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> <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>
+ *
*
*
*/
@XmlAccessorType(XmlAccessType.FIELD)
-@XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
+@XmlType(name = "", propOrder = {
+ "alcodon",
+ "alcodMap"
+})
@XmlRootElement(name = "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.
*
+ *
+ * For example, to add a new item, do as follows: + *
+ * getAlcodon().add(newItem); + ** - * @return possible object is {@link Mapping } * - */ - public Mapping getMapping() - { - return mapping; - } - - /** - * Sets the value of the mapping property. + *
+ * 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
+ * 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 }
*
- * @return possible object is {@link String }
*
*/
- public String getDnasq()
- {
- return dnasq;
+ public List Java class for anonymous complex type.
+ *
+ * The following schema fragment specifies the expected content contained within this class.
+ *
+ * Java class for anonymous complex type.
*
- * @param value
- * allowed object is {@link BigInteger }
+ * 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.
+ * 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>
+ *
*
- * @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).
- *
- *
- * <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
- {
+ /**
+ *
+ * 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.
+ *
+ * <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>
+ *
*
- * @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;
+ }
+
+ }
}