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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 SequenceSet.java

 

Coverage histogram

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

Code metrics

10
23
13
2
410
113
18
0.78
1.77
6.5
1.38

Classes

Class Line # Actions
SequenceSet 66 19 14
0.9210526392.1%
SequenceSet.SequenceSetProperties 353 4 4
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;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
34    * &lt;sequence&gt;
35    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Sequence" maxOccurs="unbounded" minOccurs="0"/&gt;
36    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}Annotation" maxOccurs="unbounded" minOccurs="0"/&gt;
37    * &lt;element name="sequenceSetProperties" maxOccurs="unbounded" minOccurs="0"&gt;
38    * &lt;complexType&gt;
39    * &lt;complexContent&gt;
40    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
41    * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
42    * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
43    * &lt;/restriction&gt;
44    * &lt;/complexContent&gt;
45    * &lt;/complexType&gt;
46    * &lt;/element&gt;
47    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}AlcodonFrame" maxOccurs="unbounded" minOccurs="0"/&gt;
48    * &lt;element name="Matrix" type="{www.vamsas.ac.uk/jalview/version2}MatrixType" maxOccurs="unbounded" minOccurs="0"/&gt;
49    * &lt;/sequence&gt;
50    * &lt;attribute name="gapChar" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
51    * &lt;attribute name="datasetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
52    * &lt;/restriction&gt;
53    * &lt;/complexContent&gt;
54    * &lt;/complexType&gt;
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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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 toggle 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    * &lt;complexType&gt;
340    * &lt;complexContent&gt;
341    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
342    * &lt;attribute name="key" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
343    * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
344    * &lt;/restriction&gt;
345    * &lt;/complexContent&gt;
346    * &lt;/complexType&gt;
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 toggle 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 toggle 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 toggle 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 toggle public void setValue(String value)
404    {
405  21 this.value = value;
406    }
407   
408    }
409   
410    }
  • 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.