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Coverage Report

  1. Project Clover database Fri Dec 6 2024 13:47:14 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
391
124
20
0.87
1.35
8.5
1.18

Classes

Class Line # Actions
Sequence 64 7 6
0.7142857371.4%
Sequence.DBRef 202 16 14
1.0100%
 

Contributing tests

This file is covered by 32 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: 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    * &lt;complexType&gt;
32    * &lt;complexContent&gt;
33    * &lt;extension base="{www.vamsas.ac.uk/jalview/version2}SequenceType"&gt;
34    * &lt;sequence&gt;
35    * &lt;element name="DBRef" maxOccurs="unbounded" minOccurs="0"&gt;
36    * &lt;complexType&gt;
37    * &lt;complexContent&gt;
38    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
39    * &lt;sequence&gt;
40    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
41    * &lt;/sequence&gt;
42    * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
43    * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
44    * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
45    * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
46    * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
47    * &lt;/restriction&gt;
48    * &lt;/complexContent&gt;
49    * &lt;/complexType&gt;
50    * &lt;/element&gt;
51    * &lt;/sequence&gt;
52    * &lt;attribute name="dsseqid" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
53    * &lt;attribute name="biotype" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
54    * &lt;/extension&gt;
55    * &lt;/complexContent&gt;
56    * &lt;/complexType&gt;
57    * </pre>
58    *
59    *
60    */
61    @XmlAccessorType(XmlAccessType.FIELD)
62    @XmlType(name = "", propOrder = { "dbRef" })
63    @XmlRootElement(name = "Sequence")
 
64    public class Sequence extends SequenceType
65    {
66   
67    @XmlElement(name = "DBRef")
68    protected List<Sequence.DBRef> dbRef;
69   
70    /**
71    * dataset sequence id for this sequence. Will be created as union of
72    * sequences.
73    *
74    */
75    @XmlAttribute(name = "dsseqid")
76    protected String dsseqid;
77   
78    /**
79    * Biotype of the sequence (if known)
80    *
81    */
82    @XmlAttribute(name = "biotype")
83    protected String biotype;
84   
85    /**
86    * Gets the value of the dbRef property.
87    *
88    * <p>
89    * This accessor method returns a reference to the live list, not a snapshot.
90    * Therefore any modification you make to the returned list will be present
91    * inside the JAXB object. This is why there is not a <CODE>set</CODE> method
92    * for the dbRef property.
93    * </p>
94    *
95    * <p>
96    * For example, to add a new item, do as follows:
97    * </p>
98    *
99    * <pre>
100    * getDBRef().add(newItem);
101    * </pre>
102    *
103    *
104    * <p>
105    * Objects of the following type(s) are allowed in the list
106    * {@link Sequence.DBRef }
107    * </p>
108    *
109    *
110    * @return The value of the dbRef property.
111    */
 
112  3509 toggle public List<Sequence.DBRef> getDBRef()
113    {
114  3509 if (dbRef == null)
115    {
116  808 dbRef = new ArrayList<Sequence.DBRef>();
117    }
118  3509 return this.dbRef;
119    }
120   
121    /**
122    * dataset sequence id for this sequence. Will be created as union of
123    * sequences.
124    *
125    * @return possible object is {@link String }
126    *
127    */
 
128  2158 toggle public String getDsseqid()
129    {
130  2158 return dsseqid;
131    }
132   
133    /**
134    * Sets the value of the dsseqid property.
135    *
136    * @param value
137    * allowed object is {@link String }
138    *
139    * @see #getDsseqid()
140    */
 
141  760 toggle public void setDsseqid(String value)
142    {
143  760 this.dsseqid = value;
144    }
145   
146    /**
147    * Biotype of the sequence (if known)
148    *
149    * @return possible object is {@link String }
150    *
151    */
 
152  0 toggle public String getBiotype()
153    {
154  0 return biotype;
155    }
156   
157    /**
158    * Sets the value of the biotype property.
159    *
160    * @param value
161    * allowed object is {@link String }
162    *
163    * @see #getBiotype()
164    */
 
165  0 toggle public void setBiotype(String value)
166    {
167  0 this.biotype = value;
168    }
169   
170    /**
171    * <p>
172    * Java class for anonymous complex type
173    * </p>
174    * .
175    *
176    * <p>
177    * The following schema fragment specifies the expected content contained
178    * within this class.
179    * </p>
180    *
181    * <pre>
182    * &lt;complexType&gt;
183    * &lt;complexContent&gt;
184    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
185    * &lt;sequence&gt;
186    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Mapping" minOccurs="0"/&gt;
187    * &lt;/sequence&gt;
188    * &lt;attribute name="source" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
189    * &lt;attribute name="version" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
190    * &lt;attribute name="accessionId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
191    * &lt;attribute name="locus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
192    * &lt;attribute name="canonical" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
193    * &lt;/restriction&gt;
194    * &lt;/complexContent&gt;
195    * &lt;/complexType&gt;
196    * </pre>
197    *
198    *
199    */
200    @XmlAccessorType(XmlAccessType.FIELD)
201    @XmlType(name = "", propOrder = { "mapping" })
 
202    public static class DBRef
203    {
204   
205    @XmlElement(name = "Mapping")
206    protected Mapping mapping;
207   
208    @XmlAttribute(name = "source")
209    protected String source;
210   
211    @XmlAttribute(name = "version")
212    protected String version;
213   
214    @XmlAttribute(name = "accessionId")
215    protected String accessionId;
216   
217    /**
218    * true for gene locus mapping, source=species, version=assembly,
219    * accession=chromosome
220    *
221    */
222    @XmlAttribute(name = "locus")
223    protected Boolean locus;
224   
225    /**
226    * true for the representative accession for databases where multiple
227    * accessions map to the same entry (eg. Uniprot)
228    *
229    */
230    @XmlAttribute(name = "canonical")
231    protected Boolean canonical;
232   
233    /**
234    * Gets the value of the mapping property.
235    *
236    * @return possible object is {@link Mapping }
237    *
238    */
 
239  1137 toggle public Mapping getMapping()
240    {
241  1137 return mapping;
242    }
243   
244    /**
245    * Sets the value of the mapping property.
246    *
247    * @param value
248    * allowed object is {@link Mapping }
249    *
250    */
 
251  2 toggle public void setMapping(Mapping value)
252    {
253  2 this.mapping = value;
254    }
255   
256    /**
257    * Gets the value of the source property.
258    *
259    * @return possible object is {@link String }
260    *
261    */
 
262  1091 toggle public String getSource()
263    {
264  1091 return source;
265    }
266   
267    /**
268    * Sets the value of the source property.
269    *
270    * @param value
271    * allowed object is {@link String }
272    *
273    */
 
274  234 toggle public void setSource(String value)
275    {
276  234 this.source = value;
277    }
278   
279    /**
280    * Gets the value of the version property.
281    *
282    * @return possible object is {@link String }
283    *
284    */
 
285  1091 toggle public String getVersion()
286    {
287  1091 return version;
288    }
289   
290    /**
291    * Sets the value of the version property.
292    *
293    * @param value
294    * allowed object is {@link String }
295    *
296    */
 
297  234 toggle public void setVersion(String value)
298    {
299  234 this.version = value;
300    }
301   
302    /**
303    * Gets the value of the accessionId property.
304    *
305    * @return possible object is {@link String }
306    *
307    */
 
308  1091 toggle public String getAccessionId()
309    {
310  1091 return accessionId;
311    }
312   
313    /**
314    * Sets the value of the accessionId property.
315    *
316    * @param value
317    * allowed object is {@link String }
318    *
319    */
 
320  234 toggle public void setAccessionId(String value)
321    {
322  234 this.accessionId = value;
323    }
324   
325    /**
326    * true for gene locus mapping, source=species, version=assembly,
327    * accession=chromosome
328    *
329    * @return possible object is {@link Boolean }
330    *
331    */
 
332  1091 toggle public boolean isLocus()
333    {
334  1091 if (locus == null)
335    {
336  1068 return false;
337    }
338    else
339    {
340  23 return locus;
341    }
342    }
343   
344    /**
345    * Sets the value of the locus property.
346    *
347    * @param value
348    * allowed object is {@link Boolean }
349    *
350    * @see #isLocus()
351    */
 
352  1 toggle public void setLocus(Boolean value)
353    {
354  1 this.locus = value;
355    }
356   
357    /**
358    * true for the representative accession for databases where multiple
359    * accessions map to the same entry (eg. Uniprot)
360    *
361    * @return possible object is {@link Boolean }
362    *
363    */
 
364  1091 toggle public boolean isCanonical()
365    {
366  1091 if (canonical == null)
367    {
368  925 return false;
369    }
370    else
371    {
372  166 return canonical;
373    }
374    }
375   
376    /**
377    * Sets the value of the canonical property.
378    *
379    * @param value
380    * allowed object is {@link Boolean }
381    *
382    * @see #isCanonical()
383    */
 
384  234 toggle public void setCanonical(Boolean value)
385    {
386  234 this.canonical = value;
387    }
388   
389    }
390   
391    }
  • Report generated by OpenClover v 4.4.1 on Fri Dec 6 2024 13:54:25 GMT using coverage data from Fri Dec 6 2024 13:54:13 GMT.
  • OpenClover is free and open-source software.