
- *
- * - * - */ -@XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "", propOrder = { - "sequence", - "annotation", - "sequenceSetProperties", - "alcodonFrame" -}) -@XmlRootElement(name = "SequenceSet") -public class SequenceSet { - - // BH testing here - private class Sequence {} - private class Annotation {} - private class AlcodonFrame {} - // - - @XmlElement(name = "Sequence") - protected List sequence; - @XmlElement(name = "Annotation") - protected List annotation; - protected List sequenceSetProperties; - @XmlElement(name = "AlcodonFrame") - protected List alcodonFrame; - @XmlAttribute(name = "gapChar", required = true) - protected String gapChar; - @XmlAttribute(name = "datasetId") - protected String datasetId; - - /** - * Gets the value of the sequence 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 sequence property. - * - *

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

-     *    getSequence().add(newItem);
-     *
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Sequence } - * - * - */ - public List getSequence() { - if (sequence == null) { - sequence = new ArrayList(); - } - return this.sequence; - } - - /** - * Gets the value of the annotation 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 annotation property. - * - *

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

-     *    getAnnotation().add(newItem);
-     *
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link Annotation } - * - * - */ - public List getAnnotation() { - if (annotation == null) { - annotation = new ArrayList(); - } - return this.annotation; - } - - /** - * Gets the value of the sequenceSetProperties 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 sequenceSetProperties property. - * - *

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

-     *    getSequenceSetProperties().add(newItem);
-     *
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link SequenceSet.SequenceSetProperties } - * - * - */ - public List getSequenceSetProperties() { - if (sequenceSetProperties == null) { - sequenceSetProperties = new ArrayList(); - } - return this.sequenceSetProperties; - } - - /** - * Gets the value of the alcodonFrame 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 alcodonFrame property. - * - *

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

-     *    getAlcodonFrame().add(newItem);
-     *
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link AlcodonFrame } - * - * - */ - public List getAlcodonFrame() { - if (alcodonFrame == null) { - alcodonFrame = new ArrayList(); - } - return this.alcodonFrame; - } - - /** - * Gets the value of the gapChar property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getGapChar() { - return gapChar; - } - - /** - * Sets the value of the gapChar property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setGapChar(String value) { - this.gapChar = value; - } - - /** - * Gets the value of the datasetId property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getDatasetId() { - return datasetId; - } - - /** - * Sets the value of the datasetId property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDatasetId(String value) { - this.datasetId = 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="key" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     *
- * - * - */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class SequenceSetProperties { - - @XmlAttribute(name = "key") - protected String key; - @XmlAttribute(name = "value") - protected String value; - - /** - * Gets the value of the key property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getKey() { - return key; - } - - /** - * Sets the value of the key property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setKey(String value) { - this.key = value; - } - - /** - * 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; - } - - } - -} diff --git a/src/jalview/xml/binding/jalviewBH/VAMSAS.java b/src/jalview/xml/binding/jalviewBH/VAMSAS.java deleted file mode 100644 index c10f7df..0000000 --- a/src/jalview/xml/binding/jalviewBH/VAMSAS.java +++ /dev/null @@ -1,109 +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 04:36:20 PM BST -// - - -package jalview.xml.binding.jalviewBH; - -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.XmlElement; -import javax.xml.bind.annotation.XmlType; - - -/** - *

Java class for VAMSAS complex type. - * - *

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

- * <complexType name="VAMSAS">
- *   <complexContent>
- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       <sequence>
- *         <element name="Tree" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
- *         <element ref="{www.vamsas.ac.uk/jalview/version2}SequenceSet" maxOccurs="unbounded" minOccurs="0"/>
- *       </sequence>
- *     </restriction>
- *   </complexContent>
- * </complexType>
- *
- * - * - */ -@XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "VAMSAS", propOrder = { - "tree", - "sequenceSet" -}) -public class VAMSAS { - - @XmlElement(name = "Tree") - protected List tree; - @XmlElement(name = "SequenceSet") - protected List sequenceSet; - - /** - * 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 String } - * - * - */ - public List getTree() { - if (tree == null) { - tree = new ArrayList(); - } - return this.tree; - } - - /** - * Gets the value of the sequenceSet 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 sequenceSet property. - * - *

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

-     *    getSequenceSet().add(newItem);
-     *
- * - * - *

- * Objects of the following type(s) are allowed in the list - * {@link SequenceSet } - * - * - */ - public List getSequenceSet() { - if (sequenceSet == null) { - sequenceSet = new ArrayList(); - } - return this.sequenceSet; - } - -} diff --git a/swingjs/SwingJS-site.zip b/swingjs/SwingJS-site.zip index 78656bb..c56ecfc 100644 Binary files a/swingjs/SwingJS-site.zip and b/swingjs/SwingJS-site.zip differ diff --git a/swingjs/net.sf.j2s.core.jar b/swingjs/net.sf.j2s.core.jar index e72f1b8..4827b38 100644 Binary files a/swingjs/net.sf.j2s.core.jar and b/swingjs/net.sf.j2s.core.jar differ diff --git a/swingjs/timestamp b/swingjs/timestamp index 2de5302..d1276fe 100644 --- a/swingjs/timestamp +++ b/swingjs/timestamp @@ -1 +1 @@ -20181101120131 +20181101203541 diff --git a/swingjs/ver/3.2.4/SwingJS-site.zip b/swingjs/ver/3.2.4/SwingJS-site.zip index 78656bb..c56ecfc 100644 Binary files a/swingjs/ver/3.2.4/SwingJS-site.zip and b/swingjs/ver/3.2.4/SwingJS-site.zip differ diff --git a/swingjs/ver/3.2.4/net.sf.j2s.core.jar b/swingjs/ver/3.2.4/net.sf.j2s.core.jar index e72f1b8..4827b38 100644 Binary files a/swingjs/ver/3.2.4/net.sf.j2s.core.jar and b/swingjs/ver/3.2.4/net.sf.j2s.core.jar differ diff --git a/swingjs/ver/3.2.4/timestamp b/swingjs/ver/3.2.4/timestamp index 2de5302..d1276fe 100644 --- a/swingjs/ver/3.2.4/timestamp +++ b/swingjs/ver/3.2.4/timestamp @@ -1 +1 @@ -20181101120131 +20181101203541