From: Jim Procter Date: Mon, 7 Feb 2022 17:04:01 +0000 (+0000) Subject: JAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTitle' into 2_11_2_develop X-Git-Tag: Release_2_11_3_0~18^2~20 X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=7b32d373b60d0af55481cfd6d377b2cc1ec035c0;p=jalview.git JAL-3785 JAL- Merge branch 'bug/JAL-3785autoOverviewTitle' into 2_11_2_develop regenerated jaxb bindings for updated schemas on develop & feature branch Conflicts: src/jalview/gui/Preferences.java src/jalview/xml/binding/jalview/JalviewModel.java src/jalview/xml/binding/jalview/ObjectFactory.java src/jalview/xml/binding/jalview/package-info.java --- 7b32d373b60d0af55481cfd6d377b2cc1ec035c0 diff --cc src/jalview/xml/binding/embl/EntrySetType.java index 09947ec,09947ec..e1e3c35 --- a/src/jalview/xml/binding/embl/EntrySetType.java +++ b/src/jalview/xml/binding/embl/EntrySetType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2018.09.14 at 02:46:00 PM BST ++// Generated on: 2022.02.07 at 04:45:21 PM GMT // @@@ -17,21 -17,21 +17,21 @@@ import javax.xml.bind.annotation.XmlTyp /** -- *

Java class for EntrySetType complex type. ++ * <p>Java class for EntrySetType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="EntrySetType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence maxOccurs="unbounded">
-- *         <element name="entry" type="{}EntryType"/>
-- *       </sequence>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="EntrySetType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence maxOccurs="unbounded"&gt; ++ * &lt;element name="entry" type="{}EntryType"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -47,20 -47,20 +47,20 @@@ public class EntrySetType /** * Gets the value of the entry property. * -- *

++ * <p> * 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 entry property. ++ * This is why there is not a <CODE>set</CODE> method for the entry property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEntry().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EntryType } * diff --cc src/jalview/xml/binding/embl/EntryType.java index 8964a3f,8964a3f..7e2ff62 --- a/src/jalview/xml/binding/embl/EntryType.java +++ b/src/jalview/xml/binding/embl/EntryType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2018.09.14 at 02:46:00 PM BST ++// Generated on: 2022.02.07 at 04:45:21 PM GMT // @@@ -22,205 -22,205 +22,205 @@@ import javax.xml.datatype.XMLGregorianC /** -- *

Java class for EntryType complex type. ++ * <p>Java class for EntryType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="EntryType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="secondaryAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="projectAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
-- *         <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *         <element name="keyword" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="reference" maxOccurs="unbounded" minOccurs="0">
-- *           <complexType>
-- *             <complexContent>
-- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                 <sequence>
-- *                   <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                   <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-- *                   <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-- *                   <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                   <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
-- *                   <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                   <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                   <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                   <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                   <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                   <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                   <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                   <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                   <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-- *                 </sequence>
-- *                 <attribute name="type" use="required">
-- *                   <simpleType>
-- *                     <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *                       <enumeration value="submission"/>
-- *                       <enumeration value="book"/>
-- *                       <enumeration value="article"/>
-- *                       <enumeration value="patent"/>
-- *                       <enumeration value="thesis"/>
-- *                       <enumeration value="unpublished"/>
-- *                     </restriction>
-- *                   </simpleType>
-- *                 </attribute>
-- *                 <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                 <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *               </restriction>
-- *             </complexContent>
-- *           </complexType>
-- *         </element>
-- *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="feature" maxOccurs="unbounded" minOccurs="0">
-- *           <complexType>
-- *             <complexContent>
-- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                 <sequence>
-- *                   <element name="taxon" minOccurs="0">
-- *                     <complexType>
-- *                       <complexContent>
-- *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                           <sequence>
-- *                             <element name="lineage" minOccurs="0">
-- *                               <complexType>
-- *                                 <complexContent>
-- *                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                                     <sequence>
-- *                                       <element name="taxon" maxOccurs="unbounded">
-- *                                         <complexType>
-- *                                           <complexContent>
-- *                                             <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                                               <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *                                             </restriction>
-- *                                           </complexContent>
-- *                                         </complexType>
-- *                                       </element>
-- *                                     </sequence>
-- *                                   </restriction>
-- *                                 </complexContent>
-- *                               </complexType>
-- *                             </element>
-- *                           </sequence>
-- *                           <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *                           <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *                           <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                         </restriction>
-- *                       </complexContent>
-- *                     </complexType>
-- *                   </element>
-- *                   <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
-- *                   <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
-- *                     <complexType>
-- *                       <complexContent>
-- *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                           <sequence>
-- *                             <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *                           </sequence>
-- *                           <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *                         </restriction>
-- *                       </complexContent>
-- *                     </complexType>
-- *                   </element>
-- *                 </sequence>
-- *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *                 <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *               </restriction>
-- *             </complexContent>
-- *           </complexType>
-- *         </element>
-- *         <element name="assembly" minOccurs="0">
-- *           <complexType>
-- *             <complexContent>
-- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                 <sequence>
-- *                   <element name="range" maxOccurs="unbounded">
-- *                     <complexType>
-- *                       <complexContent>
-- *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                           <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                           <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                           <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                           <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                           <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *                           <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                           <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-- *                         </restriction>
-- *                       </complexContent>
-- *                     </complexType>
-- *                   </element>
-- *                 </sequence>
-- *               </restriction>
-- *             </complexContent>
-- *           </complexType>
-- *         </element>
-- *         <element name="contig" minOccurs="0">
-- *           <complexType>
-- *             <complexContent>
-- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                 <sequence>
-- *                   <choice maxOccurs="unbounded" minOccurs="0">
-- *                     <element name="range">
-- *                       <complexType>
-- *                         <complexContent>
-- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                             <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                             <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                             <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                             <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                             <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *                             <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                             <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-- *                           </restriction>
-- *                         </complexContent>
-- *                       </complexType>
-- *                     </element>
-- *                     <element name="gap">
-- *                       <complexType>
-- *                         <complexContent>
-- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                             <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                             <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                             <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *                             <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
-- *                           </restriction>
-- *                         </complexContent>
-- *                       </complexType>
-- *                     </element>
-- *                   </choice>
-- *                 </sequence>
-- *               </restriction>
-- *             </complexContent>
-- *           </complexType>
-- *         </element>
-- *         <element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *       </sequence>
-- *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *       <attribute name="entryVersion" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *       <attribute name="dataClass" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="taxonomicDivision" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="moleculeType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="sequenceLength" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *       <attribute name="topology" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="circular"/>
-- *             <enumeration value="linear"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *       <attribute name="firstPublic" type="{http://www.w3.org/2001/XMLSchema}date" />
-- *       <attribute name="firstPublicRelease" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *       <attribute name="lastUpdated" type="{http://www.w3.org/2001/XMLSchema}date" />
-- *       <attribute name="lastUpdatedRelease" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="EntryType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="secondaryAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="projectAccession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; ++ * &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="keyword" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="reference" maxOccurs="unbounded" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/&gt; ++ * &lt;element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="submission"/&gt; ++ * &lt;enumeration value="book"/&gt; ++ * &lt;enumeration value="article"/&gt; ++ * &lt;enumeration value="patent"/&gt; ++ * &lt;enumeration value="thesis"/&gt; ++ * &lt;enumeration value="unpublished"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="feature" maxOccurs="unbounded" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="taxon" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="lineage" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="taxon" maxOccurs="unbounded"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="qualifier" maxOccurs="unbounded" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="assembly" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="range" maxOccurs="unbounded"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="contig" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;choice maxOccurs="unbounded" minOccurs="0"&gt; ++ * &lt;element name="range"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="gap"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/choice&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="entryVersion" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="dataClass" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="taxonomicDivision" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="moleculeType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="sequenceLength" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="topology" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="circular"/&gt; ++ * &lt;enumeration value="linear"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="firstPublic" type="{http://www.w3.org/2001/XMLSchema}date" /&gt; ++ * &lt;attribute name="firstPublicRelease" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="lastUpdated" type="{http://www.w3.org/2001/XMLSchema}date" /&gt; ++ * &lt;attribute name="lastUpdatedRelease" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -282,20 -282,20 +282,20 @@@ public class EntryType /** * Gets the value of the secondaryAccession property. * -- *

++ * <p> * 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 secondaryAccession property. ++ * This is why there is not a <CODE>set</CODE> method for the secondaryAccession property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getSecondaryAccession().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * @@@ -311,20 -311,20 +311,20 @@@ /** * Gets the value of the projectAccession property. * -- *

++ * <p> * 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 projectAccession property. ++ * This is why there is not a <CODE>set</CODE> method for the projectAccession property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getProjectAccession().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * @@@ -388,20 -388,20 +388,20 @@@ /** * Gets the value of the keyword property. * -- *

++ * <p> * 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 keyword property. ++ * This is why there is not a <CODE>set</CODE> method for the keyword property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getKeyword().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * @@@ -417,20 -417,20 +417,20 @@@ /** * Gets the value of the reference property. * -- *

++ * <p> * 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 reference property. ++ * This is why there is not a <CODE>set</CODE> method for the reference property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getReference().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EntryType.Reference } * @@@ -446,20 -446,20 +446,20 @@@ /** * Gets the value of the xref property. * -- *

++ * <p> * 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 xref property. ++ * This is why there is not a <CODE>set</CODE> method for the xref property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getXref().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link XrefType } * @@@ -475,20 -475,20 +475,20 @@@ /** * Gets the value of the feature property. * -- *

++ * <p> * 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 feature property. ++ * This is why there is not a <CODE>set</CODE> method for the feature property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getFeature().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EntryType.Feature } * @@@ -863,35 -863,35 +863,35 @@@ /** -- *

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="range" maxOccurs="unbounded">
--     *           <complexType>
--     *             <complexContent>
--     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--     *                 <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                 <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                 <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                 <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                 <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *                 <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                 <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
--     *               </restriction>
--     *             </complexContent>
--     *           </complexType>
--     *         </element>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <p>Java class for anonymous complex type. ++ * ++ * <p>The following schema fragment specifies the expected content contained within this class. ++ * ++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="range" maxOccurs="unbounded"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -907,20 -907,20 +907,20 @@@ /** * Gets the value of the range property. * -- *

++ * <p> * 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 range property. ++ * This is why there is not a <CODE>set</CODE> method for the range property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getRange().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EntryType.Assembly.Range } * @@@ -935,25 -935,25 +935,25 @@@ /** -- *

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="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--         *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
--         *     </restriction>
--         *   </complexContent>
--         * </complexType>
--         *
++ * <p>Java class for anonymous complex type. ++ * ++ * <p>The following schema fragment specifies the expected content contained within this class. ++ * ++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1154,49 -1154,49 +1154,49 @@@ /** -- *

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>
--     *         <choice maxOccurs="unbounded" minOccurs="0">
--     *           <element name="range">
--     *             <complexType>
--     *               <complexContent>
--     *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--     *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                   <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                   <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                   <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *                   <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                   <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
--     *                 </restriction>
--     *               </complexContent>
--     *             </complexType>
--     *           </element>
--     *           <element name="gap">
--     *             <complexType>
--     *               <complexContent>
--     *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--     *                   <attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                   <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *                   <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
--     *                 </restriction>
--     *               </complexContent>
--     *             </complexType>
--     *           </element>
--     *         </choice>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <p>Java class for anonymous complex type. ++ * ++ * <p>The following schema fragment specifies the expected content contained within this class. ++ * ++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;choice maxOccurs="unbounded" minOccurs="0"&gt; ++ * &lt;element name="range"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="gap"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/choice&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1215,20 -1215,20 +1215,20 @@@ /** * Gets the value of the rangeOrGap property. * -- *

++ * <p> * 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 rangeOrGap property. ++ * This is why there is not a <CODE>set</CODE> method for the rangeOrGap property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getRangeOrGap().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EntryType.Contig.Range } * {@link EntryType.Contig.Gap } @@@ -1244,22 -1244,22 +1244,22 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
--         *     </restriction>
--         *   </complexContent>
--         * </complexType>
--         *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="unknownLength" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1380,25 -1380,25 +1380,25 @@@ /** -- *

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="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--         *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *       <attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
--         *     </restriction>
--         *   </complexContent>
--         * </complexType>
--         *
++ * <p>Java class for anonymous complex type. ++ * ++ * <p>The following schema fragment specifies the expected content contained within this class. ++ * ++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="begin" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryBegin" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="primaryEnd" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="accession" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="complement" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1599,67 -1599,67 +1599,67 @@@ /** -- *

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="taxon" minOccurs="0">
--     *           <complexType>
--     *             <complexContent>
--     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--     *                 <sequence>
--     *                   <element name="lineage" minOccurs="0">
--     *                     <complexType>
--     *                       <complexContent>
--     *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--     *                           <sequence>
--     *                             <element name="taxon" maxOccurs="unbounded">
--     *                               <complexType>
--     *                                 <complexContent>
--     *                                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--     *                                     <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *                                   </restriction>
--     *                                 </complexContent>
--     *                               </complexType>
--     *                             </element>
--     *                           </sequence>
--     *                         </restriction>
--     *                       </complexContent>
--     *                     </complexType>
--     *                   </element>
--     *                 </sequence>
--     *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *                 <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *                 <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *               </restriction>
--     *             </complexContent>
--     *           </complexType>
--     *         </element>
--     *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
--     *         <element name="qualifier" maxOccurs="unbounded" minOccurs="0">
--     *           <complexType>
--     *             <complexContent>
--     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--     *                 <sequence>
--     *                   <element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *                 </sequence>
--     *                 <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *               </restriction>
--     *             </complexContent>
--     *           </complexType>
--     *         </element>
--     *       </sequence>
--     *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *       <attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <p>Java class for anonymous complex type. ++ * ++ * <p>The following schema fragment specifies the expected content contained within this class. ++ * ++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="taxon" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="lineage" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="taxon" maxOccurs="unbounded"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="qualifier" maxOccurs="unbounded" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="location" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1706,20 -1706,20 +1706,20 @@@ /** * Gets the value of the xref property. * -- *

++ * <p> * 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 xref property. ++ * This is why there is not a <CODE>set</CODE> method for the xref property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getXref().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link XrefType } * @@@ -1735,20 -1735,20 +1735,20 @@@ /** * Gets the value of the qualifier property. * -- *

++ * <p> * 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 qualifier property. ++ * This is why there is not a <CODE>set</CODE> method for the qualifier property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getQualifier().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EntryType.Feature.Qualifier } * @@@ -1811,42 -1811,42 +1811,42 @@@ /** -- *

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="lineage" minOccurs="0">
--         *           <complexType>
--         *             <complexContent>
--         *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--         *                 <sequence>
--         *                   <element name="taxon" maxOccurs="unbounded">
--         *                     <complexType>
--         *                       <complexContent>
--         *                         <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--         *                           <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--         *                         </restriction>
--         *                       </complexContent>
--         *                     </complexType>
--         *                   </element>
--         *                 </sequence>
--         *               </restriction>
--         *             </complexContent>
--         *           </complexType>
--         *         </element>
--         *       </sequence>
--         *       <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--         *       <attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" />
--         *       <attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" />
--         *     </restriction>
--         *   </complexContent>
--         * </complexType>
--         *
++ * <p>Java class for anonymous complex type. ++ * ++ * <p>The following schema fragment specifies the expected content contained within this class. ++ * ++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="lineage" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="taxon" maxOccurs="unbounded"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="commonName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="taxId" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1962,29 -1962,29 +1962,29 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="taxon" maxOccurs="unbounded">
--             *           <complexType>
--             *             <complexContent>
--             *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--             *                 <attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--             *               </restriction>
--             *             </complexContent>
--             *           </complexType>
--             *         </element>
--             *       </sequence>
--             *     </restriction>
--             *   </complexContent>
--             * </complexType>
--             *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="taxon" maxOccurs="unbounded"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -2000,20 -2000,20 +2000,20 @@@ /** * Gets the value of the taxon property. * -- *

++ * <p> * 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 taxon property. ++ * This is why there is not a <CODE>set</CODE> method for the taxon property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++                 * <pre>
                   *    getTaxon().add(newItem);
--                 *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EntryType.Feature.FeatureTaxon.Lineage.Taxon } * @@@ -2028,19 -2028,19 +2028,19 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--                 *     </restriction>
--                 *   </complexContent>
--                 * </complexType>
--                 *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="scientificName" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -2083,22 -2083,22 +2083,22 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--         *       </sequence>
--         *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--         *     </restriction>
--         *   </complexContent>
--         * </complexType>
--         *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="value" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -2166,48 -2166,48 +2166,48 @@@ /** -- *

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="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *         <element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
--     *         <element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
--     *         <element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *         <element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/>
--     *         <element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *         <element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *         <element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *         <element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *         <element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *         <element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *         <element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *         <element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
--     *         <element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/>
--     *       </sequence>
--     *       <attribute name="type" use="required">
--     *         <simpleType>
--     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
--     *             <enumeration value="submission"/>
--     *             <enumeration value="book"/>
--     *             <enumeration value="article"/>
--     *             <enumeration value="patent"/>
--     *             <enumeration value="thesis"/>
--     *             <enumeration value="unpublished"/>
--     *           </restriction>
--     *         </simpleType>
--     *       </attribute>
--     *       <attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
--     *       <attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <p>Java class for anonymous complex type. ++ * ++ * <p>The following schema fragment specifies the expected content contained within this class. ++ * ++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="author" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="applicant" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="consortium" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="submissionDate" type="{http://www.w3.org/2001/XMLSchema}date" minOccurs="0"/&gt; ++ * &lt;element name="journal" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="year" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="volume" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="issue" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="firstPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="lastPage" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="comment" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="referenceLocation" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="xref" type="{}XrefType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="submission"/&gt; ++ * &lt;enumeration value="book"/&gt; ++ * &lt;enumeration value="article"/&gt; ++ * &lt;enumeration value="patent"/&gt; ++ * &lt;enumeration value="thesis"/&gt; ++ * &lt;enumeration value="unpublished"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="number" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;attribute name="location" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -2279,20 -2279,20 +2279,20 @@@ /** * Gets the value of the author property. * -- *

++ * <p> * 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 author property. ++ * This is why there is not a <CODE>set</CODE> method for the author property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getAuthor().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * @@@ -2308,20 -2308,20 +2308,20 @@@ /** * Gets the value of the applicant property. * -- *

++ * <p> * 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 applicant property. ++ * This is why there is not a <CODE>set</CODE> method for the applicant property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getApplicant().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * @@@ -2577,20 -2577,20 +2577,20 @@@ /** * Gets the value of the xref property. * -- *

++ * <p> * 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 xref property. ++ * This is why there is not a <CODE>set</CODE> method for the xref property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getXref().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link XrefType } * diff --cc src/jalview/xml/binding/embl/ObjectFactory.java index d5629ca,d5629ca..c27ff10 --- a/src/jalview/xml/binding/embl/ObjectFactory.java +++ b/src/jalview/xml/binding/embl/ObjectFactory.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2018.09.14 at 02:46:00 PM BST ++// Generated on: 2022.02.07 at 04:45:21 PM GMT // @@@ -15,7 -15,7 +15,7 @@@ import javax.xml.bind.annotation.XmlReg * This object contains factory methods for each * Java content interface and Java element interface * generated in the jalview.xml.binding.embl package. -- *

An ObjectFactory allows you to programatically ++ * <p>An ObjectFactory allows you to programatically * construct new instances of the Java representation * for XML content. The Java representation of XML * content can consist of schema derived interfaces diff --cc src/jalview/xml/binding/embl/ROOT.java index f7f522d,f7f522d..5b30156 --- a/src/jalview/xml/binding/embl/ROOT.java +++ b/src/jalview/xml/binding/embl/ROOT.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2018.09.14 at 02:46:00 PM BST ++// Generated on: 2022.02.07 at 04:45:21 PM GMT // @@@ -15,22 -15,22 +15,22 @@@ import javax.xml.bind.annotation.XmlTyp /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType>
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <choice>
-- *         <element name="entrySet" type="{}EntrySetType"/>
-- *         <element name="entry" type="{}EntryType"/>
-- *       </choice>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;choice&gt; ++ * &lt;element name="entrySet" type="{}EntrySetType"/&gt; ++ * &lt;element name="entry" type="{}EntryType"/&gt; ++ * &lt;/choice&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/embl/XrefType.java index 9608b79,9608b79..2aea6ca --- a/src/jalview/xml/binding/embl/XrefType.java +++ b/src/jalview/xml/binding/embl/XrefType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2018.09.14 at 02:46:00 PM BST ++// Generated on: 2022.02.07 at 04:45:21 PM GMT // @@@ -17,21 -17,21 +17,21 @@@ import javax.xml.bind.annotation.XmlTyp /** * Database cross-reference. * -- *

Java class for XrefType complex type. ++ * <p>Java class for XrefType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="XrefType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <attribute name="db" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="secondaryId" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="XrefType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="db" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="secondaryId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/jalview/AlcodonFrame.java index e52eefb,cb90984..7fe5a4d --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/Annotation.java index 6c1573f,35f78f3..1751f50 --- a/src/jalview/xml/binding/jalview/Annotation.java +++ b/src/jalview/xml/binding/jalview/Annotation.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/AnnotationColourScheme.java index 1b31b22,6f5ef65..6f8efad --- a/src/jalview/xml/binding/jalview/AnnotationColourScheme.java +++ b/src/jalview/xml/binding/jalview/AnnotationColourScheme.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/AnnotationElement.java index d141272,6780323..f549cb6 --- a/src/jalview/xml/binding/jalview/AnnotationElement.java +++ b/src/jalview/xml/binding/jalview/AnnotationElement.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/DoubleMatrix.java index bff4959,5edb2e8..068c41f --- a/src/jalview/xml/binding/jalview/DoubleMatrix.java +++ b/src/jalview/xml/binding/jalview/DoubleMatrix.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/DoubleVector.java index a255c74,68ebf9b..42b4487 --- a/src/jalview/xml/binding/jalview/DoubleVector.java +++ b/src/jalview/xml/binding/jalview/DoubleVector.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/Feature.java index 73468c9,39fc0c3..2b0ec84 --- a/src/jalview/xml/binding/jalview/Feature.java +++ b/src/jalview/xml/binding/jalview/Feature.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/FeatureMatcher.java index dee9bc1d,c92f72c..e6c5430 --- a/src/jalview/xml/binding/jalview/FeatureMatcher.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcher.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/FeatureMatcherSet.java index 4c0848f,0c21215..311bee8 --- a/src/jalview/xml/binding/jalview/FeatureMatcherSet.java +++ b/src/jalview/xml/binding/jalview/FeatureMatcherSet.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/FilterBy.java index bbb84a4,36b454f..a96be30 --- a/src/jalview/xml/binding/jalview/FilterBy.java +++ b/src/jalview/xml/binding/jalview/FilterBy.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/JalviewModel.java index 90819d7,59bdb05..61c767d --- a/src/jalview/xml/binding/jalview/JalviewModel.java +++ b/src/jalview/xml/binding/jalview/JalviewModel.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2020.12.10 at 03:00:06 PM GMT ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // @@@ -24,341 -24,355 +24,355 @@@ import javax.xml.datatype.XMLGregorianC /** - *

Java class for JalviewModel complex type. + * <p>Java class for JalviewModel complex type. * - *

The following schema fragment specifies the expected content contained within this class. + * <p>The following schema fragment specifies the expected content contained within this class. * - * 

 - * <complexType name="JalviewModel">
 - *   <complexContent>
 - *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *       <sequence>
 - *         <element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/>
 - *         <element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/>
 - *         <element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/>
 - *         <sequence>
 - *           <element name="JSeq" maxOccurs="unbounded" minOccurs="0">
 - *             <complexType>
 - *               <complexContent>
 - *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                   <sequence>
 - *                     <element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/>
 - *                     <element name="pdbids" maxOccurs="unbounded" minOccurs="0">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <extension base="{www.jalview.org}pdbentry">
 - *                             <sequence>
 - *                               <element name="structureState" maxOccurs="unbounded" minOccurs="0">
 - *                                 <complexType>
 - *                                   <simpleContent>
 - *                                     <extension base="<http://www.w3.org/2001/XMLSchema>string">
 - *                                       <attGroup ref="{www.jalview.org}swingwindow"/>
 - *                                       <attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                                       <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                                       <attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 - *                                       <attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                                       <attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 - *                                       <attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                                     </extension>
 - *                                   </simpleContent>
 - *                                 </complexType>
 - *                               </element>
 - *                             </sequence>
 - *                           </extension>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                     <element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/>
 - *                     <element name="rnaViewer" maxOccurs="unbounded" minOccurs="0">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                             <sequence>
 - *                               <element name="secondaryStructure" maxOccurs="unbounded">
 - *                                 <complexType>
 - *                                   <complexContent>
 - *                                     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                                       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                                       <attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                                       <attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                                       <attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                                     </restriction>
 - *                                   </complexContent>
 - *                                 </complexType>
 - *                               </element>
 - *                             </sequence>
 - *                             <attGroup ref="{www.jalview.org}swingwindow"/>
 - *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                             <attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                             <attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                             <attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                           </restriction>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                   </sequence>
 - *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                 </restriction>
 - *               </complexContent>
 - *             </complexType>
 - *           </element>
 - *           <element name="JGroup" maxOccurs="unbounded" minOccurs="0">
 - *             <complexType>
 - *               <complexContent>
 - *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                   <sequence>
 - *                     <element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
 - *                     <element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 - *                   </sequence>
 - *                   <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 - *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 - *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                 </restriction>
 - *               </complexContent>
 - *             </complexType>
 - *           </element>
 - *           <element name="Viewport" maxOccurs="unbounded" minOccurs="0">
 - *             <complexType>
 - *               <complexContent>
 - *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                   <sequence>
 - *                     <element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/>
 - *                     <element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                             <attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                             <attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                           </restriction>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                     <element name="calcIdParam" maxOccurs="unbounded" minOccurs="0">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet">
 - *                             <attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                             <attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                             <attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                           </extension>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                     <element name="overview" minOccurs="0">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                             <attGroup ref="{www.jalview.org}swingwindow"/>
 - *                             <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                             <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                             <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                             <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                             <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                           </restriction>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                   </sequence>
 - *                   <attGroup ref="{www.jalview.org}swingwindow"/>
 - *                   <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                   <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 - *                   <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 - *                   <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                   <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                   <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                   <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 - *                   <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                   <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                   <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 - *                   <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 - *                   <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 - *                   <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                   <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                 </restriction>
 - *               </complexContent>
 - *             </complexType>
 - *           </element>
 - *           <element name="UserColours" maxOccurs="unbounded" minOccurs="0">
 - *             <complexType>
 - *               <complexContent>
 - *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                   <sequence>
 - *                     <element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/>
 - *                   </sequence>
 - *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                 </restriction>
 - *               </complexContent>
 - *             </complexType>
 - *           </element>
 - *           <element name="tree" maxOccurs="unbounded" minOccurs="0">
 - *             <complexType>
 - *               <complexContent>
 - *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                   <sequence minOccurs="0">
 - *                     <element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/>
 - *                     <element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/>
 - *                   </sequence>
 - *                   <attGroup ref="{www.jalview.org}swingwindow"/>
 - *                   <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 - *                   <attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 - *                   <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 - *                 </restriction>
 - *               </complexContent>
 - *             </complexType>
 - *           </element>
 - *           <element name="PcaViewer" maxOccurs="unbounded" minOccurs="0">
 - *             <complexType>
 - *               <complexContent>
 - *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                   <sequence>
 - *                     <element name="sequencePoint" maxOccurs="unbounded">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                             <attGroup ref="{www.jalview.org}position"/>
 - *                             <attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                           </restriction>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                     <element name="axis" maxOccurs="3" minOccurs="3">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                             <attGroup ref="{www.jalview.org}position"/>
 - *                           </restriction>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                     <element name="seqPointMin">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                             <attGroup ref="{www.jalview.org}position"/>
 - *                           </restriction>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                     <element name="seqPointMax">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                             <attGroup ref="{www.jalview.org}position"/>
 - *                           </restriction>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                     <element name="pcaData" type="{www.jalview.org}PcaDataType"/>
 - *                   </sequence>
 - *                   <attGroup ref="{www.jalview.org}SimilarityParams"/>
 - *                   <attGroup ref="{www.jalview.org}swingwindow"/>
 - *                   <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                   <attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                   <attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" />
 - *                   <attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                   <attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                 </restriction>
 - *               </complexContent>
 - *             </complexType>
 - *           </element>
 - *           <element name="FeatureSettings" minOccurs="0">
 - *             <complexType>
 - *               <complexContent>
 - *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                   <sequence>
 - *                     <element name="setting" maxOccurs="unbounded" minOccurs="0">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                             <sequence>
 - *                               <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
 - *                               <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/>
 - *                             </sequence>
 - *                             <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                             <attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                             <attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" />
 - *                             <attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                             <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
 - *                             <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
 - *                             <attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" />
 - *                             <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
 - *                             <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
 - *                             <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                             <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                           </restriction>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                     <element name="group" maxOccurs="unbounded" minOccurs="0">
 - *                       <complexType>
 - *                         <complexContent>
 - *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 - *                             <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
 - *                             <attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 - *                           </restriction>
 - *                         </complexContent>
 - *                       </complexType>
 - *                     </element>
 - *                   </sequence>
 - *                 </restriction>
 - *               </complexContent>
 - *             </complexType>
 - *           </element>
 - *         </sequence>
 - *       </sequence>
 - *     </restriction>
 - *   </complexContent>
 - * </complexType>
 - *
+ * <pre> + * &lt;complexType name="JalviewModel"&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence&gt; + * &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt; + * &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; + * &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt; + * &lt;sequence&gt; + * &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence&gt; + * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt; + * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;extension base="{www.jalview.org}pdbentry"&gt; + * &lt;sequence&gt; + * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;simpleContent&gt; + * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; + * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; + * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;/extension&gt; + * &lt;/simpleContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;/sequence&gt; + * &lt;/extension&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt; + * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence&gt; + * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;/sequence&gt; + * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; + * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;/sequence&gt; + * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence&gt; + * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt; + * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt; + * &lt;/sequence&gt; + * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence&gt; + * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt; + * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt; + * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;/extension&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; ++ * &lt;element name="overview" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; ++ * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; ++ * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; + * &lt;/sequence&gt; + * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; + * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; + * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence&gt; + * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt; + * &lt;/sequence&gt; + * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence minOccurs="0"&gt; + * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; + * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; + * &lt;/sequence&gt; + * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; + * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; + * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; + * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence&gt; + * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;attGroup ref="{www.jalview.org}position"/&gt; + * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;attGroup ref="{www.jalview.org}position"/&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="seqPointMin"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;attGroup ref="{www.jalview.org}position"/&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="seqPointMax"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;attGroup ref="{www.jalview.org}position"/&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt; + * &lt;/sequence&gt; + * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; + * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt; + * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; + * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="FeatureSettings" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence&gt; + * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence&gt; + * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt; + * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt; + * &lt;/sequence&gt; + * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; + * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt; + * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; + * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; + * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; + * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;/sequence&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;/sequence&gt; + * &lt;/sequence&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * </pre> * * */ @@@ -4736,86 -4750,100 +4750,100 @@@ public class JalviewModel /** - *

Java class for anonymous complex type. + * <p>Java class for anonymous complex type. * - *

The following schema fragment specifies the expected content contained within this class. + * <p>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>
 -     *         <element name="overview" minOccurs="0">
 -     *           <complexType>
 -     *             <complexContent>
 -     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 -     *                 <attGroup ref="{www.jalview.org}swingwindow"/>
 -     *                 <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *                 <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *                 <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *                 <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *                 <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 -     *               </restriction>
 -     *             </complexContent>
 -     *           </complexType>
 -     *         </element>
 -     *       </sequence>
 -     *       <attGroup ref="{www.jalview.org}swingwindow"/>
 -     *       <attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" />
 -     *       <attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *       <attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 -     *       <attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 -     *       <attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 -     *       <attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 -     *       <attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 -     *       <attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 -     *       <attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 -     *       <attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 -     *       <attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 -     *       <attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 -     *       <attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 -     *       <attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *       <attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *       <attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" />
 -     *       <attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *       <attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *       <attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
 -     *       <attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" />
 -     *       <attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" />
 -     *       <attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -     *       <attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *       <attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *       <attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" />
 -     *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" />
 -     *       <attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" />
 -     *       <attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 -     *       <attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
 -     *     </restriction>
 -     *   </complexContent>
 -     * </complexType>
 -     *
+ * <pre> + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;sequence&gt; + * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt; + * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; + * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt; + * &lt;complexType&gt; + * &lt;complexContent&gt; + * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt; + * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;/extension&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; ++ * &lt;element name="overview" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; ++ * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; ++ * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; + * &lt;/sequence&gt; + * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; + * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt; + * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; + * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; + * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt; + * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * </pre> * * */ @@@ -6374,6 -6429,270 +6429,270 @@@ } + + /** - *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. + * - *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. + * - * 

 -         * <complexType>
 -         *   <complexContent>
 -         *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
 -         *       <attGroup ref="{www.jalview.org}swingwindow"/>
 -         *       <attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" />
 -         *       <attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 -         *       <attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 -         *       <attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" />
 -         *       <attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" />
 -         *     </restriction>
 -         *   </complexContent>
 -         * </complexType>
 -         *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt; ++ * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; ++ * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> + * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Overview { + + @XmlAttribute(name = "showHidden") + protected Boolean showHidden; + @XmlAttribute(name = "residueColour") + protected Integer residueColour; + @XmlAttribute(name = "gapColour") + protected Integer gapColour; + @XmlAttribute(name = "hiddenColour") + protected Integer hiddenColour; + @XmlAttribute(name = "title") + protected String title; + @XmlAttribute(name = "width") + protected Integer width; + @XmlAttribute(name = "height") + protected Integer height; + @XmlAttribute(name = "xpos") + protected Integer xpos; + @XmlAttribute(name = "ypos") + protected Integer ypos; + + /** + * Gets the value of the showHidden property. + * + * @return + * possible object is + * {@link Boolean } + * + */ + public Boolean isShowHidden() { + return showHidden; + } + + /** + * Sets the value of the showHidden property. + * + * @param value + * allowed object is + * {@link Boolean } + * + */ + public void setShowHidden(Boolean value) { + this.showHidden = value; + } + + /** + * Gets the value of the residueColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getResidueColour() { + return residueColour; + } + + /** + * Sets the value of the residueColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setResidueColour(Integer value) { + this.residueColour = value; + } + + /** + * Gets the value of the gapColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getGapColour() { + return gapColour; + } + + /** + * Sets the value of the gapColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setGapColour(Integer value) { + this.gapColour = value; + } + + /** + * Gets the value of the hiddenColour property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHiddenColour() { + return hiddenColour; + } + + /** + * Sets the value of the hiddenColour property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHiddenColour(Integer value) { + this.hiddenColour = value; + } + + /** + * Gets the value of the title property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getTitle() { + return title; + } + + /** + * Sets the value of the title property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setTitle(String value) { + this.title = value; + } + + /** + * Gets the value of the width property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getWidth() { + return width; + } + + /** + * Sets the value of the width property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setWidth(Integer value) { + this.width = value; + } + + /** + * Gets the value of the height property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getHeight() { + return height; + } + + /** + * Sets the value of the height property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setHeight(Integer value) { + this.height = value; + } + + /** + * Gets the value of the xpos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getXpos() { + return xpos; + } + + /** + * Sets the value of the xpos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setXpos(Integer value) { + this.xpos = value; + } + + /** + * Gets the value of the ypos property. + * + * @return + * possible object is + * {@link Integer } + * + */ + public Integer getYpos() { + return ypos; + } + + /** + * Sets the value of the ypos property. + * + * @param value + * allowed object is + * {@link Integer } + * + */ + public void setYpos(Integer value) { + this.ypos = value; + } + + } + } } diff --cc src/jalview/xml/binding/jalview/JalviewUserColours.java index e1ee27e,c43e04c..18117b6 --- a/src/jalview/xml/binding/jalview/JalviewUserColours.java +++ b/src/jalview/xml/binding/jalview/JalviewUserColours.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/MapListType.java index c93112c,1a31d82..9c23823 --- a/src/jalview/xml/binding/jalview/MapListType.java +++ b/src/jalview/xml/binding/jalview/MapListType.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/Mapping.java index 24f5b01,5ebeb7e..38b210f --- a/src/jalview/xml/binding/jalview/Mapping.java +++ b/src/jalview/xml/binding/jalview/Mapping.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/NoValueColour.java index 7e42db8,9db4ea3..eb1bd46 --- a/src/jalview/xml/binding/jalview/NoValueColour.java +++ b/src/jalview/xml/binding/jalview/NoValueColour.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/ObjectFactory.java index b6ea489,59fee21..9b9fe2f --- a/src/jalview/xml/binding/jalview/ObjectFactory.java +++ b/src/jalview/xml/binding/jalview/ObjectFactory.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2020.12.10 at 10:15:41 AM GMT ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/PcaDataType.java index 717ce89,6234f32..355d644 --- a/src/jalview/xml/binding/jalview/PcaDataType.java +++ b/src/jalview/xml/binding/jalview/PcaDataType.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/Pdbentry.java index 6983c04,d5132ab..fb26d27 --- a/src/jalview/xml/binding/jalview/Pdbentry.java +++ b/src/jalview/xml/binding/jalview/Pdbentry.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/Sequence.java index 5381c32,b842947..d199307 --- a/src/jalview/xml/binding/jalview/Sequence.java +++ b/src/jalview/xml/binding/jalview/Sequence.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/SequenceSet.java index c69334e,6aee6ac..0c435d0 --- a/src/jalview/xml/binding/jalview/SequenceSet.java +++ b/src/jalview/xml/binding/jalview/SequenceSet.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/SequenceType.java index 29982ae,aef7543..e06cca5 --- a/src/jalview/xml/binding/jalview/SequenceType.java +++ b/src/jalview/xml/binding/jalview/SequenceType.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/ThresholdType.java index edb9152,1b3d6d4..6b5247b --- a/src/jalview/xml/binding/jalview/ThresholdType.java +++ b/src/jalview/xml/binding/jalview/ThresholdType.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/VAMSAS.java index 48b2012,5d341c3..8997095 --- a/src/jalview/xml/binding/jalview/VAMSAS.java +++ b/src/jalview/xml/binding/jalview/VAMSAS.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/WebServiceParameterSet.java index 87e275d,659eab9..c46f6ff --- a/src/jalview/xml/binding/jalview/WebServiceParameterSet.java +++ b/src/jalview/xml/binding/jalview/WebServiceParameterSet.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2019.06.07 at 02:21:15 PM BST ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // diff --cc src/jalview/xml/binding/jalview/package-info.java index 2700ffa,711e7a7..81d19f5 --- a/src/jalview/xml/binding/jalview/package-info.java +++ b/src/jalview/xml/binding/jalview/package-info.java @@@ -1,8 -1,8 +1,8 @@@ // -// 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 +// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 +// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. - // Generated on: 2021.08.30 at 11:05:22 AM BST -// Generated on: 2020.12.10 at 03:00:06 PM GMT ++// Generated on: 2022.02.07 at 04:44:47 PM GMT // @javax.xml.bind.annotation.XmlSchema(namespace = "www.vamsas.ac.uk/jalview/version2", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED) diff --cc src/jalview/xml/binding/uniprot/CitationType.java index 07adace,07adace..cf27232 --- a/src/jalview/xml/binding/uniprot/CitationType.java +++ b/src/jalview/xml/binding/uniprot/CitationType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -20,54 -20,54 +20,54 @@@ import javax.xml.bind.annotation.XmlTyp * Describes different types of citations. * Equivalent to the flat file RX-, RG-, RA-, RT- and RL-lines. * -- *

Java class for citationType complex type. ++ * <p>Java class for citationType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="citationType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *         <element name="editorList" type="{http://uniprot.org/uniprot}nameListType" minOccurs="0"/>
-- *         <element name="authorList" type="{http://uniprot.org/uniprot}nameListType" minOccurs="0"/>
-- *         <element name="locator" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded" minOccurs="0"/>
-- *       </sequence>
-- *       <attribute name="type" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="book"/>
-- *             <enumeration value="journal article"/>
-- *             <enumeration value="online journal article"/>
-- *             <enumeration value="patent"/>
-- *             <enumeration value="submission"/>
-- *             <enumeration value="thesis"/>
-- *             <enumeration value="unpublished observations"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *       <attribute name="date">
-- *         <simpleType>
-- *           <union memberTypes=" {http://www.w3.org/2001/XMLSchema}date {http://www.w3.org/2001/XMLSchema}gYearMonth {http://www.w3.org/2001/XMLSchema}gYear">
-- *           </union>
-- *         </simpleType>
-- *       </attribute>
-- *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="volume" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="first" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="last" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="publisher" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="city" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="db" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="number" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="institute" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="country" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="citationType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="editorList" type="{http://uniprot.org/uniprot}nameListType" minOccurs="0"/&gt; ++ * &lt;element name="authorList" type="{http://uniprot.org/uniprot}nameListType" minOccurs="0"/&gt; ++ * &lt;element name="locator" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="book"/&gt; ++ * &lt;enumeration value="journal article"/&gt; ++ * &lt;enumeration value="online journal article"/&gt; ++ * &lt;enumeration value="patent"/&gt; ++ * &lt;enumeration value="submission"/&gt; ++ * &lt;enumeration value="thesis"/&gt; ++ * &lt;enumeration value="unpublished observations"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="date"&gt; ++ * &lt;simpleType&gt; ++ * &lt;union memberTypes=" {http://www.w3.org/2001/XMLSchema}date {http://www.w3.org/2001/XMLSchema}gYearMonth {http://www.w3.org/2001/XMLSchema}gYear"&gt; ++ * &lt;/union&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="volume" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="first" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="last" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="publisher" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="city" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="db" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="number" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="institute" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="country" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -210,20 -210,20 +210,20 @@@ public class CitationType /** * Gets the value of the dbReference property. * -- *

++ * <p> * 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 dbReference property. ++ * This is why there is not a <CODE>set</CODE> method for the dbReference property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getDbReference().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link DbReferenceType } * diff --cc src/jalview/xml/binding/uniprot/CofactorType.java index a0d1dfa,a0d1dfa..fdc1f3c --- a/src/jalview/xml/binding/uniprot/CofactorType.java +++ b/src/jalview/xml/binding/uniprot/CofactorType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -20,23 -20,23 +20,23 @@@ import javax.xml.bind.annotation.XmlTyp /** * Describes a cofactor. * -- *

Java class for cofactorType complex type. ++ * <p>Java class for cofactorType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="cofactorType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
-- *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-- *       </sequence>
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="cofactorType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; ++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -105,20 -105,20 +105,20 @@@ public class CofactorType /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/CommentType.java index 9cc5164,9cc5164..2227f18 --- a/src/jalview/xml/binding/uniprot/CommentType.java +++ b/src/jalview/xml/binding/uniprot/CommentType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -22,153 -22,153 +22,153 @@@ import javax.xml.bind.annotation.XmlTyp * Describes different types of general annotations. * Equivalent to the flat file CC-line. * -- *

Java class for commentType complex type. ++ * <p>Java class for commentType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="commentType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="molecule" type="{http://uniprot.org/uniprot}moleculeType" minOccurs="0"/>
-- *         <choice minOccurs="0">
-- *           <group ref="{http://uniprot.org/uniprot}bpcCommentGroup"/>
-- *           <sequence>
-- *             <element name="reaction" type="{http://uniprot.org/uniprot}reactionType"/>
-- *             <element name="physiologicalReaction" type="{http://uniprot.org/uniprot}physiologicalReactionType" maxOccurs="2" minOccurs="0"/>
-- *           </sequence>
-- *           <sequence>
-- *             <element name="cofactor" type="{http://uniprot.org/uniprot}cofactorType" maxOccurs="unbounded"/>
-- *           </sequence>
-- *           <sequence>
-- *             <element name="subcellularLocation" type="{http://uniprot.org/uniprot}subcellularLocationType" maxOccurs="unbounded"/>
-- *           </sequence>
-- *           <element name="conflict">
-- *             <complexType>
-- *               <complexContent>
-- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                   <sequence>
-- *                     <element name="sequence" minOccurs="0">
-- *                       <complexType>
-- *                         <complexContent>
-- *                           <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                             <attribute name="resource" use="required">
-- *                               <simpleType>
-- *                                 <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *                                   <enumeration value="EMBL-CDS"/>
-- *                                   <enumeration value="EMBL"/>
-- *                                 </restriction>
-- *                               </simpleType>
-- *                             </attribute>
-- *                             <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *                             <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
-- *                           </restriction>
-- *                         </complexContent>
-- *                       </complexType>
-- *                     </element>
-- *                   </sequence>
-- *                   <attribute name="type" use="required">
-- *                     <simpleType>
-- *                       <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *                         <enumeration value="frameshift"/>
-- *                         <enumeration value="erroneous initiation"/>
-- *                         <enumeration value="erroneous termination"/>
-- *                         <enumeration value="erroneous gene model prediction"/>
-- *                         <enumeration value="erroneous translation"/>
-- *                         <enumeration value="miscellaneous discrepancy"/>
-- *                       </restriction>
-- *                     </simpleType>
-- *                   </attribute>
-- *                   <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *                 </restriction>
-- *               </complexContent>
-- *             </complexType>
-- *           </element>
-- *           <sequence>
-- *             <element name="link" maxOccurs="unbounded" minOccurs="0">
-- *               <complexType>
-- *                 <complexContent>
-- *                   <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                     <attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
-- *                   </restriction>
-- *                 </complexContent>
-- *               </complexType>
-- *             </element>
-- *           </sequence>
-- *           <sequence>
-- *             <element name="event" type="{http://uniprot.org/uniprot}eventType" maxOccurs="4"/>
-- *             <element name="isoform" type="{http://uniprot.org/uniprot}isoformType" maxOccurs="unbounded" minOccurs="0"/>
-- *           </sequence>
-- *           <sequence>
-- *             <element name="interactant" type="{http://uniprot.org/uniprot}interactantType" maxOccurs="2" minOccurs="2"/>
-- *             <element name="organismsDiffer" type="{http://www.w3.org/2001/XMLSchema}boolean"/>
-- *             <element name="experiments" type="{http://www.w3.org/2001/XMLSchema}int"/>
-- *           </sequence>
-- *           <element name="disease">
-- *             <complexType>
-- *               <complexContent>
-- *                 <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                   <sequence>
-- *                     <element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
-- *                     <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
-- *                     <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
-- *                     <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-- *                   </sequence>
-- *                   <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *                 </restriction>
-- *               </complexContent>
-- *             </complexType>
-- *           </element>
-- *         </choice>
-- *         <element name="location" type="{http://uniprot.org/uniprot}locationType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-- *       </sequence>
-- *       <attribute name="type" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="allergen"/>
-- *             <enumeration value="alternative products"/>
-- *             <enumeration value="biotechnology"/>
-- *             <enumeration value="biophysicochemical properties"/>
-- *             <enumeration value="catalytic activity"/>
-- *             <enumeration value="caution"/>
-- *             <enumeration value="cofactor"/>
-- *             <enumeration value="developmental stage"/>
-- *             <enumeration value="disease"/>
-- *             <enumeration value="domain"/>
-- *             <enumeration value="disruption phenotype"/>
-- *             <enumeration value="activity regulation"/>
-- *             <enumeration value="function"/>
-- *             <enumeration value="induction"/>
-- *             <enumeration value="miscellaneous"/>
-- *             <enumeration value="pathway"/>
-- *             <enumeration value="pharmaceutical"/>
-- *             <enumeration value="polymorphism"/>
-- *             <enumeration value="PTM"/>
-- *             <enumeration value="RNA editing"/>
-- *             <enumeration value="similarity"/>
-- *             <enumeration value="subcellular location"/>
-- *             <enumeration value="sequence caution"/>
-- *             <enumeration value="subunit"/>
-- *             <enumeration value="tissue specificity"/>
-- *             <enumeration value="toxic dose"/>
-- *             <enumeration value="online information"/>
-- *             <enumeration value="mass spectrometry"/>
-- *             <enumeration value="interaction"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *       <attribute name="locationType" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="mass" type="{http://www.w3.org/2001/XMLSchema}float" />
-- *       <attribute name="error" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="method" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="commentType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="molecule" type="{http://uniprot.org/uniprot}moleculeType" minOccurs="0"/&gt; ++ * &lt;choice minOccurs="0"&gt; ++ * &lt;group ref="{http://uniprot.org/uniprot}bpcCommentGroup"/&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="reaction" type="{http://uniprot.org/uniprot}reactionType"/&gt; ++ * &lt;element name="physiologicalReaction" type="{http://uniprot.org/uniprot}physiologicalReactionType" maxOccurs="2" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="cofactor" type="{http://uniprot.org/uniprot}cofactorType" maxOccurs="unbounded"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="subcellularLocation" type="{http://uniprot.org/uniprot}subcellularLocationType" maxOccurs="unbounded"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;element name="conflict"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="sequence" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="resource" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="EMBL-CDS"/&gt; ++ * &lt;enumeration value="EMBL"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="frameshift"/&gt; ++ * &lt;enumeration value="erroneous initiation"/&gt; ++ * &lt;enumeration value="erroneous termination"/&gt; ++ * &lt;enumeration value="erroneous gene model prediction"/&gt; ++ * &lt;enumeration value="erroneous translation"/&gt; ++ * &lt;enumeration value="miscellaneous discrepancy"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="link" maxOccurs="unbounded" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="event" type="{http://uniprot.org/uniprot}eventType" maxOccurs="4"/&gt; ++ * &lt;element name="isoform" type="{http://uniprot.org/uniprot}isoformType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="interactant" type="{http://uniprot.org/uniprot}interactantType" maxOccurs="2" minOccurs="2"/&gt; ++ * &lt;element name="organismsDiffer" type="{http://www.w3.org/2001/XMLSchema}boolean"/&gt; ++ * &lt;element name="experiments" type="{http://www.w3.org/2001/XMLSchema}int"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;element name="disease"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; ++ * &lt;element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; ++ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; ++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/choice&gt; ++ * &lt;element name="location" type="{http://uniprot.org/uniprot}locationType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="allergen"/&gt; ++ * &lt;enumeration value="alternative products"/&gt; ++ * &lt;enumeration value="biotechnology"/&gt; ++ * &lt;enumeration value="biophysicochemical properties"/&gt; ++ * &lt;enumeration value="catalytic activity"/&gt; ++ * &lt;enumeration value="caution"/&gt; ++ * &lt;enumeration value="cofactor"/&gt; ++ * &lt;enumeration value="developmental stage"/&gt; ++ * &lt;enumeration value="disease"/&gt; ++ * &lt;enumeration value="domain"/&gt; ++ * &lt;enumeration value="disruption phenotype"/&gt; ++ * &lt;enumeration value="activity regulation"/&gt; ++ * &lt;enumeration value="function"/&gt; ++ * &lt;enumeration value="induction"/&gt; ++ * &lt;enumeration value="miscellaneous"/&gt; ++ * &lt;enumeration value="pathway"/&gt; ++ * &lt;enumeration value="pharmaceutical"/&gt; ++ * &lt;enumeration value="polymorphism"/&gt; ++ * &lt;enumeration value="PTM"/&gt; ++ * &lt;enumeration value="RNA editing"/&gt; ++ * &lt;enumeration value="similarity"/&gt; ++ * &lt;enumeration value="subcellular location"/&gt; ++ * &lt;enumeration value="sequence caution"/&gt; ++ * &lt;enumeration value="subunit"/&gt; ++ * &lt;enumeration value="tissue specificity"/&gt; ++ * &lt;enumeration value="toxic dose"/&gt; ++ * &lt;enumeration value="online information"/&gt; ++ * &lt;enumeration value="mass spectrometry"/&gt; ++ * &lt;enumeration value="interaction"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="locationType" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="mass" type="{http://www.w3.org/2001/XMLSchema}float" /&gt; ++ * &lt;attribute name="error" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="method" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -404,20 -404,20 +404,20 @@@ public class CommentType /** * Gets the value of the physiologicalReaction property. * -- *

++ * <p> * 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 physiologicalReaction property. ++ * This is why there is not a <CODE>set</CODE> method for the physiologicalReaction property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getPhysiologicalReaction().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link PhysiologicalReactionType } * @@@ -433,20 -433,20 +433,20 @@@ /** * Gets the value of the cofactor property. * -- *

++ * <p> * 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 cofactor property. ++ * This is why there is not a <CODE>set</CODE> method for the cofactor property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getCofactor().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link CofactorType } * @@@ -462,20 -462,20 +462,20 @@@ /** * Gets the value of the subcellularLocation property. * -- *

++ * <p> * 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 subcellularLocation property. ++ * This is why there is not a <CODE>set</CODE> method for the subcellularLocation property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getSubcellularLocation().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link SubcellularLocationType } * @@@ -515,20 -515,20 +515,20 @@@ /** * Gets the value of the link property. * -- *

++ * <p> * 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 link property. ++ * This is why there is not a <CODE>set</CODE> method for the link property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getLink().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link CommentType.Link } * @@@ -544,20 -544,20 +544,20 @@@ /** * Gets the value of the event property. * -- *

++ * <p> * 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 event property. ++ * This is why there is not a <CODE>set</CODE> method for the event property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvent().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EventType } * @@@ -573,20 -573,20 +573,20 @@@ /** * Gets the value of the isoform property. * -- *

++ * <p> * 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 isoform property. ++ * This is why there is not a <CODE>set</CODE> method for the isoform property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getIsoform().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link IsoformType } * @@@ -602,20 -602,20 +602,20 @@@ /** * Gets the value of the interactant property. * -- *

++ * <p> * 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 interactant property. ++ * This is why there is not a <CODE>set</CODE> method for the interactant property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getInteractant().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link InteractantType } * @@@ -703,20 -703,20 +703,20 @@@ /** * Gets the value of the location property. * -- *

++ * <p> * 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 location property. ++ * This is why there is not a <CODE>set</CODE> method for the location property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getLocation().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link LocationType } * @@@ -732,20 -732,20 +732,20 @@@ /** * Gets the value of the text property. * -- *

++ * <p> * 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 text property. ++ * This is why there is not a <CODE>set</CODE> method for the text property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getText().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -905,20 -905,20 +905,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * @@@ -933,22 -933,22 +933,22 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
--     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="max" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/&gt; ++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -989,20 -989,20 +989,20 @@@ /** * Gets the value of the text property. * -- *

++ * <p> * 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 text property. ++ * This is why there is not a <CODE>set</CODE> method for the text property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getText().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -1019,51 -1019,51 +1019,51 @@@ /** -- *

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="sequence" minOccurs="0">
--     *           <complexType>
--     *             <complexContent>
--     *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--     *                 <attribute name="resource" use="required">
--     *                   <simpleType>
--     *                     <restriction base="{http://www.w3.org/2001/XMLSchema}string">
--     *                       <enumeration value="EMBL-CDS"/>
--     *                       <enumeration value="EMBL"/>
--     *                     </restriction>
--     *                   </simpleType>
--     *                 </attribute>
--     *                 <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *                 <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
--     *               </restriction>
--     *             </complexContent>
--     *           </complexType>
--     *         </element>
--     *       </sequence>
--     *       <attribute name="type" use="required">
--     *         <simpleType>
--     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
--     *             <enumeration value="frameshift"/>
--     *             <enumeration value="erroneous initiation"/>
--     *             <enumeration value="erroneous termination"/>
--     *             <enumeration value="erroneous gene model prediction"/>
--     *             <enumeration value="erroneous translation"/>
--     *             <enumeration value="miscellaneous discrepancy"/>
--     *           </restriction>
--     *         </simpleType>
--     *       </attribute>
--     *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <p>Java class for anonymous complex type. ++ * ++ * <p>The following schema fragment specifies the expected content contained within this class. ++ * ++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="sequence" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="resource" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="EMBL-CDS"/&gt; ++ * &lt;enumeration value="EMBL"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="frameshift"/&gt; ++ * &lt;enumeration value="erroneous initiation"/&gt; ++ * &lt;enumeration value="erroneous termination"/&gt; ++ * &lt;enumeration value="erroneous gene model prediction"/&gt; ++ * &lt;enumeration value="erroneous translation"/&gt; ++ * &lt;enumeration value="miscellaneous discrepancy"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1153,28 -1153,28 +1153,28 @@@ /** -- *

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="resource" use="required">
--         *         <simpleType>
--         *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
--         *             <enumeration value="EMBL-CDS"/>
--         *             <enumeration value="EMBL"/>
--         *           </restriction>
--         *         </simpleType>
--         *       </attribute>
--         *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--         *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" />
--         *     </restriction>
--         *   </complexContent>
--         * </complexType>
--         *
++ * <p>Java class for anonymous complex type. ++ * ++ * <p>The following schema fragment specifies the expected content contained within this class. ++ * ++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="resource" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="EMBL-CDS"/&gt; ++ * &lt;enumeration value="EMBL"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1267,25 -1267,25 +1267,25 @@@ /** -- *

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="name" type="{http://www.w3.org/2001/XMLSchema}string"/>
--     *         <element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/>
--     *         <element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/>
--     *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
--     *       </sequence>
--     *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <p>Java class for anonymous complex type. ++ * ++ * <p>The following schema fragment specifies the expected content contained within this class. ++ * ++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; ++ * &lt;element name="acronym" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; ++ * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; ++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1433,23 -1433,23 +1433,23 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
--     *         <element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
--     *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="KM" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="Vmax" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1470,20 -1470,20 +1470,20 @@@ /** * Gets the value of the km property. * -- *

++ * <p> * 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 km property. ++ * This is why there is not a <CODE>set</CODE> method for the km property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getKM().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -1499,20 -1499,20 +1499,20 @@@ /** * Gets the value of the vmax property. * -- *

++ * <p> * 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 vmax property. ++ * This is why there is not a <CODE>set</CODE> method for the vmax property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getVmax().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -1528,20 -1528,20 +1528,20 @@@ /** * Gets the value of the text property. * -- *

++ * <p> * 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 text property. ++ * This is why there is not a <CODE>set</CODE> method for the text property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getText().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -1558,19 -1558,19 +1558,19 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" />
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="uri" use="required" type="{http://www.w3.org/2001/XMLSchema}anyURI" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1610,21 -1610,21 +1610,21 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1640,20 -1640,20 +1640,20 @@@ /** * Gets the value of the text property. * -- *

++ * <p> * 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 text property. ++ * This is why there is not a <CODE>set</CODE> method for the text property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getText().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -1670,21 -1670,21 +1670,21 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1700,20 -1700,20 +1700,20 @@@ /** * Gets the value of the text property. * -- *

++ * <p> * 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 text property. ++ * This is why there is not a <CODE>set</CODE> method for the text property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getText().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -1730,21 -1730,21 +1730,21 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1760,20 -1760,20 +1760,20 @@@ /** * Gets the value of the text property. * -- *

++ * <p> * 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 text property. ++ * This is why there is not a <CODE>set</CODE> method for the text property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getText().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * diff --cc src/jalview/xml/binding/uniprot/ConsortiumType.java index b2c4fdd,b2c4fdd..316c429 --- a/src/jalview/xml/binding/uniprot/ConsortiumType.java +++ b/src/jalview/xml/binding/uniprot/ConsortiumType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,19 -18,19 +18,19 @@@ import javax.xml.bind.annotation.XmlTyp * Describes the authors of a citation when these are represented by a consortium. * Equivalent to the flat file RG-line. * -- *

Java class for consortiumType complex type. ++ * <p>Java class for consortiumType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="consortiumType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="consortiumType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/DbReferenceType.java index ea6f728,ea6f728..178ee2d --- a/src/jalview/xml/binding/uniprot/DbReferenceType.java +++ b/src/jalview/xml/binding/uniprot/DbReferenceType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -21,25 -21,25 +21,25 @@@ import javax.xml.bind.annotation.XmlTyp * Equivalent to the flat file DR-line. * * -- *

Java class for dbReferenceType complex type. ++ * <p>Java class for dbReferenceType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="dbReferenceType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="molecule" type="{http://uniprot.org/uniprot}moleculeType" minOccurs="0"/>
-- *         <element name="property" type="{http://uniprot.org/uniprot}propertyType" maxOccurs="unbounded" minOccurs="0"/>
-- *       </sequence>
-- *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="dbReferenceType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="molecule" type="{http://uniprot.org/uniprot}moleculeType" minOccurs="0"/&gt; ++ * &lt;element name="property" type="{http://uniprot.org/uniprot}propertyType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -86,20 -86,20 +86,20 @@@ public class DbReferenceType /** * Gets the value of the property property. * -- *

++ * <p> * 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 property property. ++ * This is why there is not a <CODE>set</CODE> method for the property property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getProperty().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link PropertyType } * @@@ -163,20 -163,20 +163,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/Entry.java index dc211e8,dc211e8..34a1298 --- a/src/jalview/xml/binding/uniprot/Entry.java +++ b/src/jalview/xml/binding/uniprot/Entry.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -21,46 -21,46 +21,46 @@@ import javax.xml.datatype.XMLGregorianC /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="accession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-- *         <element name="name" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-- *         <element name="protein" type="{http://uniprot.org/uniprot}proteinType"/>
-- *         <element name="gene" type="{http://uniprot.org/uniprot}geneType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="organism" type="{http://uniprot.org/uniprot}organismType"/>
-- *         <element name="organismHost" type="{http://uniprot.org/uniprot}organismType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="geneLocation" type="{http://uniprot.org/uniprot}geneLocationType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="reference" type="{http://uniprot.org/uniprot}referenceType" maxOccurs="unbounded"/>
-- *         <element name="comment" type="{http://uniprot.org/uniprot}commentType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="proteinExistence" type="{http://uniprot.org/uniprot}proteinExistenceType"/>
-- *         <element name="keyword" type="{http://uniprot.org/uniprot}keywordType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="feature" type="{http://uniprot.org/uniprot}featureType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="evidence" type="{http://uniprot.org/uniprot}evidenceType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="sequence" type="{http://uniprot.org/uniprot}sequenceType"/>
-- *       </sequence>
-- *       <attribute name="dataset" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="Swiss-Prot"/>
-- *             <enumeration value="TrEMBL"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *       <attribute name="created" use="required" type="{http://www.w3.org/2001/XMLSchema}date" />
-- *       <attribute name="modified" use="required" type="{http://www.w3.org/2001/XMLSchema}date" />
-- *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="accession" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt; ++ * &lt;element name="name" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt; ++ * &lt;element name="protein" type="{http://uniprot.org/uniprot}proteinType"/&gt; ++ * &lt;element name="gene" type="{http://uniprot.org/uniprot}geneType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="organism" type="{http://uniprot.org/uniprot}organismType"/&gt; ++ * &lt;element name="organismHost" type="{http://uniprot.org/uniprot}organismType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="geneLocation" type="{http://uniprot.org/uniprot}geneLocationType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="reference" type="{http://uniprot.org/uniprot}referenceType" maxOccurs="unbounded"/&gt; ++ * &lt;element name="comment" type="{http://uniprot.org/uniprot}commentType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="proteinExistence" type="{http://uniprot.org/uniprot}proteinExistenceType"/&gt; ++ * &lt;element name="keyword" type="{http://uniprot.org/uniprot}keywordType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="feature" type="{http://uniprot.org/uniprot}featureType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="evidence" type="{http://uniprot.org/uniprot}evidenceType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="sequence" type="{http://uniprot.org/uniprot}sequenceType"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="dataset" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="Swiss-Prot"/&gt; ++ * &lt;enumeration value="TrEMBL"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="created" use="required" type="{http://www.w3.org/2001/XMLSchema}date" /&gt; ++ * &lt;attribute name="modified" use="required" type="{http://www.w3.org/2001/XMLSchema}date" /&gt; ++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -122,20 -122,20 +122,20 @@@ public class Entry /** * Gets the value of the accession property. * -- *

++ * <p> * 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 accession property. ++ * This is why there is not a <CODE>set</CODE> method for the accession property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getAccession().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * @@@ -151,20 -151,20 +151,20 @@@ /** * Gets the value of the name property. * -- *

++ * <p> * 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 name property. ++ * This is why there is not a <CODE>set</CODE> method for the name property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getName().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * @@@ -204,20 -204,20 +204,20 @@@ /** * Gets the value of the gene property. * -- *

++ * <p> * 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 gene property. ++ * This is why there is not a <CODE>set</CODE> method for the gene property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getGene().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link GeneType } * @@@ -257,20 -257,20 +257,20 @@@ /** * Gets the value of the organismHost property. * -- *

++ * <p> * 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 organismHost property. ++ * This is why there is not a <CODE>set</CODE> method for the organismHost property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getOrganismHost().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link OrganismType } * @@@ -286,20 -286,20 +286,20 @@@ /** * Gets the value of the geneLocation property. * -- *

++ * <p> * 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 geneLocation property. ++ * This is why there is not a <CODE>set</CODE> method for the geneLocation property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getGeneLocation().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link GeneLocationType } * @@@ -315,20 -315,20 +315,20 @@@ /** * Gets the value of the reference property. * -- *

++ * <p> * 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 reference property. ++ * This is why there is not a <CODE>set</CODE> method for the reference property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getReference().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link ReferenceType } * @@@ -344,20 -344,20 +344,20 @@@ /** * Gets the value of the comment property. * -- *

++ * <p> * 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 comment property. ++ * This is why there is not a <CODE>set</CODE> method for the comment property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getComment().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link CommentType } * @@@ -373,20 -373,20 +373,20 @@@ /** * Gets the value of the dbReference property. * -- *

++ * <p> * 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 dbReference property. ++ * This is why there is not a <CODE>set</CODE> method for the dbReference property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getDbReference().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link DbReferenceType } * @@@ -426,20 -426,20 +426,20 @@@ /** * Gets the value of the keyword property. * -- *

++ * <p> * 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 keyword property. ++ * This is why there is not a <CODE>set</CODE> method for the keyword property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getKeyword().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link KeywordType } * @@@ -455,20 -455,20 +455,20 @@@ /** * Gets the value of the feature property. * -- *

++ * <p> * 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 feature property. ++ * This is why there is not a <CODE>set</CODE> method for the feature property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getFeature().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link FeatureType } * @@@ -484,20 -484,20 +484,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidenceType } * diff --cc src/jalview/xml/binding/uniprot/EventType.java index 0c3de0e,0c3de0e..90adc2c --- a/src/jalview/xml/binding/uniprot/EventType.java +++ b/src/jalview/xml/binding/uniprot/EventType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -17,28 -17,28 +17,28 @@@ import javax.xml.bind.annotation.XmlTyp /** * Describes the type of events that cause alternative products. * -- *

Java class for eventType complex type. ++ * <p>Java class for eventType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="eventType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <attribute name="type" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="alternative splicing"/>
-- *             <enumeration value="alternative initiation"/>
-- *             <enumeration value="alternative promoter"/>
-- *             <enumeration value="ribosomal frameshifting"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="eventType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="alternative splicing"/&gt; ++ * &lt;enumeration value="alternative initiation"/&gt; ++ * &lt;enumeration value="alternative promoter"/&gt; ++ * &lt;enumeration value="ribosomal frameshifting"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/EvidenceType.java index 484d42d,484d42d..bfcd025 --- a/src/jalview/xml/binding/uniprot/EvidenceType.java +++ b/src/jalview/xml/binding/uniprot/EvidenceType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -19,24 -19,24 +19,24 @@@ import javax.xml.bind.annotation.XmlTyp * Describes the evidence for an annotation. * No flat file equivalent. * -- *

Java class for evidenceType complex type. ++ * <p>Java class for evidenceType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="evidenceType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="source" type="{http://uniprot.org/uniprot}sourceType" minOccurs="0"/>
-- *         <element name="importedFrom" type="{http://uniprot.org/uniprot}importedFromType" minOccurs="0"/>
-- *       </sequence>
-- *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="evidenceType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="source" type="{http://uniprot.org/uniprot}sourceType" minOccurs="0"/&gt; ++ * &lt;element name="importedFrom" type="{http://uniprot.org/uniprot}importedFromType" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/EvidencedStringType.java index ad22872,ad22872..1bd1f93 --- a/src/jalview/xml/binding/uniprot/EvidencedStringType.java +++ b/src/jalview/xml/binding/uniprot/EvidencedStringType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,28 -18,28 +18,28 @@@ import javax.xml.bind.annotation.XmlVal /** -- *

Java class for evidencedStringType complex type. ++ * <p>Java class for evidencedStringType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="evidencedStringType">
-- *   <simpleContent>
-- *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *       <attribute name="status">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="by similarity"/>
-- *             <enumeration value="probable"/>
-- *             <enumeration value="potential"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *     </extension>
-- *   </simpleContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="evidencedStringType"&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;attribute name="status"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="by similarity"/&gt; ++ * &lt;enumeration value="probable"/&gt; ++ * &lt;enumeration value="potential"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -83,20 -83,20 +83,20 @@@ public class EvidencedStringType /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/FeatureType.java index e951659,e951659..d1ba929 --- a/src/jalview/xml/binding/uniprot/FeatureType.java +++ b/src/jalview/xml/binding/uniprot/FeatureType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -21,81 -21,81 +21,81 @@@ import javax.xml.bind.annotation.XmlTyp * Describes different types of sequence annotations. * Equivalent to the flat file FT-line. * -- *

Java class for featureType complex type. ++ * <p>Java class for featureType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="featureType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="original" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
-- *         <element name="variation" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="location" type="{http://uniprot.org/uniprot}locationType"/>
-- *       </sequence>
-- *       <attribute name="type" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="active site"/>
-- *             <enumeration value="binding site"/>
-- *             <enumeration value="calcium-binding region"/>
-- *             <enumeration value="chain"/>
-- *             <enumeration value="coiled-coil region"/>
-- *             <enumeration value="compositionally biased region"/>
-- *             <enumeration value="cross-link"/>
-- *             <enumeration value="disulfide bond"/>
-- *             <enumeration value="DNA-binding region"/>
-- *             <enumeration value="domain"/>
-- *             <enumeration value="glycosylation site"/>
-- *             <enumeration value="helix"/>
-- *             <enumeration value="initiator methionine"/>
-- *             <enumeration value="lipid moiety-binding region"/>
-- *             <enumeration value="metal ion-binding site"/>
-- *             <enumeration value="modified residue"/>
-- *             <enumeration value="mutagenesis site"/>
-- *             <enumeration value="non-consecutive residues"/>
-- *             <enumeration value="non-terminal residue"/>
-- *             <enumeration value="nucleotide phosphate-binding region"/>
-- *             <enumeration value="peptide"/>
-- *             <enumeration value="propeptide"/>
-- *             <enumeration value="region of interest"/>
-- *             <enumeration value="repeat"/>
-- *             <enumeration value="non-standard amino acid"/>
-- *             <enumeration value="sequence conflict"/>
-- *             <enumeration value="sequence variant"/>
-- *             <enumeration value="short sequence motif"/>
-- *             <enumeration value="signal peptide"/>
-- *             <enumeration value="site"/>
-- *             <enumeration value="splice variant"/>
-- *             <enumeration value="strand"/>
-- *             <enumeration value="topological domain"/>
-- *             <enumeration value="transit peptide"/>
-- *             <enumeration value="transmembrane region"/>
-- *             <enumeration value="turn"/>
-- *             <enumeration value="unsure residue"/>
-- *             <enumeration value="zinc finger region"/>
-- *             <enumeration value="intramembrane region"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *       <attribute name="status">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="by similarity"/>
-- *             <enumeration value="probable"/>
-- *             <enumeration value="potential"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="featureType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="original" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt; ++ * &lt;element name="variation" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="location" type="{http://uniprot.org/uniprot}locationType"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="active site"/&gt; ++ * &lt;enumeration value="binding site"/&gt; ++ * &lt;enumeration value="calcium-binding region"/&gt; ++ * &lt;enumeration value="chain"/&gt; ++ * &lt;enumeration value="coiled-coil region"/&gt; ++ * &lt;enumeration value="compositionally biased region"/&gt; ++ * &lt;enumeration value="cross-link"/&gt; ++ * &lt;enumeration value="disulfide bond"/&gt; ++ * &lt;enumeration value="DNA-binding region"/&gt; ++ * &lt;enumeration value="domain"/&gt; ++ * &lt;enumeration value="glycosylation site"/&gt; ++ * &lt;enumeration value="helix"/&gt; ++ * &lt;enumeration value="initiator methionine"/&gt; ++ * &lt;enumeration value="lipid moiety-binding region"/&gt; ++ * &lt;enumeration value="metal ion-binding site"/&gt; ++ * &lt;enumeration value="modified residue"/&gt; ++ * &lt;enumeration value="mutagenesis site"/&gt; ++ * &lt;enumeration value="non-consecutive residues"/&gt; ++ * &lt;enumeration value="non-terminal residue"/&gt; ++ * &lt;enumeration value="nucleotide phosphate-binding region"/&gt; ++ * &lt;enumeration value="peptide"/&gt; ++ * &lt;enumeration value="propeptide"/&gt; ++ * &lt;enumeration value="region of interest"/&gt; ++ * &lt;enumeration value="repeat"/&gt; ++ * &lt;enumeration value="non-standard amino acid"/&gt; ++ * &lt;enumeration value="sequence conflict"/&gt; ++ * &lt;enumeration value="sequence variant"/&gt; ++ * &lt;enumeration value="short sequence motif"/&gt; ++ * &lt;enumeration value="signal peptide"/&gt; ++ * &lt;enumeration value="site"/&gt; ++ * &lt;enumeration value="splice variant"/&gt; ++ * &lt;enumeration value="strand"/&gt; ++ * &lt;enumeration value="topological domain"/&gt; ++ * &lt;enumeration value="transit peptide"/&gt; ++ * &lt;enumeration value="transmembrane region"/&gt; ++ * &lt;enumeration value="turn"/&gt; ++ * &lt;enumeration value="unsure residue"/&gt; ++ * &lt;enumeration value="zinc finger region"/&gt; ++ * &lt;enumeration value="intramembrane region"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="status"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="by similarity"/&gt; ++ * &lt;enumeration value="probable"/&gt; ++ * &lt;enumeration value="potential"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="description" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -151,20 -151,20 +151,20 @@@ public class FeatureType /** * Gets the value of the variation property. * -- *

++ * <p> * 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 variation property. ++ * This is why there is not a <CODE>set</CODE> method for the variation property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getVariation().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * @@@ -300,20 -300,20 +300,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/GeneLocationType.java index 3e3da7b,3e3da7b..6b4aa3d --- a/src/jalview/xml/binding/uniprot/GeneLocationType.java +++ b/src/jalview/xml/binding/uniprot/GeneLocationType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -20,38 -20,38 +20,38 @@@ import javax.xml.bind.annotation.XmlTyp * Describes non-nuclear gene locations (organelles and plasmids). * Equivalent to the flat file OG-line. * -- *

Java class for geneLocationType complex type. ++ * <p>Java class for geneLocationType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="geneLocationType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="name" type="{http://uniprot.org/uniprot}statusType" maxOccurs="unbounded" minOccurs="0"/>
-- *       </sequence>
-- *       <attribute name="type" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="apicoplast"/>
-- *             <enumeration value="chloroplast"/>
-- *             <enumeration value="organellar chromatophore"/>
-- *             <enumeration value="cyanelle"/>
-- *             <enumeration value="hydrogenosome"/>
-- *             <enumeration value="mitochondrion"/>
-- *             <enumeration value="non-photosynthetic plastid"/>
-- *             <enumeration value="nucleomorph"/>
-- *             <enumeration value="plasmid"/>
-- *             <enumeration value="plastid"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="geneLocationType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="name" type="{http://uniprot.org/uniprot}statusType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="apicoplast"/&gt; ++ * &lt;enumeration value="chloroplast"/&gt; ++ * &lt;enumeration value="organellar chromatophore"/&gt; ++ * &lt;enumeration value="cyanelle"/&gt; ++ * &lt;enumeration value="hydrogenosome"/&gt; ++ * &lt;enumeration value="mitochondrion"/&gt; ++ * &lt;enumeration value="non-photosynthetic plastid"/&gt; ++ * &lt;enumeration value="nucleomorph"/&gt; ++ * &lt;enumeration value="plasmid"/&gt; ++ * &lt;enumeration value="plastid"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -70,20 -70,20 +70,20 @@@ public class GeneLocationType /** * Gets the value of the name property. * -- *

++ * <p> * 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 name property. ++ * This is why there is not a <CODE>set</CODE> method for the name property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getName().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link StatusType } * @@@ -123,20 -123,20 +123,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/GeneNameType.java index bd93a7c,bd93a7c..346545e --- a/src/jalview/xml/binding/uniprot/GeneNameType.java +++ b/src/jalview/xml/binding/uniprot/GeneNameType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -21,29 -21,29 +21,29 @@@ import javax.xml.bind.annotation.XmlVal * Describes different types of gene designations. * Equivalent to the flat file GN-line. * -- *

Java class for geneNameType complex type. ++ * <p>Java class for geneNameType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="geneNameType">
-- *   <simpleContent>
-- *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *       <attribute name="type" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="primary"/>
-- *             <enumeration value="synonym"/>
-- *             <enumeration value="ordered locus"/>
-- *             <enumeration value="ORF"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *     </extension>
-- *   </simpleContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="geneNameType"&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="primary"/&gt; ++ * &lt;enumeration value="synonym"/&gt; ++ * &lt;enumeration value="ordered locus"/&gt; ++ * &lt;enumeration value="ORF"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -87,20 -87,20 +87,20 @@@ public class GeneNameType /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/GeneType.java index 7440d6b,7440d6b..60e0009 --- a/src/jalview/xml/binding/uniprot/GeneType.java +++ b/src/jalview/xml/binding/uniprot/GeneType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -20,21 -20,21 +20,21 @@@ import javax.xml.bind.annotation.XmlTyp * Describes a gene. * Equivalent to the flat file GN-line. * -- *

Java class for geneType complex type. ++ * <p>Java class for geneType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="geneType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="name" type="{http://uniprot.org/uniprot}geneNameType" maxOccurs="unbounded"/>
-- *       </sequence>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="geneType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="name" type="{http://uniprot.org/uniprot}geneNameType" maxOccurs="unbounded"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -50,20 -50,20 +50,20 @@@ public class GeneType /** * Gets the value of the name property. * -- *

++ * <p> * 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 name property. ++ * This is why there is not a <CODE>set</CODE> method for the name property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getName().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link GeneNameType } * diff --cc src/jalview/xml/binding/uniprot/ImportedFromType.java index 80cdfe5,80cdfe5..feb88f0 --- a/src/jalview/xml/binding/uniprot/ImportedFromType.java +++ b/src/jalview/xml/binding/uniprot/ImportedFromType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -17,21 -17,21 +17,21 @@@ import javax.xml.bind.annotation.XmlTyp /** * Describes the source of the evidence, when it is not assigned by UniProt, but imported from an external database. * -- *

Java class for importedFromType complex type. ++ * <p>Java class for importedFromType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="importedFromType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-- *       </sequence>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="importedFromType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/InteractantType.java index 2ba310e,2ba310e..aaf9689 --- a/src/jalview/xml/binding/uniprot/InteractantType.java +++ b/src/jalview/xml/binding/uniprot/InteractantType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -15,20 -15,20 +15,20 @@@ import javax.xml.bind.annotation.XmlTyp /** -- *

Java class for interactantType complex type. ++ * <p>Java class for interactantType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="interactantType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <group ref="{http://uniprot.org/uniprot}interactantGroup" minOccurs="0"/>
-- *       <attribute name="intactId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="interactantType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;group ref="{http://uniprot.org/uniprot}interactantGroup" minOccurs="0"/&gt; ++ * &lt;attribute name="intactId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/IsoformType.java index 9d218cf,9d218cf..8468a49 --- a/src/jalview/xml/binding/uniprot/IsoformType.java +++ b/src/jalview/xml/binding/uniprot/IsoformType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -21,50 -21,50 +21,50 @@@ import javax.xml.bind.annotation.XmlVal /** * Describes isoforms in 'alternative products' annotations. * -- *

Java class for isoformType complex type. ++ * <p>Java class for isoformType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="isoformType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="id" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-- *         <element name="name" maxOccurs="unbounded">
-- *           <complexType>
-- *             <simpleContent>
-- *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *                 <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *               </extension>
-- *             </simpleContent>
-- *           </complexType>
-- *         </element>
-- *         <element name="sequence">
-- *           <complexType>
-- *             <complexContent>
-- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                 <attribute name="type" use="required">
-- *                   <simpleType>
-- *                     <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *                       <enumeration value="not described"/>
-- *                       <enumeration value="described"/>
-- *                       <enumeration value="displayed"/>
-- *                       <enumeration value="external"/>
-- *                     </restriction>
-- *                   </simpleType>
-- *                 </attribute>
-- *                 <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *               </restriction>
-- *             </complexContent>
-- *           </complexType>
-- *         </element>
-- *         <element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-- *       </sequence>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="isoformType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="id" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt; ++ * &lt;element name="name" maxOccurs="unbounded"&gt; ++ * &lt;complexType&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="sequence"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="not described"/&gt; ++ * &lt;enumeration value="described"/&gt; ++ * &lt;enumeration value="displayed"/&gt; ++ * &lt;enumeration value="external"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="text" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -88,20 -88,20 +88,20 @@@ public class IsoformType /** * Gets the value of the id property. * -- *

++ * <p> * 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 id property. ++ * This is why there is not a <CODE>set</CODE> method for the id property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getId().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * @@@ -117,20 -117,20 +117,20 @@@ /** * Gets the value of the name property. * -- *

++ * <p> * 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 name property. ++ * This is why there is not a <CODE>set</CODE> method for the name property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getName().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link IsoformType.Name } * @@@ -170,20 -170,20 +170,20 @@@ /** * Gets the value of the text property. * -- *

++ * <p> * 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 text property. ++ * This is why there is not a <CODE>set</CODE> method for the text property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getText().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -198,19 -198,19 +198,19 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

--     * <complexType>
--     *   <simpleContent>
--     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
--     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
--     *     </extension>
--     *   </simpleContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -252,20 -252,20 +252,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getEvidence().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * @@@ -282,29 -282,29 +282,29 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="type" use="required">
--     *         <simpleType>
--     *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
--     *             <enumeration value="not described"/>
--     *             <enumeration value="described"/>
--     *             <enumeration value="displayed"/>
--     *             <enumeration value="external"/>
--     *           </restriction>
--     *         </simpleType>
--     *       </attribute>
--     *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" />
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="not described"/&gt; ++ * &lt;enumeration value="described"/&gt; ++ * &lt;enumeration value="displayed"/&gt; ++ * &lt;enumeration value="external"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/KeywordType.java index 21590e4,21590e4..1933fb3 --- a/src/jalview/xml/binding/uniprot/KeywordType.java +++ b/src/jalview/xml/binding/uniprot/KeywordType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,20 -18,20 +18,20 @@@ import javax.xml.bind.annotation.XmlVal /** -- *

Java class for keywordType complex type. ++ * <p>Java class for keywordType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="keywordType">
-- *   <simpleContent>
-- *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *       <attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </extension>
-- *   </simpleContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="keywordType"&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -75,20 -75,20 +75,20 @@@ public class KeywordType /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/LocationType.java index 35d5f87,35d5f87..28532a3 --- a/src/jalview/xml/binding/uniprot/LocationType.java +++ b/src/jalview/xml/binding/uniprot/LocationType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -17,26 -17,26 +17,26 @@@ import javax.xml.bind.annotation.XmlTyp /** * Describes a sequence location as either a range with a begin and end or as a position. The 'sequence' attribute is only used when the location is not on the canonical sequence displayed in the current entry. * -- *

Java class for locationType complex type. ++ * <p>Java class for locationType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="locationType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <choice>
-- *         <sequence>
-- *           <element name="begin" type="{http://uniprot.org/uniprot}positionType"/>
-- *           <element name="end" type="{http://uniprot.org/uniprot}positionType"/>
-- *         </sequence>
-- *         <element name="position" type="{http://uniprot.org/uniprot}positionType"/>
-- *       </choice>
-- *       <attribute name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="locationType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;choice&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="begin" type="{http://uniprot.org/uniprot}positionType"/&gt; ++ * &lt;element name="end" type="{http://uniprot.org/uniprot}positionType"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;element name="position" type="{http://uniprot.org/uniprot}positionType"/&gt; ++ * &lt;/choice&gt; ++ * &lt;attribute name="sequence" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/MoleculeType.java index 197e899,197e899..80e558d --- a/src/jalview/xml/binding/uniprot/MoleculeType.java +++ b/src/jalview/xml/binding/uniprot/MoleculeType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,19 -18,19 +18,19 @@@ import javax.xml.bind.annotation.XmlVal /** * Describes a molecule by name or unique identifier. * -- *

Java class for moleculeType complex type. ++ * <p>Java class for moleculeType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="moleculeType">
-- *   <simpleContent>
-- *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *       <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </extension>
-- *   </simpleContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="moleculeType"&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/NameListType.java index 3567be6,3567be6..95dc890 --- a/src/jalview/xml/binding/uniprot/NameListType.java +++ b/src/jalview/xml/binding/uniprot/NameListType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,22 -18,22 +18,22 @@@ import javax.xml.bind.annotation.XmlTyp /** -- *

Java class for nameListType complex type. ++ * <p>Java class for nameListType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="nameListType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <choice maxOccurs="unbounded">
-- *         <element name="consortium" type="{http://uniprot.org/uniprot}consortiumType"/>
-- *         <element name="person" type="{http://uniprot.org/uniprot}personType"/>
-- *       </choice>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="nameListType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;choice maxOccurs="unbounded"&gt; ++ * &lt;element name="consortium" type="{http://uniprot.org/uniprot}consortiumType"/&gt; ++ * &lt;element name="person" type="{http://uniprot.org/uniprot}personType"/&gt; ++ * &lt;/choice&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -52,20 -52,20 +52,20 @@@ public class NameListType /** * Gets the value of the consortiumOrPerson property. * -- *

++ * <p> * 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 consortiumOrPerson property. ++ * This is why there is not a <CODE>set</CODE> method for the consortiumOrPerson property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getConsortiumOrPerson().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link ConsortiumType } * {@link PersonType } diff --cc src/jalview/xml/binding/uniprot/ObjectFactory.java index 67c3d83,67c3d83..8dcd939 --- a/src/jalview/xml/binding/uniprot/ObjectFactory.java +++ b/src/jalview/xml/binding/uniprot/ObjectFactory.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,7 -18,7 +18,7 @@@ import javax.xml.namespace.QName * This object contains factory methods for each * Java content interface and Java element interface * generated in the jalview.xml.binding.uniprot package. -- *

An ObjectFactory allows you to programatically ++ * <p>An ObjectFactory allows you to programatically * construct new instances of the Java representation * for XML content. The Java representation of XML * content can consist of schema derived interfaces @@@ -41,19 -41,19 +41,19 @@@ public class ObjectFactory } /** -- * Create an instance of {@link SourceDataType } ++ * Create an instance of {@link IsoformType } * */ -- public SourceDataType createSourceDataType() { -- return new SourceDataType(); ++ public IsoformType createIsoformType() { ++ return new IsoformType(); } /** -- * Create an instance of {@link IsoformType } ++ * Create an instance of {@link SourceDataType } * */ -- public IsoformType createIsoformType() { -- return new IsoformType(); ++ public SourceDataType createSourceDataType() { ++ return new SourceDataType(); } /** @@@ -89,6 -89,6 +89,14 @@@ } /** ++ * Create an instance of {@link Uniprot } ++ * ++ */ ++ public Uniprot createUniprot() { ++ return new Uniprot(); ++ } ++ ++ /** * Create an instance of {@link Entry } * */ @@@ -169,11 -169,11 +177,19 @@@ } /** -- * Create an instance of {@link Uniprot } ++ * Create an instance of {@link GeneNameType } * */ -- public Uniprot createUniprot() { -- return new Uniprot(); ++ public GeneNameType createGeneNameType() { ++ return new GeneNameType(); ++ } ++ ++ /** ++ * Create an instance of {@link OrganismNameType } ++ * ++ */ ++ public OrganismNameType createOrganismNameType() { ++ return new OrganismNameType(); } /** @@@ -185,11 -185,11 +201,11 @@@ } /** -- * Create an instance of {@link PositionType } ++ * Create an instance of {@link CitationType } * */ -- public PositionType createPositionType() { -- return new PositionType(); ++ public CitationType createCitationType() { ++ return new CitationType(); } /** @@@ -201,35 -201,35 +217,27 @@@ } /** -- * Create an instance of {@link GeneNameType } -- * -- */ -- public GeneNameType createGeneNameType() { -- return new GeneNameType(); -- } -- -- /** -- * Create an instance of {@link LocationType } ++ * Create an instance of {@link PersonType } * */ -- public LocationType createLocationType() { -- return new LocationType(); ++ public PersonType createPersonType() { ++ return new PersonType(); } /** -- * Create an instance of {@link CitationType } ++ * Create an instance of {@link NameListType } * */ -- public CitationType createCitationType() { -- return new CitationType(); ++ public NameListType createNameListType() { ++ return new NameListType(); } /** -- * Create an instance of {@link PropertyType } ++ * Create an instance of {@link ReactionType } * */ -- public PropertyType createPropertyType() { -- return new PropertyType(); ++ public ReactionType createReactionType() { ++ return new ReactionType(); } /** @@@ -249,59 -249,59 +257,59 @@@ } /** -- * Create an instance of {@link EvidencedStringType } ++ * Create an instance of {@link SubcellularLocationType } * */ -- public EvidencedStringType createEvidencedStringType() { -- return new EvidencedStringType(); ++ public SubcellularLocationType createSubcellularLocationType() { ++ return new SubcellularLocationType(); } /** -- * Create an instance of {@link PersonType } ++ * Create an instance of {@link EventType } * */ -- public PersonType createPersonType() { -- return new PersonType(); ++ public EventType createEventType() { ++ return new EventType(); } /** -- * Create an instance of {@link ImportedFromType } ++ * Create an instance of {@link InteractantType } * */ -- public ImportedFromType createImportedFromType() { -- return new ImportedFromType(); ++ public InteractantType createInteractantType() { ++ return new InteractantType(); } /** -- * Create an instance of {@link EventType } ++ * Create an instance of {@link PropertyType } * */ -- public EventType createEventType() { -- return new EventType(); ++ public PropertyType createPropertyType() { ++ return new PropertyType(); } /** -- * Create an instance of {@link InteractantType } ++ * Create an instance of {@link LocationType } * */ -- public InteractantType createInteractantType() { -- return new InteractantType(); ++ public LocationType createLocationType() { ++ return new LocationType(); } /** -- * Create an instance of {@link NameListType } ++ * Create an instance of {@link PositionType } * */ -- public NameListType createNameListType() { -- return new NameListType(); ++ public PositionType createPositionType() { ++ return new PositionType(); } /** -- * Create an instance of {@link ReactionType } ++ * Create an instance of {@link MoleculeType } * */ -- public ReactionType createReactionType() { -- return new ReactionType(); ++ public MoleculeType createMoleculeType() { ++ return new MoleculeType(); } /** @@@ -313,27 -313,27 +321,35 @@@ } /** -- * Create an instance of {@link MoleculeType } ++ * Create an instance of {@link ImportedFromType } * */ -- public MoleculeType createMoleculeType() { -- return new MoleculeType(); ++ public ImportedFromType createImportedFromType() { ++ return new ImportedFromType(); } /** -- * Create an instance of {@link OrganismNameType } ++ * Create an instance of {@link EvidencedStringType } * */ -- public OrganismNameType createOrganismNameType() { -- return new OrganismNameType(); ++ public EvidencedStringType createEvidencedStringType() { ++ return new EvidencedStringType(); } /** -- * Create an instance of {@link SubcellularLocationType } ++ * Create an instance of {@link IsoformType.Name } * */ -- public SubcellularLocationType createSubcellularLocationType() { -- return new SubcellularLocationType(); ++ public IsoformType.Name createIsoformTypeName() { ++ return new IsoformType.Name(); ++ } ++ ++ /** ++ * Create an instance of {@link IsoformType.Sequence } ++ * ++ */ ++ public IsoformType.Sequence createIsoformTypeSequence() { ++ return new IsoformType.Sequence(); } /** @@@ -369,22 -369,22 +385,6 @@@ } /** -- * Create an instance of {@link IsoformType.Name } -- * -- */ -- public IsoformType.Name createIsoformTypeName() { -- return new IsoformType.Name(); -- } -- -- /** -- * Create an instance of {@link IsoformType.Sequence } -- * -- */ -- public IsoformType.Sequence createIsoformTypeSequence() { -- return new IsoformType.Sequence(); -- } -- -- /** * Create an instance of {@link CommentType.Absorption } * */ @@@ -497,8 -497,8 +497,12 @@@ } /** -- * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >}} ++ * Create an instance of {@link JAXBElement }{@code <}{@link String }{@code >} * ++ * @param value ++ * Java instance representing xml element's value. ++ * @return ++ * the new instance of {@link JAXBElement }{@code <}{@link String }{@code >} */ @XmlElementDecl(namespace = "http://uniprot.org/uniprot", name = "copyright") public JAXBElement createCopyright(String value) { diff --cc src/jalview/xml/binding/uniprot/OrganismNameType.java index fc0ba68,fc0ba68..dadc185 --- a/src/jalview/xml/binding/uniprot/OrganismNameType.java +++ b/src/jalview/xml/binding/uniprot/OrganismNameType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,29 -18,29 +18,29 @@@ import javax.xml.bind.annotation.XmlVal /** * Describes different types of source organism names. * -- *

Java class for organismNameType complex type. ++ * <p>Java class for organismNameType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="organismNameType">
-- *   <simpleContent>
-- *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *       <attribute name="type" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="common"/>
-- *             <enumeration value="full"/>
-- *             <enumeration value="scientific"/>
-- *             <enumeration value="synonym"/>
-- *             <enumeration value="abbreviation"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *     </extension>
-- *   </simpleContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="organismNameType"&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="common"/&gt; ++ * &lt;enumeration value="full"/&gt; ++ * &lt;enumeration value="scientific"/&gt; ++ * &lt;enumeration value="synonym"/&gt; ++ * &lt;enumeration value="abbreviation"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/OrganismType.java index d75b9b1,d75b9b1..de53629 --- a/src/jalview/xml/binding/uniprot/OrganismType.java +++ b/src/jalview/xml/binding/uniprot/OrganismType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -20,34 -20,34 +20,34 @@@ import javax.xml.bind.annotation.XmlTyp /** * Describes the source organism. * -- *

Java class for organismType complex type. ++ * <p>Java class for organismType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="organismType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="name" type="{http://uniprot.org/uniprot}organismNameType" maxOccurs="unbounded"/>
-- *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded"/>
-- *         <element name="lineage" minOccurs="0">
-- *           <complexType>
-- *             <complexContent>
-- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                 <sequence>
-- *                   <element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
-- *                 </sequence>
-- *               </restriction>
-- *             </complexContent>
-- *           </complexType>
-- *         </element>
-- *       </sequence>
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="organismType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="name" type="{http://uniprot.org/uniprot}organismNameType" maxOccurs="unbounded"/&gt; ++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded"/&gt; ++ * &lt;element name="lineage" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -70,20 -70,20 +70,20 @@@ public class OrganismType /** * Gets the value of the name property. * -- *

++ * <p> * 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 name property. ++ * This is why there is not a <CODE>set</CODE> method for the name property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getName().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link OrganismNameType } * @@@ -99,20 -99,20 +99,20 @@@ /** * Gets the value of the dbReference property. * -- *

++ * <p> * 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 dbReference property. ++ * This is why there is not a <CODE>set</CODE> method for the dbReference property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getDbReference().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link DbReferenceType } * @@@ -152,20 -152,20 +152,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * @@@ -180,21 -180,21 +180,21 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="taxon" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -210,20 -210,20 +210,20 @@@ /** * Gets the value of the taxon property. * -- *

++ * <p> * 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 taxon property. ++ * This is why there is not a <CODE>set</CODE> method for the taxon property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getTaxon().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * diff --cc src/jalview/xml/binding/uniprot/PersonType.java index 6328682,6328682..5a34fa6 --- a/src/jalview/xml/binding/uniprot/PersonType.java +++ b/src/jalview/xml/binding/uniprot/PersonType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -15,19 -15,19 +15,19 @@@ import javax.xml.bind.annotation.XmlTyp /** -- *

Java class for personType complex type. ++ * <p>Java class for personType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="personType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="personType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java index 8dbf704,8dbf704..ce34e68 --- a/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java +++ b/src/jalview/xml/binding/uniprot/PhysiologicalReactionType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -20,30 -20,30 +20,30 @@@ import javax.xml.bind.annotation.XmlTyp /** * Describes a physiological reaction. * -- *

Java class for physiologicalReactionType complex type. ++ * <p>Java class for physiologicalReactionType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="physiologicalReactionType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/>
-- *       </sequence>
-- *       <attribute name="direction" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="left-to-right"/>
-- *             <enumeration value="right-to-left"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="physiologicalReactionType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="direction" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="left-to-right"/&gt; ++ * &lt;enumeration value="right-to-left"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -111,20 -111,20 +111,20 @@@ public class PhysiologicalReactionType /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/PositionType.java index a850dbb,a850dbb..740d01a --- a/src/jalview/xml/binding/uniprot/PositionType.java +++ b/src/jalview/xml/binding/uniprot/PositionType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -19,31 -19,31 +19,31 @@@ import javax.xml.bind.annotation.XmlTyp /** -- *

Java class for positionType complex type. ++ * <p>Java class for positionType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="positionType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <attribute name="position" type="{http://www.w3.org/2001/XMLSchema}unsignedLong" />
-- *       <attribute name="status" default="certain">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="certain"/>
-- *             <enumeration value="uncertain"/>
-- *             <enumeration value="less than"/>
-- *             <enumeration value="greater than"/>
-- *             <enumeration value="unknown"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="positionType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="position" type="{http://www.w3.org/2001/XMLSchema}unsignedLong" /&gt; ++ * &lt;attribute name="status" default="certain"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="certain"/&gt; ++ * &lt;enumeration value="uncertain"/&gt; ++ * &lt;enumeration value="less than"/&gt; ++ * &lt;enumeration value="greater than"/&gt; ++ * &lt;enumeration value="unknown"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -114,20 -114,20 +114,20 @@@ public class PositionType /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/PropertyType.java index 977e428,977e428..ab7477a --- a/src/jalview/xml/binding/uniprot/PropertyType.java +++ b/src/jalview/xml/binding/uniprot/PropertyType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -15,20 -15,20 +15,20 @@@ import javax.xml.bind.annotation.XmlTyp /** -- *

Java class for propertyType complex type. ++ * <p>Java class for propertyType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="propertyType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="propertyType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="value" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/ProteinExistenceType.java index fb12cd6,fb12cd6..41f2bdd --- a/src/jalview/xml/binding/uniprot/ProteinExistenceType.java +++ b/src/jalview/xml/binding/uniprot/ProteinExistenceType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,29 -18,29 +18,29 @@@ import javax.xml.bind.annotation.XmlTyp * Describes the evidence for the protein's existence. * Equivalent to the flat file PE-line. * -- *

Java class for proteinExistenceType complex type. ++ * <p>Java class for proteinExistenceType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="proteinExistenceType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <attribute name="type" use="required">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="evidence at protein level"/>
-- *             <enumeration value="evidence at transcript level"/>
-- *             <enumeration value="inferred from homology"/>
-- *             <enumeration value="predicted"/>
-- *             <enumeration value="uncertain"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="proteinExistenceType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;attribute name="type" use="required"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="evidence at protein level"/&gt; ++ * &lt;enumeration value="evidence at transcript level"/&gt; ++ * &lt;enumeration value="inferred from homology"/&gt; ++ * &lt;enumeration value="predicted"/&gt; ++ * &lt;enumeration value="uncertain"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/ProteinType.java index defaff2,defaff2..14e6614 --- a/src/jalview/xml/binding/uniprot/ProteinType.java +++ b/src/jalview/xml/binding/uniprot/ProteinType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -20,39 -20,39 +20,39 @@@ import javax.xml.bind.annotation.XmlTyp * Describes the names for the protein and parts thereof. * Equivalent to the flat file DE-line. * -- *

Java class for proteinType complex type. ++ * <p>Java class for proteinType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="proteinType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-- *         <element name="domain" maxOccurs="unbounded" minOccurs="0">
-- *           <complexType>
-- *             <complexContent>
-- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                 <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-- *               </restriction>
-- *             </complexContent>
-- *           </complexType>
-- *         </element>
-- *         <element name="component" maxOccurs="unbounded" minOccurs="0">
-- *           <complexType>
-- *             <complexContent>
-- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *                 <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
-- *               </restriction>
-- *             </complexContent>
-- *           </complexType>
-- *         </element>
-- *       </sequence>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="proteinType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/&gt; ++ * &lt;element name="domain" maxOccurs="unbounded" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="component" maxOccurs="unbounded" minOccurs="0"&gt; ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -107,20 -107,20 +107,20 @@@ public class ProteinType /** * Gets the value of the alternativeName property. * -- *

++ * <p> * 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 alternativeName property. ++ * This is why there is not a <CODE>set</CODE> method for the alternativeName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getAlternativeName().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link ProteinType.AlternativeName } * @@@ -136,20 -136,20 +136,20 @@@ /** * Gets the value of the submittedName property. * -- *

++ * <p> * 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 submittedName property. ++ * This is why there is not a <CODE>set</CODE> method for the submittedName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getSubmittedName().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link ProteinType.SubmittedName } * @@@ -213,20 -213,20 +213,20 @@@ /** * Gets the value of the cdAntigenName property. * -- *

++ * <p> * 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 cdAntigenName property. ++ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getCdAntigenName().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -242,20 -242,20 +242,20 @@@ /** * Gets the value of the innName property. * -- *

++ * <p> * 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 innName property. ++ * This is why there is not a <CODE>set</CODE> method for the innName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getInnName().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -271,20 -271,20 +271,20 @@@ /** * Gets the value of the domain property. * -- *

++ * <p> * 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 domain property. ++ * This is why there is not a <CODE>set</CODE> method for the domain property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getDomain().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link ProteinType.Domain } * @@@ -300,20 -300,20 +300,20 @@@ /** * Gets the value of the component property. * -- *

++ * <p> * 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 component property. ++ * This is why there is not a <CODE>set</CODE> method for the component property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getComponent().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link ProteinType.Component } * @@@ -328,23 -328,23 +328,23 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/>
--     *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
--     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType" minOccurs="0"/&gt; ++ * &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -387,20 -387,20 +387,20 @@@ /** * Gets the value of the shortName property. * -- *

++ * <p> * 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 shortName property. ++ * This is why there is not a <CODE>set</CODE> method for the shortName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getShortName().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -416,20 -416,20 +416,20 @@@ /** * Gets the value of the ecNumber property. * -- *

++ * <p> * 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 ecNumber property. ++ * This is why there is not a <CODE>set</CODE> method for the ecNumber property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getEcNumber().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -446,19 -446,19 +446,19 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

--     * <complexType>
--     *   <complexContent>
--     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--     *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -509,20 -509,20 +509,20 @@@ /** * Gets the value of the alternativeName property. * -- *

++ * <p> * 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 alternativeName property. ++ * This is why there is not a <CODE>set</CODE> method for the alternativeName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getAlternativeName().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link ProteinType.AlternativeName } * @@@ -538,20 -538,20 +538,20 @@@ /** * Gets the value of the submittedName property. * -- *

++ * <p> * 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 submittedName property. ++ * This is why there is not a <CODE>set</CODE> method for the submittedName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getSubmittedName().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link ProteinType.SubmittedName } * @@@ -615,20 -615,20 +615,20 @@@ /** * Gets the value of the cdAntigenName property. * -- *

++ * <p> * 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 cdAntigenName property. ++ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getCdAntigenName().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -644,20 -644,20 +644,20 @@@ /** * Gets the value of the innName property. * -- *

++ * <p> * 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 innName property. ++ * This is why there is not a <CODE>set</CODE> method for the innName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getInnName().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -674,19 -674,19 +674,19 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

--     * <complexType>
--     *   <complexContent>
--     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
--     *       <group ref="{http://uniprot.org/uniprot}proteinNameGroup"/>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;group ref="{http://uniprot.org/uniprot}proteinNameGroup"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -737,20 -737,20 +737,20 @@@ /** * Gets the value of the alternativeName property. * -- *

++ * <p> * 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 alternativeName property. ++ * This is why there is not a <CODE>set</CODE> method for the alternativeName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getAlternativeName().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link ProteinType.AlternativeName } * @@@ -766,20 -766,20 +766,20 @@@ /** * Gets the value of the submittedName property. * -- *

++ * <p> * 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 submittedName property. ++ * This is why there is not a <CODE>set</CODE> method for the submittedName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getSubmittedName().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link ProteinType.SubmittedName } * @@@ -843,20 -843,20 +843,20 @@@ /** * Gets the value of the cdAntigenName property. * -- *

++ * <p> * 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 cdAntigenName property. ++ * This is why there is not a <CODE>set</CODE> method for the cdAntigenName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getCdAntigenName().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -872,20 -872,20 +872,20 @@@ /** * Gets the value of the innName property. * -- *

++ * <p> * 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 innName property. ++ * This is why there is not a <CODE>set</CODE> method for the innName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getInnName().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -902,23 -902,23 +902,23 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
--     *         <element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
--     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/&gt; ++ * &lt;element name="shortName" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -962,20 -962,20 +962,20 @@@ /** * Gets the value of the shortName property. * -- *

++ * <p> * 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 shortName property. ++ * This is why there is not a <CODE>set</CODE> method for the shortName property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getShortName().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -991,20 -991,20 +991,20 @@@ /** * Gets the value of the ecNumber property. * -- *

++ * <p> * 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 ecNumber property. ++ * This is why there is not a <CODE>set</CODE> method for the ecNumber property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getEcNumber().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -1021,22 -1021,22 +1021,22 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/>
--     *         <element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
--     *       </sequence>
--     *     </restriction>
--     *   </complexContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="fullName" type="{http://uniprot.org/uniprot}evidencedStringType"/&gt; ++ * &lt;element name="ecNumber" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -1078,20 -1078,20 +1078,20 @@@ /** * Gets the value of the ecNumber property. * -- *

++ * <p> * 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 ecNumber property. ++ * This is why there is not a <CODE>set</CODE> method for the ecNumber property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getEcNumber().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * diff --cc src/jalview/xml/binding/uniprot/ReactionType.java index 800f518,800f518..fedebd8 --- a/src/jalview/xml/binding/uniprot/ReactionType.java +++ b/src/jalview/xml/binding/uniprot/ReactionType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -20,23 -20,23 +20,23 @@@ import javax.xml.bind.annotation.XmlTyp /** * Describes a chemical reaction. * -- *

Java class for reactionType complex type. ++ * <p>Java class for reactionType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="reactionType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="text" type="{http://www.w3.org/2001/XMLSchema}string"/>
-- *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded"/>
-- *       </sequence>
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="reactionType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="text" type="{http://www.w3.org/2001/XMLSchema}string"/&gt; ++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" maxOccurs="unbounded"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -81,20 -81,20 +81,20 @@@ public class ReactionType /** * Gets the value of the dbReference property. * -- *

++ * <p> * 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 dbReference property. ++ * This is why there is not a <CODE>set</CODE> method for the dbReference property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getDbReference().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link DbReferenceType } * @@@ -110,20 -110,20 +110,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/ReferenceType.java index 75fb044,75fb044..ba47ec7 --- a/src/jalview/xml/binding/uniprot/ReferenceType.java +++ b/src/jalview/xml/binding/uniprot/ReferenceType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -21,24 -21,24 +21,24 @@@ import javax.xml.bind.annotation.XmlTyp * Describes a citation and a summary of its content. * Equivalent to the flat file RN-, RP-, RC-, RX-, RG-, RA-, RT- and RL-lines. * -- *

Java class for referenceType complex type. ++ * <p>Java class for referenceType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="referenceType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="citation" type="{http://uniprot.org/uniprot}citationType"/>
-- *         <group ref="{http://uniprot.org/uniprot}sptrCitationGroup"/>
-- *       </sequence>
-- *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *       <attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="referenceType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="citation" type="{http://uniprot.org/uniprot}citationType"/&gt; ++ * &lt;group ref="{http://uniprot.org/uniprot}sptrCitationGroup"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;attribute name="key" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -87,20 -87,20 +87,20 @@@ public class ReferenceType /** * Gets the value of the scope property. * -- *

++ * <p> * 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 scope property. ++ * This is why there is not a <CODE>set</CODE> method for the scope property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getScope().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link String } * @@@ -140,20 -140,20 +140,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEvidence().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/SequenceType.java index 8c10faf,8c10faf..a5f7749 --- a/src/jalview/xml/binding/uniprot/SequenceType.java +++ b/src/jalview/xml/binding/uniprot/SequenceType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,32 -18,32 +18,32 @@@ import javax.xml.datatype.XMLGregorianC /** -- *

Java class for sequenceType complex type. ++ * <p>Java class for sequenceType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="sequenceType">
-- *   <simpleContent>
-- *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *       <attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-- *       <attribute name="mass" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-- *       <attribute name="checksum" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
-- *       <attribute name="modified" use="required" type="{http://www.w3.org/2001/XMLSchema}date" />
-- *       <attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}int" />
-- *       <attribute name="precursor" type="{http://www.w3.org/2001/XMLSchema}boolean" />
-- *       <attribute name="fragment">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="single"/>
-- *             <enumeration value="multiple"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *     </extension>
-- *   </simpleContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="sequenceType"&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="length" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="mass" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="checksum" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; ++ * &lt;attribute name="modified" use="required" type="{http://www.w3.org/2001/XMLSchema}date" /&gt; ++ * &lt;attribute name="version" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt; ++ * &lt;attribute name="precursor" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt; ++ * &lt;attribute name="fragment"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="single"/&gt; ++ * &lt;enumeration value="multiple"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/SourceDataType.java index c3838ec,c3838ec..aad1a5f --- a/src/jalview/xml/binding/uniprot/SourceDataType.java +++ b/src/jalview/xml/binding/uniprot/SourceDataType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -23,56 -23,56 +23,56 @@@ import javax.xml.bind.annotation.XmlVal * Describes the source of the sequence according to the citation. * Equivalent to the flat file RC-line. * -- *

Java class for sourceDataType complex type. ++ * <p>Java class for sourceDataType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="sourceDataType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <choice maxOccurs="unbounded">
-- *         <element name="strain">
-- *           <complexType>
-- *             <simpleContent>
-- *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *                 <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *               </extension>
-- *             </simpleContent>
-- *           </complexType>
-- *         </element>
-- *         <element name="plasmid">
-- *           <complexType>
-- *             <simpleContent>
-- *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *                 <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *               </extension>
-- *             </simpleContent>
-- *           </complexType>
-- *         </element>
-- *         <element name="transposon">
-- *           <complexType>
-- *             <simpleContent>
-- *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *                 <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *               </extension>
-- *             </simpleContent>
-- *           </complexType>
-- *         </element>
-- *         <element name="tissue">
-- *           <complexType>
-- *             <simpleContent>
-- *               <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *                 <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
-- *               </extension>
-- *             </simpleContent>
-- *           </complexType>
-- *         </element>
-- *       </choice>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="sourceDataType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;choice maxOccurs="unbounded"&gt; ++ * &lt;element name="strain"&gt; ++ * &lt;complexType&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="plasmid"&gt; ++ * &lt;complexType&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="transposon"&gt; ++ * &lt;complexType&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;element name="tissue"&gt; ++ * &lt;complexType&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * &lt;/element&gt; ++ * &lt;/choice&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -93,20 -93,20 +93,20 @@@ public class SourceDataType /** * Gets the value of the strainOrPlasmidOrTransposon property. * -- *

++ * <p> * 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 strainOrPlasmidOrTransposon property. ++ * This is why there is not a <CODE>set</CODE> method for the strainOrPlasmidOrTransposon property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getStrainOrPlasmidOrTransposon().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link SourceDataType.Strain } * {@link SourceDataType.Plasmid } @@@ -124,19 -124,19 +124,19 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

--     * <complexType>
--     *   <simpleContent>
--     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
--     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
--     *     </extension>
--     *   </simpleContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -178,20 -178,20 +178,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getEvidence().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * @@@ -208,19 -208,19 +208,19 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

--     * <complexType>
--     *   <simpleContent>
--     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
--     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
--     *     </extension>
--     *   </simpleContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -262,20 -262,20 +262,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getEvidence().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * @@@ -292,19 -292,19 +292,19 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

--     * <complexType>
--     *   <simpleContent>
--     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
--     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
--     *     </extension>
--     *   </simpleContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -346,20 -346,20 +346,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getEvidence().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * @@@ -376,19 -376,19 +376,19 @@@ /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

--     * <complexType>
--     *   <simpleContent>
--     *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
--     *       <attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" />
--     *     </extension>
--     *   </simpleContent>
--     * </complexType>
--     *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="evidence" type="{http://uniprot.org/uniprot}intListType" /&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -430,20 -430,20 +430,20 @@@ /** * Gets the value of the evidence property. * -- *

++ * <p> * 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 evidence property. ++ * This is why there is not a <CODE>set</CODE> method for the evidence property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++         * <pre>
           *    getEvidence().add(newItem);
--         *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Integer } * diff --cc src/jalview/xml/binding/uniprot/SourceType.java index 2814911,2814911..6b4a612 --- a/src/jalview/xml/binding/uniprot/SourceType.java +++ b/src/jalview/xml/binding/uniprot/SourceType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,22 -18,22 +18,22 @@@ import javax.xml.bind.annotation.XmlTyp /** * Describes the source of the data using a database cross-reference (or a 'ref' attribute when the source cannot be found in a public data source, such as PubMed, and is cited only within the UniProtKB entry). * -- *

Java class for sourceType complex type. ++ * <p>Java class for sourceType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="sourceType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" minOccurs="0"/>
-- *       </sequence>
-- *       <attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}integer" />
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="sourceType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="dbReference" type="{http://uniprot.org/uniprot}dbReferenceType" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;attribute name="ref" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/StatusType.java index 3f956c3,3f956c3..ef4cc70 --- a/src/jalview/xml/binding/uniprot/StatusType.java +++ b/src/jalview/xml/binding/uniprot/StatusType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,26 -18,26 +18,26 @@@ import javax.xml.bind.annotation.XmlVal /** * Indicates whether the name of a plasmid is known or unknown. * -- *

Java class for statusType complex type. ++ * <p>Java class for statusType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="statusType">
-- *   <simpleContent>
-- *     <extension base="<http://www.w3.org/2001/XMLSchema>string">
-- *       <attribute name="status" default="known">
-- *         <simpleType>
-- *           <restriction base="{http://www.w3.org/2001/XMLSchema}string">
-- *             <enumeration value="known"/>
-- *             <enumeration value="unknown"/>
-- *           </restriction>
-- *         </simpleType>
-- *       </attribute>
-- *     </extension>
-- *   </simpleContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="statusType"&gt; ++ * &lt;simpleContent&gt; ++ * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt; ++ * &lt;attribute name="status" default="known"&gt; ++ * &lt;simpleType&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}string"&gt; ++ * &lt;enumeration value="known"/&gt; ++ * &lt;enumeration value="unknown"/&gt; ++ * &lt;/restriction&gt; ++ * &lt;/simpleType&gt; ++ * &lt;/attribute&gt; ++ * &lt;/extension&gt; ++ * &lt;/simpleContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ diff --cc src/jalview/xml/binding/uniprot/SubcellularLocationType.java index b9ff7d3,b9ff7d3..fad1fea --- a/src/jalview/xml/binding/uniprot/SubcellularLocationType.java +++ b/src/jalview/xml/binding/uniprot/SubcellularLocationType.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -19,23 -19,23 +19,23 @@@ import javax.xml.bind.annotation.XmlTyp /** * Describes the subcellular location and optionally the topology and orientation of a molecule. * -- *

Java class for subcellularLocationType complex type. ++ * <p>Java class for subcellularLocationType complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>The following schema fragment specifies the expected content contained within this class. * -- * 

-- * <complexType name="subcellularLocationType">
-- *   <complexContent>
-- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-- *       <sequence>
-- *         <element name="location" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/>
-- *         <element name="topology" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-- *         <element name="orientation" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/>
-- *       </sequence>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType name="subcellularLocationType"&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element name="location" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded"/&gt; ++ * &lt;element name="topology" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;element name="orientation" type="{http://uniprot.org/uniprot}evidencedStringType" maxOccurs="unbounded" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -55,20 -55,20 +55,20 @@@ public class SubcellularLocationType /** * Gets the value of the location property. * -- *

++ * <p> * 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 location property. ++ * This is why there is not a <CODE>set</CODE> method for the location property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getLocation().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -84,20 -84,20 +84,20 @@@ /** * Gets the value of the topology property. * -- *

++ * <p> * 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 topology property. ++ * This is why there is not a <CODE>set</CODE> method for the topology property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getTopology().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * @@@ -113,20 -113,20 +113,20 @@@ /** * Gets the value of the orientation property. * -- *

++ * <p> * 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 orientation property. ++ * This is why there is not a <CODE>set</CODE> method for the orientation property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getOrientation().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link EvidencedStringType } * diff --cc src/jalview/xml/binding/uniprot/Uniprot.java index 5751e61,5751e61..07e9562 --- a/src/jalview/xml/binding/uniprot/Uniprot.java +++ b/src/jalview/xml/binding/uniprot/Uniprot.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @@@ -18,22 -18,22 +18,22 @@@ import javax.xml.bind.annotation.XmlTyp /** -- *

Java class for anonymous complex type. ++ * <p>Java class for anonymous complex type. * -- *

The following schema fragment specifies the expected content contained within this class. ++ * <p>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="{http://uniprot.org/uniprot}entry" maxOccurs="unbounded"/>
-- *         <element ref="{http://uniprot.org/uniprot}copyright" minOccurs="0"/>
-- *       </sequence>
-- *     </restriction>
-- *   </complexContent>
-- * </complexType>
-- *
++ * <pre> ++ * &lt;complexType&gt; ++ * &lt;complexContent&gt; ++ * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; ++ * &lt;sequence&gt; ++ * &lt;element ref="{http://uniprot.org/uniprot}entry" maxOccurs="unbounded"/&gt; ++ * &lt;element ref="{http://uniprot.org/uniprot}copyright" minOccurs="0"/&gt; ++ * &lt;/sequence&gt; ++ * &lt;/restriction&gt; ++ * &lt;/complexContent&gt; ++ * &lt;/complexType&gt; ++ * </pre> * * */ @@@ -52,20 -52,20 +52,20 @@@ public class Uniprot /** * Gets the value of the entry property. * -- *

++ * <p> * 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 entry property. ++ * This is why there is not a <CODE>set</CODE> method for the entry property. * -- *

++ * <p> * For example, to add a new item, do as follows: -- * 

++     * <pre>
       *    getEntry().add(newItem);
--     *
++ * </pre> * * -- *

++ * <p> * Objects of the following type(s) are allowed in the list * {@link Entry } * diff --cc src/jalview/xml/binding/uniprot/package-info.java index 71f7eaa,71f7eaa..c30f9a9 --- a/src/jalview/xml/binding/uniprot/package-info.java +++ b/src/jalview/xml/binding/uniprot/package-info.java @@@ -1,8 -1,8 +1,8 @@@ // --// 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 ++// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 ++// See https://eclipse-ee4j.github.io/jaxb-ri // Any modifications to this file will be lost upon recompilation of the source schema. --// Generated on: 2019.04.05 at 08:01:44 AM BST ++// Generated on: 2022.02.07 at 04:44:21 PM GMT // @javax.xml.bind.annotation.XmlSchema(namespace = "http://uniprot.org/uniprot", elementFormDefault = javax.xml.bind.annotation.XmlNsForm.QUALIFIED)