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Coverage Report

  1. Project Clover database Mon Sep 2 2024 17:57:51 BST
  2. Package jalview.xml.binding.jalview

File Annotation.java

 

Coverage histogram

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

Code metrics

12
61
49
2
809
300
55
0.9
1.24
24.5
1.12

Classes

Class Line # Actions
Annotation 85 55 49
0.9181818491.8%
Annotation.ThresholdLine 726 6 6
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, v2.3.3
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: 2023.11.01 at 07:03:09 PM GMT
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>Java class for anonymous complex type.
21    *
22    * <p>The following schema fragment specifies the expected content
23    * contained within this class.
24    *
25    * <pre> <complexType> <complexContent>
26    * <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
27    * <sequence> <element
28    * ref="{www.vamsas.ac.uk/jalview/version2}annotationElement"
29    * maxOccurs="unbounded" minOccurs="0"/> <element name="label"
30    * type="{http://www.w3.org/2001/XMLSchema}string"/> <element
31    * name="description" type="{http://www.w3.org/2001/XMLSchema}string"
32    * minOccurs="0"/> <element name="thresholdLine"
33    * minOccurs="0"> <complexType>
34    * <complexContent> <restriction
35    * base="{http://www.w3.org/2001/XMLSchema}anyType"> <attribute
36    * name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
37    * <attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float"
38    * /> <attribute name="colour"
39    * type="{http://www.w3.org/2001/XMLSchema}int" />
40    * </restriction> </complexContent>
41    * </complexType> </element> <element
42    * name="contactmatrix"
43    * type="{www.vamsas.ac.uk/jalview/version2}MapOnAMatrixType"
44    * maxOccurs="unbounded" minOccurs="0"/> <element name="property"
45    * type="{www.vamsas.ac.uk/jalview/version2}property" maxOccurs="unbounded"
46    * minOccurs="0"/> </sequence> <attribute
47    * name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean"
48    * /> <attribute name="graphType"
49    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
50    * name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
51    * <attribute name="groupRef"
52    * type="{http://www.w3.org/2001/XMLSchema}string" /> <attribute
53    * name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
54    * <attribute name="graphGroup"
55    * type="{http://www.w3.org/2001/XMLSchema}int" /> <attribute
56    * name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
57    * <attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string"
58    * /> <attribute name="scoreOnly"
59    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
60    * <attribute name="score"
61    * type="{http://www.w3.org/2001/XMLSchema}double" /> <attribute
62    * name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
63    * <attribute name="centreColLabels"
64    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
65    * name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean"
66    * /> <attribute name="showAllColLabels"
67    * type="{http://www.w3.org/2001/XMLSchema}boolean" /> <attribute
68    * name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean"
69    * default="false" /> <attribute name="belowAlignment"
70    * type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
71    * <attribute name="calcId"
72    * type="{http://www.w3.org/2001/XMLSchema}string" />
73    * </restriction> </complexContent>
74    * </complexType> </pre>
75    *
76    *
77    */
78    @XmlAccessorType(XmlAccessType.FIELD)
79    @XmlType(
80    name = "",
81    propOrder =
82    { "annotationElement", "label", "description", "thresholdLine",
83    "contactmatrix", "property" })
84    @XmlRootElement(name = "Annotation")
 
85    public class Annotation
86    {
87   
88    protected List<AnnotationElement> annotationElement;
89   
90    @XmlElement(required = true)
91    protected String label;
92   
93    protected String description;
94   
95    protected Annotation.ThresholdLine thresholdLine;
96   
97    protected List<MapOnAMatrixType> contactmatrix;
98   
99    protected List<Property> property;
100   
101    @XmlAttribute(name = "graph", required = true)
102    protected boolean graph;
103   
104    @XmlAttribute(name = "graphType")
105    protected Integer graphType;
106   
107    @XmlAttribute(name = "sequenceRef")
108    protected String sequenceRef;
109   
110    @XmlAttribute(name = "groupRef")
111    protected String groupRef;
112   
113    @XmlAttribute(name = "graphColour")
114    protected Integer graphColour;
115   
116    @XmlAttribute(name = "graphGroup")
117    protected Integer graphGroup;
118   
119    @XmlAttribute(name = "graphHeight")
120    protected Integer graphHeight;
121   
122    @XmlAttribute(name = "id")
123    protected String id;
124   
125    @XmlAttribute(name = "scoreOnly")
126    protected Boolean scoreOnly;
127   
128    @XmlAttribute(name = "score")
129    protected Double score;
130   
131    @XmlAttribute(name = "visible")
132    protected Boolean visible;
133   
134    @XmlAttribute(name = "centreColLabels")
135    protected Boolean centreColLabels;
136   
137    @XmlAttribute(name = "scaleColLabels")
138    protected Boolean scaleColLabels;
139   
140    @XmlAttribute(name = "showAllColLabels")
141    protected Boolean showAllColLabels;
142   
143    @XmlAttribute(name = "autoCalculated")
144    protected Boolean autoCalculated;
145   
146    @XmlAttribute(name = "belowAlignment")
147    protected Boolean belowAlignment;
148   
149    @XmlAttribute(name = "calcId")
150    protected String calcId;
151   
152    /**
153    * Gets the value of the annotationElement property.
154    *
155    * &lt;p&gt; This accessor method returns a reference to the live list, not a
156    * snapshot. Therefore any modification you make to the returned list will be
157    * present inside the JAXB object. This is why there is not a
158    * &lt;CODE&gt;set&lt;/CODE&gt; method for the annotationElement property.
159    *
160    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
161    * getAnnotationElement().add(newItem); &lt;/pre&gt;
162    *
163    *
164    * &lt;p&gt; Objects of the following type(s) are allowed in the list
165    * {@link AnnotationElement }
166    *
167    *
168    */
 
169  47480 toggle public List<AnnotationElement> getAnnotationElement()
170    {
171  47480 if (annotationElement == null)
172    {
173  447 annotationElement = new ArrayList<AnnotationElement>();
174    }
175  47480 return this.annotationElement;
176    }
177   
178    /**
179    * Gets the value of the label property.
180    *
181    * @return possible object is {@link String }
182    *
183    */
 
184  2166 toggle public String getLabel()
185    {
186  2166 return label;
187    }
188   
189    /**
190    * Sets the value of the label property.
191    *
192    * @param value
193    * allowed object is {@link String }
194    *
195    */
 
196  447 toggle public void setLabel(String value)
197    {
198  447 this.label = value;
199    }
200   
201    /**
202    * Gets the value of the description property.
203    *
204    * @return possible object is {@link String }
205    *
206    */
 
207  594 toggle public String getDescription()
208    {
209  594 return description;
210    }
211   
212    /**
213    * Sets the value of the description property.
214    *
215    * @param value
216    * allowed object is {@link String }
217    *
218    */
 
219  447 toggle public void setDescription(String value)
220    {
221  447 this.description = value;
222    }
223   
224    /**
225    * Gets the value of the thresholdLine property.
226    *
227    * @return possible object is {@link Annotation.ThresholdLine }
228    *
229    */
 
230  500 toggle public Annotation.ThresholdLine getThresholdLine()
231    {
232  500 return thresholdLine;
233    }
234   
235    /**
236    * Sets the value of the thresholdLine property.
237    *
238    * @param value
239    * allowed object is {@link Annotation.ThresholdLine }
240    *
241    */
 
242  30 toggle public void setThresholdLine(Annotation.ThresholdLine value)
243    {
244  30 this.thresholdLine = value;
245    }
246   
247    /**
248    * Gets the value of the contactmatrix property.
249    *
250    * &lt;p&gt; This accessor method returns a reference to the live list, not a
251    * snapshot. Therefore any modification you make to the returned list will be
252    * present inside the JAXB object. This is why there is not a
253    * &lt;CODE&gt;set&lt;/CODE&gt; method for the contactmatrix property.
254    *
255    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
256    * getContactmatrix().add(newItem); &lt;/pre&gt;
257    *
258    *
259    * &lt;p&gt; Objects of the following type(s) are allowed in the list
260    * {@link MapOnAMatrixType }
261    *
262    *
263    */
 
264  18 toggle public List<MapOnAMatrixType> getContactmatrix()
265    {
266  18 if (contactmatrix == null)
267    {
268  9 contactmatrix = new ArrayList<MapOnAMatrixType>();
269    }
270  18 return this.contactmatrix;
271    }
272   
273    /**
274    * Gets the value of the property property.
275    *
276    * &lt;p&gt; This accessor method returns a reference to the live list, not a
277    * snapshot. Therefore any modification you make to the returned list will be
278    * present inside the JAXB object. This is why there is not a
279    * &lt;CODE&gt;set&lt;/CODE&gt; method for the property property.
280    *
281    * &lt;p&gt; For example, to add a new item, do as follows: &lt;pre&gt;
282    * getProperty().add(newItem); &lt;/pre&gt;
283    *
284    *
285    * &lt;p&gt; Objects of the following type(s) are allowed in the list
286    * {@link Property }
287    *
288    *
289    */
 
290  594 toggle public List<Property> getProperty()
291    {
292  594 if (property == null)
293    {
294  594 property = new ArrayList<Property>();
295    }
296  594 return this.property;
297    }
298   
299    /**
300    * Gets the value of the graph property.
301    *
302    */
 
303  594 toggle public boolean isGraph()
304    {
305  594 return graph;
306    }
307   
308    /**
309    * Sets the value of the graph property.
310    *
311    */
 
312  447 toggle public void setGraph(boolean value)
313    {
314  447 this.graph = value;
315    }
316   
317    /**
318    * Gets the value of the graphType property.
319    *
320    * @return possible object is {@link Integer }
321    *
322    */
 
323  410 toggle public Integer getGraphType()
324    {
325  410 return graphType;
326    }
327   
328    /**
329    * Sets the value of the graphType property.
330    *
331    * @param value
332    * allowed object is {@link Integer }
333    *
334    */
 
335  283 toggle public void setGraphType(Integer value)
336    {
337  283 this.graphType = value;
338    }
339   
340    /**
341    * Gets the value of the sequenceRef property.
342    *
343    * @return possible object is {@link String }
344    *
345    */
 
346  594 toggle public String getSequenceRef()
347    {
348  594 return sequenceRef;
349    }
350   
351    /**
352    * Sets the value of the sequenceRef property.
353    *
354    * @param value
355    * allowed object is {@link String }
356    *
357    */
 
358  229 toggle public void setSequenceRef(String value)
359    {
360  229 this.sequenceRef = value;
361    }
362   
363    /**
364    * Gets the value of the groupRef property.
365    *
366    * @return possible object is {@link String }
367    *
368    */
 
369  678 toggle public String getGroupRef()
370    {
371  678 return groupRef;
372    }
373   
374    /**
375    * Sets the value of the groupRef property.
376    *
377    * @param value
378    * allowed object is {@link String }
379    *
380    */
 
381  12 toggle public void setGroupRef(String value)
382    {
383  12 this.groupRef = value;
384    }
385   
386    /**
387    * Gets the value of the graphColour property.
388    *
389    * @return possible object is {@link Integer }
390    *
391    */
 
392  0 toggle public Integer getGraphColour()
393    {
394  0 return graphColour;
395    }
396   
397    /**
398    * Sets the value of the graphColour property.
399    *
400    * @param value
401    * allowed object is {@link Integer }
402    *
403    */
 
404  0 toggle public void setGraphColour(Integer value)
405    {
406  0 this.graphColour = value;
407    }
408   
409    /**
410    * Gets the value of the graphGroup property.
411    *
412    * @return possible object is {@link Integer }
413    *
414    */
 
415  410 toggle public Integer getGraphGroup()
416    {
417  410 return graphGroup;
418    }
419   
420    /**
421    * Sets the value of the graphGroup property.
422    *
423    * @param value
424    * allowed object is {@link Integer }
425    *
426    */
 
427  283 toggle public void setGraphGroup(Integer value)
428    {
429  283 this.graphGroup = value;
430    }
431   
432    /**
433    * Gets the value of the graphHeight property.
434    *
435    * @return possible object is {@link Integer }
436    *
437    */
 
438  1188 toggle public Integer getGraphHeight()
439    {
440  1188 return graphHeight;
441    }
442   
443    /**
444    * Sets the value of the graphHeight property.
445    *
446    * @param value
447    * allowed object is {@link Integer }
448    *
449    */
 
450  447 toggle public void setGraphHeight(Integer value)
451    {
452  447 this.graphHeight = value;
453    }
454   
455    /**
456    * Gets the value of the id property.
457    *
458    * @return possible object is {@link String }
459    *
460    */
 
461  1774 toggle public String getId()
462    {
463  1774 return id;
464    }
465   
466    /**
467    * Sets the value of the id property.
468    *
469    * @param value
470    * allowed object is {@link String }
471    *
472    */
 
473  751 toggle public void setId(String value)
474    {
475  751 this.id = value;
476    }
477   
478    /**
479    * Gets the value of the scoreOnly property.
480    *
481    * @return possible object is {@link Boolean }
482    *
483    */
 
484  594 toggle public boolean isScoreOnly()
485    {
486  594 if (scoreOnly == null)
487    {
488  0 return false;
489    }
490    else
491    {
492  594 return scoreOnly;
493    }
494    }
495   
496    /**
497    * Sets the value of the scoreOnly property.
498    *
499    * @param value
500    * allowed object is {@link Boolean }
501    *
502    */
 
503  447 toggle public void setScoreOnly(Boolean value)
504    {
505  447 this.scoreOnly = value;
506    }
507   
508    /**
509    * Gets the value of the score property.
510    *
511    * @return possible object is {@link Double }
512    *
513    */
 
514  733 toggle public Double getScore()
515    {
516  733 return score;
517    }
518   
519    /**
520    * Sets the value of the score property.
521    *
522    * @param value
523    * allowed object is {@link Double }
524    *
525    */
 
526  139 toggle public void setScore(Double value)
527    {
528  139 this.score = value;
529    }
530   
531    /**
532    * Gets the value of the visible property.
533    *
534    * @return possible object is {@link Boolean }
535    *
536    */
 
537  1200 toggle public Boolean isVisible()
538    {
539  1200 return visible;
540    }
541   
542    /**
543    * Sets the value of the visible property.
544    *
545    * @param value
546    * allowed object is {@link Boolean }
547    *
548    */
 
549  447 toggle public void setVisible(Boolean value)
550    {
551  447 this.visible = value;
552    }
553   
554    /**
555    * Gets the value of the centreColLabels property.
556    *
557    * @return possible object is {@link Boolean }
558    *
559    */
 
560  1188 toggle public Boolean isCentreColLabels()
561    {
562  1188 return centreColLabels;
563    }
564   
565    /**
566    * Sets the value of the centreColLabels property.
567    *
568    * @param value
569    * allowed object is {@link Boolean }
570    *
571    */
 
572  447 toggle public void setCentreColLabels(Boolean value)
573    {
574  447 this.centreColLabels = value;
575    }
576   
577    /**
578    * Gets the value of the scaleColLabels property.
579    *
580    * @return possible object is {@link Boolean }
581    *
582    */
 
583  1188 toggle public Boolean isScaleColLabels()
584    {
585  1188 return scaleColLabels;
586    }
587   
588    /**
589    * Sets the value of the scaleColLabels property.
590    *
591    * @param value
592    * allowed object is {@link Boolean }
593    *
594    */
 
595  447 toggle public void setScaleColLabels(Boolean value)
596    {
597  447 this.scaleColLabels = value;
598    }
599   
600    /**
601    * Gets the value of the showAllColLabels property.
602    *
603    * @return possible object is {@link Boolean }
604    *
605    */
 
606  0 toggle public Boolean isShowAllColLabels()
607    {
608  0 return showAllColLabels;
609    }
610   
611    /**
612    * Sets the value of the showAllColLabels property.
613    *
614    * @param value
615    * allowed object is {@link Boolean }
616    *
617    */
 
618  447 toggle public void setShowAllColLabels(Boolean value)
619    {
620  447 this.showAllColLabels = value;
621    }
622   
623    /**
624    * Gets the value of the autoCalculated property.
625    *
626    * @return possible object is {@link Boolean }
627    *
628    */
 
629  1142 toggle public boolean isAutoCalculated()
630    {
631  1142 if (autoCalculated == null)
632    {
633  692 return false;
634    }
635    else
636    {
637  450 return autoCalculated;
638    }
639    }
640   
641    /**
642    * Sets the value of the autoCalculated property.
643    *
644    * @param value
645    * allowed object is {@link Boolean }
646    *
647    */
 
648  193 toggle public void setAutoCalculated(Boolean value)
649    {
650  193 this.autoCalculated = value;
651    }
652   
653    /**
654    * Gets the value of the belowAlignment property.
655    *
656    * @return possible object is {@link Boolean }
657    *
658    */
 
659  594 toggle public boolean isBelowAlignment()
660    {
661  594 if (belowAlignment == null)
662    {
663  144 return true;
664    }
665    else
666    {
667  450 return belowAlignment;
668    }
669    }
670   
671    /**
672    * Sets the value of the belowAlignment property.
673    *
674    * @param value
675    * allowed object is {@link Boolean }
676    *
677    */
 
678  447 toggle public void setBelowAlignment(Boolean value)
679    {
680  447 this.belowAlignment = value;
681    }
682   
683    /**
684    * Gets the value of the calcId property.
685    *
686    * @return possible object is {@link String }
687    *
688    */
 
689  594 toggle public String getCalcId()
690    {
691  594 return calcId;
692    }
693   
694    /**
695    * Sets the value of the calcId property.
696    *
697    * @param value
698    * allowed object is {@link String }
699    *
700    */
 
701  423 toggle public void setCalcId(String value)
702    {
703  423 this.calcId = value;
704    }
705   
706    /**
707    * &lt;p&gt;Java class for anonymous complex type.
708    *
709    * &lt;p&gt;The following schema fragment specifies the expected content
710    * contained within this class.
711    *
712    * &lt;pre&gt; &amp;lt;complexType&amp;gt; &amp;lt;complexContent&amp;gt;
713    * &amp;lt;restriction
714    * base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt; &amp;lt;attribute
715    * name="label" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
716    * &amp;lt;attribute name="value"
717    * type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt; &amp;lt;attribute
718    * name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&amp;gt;
719    * &amp;lt;/restriction&amp;gt; &amp;lt;/complexContent&amp;gt;
720    * &amp;lt;/complexType&amp;gt; &lt;/pre&gt;
721    *
722    *
723    */
724    @XmlAccessorType(XmlAccessType.FIELD)
725    @XmlType(name = "")
 
726    public static class ThresholdLine
727    {
728   
729    @XmlAttribute(name = "label")
730    protected String label;
731   
732    @XmlAttribute(name = "value")
733    protected Float value;
734   
735    @XmlAttribute(name = "colour")
736    protected Integer colour;
737   
738    /**
739    * Gets the value of the label property.
740    *
741    * @return possible object is {@link String }
742    *
743    */
 
744  30 toggle public String getLabel()
745    {
746  30 return label;
747    }
748   
749    /**
750    * Sets the value of the label property.
751    *
752    * @param value
753    * allowed object is {@link String }
754    *
755    */
 
756  30 toggle public void setLabel(String value)
757    {
758  30 this.label = value;
759    }
760   
761    /**
762    * Gets the value of the value property.
763    *
764    * @return possible object is {@link Float }
765    *
766    */
 
767  30 toggle public Float getValue()
768    {
769  30 return value;
770    }
771   
772    /**
773    * Sets the value of the value property.
774    *
775    * @param value
776    * allowed object is {@link Float }
777    *
778    */
 
779  30 toggle public void setValue(Float value)
780    {
781  30 this.value = value;
782    }
783   
784    /**
785    * Gets the value of the colour property.
786    *
787    * @return possible object is {@link Integer }
788    *
789    */
 
790  30 toggle public Integer getColour()
791    {
792  30 return colour;
793    }
794   
795    /**
796    * Sets the value of the colour property.
797    *
798    * @param value
799    * allowed object is {@link Integer }
800    *
801    */
 
802  30 toggle public void setColour(Integer value)
803    {
804  30 this.colour = value;
805    }
806   
807    }
808   
809    }
  • Report generated by OpenClover v 4.4.1 on Mon Sep 2 2024 18:05:00 BST using coverage data from Mon Sep 2 2024 18:04:45 BST.
  • OpenClover is free and open-source software.