Coverage Report
File AlcodonFrame.java
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60% of files have more coverage
Classes
| Class | Line # | Actions | |||
|---|---|---|---|---|---|
| AlcodonFrame | 69 | 6 | 4 | ||
| AlcodonFrame.AlcodMap | 163 | 4 | 4 | ||
| AlcodonFrame.Alcodon | 263 | 6 | 6 |
Contributing tests
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| 1 | // | |
| 2 | // This file was generated by the Eclipse Implementation of JAXB, v2.3.9 | |
| 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: 2025.04.17 at 04:05:44 PM BST | |
| 6 | // | |
| 7 | ||
| 8 | ||
| 9 | package jalview.xml.binding.jalview; | |
| 10 | ||
| 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; | |
| 20 | ||
| 21 | ||
| 22 | /** | |
| 23 | * <p>Java class for anonymous complex type</p>. | |
| 24 | * | |
| 25 | * <p>The following schema fragment specifies the expected content contained within this class.</p> | |
| 26 | * | |
| 27 | * <pre> | |
| 28 | * <complexType> | |
| 29 | * <complexContent> | |
| 30 | * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> | |
| 31 | * <sequence> | |
| 32 | * <element name="alcodon" maxOccurs="unbounded" minOccurs="0"> | |
| 33 | * <complexType> | |
| 34 | * <complexContent> | |
| 35 | * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> | |
| 36 | * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /> | |
| 37 | * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /> | |
| 38 | * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /> | |
| 39 | * </restriction> | |
| 40 | * </complexContent> | |
| 41 | * </complexType> | |
| 42 | * </element> | |
| 43 | * <element name="alcodMap" maxOccurs="unbounded" minOccurs="0"> | |
| 44 | * <complexType> | |
| 45 | * <complexContent> | |
| 46 | * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> | |
| 47 | * <sequence> | |
| 48 | * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/> | |
| 49 | * </sequence> | |
| 50 | * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> | |
| 51 | * </restriction> | |
| 52 | * </complexContent> | |
| 53 | * </complexType> | |
| 54 | * </element> | |
| 55 | * </sequence> | |
| 56 | * </restriction> | |
| 57 | * </complexContent> | |
| 58 | * </complexType> | |
| 59 | * </pre> | |
| 60 | * | |
| 61 | * | |
| 62 | */ | |
| 63 | @XmlAccessorType(XmlAccessType.FIELD) | |
| 64 | @XmlType(name = "", propOrder = { | |
| 65 | "alcodon", | |
| 66 | "alcodMap" | |
| 67 | }) | |
| 68 | @XmlRootElement(name = "AlcodonFrame") | |
| 69 | public class AlcodonFrame { | |
| 70 | ||
| 71 | protected List<AlcodonFrame.Alcodon> alcodon; | |
| 72 | protected List<AlcodonFrame.AlcodMap> alcodMap; | |
| 73 | ||
| 74 | /** | |
| 75 | * Gets the value of the alcodon property. | |
| 76 | * | |
| 77 | * <p>This accessor method returns a reference to the live list, | |
| 78 | * not a snapshot. Therefore any modification you make to the | |
| 79 | * returned list will be present inside the JAXB object. | |
| 80 | * This is why there is not a <CODE>set</CODE> method for the alcodon property.</p> | |
| 81 | * | |
| 82 | * <p> | |
| 83 | * For example, to add a new item, do as follows: | |
| 84 | * </p> | |
| 85 | * <pre> | |
| 86 | * getAlcodon().add(newItem); | |
| 87 | * </pre> | |
| 88 | * | |
| 89 | * | |
| 90 | * <p> | |
| 91 | * Objects of the following type(s) are allowed in the list | |
| 92 | * {@link AlcodonFrame.Alcodon } | |
| 93 | * </p> | |
| 94 | * | |
| 95 | * | |
| 96 | * @return | |
| 97 | * The value of the alcodon property. | |
| 98 | */ | |
| 99 | 0 |  public List<AlcodonFrame.Alcodon> getAlcodon() { |
| 100 | 0 | if (alcodon == null) { |
| 101 | 0 | alcodon = new ArrayList<AlcodonFrame.Alcodon>(); |
| 102 | } | |
| 103 | 0 | return this.alcodon; |
| 104 | } | |
| 105 | ||
| 106 | /** | |
| 107 | * Gets the value of the alcodMap property. | |
| 108 | * | |
| 109 | * <p>This accessor method returns a reference to the live list, | |
| 110 | * not a snapshot. Therefore any modification you make to the | |
| 111 | * returned list will be present inside the JAXB object. | |
| 112 | * This is why there is not a <CODE>set</CODE> method for the alcodMap property.</p> | |
| 113 | * | |
| 114 | * <p> | |
| 115 | * For example, to add a new item, do as follows: | |
| 116 | * </p> | |
| 117 | * <pre> | |
| 118 | * getAlcodMap().add(newItem); | |
| 119 | * </pre> | |
| 120 | * | |
| 121 | * | |
| 122 | * <p> | |
| 123 | * Objects of the following type(s) are allowed in the list | |
| 124 | * {@link AlcodonFrame.AlcodMap } | |
| 125 | * </p> | |
| 126 | * | |
| 127 | * | |
| 128 | * @return | |
| 129 | * The value of the alcodMap property. | |
| 130 | */ | |
| 131 | 0 | public List<AlcodonFrame.AlcodMap> getAlcodMap() { |
| 132 | 0 | if (alcodMap == null) { |
| 133 | 0 | alcodMap = new ArrayList<AlcodonFrame.AlcodMap>(); |
| 134 | } | |
| 135 | 0 | return this.alcodMap; |
| 136 | } | |
| 137 | ||
| 138 | ||
| 139 | /** | |
| 140 | * <p>Java class for anonymous complex type</p>. | |
| 141 | * | |
| 142 | * <p>The following schema fragment specifies the expected content contained within this class.</p> | |
| 143 | * | |
| 144 | * <pre> | |
| 145 | * <complexType> | |
| 146 | * <complexContent> | |
| 147 | * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> | |
| 148 | * <sequence> | |
| 149 | * <element ref="{www.vamsas.ac.uk/jalview/version2}Mapping"/> | |
| 150 | * </sequence> | |
| 151 | * <attribute name="dnasq" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> | |
| 152 | * </restriction> | |
| 153 | * </complexContent> | |
| 154 | * </complexType> | |
| 155 | * </pre> | |
| 156 | * | |
| 157 | * | |
| 158 | */ | |
| 159 | @XmlAccessorType(XmlAccessType.FIELD) | |
| 160 | @XmlType(name = "", propOrder = { | |
| 161 | "mapping" | |
| 162 | }) | |
| 163 | public static class AlcodMap { | |
| 164 | ||
| 165 | /** | |
| 166 | * a Mapping entry and an associated protein | |
| 167 | * sequence | |
| 168 | * | |
| 169 | */ | |
| 170 | @XmlElement(name = "Mapping", required = true) | |
| 171 | protected Mapping mapping; | |
| 172 | /** | |
| 173 | * internal jalview id for the dnasq for this | |
| 174 | * mapping. | |
| 175 | * | |
| 176 | */ | |
| 177 | @XmlAttribute(name = "dnasq", required = true) | |
| 178 | protected String dnasq; | |
| 179 | ||
| 180 | /** | |
| 181 | * a Mapping entry and an associated protein | |
| 182 | * sequence | |
| 183 | * | |
| 184 | * @return | |
| 185 | * possible object is | |
| 186 | * {@link Mapping } | |
| 187 | * | |
| 188 | */ | |
| 189 | 0 | public Mapping getMapping() { |
| 190 | 0 | return mapping; |
| 191 | } | |
| 192 | ||
| 193 | /** | |
| 194 | * Sets the value of the mapping property. | |
| 195 | * | |
| 196 | * @param value | |
| 197 | * allowed object is | |
| 198 | * {@link Mapping } | |
| 199 | * | |
| 200 | * @see #getMapping() | |
| 201 | */ | |
| 202 | 0 | public void setMapping(Mapping value) { |
| 203 | 0 | this.mapping = value; |
| 204 | } | |
| 205 | ||
| 206 | /** | |
| 207 | * internal jalview id for the dnasq for this | |
| 208 | * mapping. | |
| 209 | * | |
| 210 | * @return | |
| 211 | * possible object is | |
| 212 | * {@link String } | |
| 213 | * | |
| 214 | */ | |
| 215 | 0 | public String getDnasq() { |
| 216 | 0 | return dnasq; |
| 217 | } | |
| 218 | ||
| 219 | /** | |
| 220 | * Sets the value of the dnasq property. | |
| 221 | * | |
| 222 | * @param value | |
| 223 | * allowed object is | |
| 224 | * {@link String } | |
| 225 | * | |
| 226 | * @see #getDnasq() | |
| 227 | */ | |
| 228 | 0 | public void setDnasq(String value) { |
| 229 | 0 | this.dnasq = value; |
| 230 | } | |
| 231 | ||
| 232 | } | |
| 233 | ||
| 234 | ||
| 235 | /** | |
| 236 | * specifies a series of aligned codons from an | |
| 237 | * associated DNA sequence alignment that when translated | |
| 238 | * correspond to columns of a peptide alignment. | |
| 239 | * Element may have | |
| 240 | * either all pos1,2,3 attributes specified, or none at all | |
| 241 | * (indicating a gapped column with no translated peptide). | |
| 242 | * | |
| 243 | * <p>Java class for anonymous complex type</p>. | |
| 244 | * | |
| 245 | * <p>The following schema fragment specifies the expected content contained within this class.</p> | |
| 246 | * | |
| 247 | * <pre> | |
| 248 | * <complexType> | |
| 249 | * <complexContent> | |
| 250 | * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> | |
| 251 | * <attribute name="pos1" type="{http://www.w3.org/2001/XMLSchema}integer" /> | |
| 252 | * <attribute name="pos2" type="{http://www.w3.org/2001/XMLSchema}integer" /> | |
| 253 | * <attribute name="pos3" type="{http://www.w3.org/2001/XMLSchema}integer" /> | |
| 254 | * </restriction> | |
| 255 | * </complexContent> | |
| 256 | * </complexType> | |
| 257 | * </pre> | |
| 258 | * | |
| 259 | * | |
| 260 | */ | |
| 261 | @XmlAccessorType(XmlAccessType.FIELD) | |
| 262 | @XmlType(name = "") | |
| 263 | public static class Alcodon { | |
| 264 | ||
| 265 | @XmlAttribute(name = "pos1") | |
| 266 | protected BigInteger pos1; | |
| 267 | @XmlAttribute(name = "pos2") | |
| 268 | protected BigInteger pos2; | |
| 269 | @XmlAttribute(name = "pos3") | |
| 270 | protected BigInteger pos3; | |
| 271 | ||
| 272 | /** | |
| 273 | * Gets the value of the pos1 property. | |
| 274 | * | |
| 275 | * @return | |
| 276 | * possible object is | |
| 277 | * {@link BigInteger } | |
| 278 | * | |
| 279 | */ | |
| 280 | 0 | public BigInteger getPos1() { |
| 281 | 0 | return pos1; |
| 282 | } | |
| 283 | ||
| 284 | /** | |
| 285 | * Sets the value of the pos1 property. | |
| 286 | * | |
| 287 | * @param value | |
| 288 | * allowed object is | |
| 289 | * {@link BigInteger } | |
| 290 | * | |
| 291 | */ | |
| 292 | 0 | public void setPos1(BigInteger value) { |
| 293 | 0 | this.pos1 = value; |
| 294 | } | |
| 295 | ||
| 296 | /** | |
| 297 | * Gets the value of the pos2 property. | |
| 298 | * | |
| 299 | * @return | |
| 300 | * possible object is | |
| 301 | * {@link BigInteger } | |
| 302 | * | |
| 303 | */ | |
| 304 | 0 | public BigInteger getPos2() { |
| 305 | 0 | return pos2; |
| 306 | } | |
| 307 | ||
| 308 | /** | |
| 309 | * Sets the value of the pos2 property. | |
| 310 | * | |
| 311 | * @param value | |
| 312 | * allowed object is | |
| 313 | * {@link BigInteger } | |
| 314 | * | |
| 315 | */ | |
| 316 | 0 | public void setPos2(BigInteger value) { |
| 317 | 0 | this.pos2 = value; |
| 318 | } | |
| 319 | ||
| 320 | /** | |
| 321 | * Gets the value of the pos3 property. | |
| 322 | * | |
| 323 | * @return | |
| 324 | * possible object is | |
| 325 | * {@link BigInteger } | |
| 326 | * | |
| 327 | */ | |
| 328 | 0 | public BigInteger getPos3() { |
| 329 | 0 | return pos3; |
| 330 | } | |
| 331 | ||
| 332 | /** | |
| 333 | * Sets the value of the pos3 property. | |
| 334 | * | |
| 335 | * @param value | |
| 336 | * allowed object is | |
| 337 | * {@link BigInteger } | |
| 338 | * | |
| 339 | */ | |
| 340 | 0 | public void setPos3(BigInteger value) { |
| 341 | 0 | this.pos3 = value; |
| 342 | } | |
| 343 | ||
| 344 | } | |
| 345 | ||
| 346 | } |