Class |
Line # |
Actions |
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SequenceSet | 66 | 19 | 14 | ||
SequenceSet.SequenceSetProperties | 353 | 4 | 4 |
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: 2024.07.25 at 04:43:38 PM BST | |
6 | // | |
7 | ||
8 | package jalview.xml.binding.jalview; | |
9 | ||
10 | import java.util.ArrayList; | |
11 | import java.util.List; | |
12 | import javax.xml.bind.annotation.XmlAccessType; | |
13 | import javax.xml.bind.annotation.XmlAccessorType; | |
14 | import javax.xml.bind.annotation.XmlAttribute; | |
15 | import javax.xml.bind.annotation.XmlElement; | |
16 | import javax.xml.bind.annotation.XmlRootElement; | |
17 | import javax.xml.bind.annotation.XmlType; | |
18 | ||
19 | /** | |
20 | * <p> | |
21 | * Java class for anonymous complex type | |
22 | * </p> | |
23 | * . | |
24 | * | |
25 | * <p> | |
26 | * The following schema fragment specifies the expected content contained within | |
27 | * this class. | |
28 | * </p> | |
29 | * | |
30 | * <pre> | |
31 | * <complexType> | |
32 | * <complexContent> | |
33 | * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> | |
34 | * <sequence> | |
35 | * <element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/> | |
36 | * <element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/> | |
37 | * <element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0"> | |
38 | * <complexType> | |
39 | * <complexContent> | |
40 | * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> | |
41 | * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /> | |
42 | * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /> | |
43 | * </restriction> | |
44 | * </complexContent> | |
45 | * </complexType> | |
46 | * </element> | |
47 | * <element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/> | |
48 | * <element name="Matrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/> | |
49 | * </sequence> | |
50 | * <attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /> | |
51 | * <attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" /> | |
52 | * </restriction> | |
53 | * </complexContent> | |
54 | * </complexType> | |
55 | * </pre> | |
56 | * | |
57 | * | |
58 | */ | |
59 | @XmlAccessorType(XmlAccessType.FIELD) | |
60 | @XmlType( | |
61 | name = "", | |
62 | propOrder = | |
63 | { "sequence", "annotation", "sequenceSetProperties", "alcodonFrame", | |
64 | "matrix" }) | |
65 | @XmlRootElement(name = "SequenceSet") | |
66 | public class SequenceSet | |
67 | { | |
68 | ||
69 | @XmlElement(name = "Sequence") | |
70 | protected List<Sequence> sequence; | |
71 | ||
72 | @XmlElement(name = "Annotation") | |
73 | protected List<Annotation> annotation; | |
74 | ||
75 | protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties; | |
76 | ||
77 | @XmlElement(name = "AlcodonFrame") | |
78 | protected List<AlcodonFrame> alcodonFrame; | |
79 | ||
80 | /** | |
81 | * Matrices referred to by this set of sequences. | |
82 | * | |
83 | */ | |
84 | @XmlElement(name = "Matrix") | |
85 | protected List<MatrixType> matrix; | |
86 | ||
87 | @XmlAttribute(name = "gapChar", required = true) | |
88 | protected String gapChar; | |
89 | ||
90 | /** | |
91 | * reference to set where jalview will gather the dataset sequences for all | |
92 | * sequences in the set. | |
93 | * | |
94 | */ | |
95 | @XmlAttribute(name = "datasetId") | |
96 | protected String datasetId; | |
97 | ||
98 | /** | |
99 | * Gets the value of the sequence property. | |
100 | * | |
101 | * <p> | |
102 | * This accessor method returns a reference to the live list, not a snapshot. | |
103 | * Therefore any modification you make to the returned list will be present | |
104 | * inside the JAXB object. This is why there is not a <CODE>set</CODE> method | |
105 | * for the sequence property. | |
106 | * </p> | |
107 | * | |
108 | * <p> | |
109 | * For example, to add a new item, do as follows: | |
110 | * </p> | |
111 | * | |
112 | * <pre> | |
113 | * getSequence().add(newItem); | |
114 | * </pre> | |
115 | * | |
116 | * | |
117 | * <p> | |
118 | * Objects of the following type(s) are allowed in the list {@link Sequence } | |
119 | * </p> | |
120 | * | |
121 | * | |
122 | * @return The value of the sequence property. | |
123 | */ | |
124 | 1867 | public List<Sequence> getSequence() |
125 | { | |
126 | 1867 | if (sequence == null) |
127 | { | |
128 | 103 | sequence = new ArrayList<Sequence>(); |
129 | } | |
130 | 1867 | return this.sequence; |
131 | } | |
132 | ||
133 | /** | |
134 | * Gets the value of the annotation property. | |
135 | * | |
136 | * <p> | |
137 | * This accessor method returns a reference to the live list, not a snapshot. | |
138 | * Therefore any modification you make to the returned list will be present | |
139 | * inside the JAXB object. This is why there is not a <CODE>set</CODE> method | |
140 | * for the annotation property. | |
141 | * </p> | |
142 | * | |
143 | * <p> | |
144 | * For example, to add a new item, do as follows: | |
145 | * </p> | |
146 | * | |
147 | * <pre> | |
148 | * getAnnotation().add(newItem); | |
149 | * </pre> | |
150 | * | |
151 | * | |
152 | * <p> | |
153 | * Objects of the following type(s) are allowed in the list {@link Annotation | |
154 | * } | |
155 | * </p> | |
156 | * | |
157 | * | |
158 | * @return The value of the annotation property. | |
159 | */ | |
160 | 643 | public List<Annotation> getAnnotation() |
161 | { | |
162 | 643 | if (annotation == null) |
163 | { | |
164 | 75 | annotation = new ArrayList<Annotation>(); |
165 | } | |
166 | 643 | return this.annotation; |
167 | } | |
168 | ||
169 | /** | |
170 | * Gets the value of the sequenceSetProperties property. | |
171 | * | |
172 | * <p> | |
173 | * This accessor method returns a reference to the live list, not a snapshot. | |
174 | * Therefore any modification you make to the returned list will be present | |
175 | * inside the JAXB object. This is why there is not a <CODE>set</CODE> method | |
176 | * for the sequenceSetProperties property. | |
177 | * </p> | |
178 | * | |
179 | * <p> | |
180 | * For example, to add a new item, do as follows: | |
181 | * </p> | |
182 | * | |
183 | * <pre> | |
184 | * getSequenceSetProperties().add(newItem); | |
185 | * </pre> | |
186 | * | |
187 | * | |
188 | * <p> | |
189 | * Objects of the following type(s) are allowed in the list | |
190 | * {@link SequenceSet.SequenceSetProperties } | |
191 | * </p> | |
192 | * | |
193 | * | |
194 | * @return The value of the sequenceSetProperties property. | |
195 | */ | |
196 | 173 | public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() |
197 | { | |
198 | 173 | if (sequenceSetProperties == null) |
199 | { | |
200 | 110 | sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>(); |
201 | } | |
202 | 173 | return this.sequenceSetProperties; |
203 | } | |
204 | ||
205 | /** | |
206 | * Gets the value of the alcodonFrame property. | |
207 | * | |
208 | * <p> | |
209 | * This accessor method returns a reference to the live list, not a snapshot. | |
210 | * Therefore any modification you make to the returned list will be present | |
211 | * inside the JAXB object. This is why there is not a <CODE>set</CODE> method | |
212 | * for the alcodonFrame property. | |
213 | * </p> | |
214 | * | |
215 | * <p> | |
216 | * For example, to add a new item, do as follows: | |
217 | * </p> | |
218 | * | |
219 | * <pre> | |
220 | * getAlcodonFrame().add(newItem); | |
221 | * </pre> | |
222 | * | |
223 | * | |
224 | * <p> | |
225 | * Objects of the following type(s) are allowed in the list | |
226 | * {@link AlcodonFrame } | |
227 | * </p> | |
228 | * | |
229 | * | |
230 | * @return The value of the alcodonFrame property. | |
231 | */ | |
232 | 110 | public List<AlcodonFrame> getAlcodonFrame() |
233 | { | |
234 | 110 | if (alcodonFrame == null) |
235 | { | |
236 | 110 | alcodonFrame = new ArrayList<AlcodonFrame>(); |
237 | } | |
238 | 110 | return this.alcodonFrame; |
239 | } | |
240 | ||
241 | /** | |
242 | * Matrices referred to by this set of sequences. | |
243 | * | |
244 | * Gets the value of the matrix property. | |
245 | * | |
246 | * <p> | |
247 | * This accessor method returns a reference to the live list, not a snapshot. | |
248 | * Therefore any modification you make to the returned list will be present | |
249 | * inside the JAXB object. This is why there is not a <CODE>set</CODE> method | |
250 | * for the matrix property. | |
251 | * </p> | |
252 | * | |
253 | * <p> | |
254 | * For example, to add a new item, do as follows: | |
255 | * </p> | |
256 | * | |
257 | * <pre> | |
258 | * getMatrix().add(newItem); | |
259 | * </pre> | |
260 | * | |
261 | * | |
262 | * <p> | |
263 | * Objects of the following type(s) are allowed in the list {@link MatrixType | |
264 | * } | |
265 | * </p> | |
266 | * | |
267 | * | |
268 | * @return The value of the matrix property. | |
269 | */ | |
270 | 224 | public List<MatrixType> getMatrix() |
271 | { | |
272 | 224 | if (matrix == null) |
273 | { | |
274 | 110 | matrix = new ArrayList<MatrixType>(); |
275 | } | |
276 | 224 | return this.matrix; |
277 | } | |
278 | ||
279 | /** | |
280 | * Gets the value of the gapChar property. | |
281 | * | |
282 | * @return possible object is {@link String } | |
283 | * | |
284 | */ | |
285 | 0 | public String getGapChar() |
286 | { | |
287 | 0 | return gapChar; |
288 | } | |
289 | ||
290 | /** | |
291 | * Sets the value of the gapChar property. | |
292 | * | |
293 | * @param value | |
294 | * allowed object is {@link String } | |
295 | * | |
296 | */ | |
297 | 73 | public void setGapChar(String value) |
298 | { | |
299 | 73 | this.gapChar = value; |
300 | } | |
301 | ||
302 | /** | |
303 | * reference to set where jalview will gather the dataset sequences for all | |
304 | * sequences in the set. | |
305 | * | |
306 | * @return possible object is {@link String } | |
307 | * | |
308 | */ | |
309 | 399 | public String getDatasetId() |
310 | { | |
311 | 399 | return datasetId; |
312 | } | |
313 | ||
314 | /** | |
315 | * Sets the value of the datasetId property. | |
316 | * | |
317 | * @param value | |
318 | * allowed object is {@link String } | |
319 | * | |
320 | * @see #getDatasetId() | |
321 | */ | |
322 | 73 | public void setDatasetId(String value) |
323 | { | |
324 | 73 | this.datasetId = value; |
325 | } | |
326 | ||
327 | /** | |
328 | * <p> | |
329 | * Java class for anonymous complex type | |
330 | * </p> | |
331 | * . | |
332 | * | |
333 | * <p> | |
334 | * The following schema fragment specifies the expected content contained | |
335 | * within this class. | |
336 | * </p> | |
337 | * | |
338 | * <pre> | |
339 | * <complexType> | |
340 | * <complexContent> | |
341 | * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType"> | |
342 | * <attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /> | |
343 | * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /> | |
344 | * </restriction> | |
345 | * </complexContent> | |
346 | * </complexType> | |
347 | * </pre> | |
348 | * | |
349 | * | |
350 | */ | |
351 | @XmlAccessorType(XmlAccessType.FIELD) | |
352 | @XmlType(name = "") | |
353 | public static class SequenceSetProperties | |
354 | { | |
355 | ||
356 | @XmlAttribute(name = "key") | |
357 | protected String key; | |
358 | ||
359 | @XmlAttribute(name = "value") | |
360 | protected String value; | |
361 | ||
362 | /** | |
363 | * Gets the value of the key property. | |
364 | * | |
365 | * @return possible object is {@link String } | |
366 | * | |
367 | */ | |
368 | 21 | public String getKey() |
369 | { | |
370 | 21 | return key; |
371 | } | |
372 | ||
373 | /** | |
374 | * Sets the value of the key property. | |
375 | * | |
376 | * @param value | |
377 | * allowed object is {@link String } | |
378 | * | |
379 | */ | |
380 | 21 | public void setKey(String value) |
381 | { | |
382 | 21 | this.key = value; |
383 | } | |
384 | ||
385 | /** | |
386 | * Gets the value of the value property. | |
387 | * | |
388 | * @return possible object is {@link String } | |
389 | * | |
390 | */ | |
391 | 21 | public String getValue() |
392 | { | |
393 | 21 | return value; |
394 | } | |
395 | ||
396 | /** | |
397 | * Sets the value of the value property. | |
398 | * | |
399 | * @param value | |
400 | * allowed object is {@link String } | |
401 | * | |
402 | */ | |
403 | 21 | public void setValue(String value) |
404 | { | |
405 | 21 | this.value = value; |
406 | } | |
407 | ||
408 | } | |
409 | ||
410 | } |