X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FAlcodonFrame.java;h=5dcc0bd63db18266709c90e5c0e34f07a935d5a3;hb=beb2fee66dde629e3bbb7febb38d0116e1a64df2;hp=7fe5a4dd3b4d26325299922206802062dd7f1ec1;hpb=7b32d373b60d0af55481cfd6d377b2cc1ec035c0;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index 7fe5a4d..6b98b6a 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -1,11 +1,10 @@ // -// This file was generated by the Eclipse Implementation of JAXB, v2.3.3 -// See https://eclipse-ee4j.github.io/jaxb-ri +// This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802 +// See http://java.sun.com/xml/jaxb // Any modifications to this file will be lost upon recompilation of the source schema. -// Generated on: 2022.02.07 at 04:44:47 PM GMT +// Generated on: 2023.05.13 at 06:58:41 PM BST // - package jalview.xml.binding.jalview; import java.math.BigInteger; @@ -18,309 +17,320 @@ import javax.xml.bind.annotation.XmlElement; import javax.xml.bind.annotation.XmlRootElement; import javax.xml.bind.annotation.XmlType; - /** - * <p>Java class for anonymous complex type. + *

+ * Java class for anonymous complex type. * - * <p>The following schema fragment specifies the expected content contained within this class. + *

+ * 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="alcodon" 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="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;/restriction&gt; - * &lt;/complexContent&gt; - * &lt;/complexType&gt; - * &lt;/element&gt; - * &lt;element name="alcodMap" 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"/&gt; - * &lt;/sequence&gt; - * &lt;attribute name="dnasq" 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> + * 

+ * <complexType>
+ *   <complexContent>
+ *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *       <sequence>
+ *         <element name="alcodon" maxOccurs="unbounded" minOccurs="0">
+ *           <complexType>
+ *             <complexContent>
+ *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+ *                 <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *                 <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *         <element name="alcodMap" 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"/>
+ *                 </sequence>
+ *                 <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+ *               </restriction>
+ *             </complexContent>
+ *           </complexType>
+ *         </element>
+ *       </sequence>
+ *     </restriction>
+ *   </complexContent>
+ * </complexType>
+ *
* * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "", propOrder = { - "alcodon", - "alcodMap" -}) +@XmlType(name = "", propOrder = { "alcodon", "alcodMap" }) @XmlRootElement(name = "AlcodonFrame") -public class AlcodonFrame { +public class AlcodonFrame +{ + + protected List alcodon; + + protected List alcodMap; - protected List alcodon; - protected List alcodMap; + /** + * Gets the value of the alcodon 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 alcodon property. + * + *

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

+   * getAlcodon().add(newItem);
+   *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link AlcodonFrame.Alcodon } + * + * + */ + public List getAlcodon() + { + if (alcodon == null) + { + alcodon = new ArrayList(); + } + return this.alcodon; + } + + /** + * Gets the value of the alcodMap 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 alcodMap property. + * + *

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

+   * getAlcodMap().add(newItem);
+   *
+ * + * + *

+ * Objects of the following type(s) are allowed in the list + * {@link AlcodonFrame.AlcodMap } + * + * + */ + public List getAlcodMap() + { + if (alcodMap == null) + { + alcodMap = new ArrayList(); + } + return this.alcodMap; + } + + /** + *

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

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

+   * <complexType>
+   *   <complexContent>
+   *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
+   *       <sequence>
+   *         <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
+   *       </sequence>
+   *       <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "", propOrder = { "mapping" }) + public static class AlcodMap + { + + @XmlElement(name = "Mapping", required = true) + protected Mapping mapping; + + @XmlAttribute(name = "dnasq", required = true) + protected String dnasq; /** - * Gets the value of the alcodon 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 alcodon property. + * a Mapping entry and an associated protein sequence * - * <p> - * For example, to add a new item, do as follows: - * <pre> - * getAlcodon().add(newItem); - * </pre> - * - * - * <p> - * Objects of the following type(s) are allowed in the list - * {@link AlcodonFrame.Alcodon } * + * @return possible object is {@link Mapping } * */ - public List getAlcodon() { - if (alcodon == null) { - alcodon = new ArrayList(); - } - return this.alcodon; + public Mapping getMapping() + { + return mapping; } /** - * Gets the value of the alcodMap 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 alcodMap property. - * - * <p> - * For example, to add a new item, do as follows: - * <pre> - * getAlcodMap().add(newItem); - * </pre> - * - * - * <p> - * Objects of the following type(s) are allowed in the list - * {@link AlcodonFrame.AlcodMap } + * Sets the value of the mapping property. * + * @param value + * allowed object is {@link Mapping } * */ - public List getAlcodMap() { - if (alcodMap == null) { - alcodMap = new ArrayList(); - } - return this.alcodMap; + public void setMapping(Mapping value) + { + this.mapping = value; } - /** - * <p>Java class for anonymous complex type. + * Gets the value of the dnasq property. * - * <p>The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link String } * - * <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"/&gt; - * &lt;/sequence&gt; - * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt; - * &lt;/restriction&gt; - * &lt;/complexContent&gt; - * &lt;/complexType&gt; - * </pre> + */ + public String getDnasq() + { + return dnasq; + } + + /** + * Sets the value of the dnasq property. * + * @param value + * allowed object is {@link String } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "", propOrder = { - "mapping" - }) - public static class AlcodMap { + public void setDnasq(String value) + { + this.dnasq = value; + } - @XmlElement(name = "Mapping", required = true) - protected Mapping mapping; - @XmlAttribute(name = "dnasq", required = true) - protected String dnasq; + } - /** - * - * a Mapping entry and an associated protein sequence - * - * - * @return - * possible object is - * {@link Mapping } - * - */ - public Mapping getMapping() { - return mapping; - } + /** + * + * specifies a series of aligned codons from an associated DNA sequence + * alignment that when translated correspond to columns of a peptide + * alignment. Element may have either all pos1,2,3 attributes specified, or + * none at all (indicating a gapped column with no translated peptide). + * + * + *

+ * 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="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *       <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
+   *     </restriction>
+   *   </complexContent>
+   * </complexType>
+   *
+ * + * + */ + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Alcodon + { - /** - * Sets the value of the mapping property. - * - * @param value - * allowed object is - * {@link Mapping } - * - */ - public void setMapping(Mapping value) { - this.mapping = value; - } + @XmlAttribute(name = "pos1") + protected BigInteger pos1; - /** - * Gets the value of the dnasq property. - * - * @return - * possible object is - * {@link String } - * - */ - public String getDnasq() { - return dnasq; - } + @XmlAttribute(name = "pos2") + protected BigInteger pos2; - /** - * Sets the value of the dnasq property. - * - * @param value - * allowed object is - * {@link String } - * - */ - public void setDnasq(String value) { - this.dnasq = value; - } + @XmlAttribute(name = "pos3") + protected BigInteger pos3; + /** + * Gets the value of the pos1 property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getPos1() + { + return pos1; } - /** + * Sets the value of the pos1 property. * - * specifies a series of aligned codons from an associated DNA sequence alignment that when translated correspond to columns of a peptide alignment. - * Element may have either all pos1,2,3 attributes specified, or none at all (indicating a gapped column with no translated peptide). - * + * @param value + * allowed object is {@link BigInteger } * - * <p>Java class for anonymous complex type. + */ + public void setPos1(BigInteger value) + { + this.pos1 = value; + } + + /** + * Gets the value of the pos2 property. * - * <p>The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link BigInteger } * - * <pre> - * &lt;complexType&gt; - * &lt;complexContent&gt; - * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt; - * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt; - * &lt;/restriction&gt; - * &lt;/complexContent&gt; - * &lt;/complexType&gt; - * </pre> + */ + public BigInteger getPos2() + { + return pos2; + } + + /** + * Sets the value of the pos2 property. * + * @param value + * allowed object is {@link BigInteger } * */ - @XmlAccessorType(XmlAccessType.FIELD) - @XmlType(name = "") - public static class Alcodon { - - @XmlAttribute(name = "pos1") - protected BigInteger pos1; - @XmlAttribute(name = "pos2") - protected BigInteger pos2; - @XmlAttribute(name = "pos3") - protected BigInteger pos3; - - /** - * Gets the value of the pos1 property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getPos1() { - return pos1; - } - - /** - * Sets the value of the pos1 property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setPos1(BigInteger value) { - this.pos1 = value; - } - - /** - * Gets the value of the pos2 property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getPos2() { - return pos2; - } - - /** - * Sets the value of the pos2 property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setPos2(BigInteger value) { - this.pos2 = value; - } - - /** - * Gets the value of the pos3 property. - * - * @return - * possible object is - * {@link BigInteger } - * - */ - public BigInteger getPos3() { - return pos3; - } + public void setPos2(BigInteger value) + { + this.pos2 = value; + } - /** - * Sets the value of the pos3 property. - * - * @param value - * allowed object is - * {@link BigInteger } - * - */ - public void setPos3(BigInteger value) { - this.pos3 = value; - } + /** + * Gets the value of the pos3 property. + * + * @return possible object is {@link BigInteger } + * + */ + public BigInteger getPos3() + { + return pos3; + } + /** + * Sets the value of the pos3 property. + * + * @param value + * allowed object is {@link BigInteger } + * + */ + public void setPos3(BigInteger value) + { + this.pos3 = value; } + } + }