2 // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
3 // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
4 // Any modifications to this file will be lost upon recompilation of the source schema.
5 // Generated on: 2023.05.13 at 06:58:41 PM BST
8 package jalview.xml.binding.jalview;
10 import java.math.BigInteger;
11 import java.util.ArrayList;
12 import java.util.List;
13 import javax.xml.bind.annotation.XmlAccessType;
14 import javax.xml.bind.annotation.XmlAccessorType;
15 import javax.xml.bind.annotation.XmlAttribute;
16 import javax.xml.bind.annotation.XmlElement;
17 import javax.xml.bind.annotation.XmlRootElement;
18 import javax.xml.bind.annotation.XmlType;
22 * Java class for anonymous complex type.
25 * The following schema fragment specifies the expected content contained within
31 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
33 * <element name="alcodon" maxOccurs="unbounded" minOccurs="0">
36 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
37 * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
38 * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
39 * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
41 * </complexContent>
44 * <element name="alcodMap" maxOccurs="unbounded" minOccurs="0">
47 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
49 * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
51 * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
53 * </complexContent>
58 * </complexContent>
64 @XmlAccessorType(XmlAccessType.FIELD)
65 @XmlType(name = "", propOrder = { "alcodon", "alcodMap" })
66 @XmlRootElement(name = "AlcodonFrame")
67 public class AlcodonFrame
70 protected List<AlcodonFrame.Alcodon> alcodon;
72 protected List<AlcodonFrame.AlcodMap> alcodMap;
75 * Gets the value of the alcodon property.
78 * This accessor method returns a reference to the live list, not a snapshot.
79 * Therefore any modification you make to the returned list will be present
80 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
81 * for the alcodon property.
84 * For example, to add a new item, do as follows:
87 * getAlcodon().add(newItem);
92 * Objects of the following type(s) are allowed in the list
93 * {@link AlcodonFrame.Alcodon }
97 public List<AlcodonFrame.Alcodon> getAlcodon()
101 alcodon = new ArrayList<AlcodonFrame.Alcodon>();
107 * Gets the value of the alcodMap property.
110 * This accessor method returns a reference to the live list, not a snapshot.
111 * Therefore any modification you make to the returned list will be present
112 * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
113 * for the alcodMap property.
116 * For example, to add a new item, do as follows:
119 * getAlcodMap().add(newItem);
124 * Objects of the following type(s) are allowed in the list
125 * {@link AlcodonFrame.AlcodMap }
129 public List<AlcodonFrame.AlcodMap> getAlcodMap()
131 if (alcodMap == null)
133 alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
135 return this.alcodMap;
140 * Java class for anonymous complex type.
143 * The following schema fragment specifies the expected content contained
148 * <complexContent>
149 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
151 * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/>
153 * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
155 * </complexContent>
161 @XmlAccessorType(XmlAccessType.FIELD)
162 @XmlType(name = "", propOrder = { "mapping" })
163 public static class AlcodMap
166 @XmlElement(name = "Mapping", required = true)
167 protected Mapping mapping;
169 @XmlAttribute(name = "dnasq", required = true)
170 protected String dnasq;
174 * a Mapping entry and an associated protein sequence
177 * @return possible object is {@link Mapping }
180 public Mapping getMapping()
186 * Sets the value of the mapping property.
189 * allowed object is {@link Mapping }
192 public void setMapping(Mapping value)
194 this.mapping = value;
198 * Gets the value of the dnasq property.
200 * @return possible object is {@link String }
203 public String getDnasq()
209 * Sets the value of the dnasq property.
212 * allowed object is {@link String }
215 public void setDnasq(String value)
224 * specifies a series of aligned codons from an associated DNA sequence
225 * alignment that when translated correspond to columns of a peptide
226 * alignment. Element may have either all pos1,2,3 attributes specified, or
227 * none at all (indicating a gapped column with no translated peptide).
231 * Java class for anonymous complex type.
234 * The following schema fragment specifies the expected content contained
239 * <complexContent>
240 * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
241 * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" />
242 * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" />
243 * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" />
245 * </complexContent>
251 @XmlAccessorType(XmlAccessType.FIELD)
253 public static class Alcodon
256 @XmlAttribute(name = "pos1")
257 protected BigInteger pos1;
259 @XmlAttribute(name = "pos2")
260 protected BigInteger pos2;
262 @XmlAttribute(name = "pos3")
263 protected BigInteger pos3;
266 * Gets the value of the pos1 property.
268 * @return possible object is {@link BigInteger }
271 public BigInteger getPos1()
277 * Sets the value of the pos1 property.
280 * allowed object is {@link BigInteger }
283 public void setPos1(BigInteger value)
289 * Gets the value of the pos2 property.
291 * @return possible object is {@link BigInteger }
294 public BigInteger getPos2()
300 * Sets the value of the pos2 property.
303 * allowed object is {@link BigInteger }
306 public void setPos2(BigInteger value)
312 * Gets the value of the pos3 property.
314 * @return possible object is {@link BigInteger }
317 public BigInteger getPos3()
323 * Sets the value of the pos3 property.
326 * allowed object is {@link BigInteger }
329 public void setPos3(BigInteger value)