X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FAlcodonFrame.java;h=c412c36eeb78e9c02b21c1c196aea46e78f1ca9d;hb=893f21fe8df6a9d47ced8140e3ba75f03407be00;hp=5dcc0bd63db18266709c90e5c0e34f07a935d5a3;hpb=4b7d3640209c4434d569c746672cf9eed4250ace;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index 5dcc0bd..c412c36 100644 --- a/src/jalview/xml/binding/jalview/AlcodonFrame.java +++ b/src/jalview/xml/binding/jalview/AlcodonFrame.java @@ -1,10 +1,11 @@ // -// 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: 2023.03.17 at 05:31:44 PM GMT +// Generated on: 2023.11.01 at 07:03:09 PM GMT // + package jalview.xml.binding.jalview; import java.math.BigInteger; @@ -17,320 +18,314 @@ 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>
- *     <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>
- *
+ * <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> * * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "", propOrder = { "alcodon", "alcodMap" }) +@XmlType(name = "", propOrder = { + "alcodon", + "alcodMap" +}) @XmlRootElement(name = "AlcodonFrame") -public class AlcodonFrame -{ - - protected List alcodon; - - protected List alcodMap; +public class AlcodonFrame { - /** - * 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; + protected List alcodon; + protected List alcodMap; /** + * Gets the value of the alcodon property. * - * a Mapping entry and an associated protein sequence + * <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. * + * <p> + * For example, to add a new item, do as follows: + * <pre> + * getAlcodon().add(newItem); + * </pre> * - * @return possible object is {@link Mapping } * - */ - public Mapping getMapping() - { - return mapping; - } - - /** - * Sets the value of the mapping property. + * <p> + * Objects of the following type(s) are allowed in the list + * {@link AlcodonFrame.Alcodon } * - * @param value - * allowed object is {@link Mapping } * */ - public void setMapping(Mapping value) - { - this.mapping = value; + public List getAlcodon() { + if (alcodon == null) { + alcodon = new ArrayList(); + } + return this.alcodon; } /** - * Gets the value of the dnasq property. + * 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 } * - * @return possible object is {@link String } * */ - public String getDnasq() - { - return dnasq; + public List getAlcodMap() { + if (alcodMap == null) { + alcodMap = new ArrayList(); + } + return this.alcodMap; } + /** - * Sets the value of the dnasq property. + * <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"/&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> * - * @param value - * allowed object is {@link String } * */ - public void setDnasq(String value) - { - this.dnasq = value; - } + @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; - /** - * - * 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 - { + /** + * + * a Mapping entry and an associated protein + * sequence + * + * + * @return + * possible object is + * {@link Mapping } + * + */ + public Mapping getMapping() { + return mapping; + } - @XmlAttribute(name = "pos1") - protected BigInteger pos1; + /** + * Sets the value of the mapping property. + * + * @param value + * allowed object is + * {@link Mapping } + * + */ + public void setMapping(Mapping value) { + this.mapping = value; + } - @XmlAttribute(name = "pos2") - protected BigInteger pos2; + /** + * Gets the value of the dnasq property. + * + * @return + * possible object is + * {@link String } + * + */ + public String getDnasq() { + return dnasq; + } - @XmlAttribute(name = "pos3") - protected BigInteger pos3; + /** + * Sets the value of the dnasq property. + * + * @param value + * allowed object is + * {@link String } + * + */ + public void setDnasq(String value) { + this.dnasq = value; + } - /** - * 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 } + * 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). + * * - */ - public BigInteger getPos2() - { - return pos2; - } - - /** - * Sets the value of the pos2 property. + * <p>Java class for anonymous complex type. * - * @param value - * allowed object is {@link BigInteger } + * <p>The following schema fragment specifies the expected content contained within this class. * - */ - public void setPos2(BigInteger value) - { - this.pos2 = value; - } - - /** - * Gets the value of the pos3 property. + * <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> * - * @return possible object is {@link BigInteger } * */ - public BigInteger getPos3() - { - return pos3; - } + @XmlAccessorType(XmlAccessType.FIELD) + @XmlType(name = "") + public static class Alcodon { - /** - * Sets the value of the pos3 property. - * - * @param value - * allowed object is {@link BigInteger } - * - */ - public void setPos3(BigInteger value) - { - this.pos3 = value; - } + @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; + } + + /** + * Sets the value of the pos3 property. + * + * @param value + * allowed object is + * {@link BigInteger } + * + */ + public void setPos3(BigInteger value) { + this.pos3 = value; + } + + } }