X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fxml%2Fbinding%2Fjalview%2FAlcodonFrame.java;h=bb263038a90303639d936d8c80bc14beb82e7992;hb=4a28fee3e0c129a01268d26e1396b045bd893fb8;hp=cb90984c07a35a15a29be778ed2e55a4798c95d3;hpb=71d8702f4f5f12c9c2f1dcb119091704dc738522;p=jalview.git diff --git a/src/jalview/xml/binding/jalview/AlcodonFrame.java b/src/jalview/xml/binding/jalview/AlcodonFrame.java index cb90984..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: 2019.06.07 at 02:21:15 PM BST +// 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> <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> * * */ @XmlAccessorType(XmlAccessType.FIELD) -@XmlType(name = "", propOrder = { - "alcodon", - "alcodMap" -}) +@XmlType(name = "", propOrder = { "alcodon", "alcodMap" }) @XmlRootElement(name = "AlcodonFrame") -public class AlcodonFrame { +public class AlcodonFrame +{ + + protected List
- * 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
- * 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
- * For example, to add a new item, do as follows:
- *
- * 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 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 }
*
- * 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 }
*
- * set
method for the alcodMap property.
- *
- *
- * getAlcodMap().add(newItem);
- *
- *
- *
- *
- * <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> <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> </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 }
*
- *
- * <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;
}
+ }
+
}