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Coverage Report

  1. Project Clover database Tue Nov 4 2025 11:21:43 GMT
  2. Package jalview.xml.binding.jalview

File Sequence.java

 

Coverage histogram

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

Code metrics

6
23
17
2
379
104
20
0.87
1.35
8.5
1.18

Classes

Class Line # Actions
Sequence 62 7 6
0.7142857371.4%
Sequence.DBRef 194 16 14
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;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
30    * &lt;sequence&gt;
31    * &lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0"&gt;
32    * &lt;complexType&gt;
33    * &lt;complexContent&gt;
34    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
35    * &lt;sequence&gt;
36    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
37    * &lt;/sequence&gt;
38    * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
39    * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
40    * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
41    * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
42    * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
43    * &lt;/restriction&gt;
44    * &lt;/complexContent&gt;
45    * &lt;/complexType&gt;
46    * &lt;/element&gt;
47    * &lt;/sequence&gt;
48    * &lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
49    * &lt;attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
50    * &lt;/extension&gt;
51    * &lt;/complexContent&gt;
52    * &lt;/complexType&gt;
53    * </pre>
54    *
55    *
56    */
57    @XmlAccessorType(XmlAccessType.FIELD)
58    @XmlType(name = "", propOrder = {
59    "dbRef"
60    })
61    @XmlRootElement(name = "Sequence")
 
62    public class Sequence
63    extends SequenceType
64    {
65   
66    @XmlElement(name = "DBRef")
67    protected List<Sequence.DBRef> dbRef;
68    /**
69    * dataset sequence id for this sequence. Will be
70    * created as union of sequences.
71    *
72    */
73    @XmlAttribute(name = "dsseqid")
74    protected String dsseqid;
75    /**
76    * Biotype of the sequence (if known)
77    *
78    */
79    @XmlAttribute(name = "biotype")
80    protected String biotype;
81   
82    /**
83    * Gets the value of the dbRef property.
84    *
85    * <p>This accessor method returns a reference to the live list,
86    * not a snapshot. Therefore any modification you make to the
87    * returned list will be present inside the JAXB object.
88    * This is why there is not a <CODE>set</CODE> method for the dbRef property.</p>
89    *
90    * <p>
91    * For example, to add a new item, do as follows:
92    * </p>
93    * <pre>
94    * getDBRef().add(newItem);
95    * </pre>
96    *
97    *
98    * <p>
99    * Objects of the following type(s) are allowed in the list
100    * {@link Sequence.DBRef }
101    * </p>
102    *
103    *
104    * @return
105    * The value of the dbRef property.
106    */
 
107  22527 toggle public List<Sequence.DBRef> getDBRef() {
108  22527 if (dbRef == null) {
109  15610 dbRef = new ArrayList<Sequence.DBRef>();
110    }
111  22527 return this.dbRef;
112    }
113   
114    /**
115    * dataset sequence id for this sequence. Will be
116    * created as union of sequences.
117    *
118    * @return
119    * possible object is
120    * {@link String }
121    *
122    */
 
123  31926 toggle public String getDsseqid() {
124  31926 return dsseqid;
125    }
126   
127    /**
128    * Sets the value of the dsseqid property.
129    *
130    * @param value
131    * allowed object is
132    * {@link String }
133    *
134    * @see #getDsseqid()
135    */
 
136  8172 toggle public void setDsseqid(String value) {
137  8172 this.dsseqid = value;
138    }
139   
140    /**
141    * Biotype of the sequence (if known)
142    *
143    * @return
144    * possible object is
145    * {@link String }
146    *
147    */
 
148  0 toggle public String getBiotype() {
149  0 return biotype;
150    }
151   
152    /**
153    * Sets the value of the biotype property.
154    *
155    * @param value
156    * allowed object is
157    * {@link String }
158    *
159    * @see #getBiotype()
160    */
 
161  0 toggle public void setBiotype(String value) {
162  0 this.biotype = value;
163    }
164   
165   
166    /**
167    * <p>Java class for anonymous complex type</p>.
168    *
169    * <p>The following schema fragment specifies the expected content contained within this class.</p>
170    *
171    * <pre>
172    * &lt;complexType&gt;
173    * &lt;complexContent&gt;
174    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
175    * &lt;sequence&gt;
176    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
177    * &lt;/sequence&gt;
178    * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
179    * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
180    * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
181    * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
182    * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
183    * &lt;/restriction&gt;
184    * &lt;/complexContent&gt;
185    * &lt;/complexType&gt;
186    * </pre>
187    *
188    *
189    */
190    @XmlAccessorType(XmlAccessType.FIELD)
191    @XmlType(name = "", propOrder = {
192    "mapping"
193    })
 
194    public static class DBRef {
195   
196    @XmlElement(name = "Mapping")
197    protected Mapping mapping;
198    @XmlAttribute(name = "source")
199    protected String source;
200    @XmlAttribute(name = "version")
201    protected String version;
202    @XmlAttribute(name = "accessionId")
203    protected String accessionId;
204    /**
205    * true for gene locus mapping, source=species,
206    * version=assembly, accession=chromosome
207    *
208    */
209    @XmlAttribute(name = "locus")
210    protected Boolean locus;
211    /**
212    * true for the representative accession for
213    * databases where multiple accessions map to the same entry
214    * (eg. Uniprot)
215    *
216    */
217    @XmlAttribute(name = "canonical")
218    protected Boolean canonical;
219   
220    /**
221    * Gets the value of the mapping property.
222    *
223    * @return
224    * possible object is
225    * {@link Mapping }
226    *
227    */
 
228  2797 toggle public Mapping getMapping() {
229  2797 return mapping;
230    }
231   
232    /**
233    * Sets the value of the mapping property.
234    *
235    * @param value
236    * allowed object is
237    * {@link Mapping }
238    *
239    */
 
240  2 toggle public void setMapping(Mapping value) {
241  2 this.mapping = value;
242    }
243   
244    /**
245    * Gets the value of the source property.
246    *
247    * @return
248    * possible object is
249    * {@link String }
250    *
251    */
 
252  2751 toggle public String getSource() {
253  2751 return source;
254    }
255   
256    /**
257    * Sets the value of the source property.
258    *
259    * @param value
260    * allowed object is
261    * {@link String }
262    *
263    */
 
264  1064 toggle public void setSource(String value) {
265  1064 this.source = value;
266    }
267   
268    /**
269    * Gets the value of the version property.
270    *
271    * @return
272    * possible object is
273    * {@link String }
274    *
275    */
 
276  2751 toggle public String getVersion() {
277  2751 return version;
278    }
279   
280    /**
281    * Sets the value of the version property.
282    *
283    * @param value
284    * allowed object is
285    * {@link String }
286    *
287    */
 
288  1064 toggle public void setVersion(String value) {
289  1064 this.version = value;
290    }
291   
292    /**
293    * Gets the value of the accessionId property.
294    *
295    * @return
296    * possible object is
297    * {@link String }
298    *
299    */
 
300  2751 toggle public String getAccessionId() {
301  2751 return accessionId;
302    }
303   
304    /**
305    * Sets the value of the accessionId property.
306    *
307    * @param value
308    * allowed object is
309    * {@link String }
310    *
311    */
 
312  1064 toggle public void setAccessionId(String value) {
313  1064 this.accessionId = value;
314    }
315   
316    /**
317    * true for gene locus mapping, source=species,
318    * version=assembly, accession=chromosome
319    *
320    * @return
321    * possible object is
322    * {@link Boolean }
323    *
324    */
 
325  2751 toggle public boolean isLocus() {
326  2751 if (locus == null) {
327  2728 return false;
328    } else {
329  23 return locus;
330    }
331    }
332   
333    /**
334    * Sets the value of the locus property.
335    *
336    * @param value
337    * allowed object is
338    * {@link Boolean }
339    *
340    * @see #isLocus()
341    */
 
342  1 toggle public void setLocus(Boolean value) {
343  1 this.locus = value;
344    }
345   
346    /**
347    * true for the representative accession for
348    * databases where multiple accessions map to the same entry
349    * (eg. Uniprot)
350    *
351    * @return
352    * possible object is
353    * {@link Boolean }
354    *
355    */
 
356  2751 toggle public boolean isCanonical() {
357  2751 if (canonical == null) {
358  925 return false;
359    } else {
360  1826 return canonical;
361    }
362    }
363   
364    /**
365    * Sets the value of the canonical property.
366    *
367    * @param value
368    * allowed object is
369    * {@link Boolean }
370    *
371    * @see #isCanonical()
372    */
 
373  1064 toggle public void setCanonical(Boolean value) {
374  1064 this.canonical = value;
375    }
376   
377    }
378   
379    }
  • Report generated by OpenClover v 4.4.1 on Tue Nov 4 2025 11:32:25 GMT using coverage data from Tue Nov 4 2025 11:32:11 GMT.
  • OpenClover is free and open-source software.