X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FSequence.java;h=200184531823d56b909d5fce35a2bc358c77f0e6;hb=57738a1f3c19b1c3a00bd3ac5108f8cd0af32f99;hp=abb40c9ec8c2ede7955bfcfc7f04b65e90115dd2;hpb=c25cfde239527da78fecce55a877330afa90701d;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/Sequence.java b/src/jalview/xml/binding/jalview/Sequence.java index abb40c9..2001845 100644 --- a/src/jalview/xml/binding/jalview/Sequence.java +++ b/src/jalview/xml/binding/jalview/Sequence.java @@ -1,11 +1,10 @@ // -// 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: 2018.12.20 at 11:47:26 AM GMT +// Generated on: 2021.08.30 at 11:05:22 AM BST // - package jalview.xml.binding.jalview; import java.util.ArrayList; @@ -17,241 +16,325 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; - /** - *

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>
- *     <extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType">
- *       <sequence>
- *         <element name="DBRef" maxOccurs="unbounded" minOccurs="0">
- *           <complexType>
- *             <complexContent>
- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 <sequence>
- *                   <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
- *                 </sequence>
- *                 <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *               </restriction>
- *             </complexContent>
- *           </complexType>
- *         </element>
- *       </sequence>
- *       <attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     </extension>
- *   </complexContent>
- * </complexType>
- *
+ * <pre> &lt;complexType&gt; &lt;complexContent&gt; + * &lt;extension + * base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt; + * &lt;sequence&gt; &lt;element name="DBRef" 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 + * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt; + * &lt;/sequence&gt; &lt;attribute name="source" + * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute + * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="accessionId" + * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute + * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" + * /&gt; &lt;attribute name="canonical" + * 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;attribute name="dsseqid" + * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute + * name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;/extension&gt; &lt;/complexContent&gt; + * &lt;/complexType&gt; </pre> * * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "", propOrder = { - "dbRef" -}) +@XmlType(name = "", propOrder = { "dbRef" }) @XmlRootElement(name = "Sequence") -public class Sequence - extends SequenceType +public class Sequence extends SequenceType { - @XmlElement(name = "DBRef") - protected List dbRef; - @XmlAttribute(name = "dsseqid") - protected String dsseqid; + @XmlElement(name = "DBRef") + protected List dbRef; + + @XmlAttribute(name = "dsseqid") + protected String dsseqid; + + @XmlAttribute(name = "biotype") + protected String biotype; + + /** + * Gets the value of the dbRef 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 + * <CODE>set</CODE> method for the dbRef property. + * + * <p> For example, to add a new item, do as follows: <pre> + * getDBRef().add(newItem); </pre> + * + * + * <p> Objects of the following type(s) are allowed in the list + * {@link Sequence.DBRef } + * + * + */ + public List getDBRef() + { + if (dbRef == null) + { + dbRef = new ArrayList(); + } + return this.dbRef; + } + + /** + * Gets the value of the dsseqid property. + * + * @return possible object is {@link String } + * + */ + public String getDsseqid() + { + return dsseqid; + } + + /** + * Sets the value of the dsseqid property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setDsseqid(String value) + { + this.dsseqid = value; + } + + /** + * Gets the value of the biotype property. + * + * @return possible object is {@link String } + * + */ + public String getBiotype() + { + return biotype; + } + + /** + * Sets the value of the biotype property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setBiotype(String value) + { + this.biotype = value; + } + + /** + * <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 + * ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt; + * &lt;/sequence&gt; &lt;attribute name="source" + * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute + * name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="accessionId" + * type="{http://www.w3.org/2001/XMLSchema}string" /&gt; &lt;attribute + * name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" + * default="false" /&gt; &lt;attribute name="canonical" + * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt; + * &lt;/restriction&gt; &lt;/complexContent&gt; + * &lt;/complexType&gt; </pre> + * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "mapping" }) + public static class DBRef + { + + @XmlElement(name = "Mapping") + protected Mapping mapping; + + @XmlAttribute(name = "source") + protected String source; + + @XmlAttribute(name = "version") + protected String version; + + @XmlAttribute(name = "accessionId") + protected String accessionId; + + @XmlAttribute(name = "locus") + protected Boolean locus; + + @XmlAttribute(name = "canonical") + protected Boolean canonical; /** - * Gets the value of the dbRef property. + * Gets the value of the mapping property. * - *

- * This accessor method returns a reference to the live list, - * not a snapshot. Therefore any modification you make to the - * returned list will be present inside the JAXB object. - * This is why there is not a set method for the dbRef property. + * @return possible object is {@link Mapping } * - *

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

-     *    getDBRef().add(newItem);
-     *
+ */ + public Mapping getMapping() + { + return mapping; + } + + /** + * Sets the value of the mapping property. * + * @param value + * allowed object is {@link Mapping } * - *

- * Objects of the following type(s) are allowed in the list - * {@link Sequence.DBRef } + */ + public void setMapping(Mapping value) + { + this.mapping = value; + } + + /** + * Gets the value of the source property. * + * @return possible object is {@link String } * */ - public List getDBRef() { - if (dbRef == null) { - dbRef = new ArrayList(); - } - return this.dbRef; + public String getSource() + { + return source; } /** - * Gets the value of the dsseqid property. + * Sets the value of the source property. + * + * @param value + * allowed object is {@link String } * - * @return - * possible object is - * {@link String } - * */ - public String getDsseqid() { - return dsseqid; + public void setSource(String value) + { + this.source = value; } /** - * Sets the value of the dsseqid property. + * Gets the value of the version property. + * + * @return possible object is {@link String } + * + */ + public String getVersion() + { + return version; + } + + /** + * Sets the value of the version property. + * + * @param value + * allowed object is {@link String } + * + */ + public void setVersion(String value) + { + this.version = value; + } + + /** + * Gets the value of the accessionId property. + * + * @return possible object is {@link String } + * + */ + public String getAccessionId() + { + return accessionId; + } + + /** + * Sets the value of the accessionId property. * * @param value - * allowed object is - * {@link String } - * + * allowed object is {@link String } + * */ - public void setDsseqid(String value) { - this.dsseqid = value; + public void setAccessionId(String value) + { + this.accessionId = value; } + /** + * Gets the value of the locus property. + * + * @return possible object is {@link Boolean } + * + */ + public boolean isLocus() + { + if (locus == null) + { + return false; + } + else + { + return locus; + } + } /** - *

Java class for anonymous complex type. + * Sets the value of the locus property. * - *

The following schema fragment specifies the expected content contained within this class. + * @param value + * allowed object is {@link Boolean } * - * 

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <sequence>
-     *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/>
-     *       </sequence>
-     *       <attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     *
+ */ + public void setLocus(Boolean value) + { + this.locus = value; + } + + /** + * Gets the value of the canonical property. * + * @return possible object is {@link Boolean } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "mapping" - }) - public static class DBRef { - - @XmlElement(name = "Mapping") - protected Mapping mapping; - @XmlAttribute(name = "source") - protected String source; - @XmlAttribute(name = "version") - protected String version; - @XmlAttribute(name = "accessionId") - protected String accessionId; - - /** - * Gets the value of the mapping property. - * - * @return - * possible object is - * {@link Mapping } - * - */ - public Mapping getMapping() { - return mapping; - } - - /** - * Sets the value of the mapping property. - * - * @param value - * allowed object is - * {@link Mapping } - * - */ - public void setMapping(Mapping value) { - this.mapping = value; - } - - /** - * Gets the value of the source property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getSource() { - return source; - } - - /** - * Sets the value of the source property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setSource(String value) { - this.source = value; - } - - /** - * Gets the value of the version property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getVersion() { - return version; - } - - /** - * Sets the value of the version property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setVersion(String value) { - this.version = value; - } - - /** - * Gets the value of the accessionId property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getAccessionId() { - return accessionId; - } - - /** - * Sets the value of the accessionId property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setAccessionId(String value) { - this.accessionId = value; - } + public boolean isCanonical() + { + if (canonical == null) + { + return false; + } + else + { + return canonical; + } + } + /** + * Sets the value of the canonical property. + * + * @param value + * allowed object is {@link Boolean } + * + */ + public void setCanonical(Boolean value) + { + this.canonical = value; } + } + }