2 // This file was generated by the Eclipse Implementation of JAXB, v2.3.3
3 // See https://eclipse-ee4j.github.io/jaxb-ri
4 // Any modifications to this file will be lost upon recompilation of the source schema.
5 // Generated on: 2023.11.01 at 07:03:09 PM GMT
9 package jalview.xml.binding.jalview;
11 import java.math.BigInteger;
12 import java.util.ArrayList;
13 import java.util.List;
14 import javax.xml.bind.annotation.XmlAccessType;
15 import javax.xml.bind.annotation.XmlAccessorType;
16 import javax.xml.bind.annotation.XmlAttribute;
17 import javax.xml.bind.annotation.XmlElement;
18 import javax.xml.bind.annotation.XmlRootElement;
19 import javax.xml.bind.annotation.XmlType;
23 * <p>Java class for anonymous complex type.
25 * <p>The following schema fragment specifies the expected content contained within this class.
28 * &lt;complexType&gt;
29 * &lt;complexContent&gt;
30 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
31 * &lt;sequence&gt;
32 * &lt;element name="alcodon" maxOccurs="unbounded" minOccurs="0"&gt;
33 * &lt;complexType&gt;
34 * &lt;complexContent&gt;
35 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
36 * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
37 * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
38 * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
39 * &lt;/restriction&gt;
40 * &lt;/complexContent&gt;
41 * &lt;/complexType&gt;
42 * &lt;/element&gt;
43 * &lt;element name="alcodMap" maxOccurs="unbounded" minOccurs="0"&gt;
44 * &lt;complexType&gt;
45 * &lt;complexContent&gt;
46 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
47 * &lt;sequence&gt;
48 * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
49 * &lt;/sequence&gt;
50 * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
51 * &lt;/restriction&gt;
52 * &lt;/complexContent&gt;
53 * &lt;/complexType&gt;
54 * &lt;/element&gt;
55 * &lt;/sequence&gt;
56 * &lt;/restriction&gt;
57 * &lt;/complexContent&gt;
58 * &lt;/complexType&gt;
63 @XmlAccessorType(XmlAccessType.FIELD)
64 @XmlType(name = "", propOrder = {
68 @XmlRootElement(name = "AlcodonFrame")
69 public class AlcodonFrame {
71 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,
79 * not a snapshot. Therefore any modification you make to the
80 * returned list will be present inside the JAXB object.
81 * This is why there is not a <CODE>set</CODE> method for the alcodon property.
84 * For example, to add a new item, do as follows:
86 * getAlcodon().add(newItem);
91 * Objects of the following type(s) are allowed in the list
92 * {@link AlcodonFrame.Alcodon }
96 public List<AlcodonFrame.Alcodon> getAlcodon() {
97 if (alcodon == null) {
98 alcodon = new ArrayList<AlcodonFrame.Alcodon>();
104 * Gets the value of the alcodMap property.
107 * This accessor method returns a reference to the live list,
108 * not a snapshot. Therefore any modification you make to the
109 * returned list will be present inside the JAXB object.
110 * This is why there is not a <CODE>set</CODE> method for the alcodMap property.
113 * For example, to add a new item, do as follows:
115 * getAlcodMap().add(newItem);
120 * Objects of the following type(s) are allowed in the list
121 * {@link AlcodonFrame.AlcodMap }
125 public List<AlcodonFrame.AlcodMap> getAlcodMap() {
126 if (alcodMap == null) {
127 alcodMap = new ArrayList<AlcodonFrame.AlcodMap>();
129 return this.alcodMap;
134 * <p>Java class for anonymous complex type.
136 * <p>The following schema fragment specifies the expected content contained within this class.
139 * &lt;complexType&gt;
140 * &lt;complexContent&gt;
141 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
142 * &lt;sequence&gt;
143 * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/&gt;
144 * &lt;/sequence&gt;
145 * &lt;attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
146 * &lt;/restriction&gt;
147 * &lt;/complexContent&gt;
148 * &lt;/complexType&gt;
153 @XmlAccessorType(XmlAccessType.FIELD)
154 @XmlType(name = "", propOrder = {
157 public static class AlcodMap {
159 @XmlElement(name = "Mapping", required = true)
160 protected Mapping mapping;
161 @XmlAttribute(name = "dnasq", required = true)
162 protected String dnasq;
166 * a Mapping entry and an associated protein
175 public Mapping getMapping() {
180 * Sets the value of the mapping property.
187 public void setMapping(Mapping value) {
188 this.mapping = value;
192 * Gets the value of the dnasq property.
199 public String getDnasq() {
204 * Sets the value of the dnasq property.
211 public void setDnasq(String value) {
220 * specifies a series of aligned codons from an
221 * associated DNA sequence alignment that when translated
222 * correspond to columns of a peptide alignment.
224 * either all pos1,2,3 attributes specified, or none at all
225 * (indicating a gapped column with no translated peptide).
228 * <p>Java class for anonymous complex type.
230 * <p>The following schema fragment specifies the expected content contained within this class.
233 * &lt;complexType&gt;
234 * &lt;complexContent&gt;
235 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
236 * &lt;attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
237 * &lt;attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
238 * &lt;attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /&gt;
239 * &lt;/restriction&gt;
240 * &lt;/complexContent&gt;
241 * &lt;/complexType&gt;
246 @XmlAccessorType(XmlAccessType.FIELD)
248 public static class Alcodon {
250 @XmlAttribute(name = "pos1")
251 protected BigInteger pos1;
252 @XmlAttribute(name = "pos2")
253 protected BigInteger pos2;
254 @XmlAttribute(name = "pos3")
255 protected BigInteger pos3;
258 * Gets the value of the pos1 property.
262 * {@link BigInteger }
265 public BigInteger getPos1() {
270 * Sets the value of the pos1 property.
274 * {@link BigInteger }
277 public void setPos1(BigInteger value) {
282 * Gets the value of the pos2 property.
286 * {@link BigInteger }
289 public BigInteger getPos2() {
294 * Sets the value of the pos2 property.
298 * {@link BigInteger }
301 public void setPos2(BigInteger value) {
306 * Gets the value of the pos3 property.
310 * {@link BigInteger }
313 public BigInteger getPos3() {
318 * Sets the value of the pos3 property.
322 * {@link BigInteger }
325 public void setPos3(BigInteger value) {