X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FSequenceSet.java;h=751f6cab1f427ae6c9badc741d9c07bde8a64c12;hb=6ca8a32d88328b8f2162512f41c657c87e131045;hp=a09195016afcaa40e8cf43c70dc291dc7f3e1675;hpb=f3d6a13271e3f34dfb4e40d6a2a7df1d392f8014;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/SequenceSet.java b/src/jalview/xml/binding/jalview/SequenceSet.java index a091950..751f6ca 100644 --- a/src/jalview/xml/binding/jalview/SequenceSet.java +++ b/src/jalview/xml/binding/jalview/SequenceSet.java @@ -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: 2023.05.13 at 06:58:41 PM BST +// Generated on: 2023.11.01 at 07:03:09 PM GMT // @@ -19,35 +19,36 @@ 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>
- *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *       <sequence>
- *         <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/>
- *         <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/>
- *         <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0">
- *           <complexType>
- *             <complexContent>
- *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
- *                 <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
- *                 <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
- *               </restriction>
- *             </complexContent>
- *           </complexType>
- *         </element>
- *         <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/>
- *       </sequence>
- *       <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
- *       <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" />
- *     </restriction>
- *   </complexContent>
- * </complexType>
- *
+ * <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}Sequence" maxOccurs="unbounded" minOccurs="0"/&gt; + * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/&gt; + * &lt;element name="sequenceSetProperties" 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="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * &lt;/element&gt; + * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/&gt; + * &lt;element name="Matrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/&gt; + * &lt;/sequence&gt; + * &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * </pre> * * */ @@ -56,7 +57,8 @@ import javax.xml.bind.annotation.XmlType; "sequence", "annotation", "sequenceSetProperties", - "alcodonFrame" + "alcodonFrame", + "matrix" }) @XmlRootElement(name = "SequenceSet") public class SequenceSet { @@ -68,6 +70,8 @@ public class SequenceSet { protected List sequenceSetProperties; @XmlElement(name = "AlcodonFrame") protected List alcodonFrame; + @XmlElement(name = "Matrix") + protected List matrix; @XmlAttribute(name = "gapChar", required = true) protected String gapChar; @XmlAttribute(name = "datasetId") @@ -76,20 +80,20 @@ public class SequenceSet { /** * Gets the value of the sequence 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 sequence property. + * This is why there is not a <CODE>set</CODE> method for the sequence property. * - *

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

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

+ * <p> * Objects of the following type(s) are allowed in the list * {@link Sequence } * @@ -105,20 +109,20 @@ public class SequenceSet { /** * Gets the value of the annotation 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 annotation property. + * This is why there is not a <CODE>set</CODE> method for the annotation property. * - *

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

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

+ * <p> * Objects of the following type(s) are allowed in the list * {@link Annotation } * @@ -134,20 +138,20 @@ public class SequenceSet { /** * Gets the value of the sequenceSetProperties 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 sequenceSetProperties property. + * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property. * - *

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

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

+ * <p> * Objects of the following type(s) are allowed in the list * {@link SequenceSet.SequenceSetProperties } * @@ -163,20 +167,20 @@ public class SequenceSet { /** * Gets the value of the alcodonFrame 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 alcodonFrame property. + * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property. * - *

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

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

+ * <p> * Objects of the following type(s) are allowed in the list * {@link AlcodonFrame } * @@ -190,6 +194,35 @@ public class SequenceSet { } /** + * Gets the value of the matrix 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 matrix property. + * + * <p> + * For example, to add a new item, do as follows: + * <pre> + * getMatrix().add(newItem); + * </pre> + * + * + * <p> + * Objects of the following type(s) are allowed in the list + * {@link MatrixType } + * + * + */ + public List getMatrix() { + if (matrix == null) { + matrix = new ArrayList(); + } + return this.matrix; + } + + /** * Gets the value of the gapChar property. * * @return @@ -239,20 +272,20 @@ public class SequenceSet { /** - *

Java class for anonymous complex type. - * - *

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

-     * <complexType>
-     *   <complexContent>
-     *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
-     *       <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *       <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
-     *     </restriction>
-     *   </complexContent>
-     * </complexType>
-     *
+ * <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="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; + * &lt;/restriction&gt; + * &lt;/complexContent&gt; + * &lt;/complexType&gt; + * </pre> * * */