X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FAlcodonFrame.java;h=bb263038a90303639d936d8c80bc14beb82e7992;hb=4a28fee3e0c129a01268d26e1396b045bd893fb8;hp=83f1ee28b51301cd4b4b92c03cc1b270a76e6870;hpb=c25cfde239527da78fecce55a877330afa90701d;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index 83f1ee2..bb26303 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 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: 2023.11.01 at 07:03:09 PM GMT // - package jalview.xml.binding.jalview; import java.math.BigInteger; @@ -18,309 +17,288 @@ 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 { +public class AlcodonFrame +{ + + protected List alcodon; + + protected List alcodMap; - protected List alcodon; - protected List alcodMap; + /** + * 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. + * + * <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 } + * + * + */ + public List getAlcodon() + { + if (alcodon == null) + { + alcodon = new ArrayList(); + } + return this.alcodon; + } + + /** + * 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 } + * + * + */ + public List getAlcodMap() + { + if (alcodMap == null) + { + alcodMap = new ArrayList(); + } + return this.alcodMap; + } + + /** + * <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> + * + * + */ + @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. * - *

- * 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. + * a Mapping entry and an associated protein sequence * - *

- * 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 } * + * @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. - * - *

- * 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 } + * 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; } - /** - *

Java class for anonymous complex type. + * Gets the value of the dnasq property. * - *

The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link String } * - * 

-     * <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>
-     *
+ */ + 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). + * + * + * <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="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> + * + * + */ + @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 } * - *

Java class for anonymous complex type. + */ + public void setPos1(BigInteger value) + { + this.pos1 = value; + } + + /** + * Gets the value of the pos2 property. * - *

The following schema fragment specifies the expected content contained within this class. + * @return possible object is {@link BigInteger } * - * 

-     * <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>
-     *
+ */ + 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; } + } + }