//
-// 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 <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
// Any modifications to this file will be lost upon recompilation of the source schema.
-// Generated on: 2021.08.30 at 11:05:22 AM BST
+// Generated on: 2023.01.31 at 04:07:08 PM GMT
//
+
package jalview.xml.binding.jalview;
import java.math.BigInteger;
import javax.xml.bind.annotation.XmlRootElement;
import javax.xml.bind.annotation.XmlType;
+
/**
- * <p>Java class for anonymous complex type.
+ * <p>Java class for anonymous complex type.
*
- * <p>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.
*
- * <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>
+ * <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
-{
-
- protected List<AlcodonFrame.Alcodon> alcodon;
-
- protected List<AlcodonFrame.AlcodMap> alcodMap;
+public class AlcodonFrame {
- /**
- * 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<AlcodonFrame.Alcodon> getAlcodon()
- {
- if (alcodon == null)
- {
- alcodon = new ArrayList<AlcodonFrame.Alcodon>();
- }
- 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<AlcodonFrame.AlcodMap> getAlcodMap()
- {
- if (alcodMap == null)
- {
- alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
- }
- 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;
+ protected List<AlcodonFrame.Alcodon> alcodon;
+ protected List<AlcodonFrame.AlcodMap> 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<AlcodonFrame.Alcodon> getAlcodon() {
+ if (alcodon == null) {
+ alcodon = new ArrayList<AlcodonFrame.Alcodon>();
+ }
+ 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<AlcodonFrame.AlcodMap> getAlcodMap() {
+ if (alcodMap == null) {
+ alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
+ }
+ 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>
+ * <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>
+ * </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).
- *
- *
- * <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
- {
+ /**
+ *
+ * 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>
+ * <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>
*
- * @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;
+ }
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff