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Coverage Report

  1. Project Clover database Thu Nov 27 2025 16:51:35 GMT
  2. Package jalview.xml.binding.jalview

File SequenceSet.java

 

Coverage histogram

../../../../img/srcFileCovDistChart10.png
0% of files have more coverage

Code metrics

10
23
13
2
379
95
18
0.78
1.77
6.5
1.38

Classes

Class Line # Actions
SequenceSet 64 19 14
0.9210526392.1%
SequenceSet.SequenceSetProperties 322 4 4
1.0100%
 

Contributing tests

This file is covered by 34 tests. .

Source view

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.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;
19   
20   
21    /**
22    * <p>Java class for anonymous complex type</p>.
23    *
24    * <p>The following schema fragment specifies the expected content contained within this class.</p>
25    *
26    * <pre>
27    * &lt;complexType&gt;
28    * &lt;complexContent&gt;
29    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
30    * &lt;sequence&gt;
31    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/&gt;
32    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/&gt;
33    * &lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0"&gt;
34    * &lt;complexType&gt;
35    * &lt;complexContent&gt;
36    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
37    * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
38    * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
39    * &lt;/restriction&gt;
40    * &lt;/complexContent&gt;
41    * &lt;/complexType&gt;
42    * &lt;/element&gt;
43    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/&gt;
44    * &lt;element name="Matrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/&gt;
45    * &lt;/sequence&gt;
46    * &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
47    * &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
48    * &lt;/restriction&gt;
49    * &lt;/complexContent&gt;
50    * &lt;/complexType&gt;
51    * </pre>
52    *
53    *
54    */
55    @XmlAccessorType(XmlAccessType.FIELD)
56    @XmlType(name = "", propOrder = {
57    "sequence",
58    "annotation",
59    "sequenceSetProperties",
60    "alcodonFrame",
61    "matrix"
62    })
63    @XmlRootElement(name = "SequenceSet")
 
64    public class SequenceSet {
65   
66    @XmlElement(name = "Sequence")
67    protected List<Sequence> sequence;
68    @XmlElement(name = "Annotation")
69    protected List<Annotation> annotation;
70    protected List<SequenceSet.SequenceSetProperties> sequenceSetProperties;
71    @XmlElement(name = "AlcodonFrame")
72    protected List<AlcodonFrame> alcodonFrame;
73    /**
74    * Matrices referred to by this set of sequences.
75    *
76    */
77    @XmlElement(name = "Matrix")
78    protected List<MatrixType> matrix;
79    @XmlAttribute(name = "gapChar", required = true)
80    protected String gapChar;
81    /**
82    * reference to set where jalview will gather the
83    * dataset sequences for all sequences in the set.
84    *
85    */
86    @XmlAttribute(name = "datasetId")
87    protected String datasetId;
88   
89    /**
90    * Gets the value of the sequence property.
91    *
92    * <p>This accessor method returns a reference to the live list,
93    * not a snapshot. Therefore any modification you make to the
94    * returned list will be present inside the JAXB object.
95    * This is why there is not a <CODE>set</CODE> method for the sequence property.</p>
96    *
97    * <p>
98    * For example, to add a new item, do as follows:
99    * </p>
100    * <pre>
101    * getSequence().add(newItem);
102    * </pre>
103    *
104    *
105    * <p>
106    * Objects of the following type(s) are allowed in the list
107    * {@link Sequence }
108    * </p>
109    *
110    *
111    * @return
112    * The value of the sequence property.
113    */
 
114  24135 toggle public List<Sequence> getSequence() {
115  24135 if (sequence == null) {
116  107 sequence = new ArrayList<Sequence>();
117    }
118  24135 return this.sequence;
119    }
120   
121    /**
122    * Gets the value of the annotation property.
123    *
124    * <p>This accessor method returns a reference to the live list,
125    * not a snapshot. Therefore any modification you make to the
126    * returned list will be present inside the JAXB object.
127    * This is why there is not a <CODE>set</CODE> method for the annotation property.</p>
128    *
129    * <p>
130    * For example, to add a new item, do as follows:
131    * </p>
132    * <pre>
133    * getAnnotation().add(newItem);
134    * </pre>
135    *
136    *
137    * <p>
138    * Objects of the following type(s) are allowed in the list
139    * {@link Annotation }
140    * </p>
141    *
142    *
143    * @return
144    * The value of the annotation property.
145    */
 
146  964 toggle public List<Annotation> getAnnotation() {
147  964 if (annotation == null) {
148  79 annotation = new ArrayList<Annotation>();
149    }
150  964 return this.annotation;
151    }
152   
153    /**
154    * Gets the value of the sequenceSetProperties property.
155    *
156    * <p>This accessor method returns a reference to the live list,
157    * not a snapshot. Therefore any modification you make to the
158    * returned list will be present inside the JAXB object.
159    * This is why there is not a <CODE>set</CODE> method for the sequenceSetProperties property.</p>
160    *
161    * <p>
162    * For example, to add a new item, do as follows:
163    * </p>
164    * <pre>
165    * getSequenceSetProperties().add(newItem);
166    * </pre>
167    *
168    *
169    * <p>
170    * Objects of the following type(s) are allowed in the list
171    * {@link SequenceSet.SequenceSetProperties }
172    * </p>
173    *
174    *
175    * @return
176    * The value of the sequenceSetProperties property.
177    */
 
178  181 toggle public List<SequenceSet.SequenceSetProperties> getSequenceSetProperties() {
179  181 if (sequenceSetProperties == null) {
180  118 sequenceSetProperties = new ArrayList<SequenceSet.SequenceSetProperties>();
181    }
182  181 return this.sequenceSetProperties;
183    }
184   
185    /**
186    * Gets the value of the alcodonFrame property.
187    *
188    * <p>This accessor method returns a reference to the live list,
189    * not a snapshot. Therefore any modification you make to the
190    * returned list will be present inside the JAXB object.
191    * This is why there is not a <CODE>set</CODE> method for the alcodonFrame property.</p>
192    *
193    * <p>
194    * For example, to add a new item, do as follows:
195    * </p>
196    * <pre>
197    * getAlcodonFrame().add(newItem);
198    * </pre>
199    *
200    *
201    * <p>
202    * Objects of the following type(s) are allowed in the list
203    * {@link AlcodonFrame }
204    * </p>
205    *
206    *
207    * @return
208    * The value of the alcodonFrame property.
209    */
 
210  118 toggle public List<AlcodonFrame> getAlcodonFrame() {
211  118 if (alcodonFrame == null) {
212  118 alcodonFrame = new ArrayList<AlcodonFrame>();
213    }
214  118 return this.alcodonFrame;
215    }
216   
217    /**
218    * Matrices referred to by this set of sequences.
219    *
220    * Gets the value of the matrix property.
221    *
222    * <p>This accessor method returns a reference to the live list,
223    * not a snapshot. Therefore any modification you make to the
224    * returned list will be present inside the JAXB object.
225    * This is why there is not a <CODE>set</CODE> method for the matrix property.</p>
226    *
227    * <p>
228    * For example, to add a new item, do as follows:
229    * </p>
230    * <pre>
231    * getMatrix().add(newItem);
232    * </pre>
233    *
234    *
235    * <p>
236    * Objects of the following type(s) are allowed in the list
237    * {@link MatrixType }
238    * </p>
239    *
240    *
241    * @return
242    * The value of the matrix property.
243    */
 
244  246 toggle public List<MatrixType> getMatrix() {
245  246 if (matrix == null) {
246  116 matrix = new ArrayList<MatrixType>();
247    }
248  246 return this.matrix;
249    }
250   
251    /**
252    * Gets the value of the gapChar property.
253    *
254    * @return
255    * possible object is
256    * {@link String }
257    *
258    */
 
259  0 toggle public String getGapChar() {
260  0 return gapChar;
261    }
262   
263    /**
264    * Sets the value of the gapChar property.
265    *
266    * @param value
267    * allowed object is
268    * {@link String }
269    *
270    */
 
271  77 toggle public void setGapChar(String value) {
272  77 this.gapChar = value;
273    }
274   
275    /**
276    * reference to set where jalview will gather the
277    * dataset sequences for all sequences in the set.
278    *
279    * @return
280    * possible object is
281    * {@link String }
282    *
283    */
 
284  439 toggle public String getDatasetId() {
285  439 return datasetId;
286    }
287   
288    /**
289    * Sets the value of the datasetId property.
290    *
291    * @param value
292    * allowed object is
293    * {@link String }
294    *
295    * @see #getDatasetId()
296    */
 
297  77 toggle public void setDatasetId(String value) {
298  77 this.datasetId = value;
299    }
300   
301   
302    /**
303    * <p>Java class for anonymous complex type</p>.
304    *
305    * <p>The following schema fragment specifies the expected content contained within this class.</p>
306    *
307    * <pre>
308    * &lt;complexType&gt;
309    * &lt;complexContent&gt;
310    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
311    * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
312    * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
313    * &lt;/restriction&gt;
314    * &lt;/complexContent&gt;
315    * &lt;/complexType&gt;
316    * </pre>
317    *
318    *
319    */
320    @XmlAccessorType(XmlAccessType.FIELD)
321    @XmlType(name = "")
 
322    public static class SequenceSetProperties {
323   
324    @XmlAttribute(name = "key")
325    protected String key;
326    @XmlAttribute(name = "value")
327    protected String value;
328   
329    /**
330    * Gets the value of the key property.
331    *
332    * @return
333    * possible object is
334    * {@link String }
335    *
336    */
 
337  21 toggle public String getKey() {
338  21 return key;
339    }
340   
341    /**
342    * Sets the value of the key property.
343    *
344    * @param value
345    * allowed object is
346    * {@link String }
347    *
348    */
 
349  21 toggle public void setKey(String value) {
350  21 this.key = value;
351    }
352   
353    /**
354    * Gets the value of the value property.
355    *
356    * @return
357    * possible object is
358    * {@link String }
359    *
360    */
 
361  21 toggle public String getValue() {
362  21 return value;
363    }
364   
365    /**
366    * Sets the value of the value property.
367    *
368    * @param value
369    * allowed object is
370    * {@link String }
371    *
372    */
 
373  21 toggle public void setValue(String value) {
374  21 this.value = value;
375    }
376   
377    }
378   
379    }
  • Report generated by OpenClover v 4.4.1 on Thu Nov 27 2025 17:01:26 GMT using coverage data from Thu Nov 27 2025 17:01:12 GMT.
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