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Coverage Report

  1. Project Clover database Thu Aug 13 2020 12:04:21 BST
  2. Package jalview.xml.binding.jalview

File Annotation.java

 

Coverage histogram

../../../../img/srcFileCovDistChart9.png
12% of files have more coverage

Code metrics

10
62
52
3
857
252
57
0.92
1.19
17.33
1.1

Classes

Class Line # Actions
Annotation 89 52 47
0.9134615791.3%
Annotation.Property 695 4 4
0.00%
Annotation.ThresholdLine 774 6 6
1.0100%
 

Contributing tests

This file is covered by 22 tests. .

Source view

1    //
2    // This file was generated by the JavaTM Architecture for XML Binding(JAXB) Reference Implementation, v2.2.8-b130911.1802
3    // See <a href="http://java.sun.com/xml/jaxb">http://java.sun.com/xml/jaxb</a>
4    // Any modifications to this file will be lost upon recompilation of the source schema.
5    // Generated on: 2019.06.07 at 02:21:15 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.
23    *
24    * <p>The following schema fragment specifies the expected content contained within this class.
25    *
26    * <pre>
27    * &lt;complexType>
28    * &lt;complexContent>
29    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
30    * &lt;sequence>
31    * &lt;element ref="{www.vamsas.ac.uk/jalview/version2}annotationElement" maxOccurs="unbounded" minOccurs="0"/>
32    * &lt;element name="label" type="{http://www.w3.org/2001/XMLSchema}string"/>
33    * &lt;element name="description" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
34    * &lt;element name="thresholdLine" minOccurs="0">
35    * &lt;complexType>
36    * &lt;complexContent>
37    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
38    * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
39    * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
40    * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
41    * &lt;/restriction>
42    * &lt;/complexContent>
43    * &lt;/complexType>
44    * &lt;/element>
45    * &lt;element name="property" maxOccurs="unbounded" minOccurs="0">
46    * &lt;complexType>
47    * &lt;complexContent>
48    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
49    * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
50    * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
51    * &lt;/restriction>
52    * &lt;/complexContent>
53    * &lt;/complexType>
54    * &lt;/element>
55    * &lt;/sequence>
56    * &lt;attribute name="graph" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" />
57    * &lt;attribute name="graphType" type="{http://www.w3.org/2001/XMLSchema}int" />
58    * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" />
59    * &lt;attribute name="groupRef" type="{http://www.w3.org/2001/XMLSchema}string" />
60    * &lt;attribute name="graphColour" type="{http://www.w3.org/2001/XMLSchema}int" />
61    * &lt;attribute name="graphGroup" type="{http://www.w3.org/2001/XMLSchema}int" />
62    * &lt;attribute name="graphHeight" type="{http://www.w3.org/2001/XMLSchema}int" />
63    * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" />
64    * &lt;attribute name="scoreOnly" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
65    * &lt;attribute name="score" type="{http://www.w3.org/2001/XMLSchema}double" />
66    * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" />
67    * &lt;attribute name="centreColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
68    * &lt;attribute name="scaleColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
69    * &lt;attribute name="showAllColLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" />
70    * &lt;attribute name="autoCalculated" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" />
71    * &lt;attribute name="belowAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" />
72    * &lt;attribute name="calcId" type="{http://www.w3.org/2001/XMLSchema}string" />
73    * &lt;/restriction>
74    * &lt;/complexContent>
75    * &lt;/complexType>
76    * </pre>
77    *
78    *
79    */
80    @XmlAccessorType(XmlAccessType.FIELD)
81    @XmlType(name = "", propOrder = {
82    "annotationElement",
83    "label",
84    "description",
85    "thresholdLine",
86    "property"
87    })
88    @XmlRootElement(name = "Annotation")
 
89    public class Annotation {
90   
91    protected List<AnnotationElement> annotationElement;
92    @XmlElement(required = true)
93    protected String label;
94    protected String description;
95    protected Annotation.ThresholdLine thresholdLine;
96    protected List<Annotation.Property> property;
97    @XmlAttribute(name = "graph", required = true)
98    protected boolean graph;
99    @XmlAttribute(name = "graphType")
100    protected Integer graphType;
101    @XmlAttribute(name = "sequenceRef")
102    protected String sequenceRef;
103    @XmlAttribute(name = "groupRef")
104    protected String groupRef;
105    @XmlAttribute(name = "graphColour")
106    protected Integer graphColour;
107    @XmlAttribute(name = "graphGroup")
108    protected Integer graphGroup;
109    @XmlAttribute(name = "graphHeight")
110    protected Integer graphHeight;
111    @XmlAttribute(name = "id")
112    protected String id;
113    @XmlAttribute(name = "scoreOnly")
114    protected Boolean scoreOnly;
115    @XmlAttribute(name = "score")
116    protected Double score;
117    @XmlAttribute(name = "visible")
118    protected Boolean visible;
119    @XmlAttribute(name = "centreColLabels")
120    protected Boolean centreColLabels;
121    @XmlAttribute(name = "scaleColLabels")
122    protected Boolean scaleColLabels;
123    @XmlAttribute(name = "showAllColLabels")
124    protected Boolean showAllColLabels;
125    @XmlAttribute(name = "autoCalculated")
126    protected Boolean autoCalculated;
127    @XmlAttribute(name = "belowAlignment")
128    protected Boolean belowAlignment;
129    @XmlAttribute(name = "calcId")
130    protected String calcId;
131   
132    /**
133    * Gets the value of the annotationElement property.
134    *
135    * <p>
136    * This accessor method returns a reference to the live list,
137    * not a snapshot. Therefore any modification you make to the
138    * returned list will be present inside the JAXB object.
139    * This is why there is not a <CODE>set</CODE> method for the annotationElement property.
140    *
141    * <p>
142    * For example, to add a new item, do as follows:
143    * <pre>
144    * getAnnotationElement().add(newItem);
145    * </pre>
146    *
147    *
148    * <p>
149    * Objects of the following type(s) are allowed in the list
150    * {@link AnnotationElement }
151    *
152    *
153    */
 
154  39843 toggle public List<AnnotationElement> getAnnotationElement() {
155  39843 if (annotationElement == null) {
156  357 annotationElement = new ArrayList<AnnotationElement>();
157    }
158  39843 return this.annotationElement;
159    }
160   
161    /**
162    * Gets the value of the label property.
163    *
164    * @return
165    * possible object is
166    * {@link String }
167    *
168    */
 
169  1884 toggle public String getLabel() {
170  1884 return label;
171    }
172   
173    /**
174    * Sets the value of the label property.
175    *
176    * @param value
177    * allowed object is
178    * {@link String }
179    *
180    */
 
181  357 toggle public void setLabel(String value) {
182  357 this.label = value;
183    }
184   
185    /**
186    * Gets the value of the description property.
187    *
188    * @return
189    * possible object is
190    * {@link String }
191    *
192    */
 
193  516 toggle public String getDescription() {
194  516 return description;
195    }
196   
197    /**
198    * Sets the value of the description property.
199    *
200    * @param value
201    * allowed object is
202    * {@link String }
203    *
204    */
 
205  357 toggle public void setDescription(String value) {
206  357 this.description = value;
207    }
208   
209    /**
210    * Gets the value of the thresholdLine property.
211    *
212    * @return
213    * possible object is
214    * {@link Annotation.ThresholdLine }
215    *
216    */
 
217  431 toggle public Annotation.ThresholdLine getThresholdLine() {
218  431 return thresholdLine;
219    }
220   
221    /**
222    * Sets the value of the thresholdLine property.
223    *
224    * @param value
225    * allowed object is
226    * {@link Annotation.ThresholdLine }
227    *
228    */
 
229  30 toggle public void setThresholdLine(Annotation.ThresholdLine value) {
230  30 this.thresholdLine = value;
231    }
232   
233    /**
234    * Gets the value of the property property.
235    *
236    * <p>
237    * This accessor method returns a reference to the live list,
238    * not a snapshot. Therefore any modification you make to the
239    * returned list will be present inside the JAXB object.
240    * This is why there is not a <CODE>set</CODE> method for the property property.
241    *
242    * <p>
243    * For example, to add a new item, do as follows:
244    * <pre>
245    * getProperty().add(newItem);
246    * </pre>
247    *
248    *
249    * <p>
250    * Objects of the following type(s) are allowed in the list
251    * {@link Annotation.Property }
252    *
253    *
254    */
 
255  516 toggle public List<Annotation.Property> getProperty() {
256  516 if (property == null) {
257  516 property = new ArrayList<Annotation.Property>();
258    }
259  516 return this.property;
260    }
261   
262    /**
263    * Gets the value of the graph property.
264    *
265    */
 
266  516 toggle public boolean isGraph() {
267  516 return graph;
268    }
269   
270    /**
271    * Sets the value of the graph property.
272    *
273    */
 
274  357 toggle public void setGraph(boolean value) {
275  357 this.graph = value;
276    }
277   
278    /**
279    * Gets the value of the graphType property.
280    *
281    * @return
282    * possible object is
283    * {@link Integer }
284    *
285    */
 
286  341 toggle public Integer getGraphType() {
287  341 return graphType;
288    }
289   
290    /**
291    * Sets the value of the graphType property.
292    *
293    * @param value
294    * allowed object is
295    * {@link Integer }
296    *
297    */
 
298  198 toggle public void setGraphType(Integer value) {
299  198 this.graphType = value;
300    }
301   
302    /**
303    * Gets the value of the sequenceRef property.
304    *
305    * @return
306    * possible object is
307    * {@link String }
308    *
309    */
 
310  516 toggle public String getSequenceRef() {
311  516 return sequenceRef;
312    }
313   
314    /**
315    * Sets the value of the sequenceRef property.
316    *
317    * @param value
318    * allowed object is
319    * {@link String }
320    *
321    */
 
322  219 toggle public void setSequenceRef(String value) {
323  219 this.sequenceRef = value;
324    }
325   
326    /**
327    * Gets the value of the groupRef property.
328    *
329    * @return
330    * possible object is
331    * {@link String }
332    *
333    */
 
334  588 toggle public String getGroupRef() {
335  588 return groupRef;
336    }
337   
338    /**
339    * Sets the value of the groupRef property.
340    *
341    * @param value
342    * allowed object is
343    * {@link String }
344    *
345    */
 
346  6 toggle public void setGroupRef(String value) {
347  6 this.groupRef = value;
348    }
349   
350    /**
351    * Gets the value of the graphColour property.
352    *
353    * @return
354    * possible object is
355    * {@link Integer }
356    *
357    */
 
358  0 toggle public Integer getGraphColour() {
359  0 return graphColour;
360    }
361   
362    /**
363    * Sets the value of the graphColour property.
364    *
365    * @param value
366    * allowed object is
367    * {@link Integer }
368    *
369    */
 
370  0 toggle public void setGraphColour(Integer value) {
371  0 this.graphColour = value;
372    }
373   
374    /**
375    * Gets the value of the graphGroup property.
376    *
377    * @return
378    * possible object is
379    * {@link Integer }
380    *
381    */
 
382  341 toggle public Integer getGraphGroup() {
383  341 return graphGroup;
384    }
385   
386    /**
387    * Sets the value of the graphGroup property.
388    *
389    * @param value
390    * allowed object is
391    * {@link Integer }
392    *
393    */
 
394  198 toggle public void setGraphGroup(Integer value) {
395  198 this.graphGroup = value;
396    }
397   
398    /**
399    * Gets the value of the graphHeight property.
400    *
401    * @return
402    * possible object is
403    * {@link Integer }
404    *
405    */
 
406  1032 toggle public Integer getGraphHeight() {
407  1032 return graphHeight;
408    }
409   
410    /**
411    * Sets the value of the graphHeight property.
412    *
413    * @param value
414    * allowed object is
415    * {@link Integer }
416    *
417    */
 
418  357 toggle public void setGraphHeight(Integer value) {
419  357 this.graphHeight = value;
420    }
421   
422    /**
423    * Gets the value of the id property.
424    *
425    * @return
426    * possible object is
427    * {@link String }
428    *
429    */
 
430  1588 toggle public String getId() {
431  1588 return id;
432    }
433   
434    /**
435    * Sets the value of the id property.
436    *
437    * @param value
438    * allowed object is
439    * {@link String }
440    *
441    */
 
442  595 toggle public void setId(String value) {
443  595 this.id = value;
444    }
445   
446    /**
447    * Gets the value of the scoreOnly property.
448    *
449    * @return
450    * possible object is
451    * {@link Boolean }
452    *
453    */
 
454  516 toggle public boolean isScoreOnly() {
455  516 if (scoreOnly == null) {
456  0 return false;
457    } else {
458  516 return scoreOnly;
459    }
460    }
461   
462    /**
463    * Sets the value of the scoreOnly property.
464    *
465    * @param value
466    * allowed object is
467    * {@link Boolean }
468    *
469    */
 
470  357 toggle public void setScoreOnly(Boolean value) {
471  357 this.scoreOnly = value;
472    }
473   
474    /**
475    * Gets the value of the score property.
476    *
477    * @return
478    * possible object is
479    * {@link Double }
480    *
481    */
 
482  655 toggle public Double getScore() {
483  655 return score;
484    }
485   
486    /**
487    * Sets the value of the score property.
488    *
489    * @param value
490    * allowed object is
491    * {@link Double }
492    *
493    */
 
494  139 toggle public void setScore(Double value) {
495  139 this.score = value;
496    }
497   
498    /**
499    * Gets the value of the visible property.
500    *
501    * @return
502    * possible object is
503    * {@link Boolean }
504    *
505    */
 
506  1032 toggle public Boolean isVisible() {
507  1032 return visible;
508    }
509   
510    /**
511    * Sets the value of the visible property.
512    *
513    * @param value
514    * allowed object is
515    * {@link Boolean }
516    *
517    */
 
518  357 toggle public void setVisible(Boolean value) {
519  357 this.visible = value;
520    }
521   
522    /**
523    * Gets the value of the centreColLabels property.
524    *
525    * @return
526    * possible object is
527    * {@link Boolean }
528    *
529    */
 
530  1032 toggle public Boolean isCentreColLabels() {
531  1032 return centreColLabels;
532    }
533   
534    /**
535    * Sets the value of the centreColLabels property.
536    *
537    * @param value
538    * allowed object is
539    * {@link Boolean }
540    *
541    */
 
542  357 toggle public void setCentreColLabels(Boolean value) {
543  357 this.centreColLabels = value;
544    }
545   
546    /**
547    * Gets the value of the scaleColLabels property.
548    *
549    * @return
550    * possible object is
551    * {@link Boolean }
552    *
553    */
 
554  1032 toggle public Boolean isScaleColLabels() {
555  1032 return scaleColLabels;
556    }
557   
558    /**
559    * Sets the value of the scaleColLabels property.
560    *
561    * @param value
562    * allowed object is
563    * {@link Boolean }
564    *
565    */
 
566  357 toggle public void setScaleColLabels(Boolean value) {
567  357 this.scaleColLabels = value;
568    }
569   
570    /**
571    * Gets the value of the showAllColLabels property.
572    *
573    * @return
574    * possible object is
575    * {@link Boolean }
576    *
577    */
 
578  0 toggle public Boolean isShowAllColLabels() {
579  0 return showAllColLabels;
580    }
581   
582    /**
583    * Sets the value of the showAllColLabels property.
584    *
585    * @param value
586    * allowed object is
587    * {@link Boolean }
588    *
589    */
 
590  357 toggle public void setShowAllColLabels(Boolean value) {
591  357 this.showAllColLabels = value;
592    }
593   
594    /**
595    * Gets the value of the autoCalculated property.
596    *
597    * @return
598    * possible object is
599    * {@link Boolean }
600    *
601    */
 
602  1005 toggle public boolean isAutoCalculated() {
603  1005 if (autoCalculated == null) {
604  659 return false;
605    } else {
606  346 return autoCalculated;
607    }
608    }
609   
610    /**
611    * Sets the value of the autoCalculated property.
612    *
613    * @param value
614    * allowed object is
615    * {@link Boolean }
616    *
617    */
 
618  117 toggle public void setAutoCalculated(Boolean value) {
619  117 this.autoCalculated = value;
620    }
621   
622    /**
623    * Gets the value of the belowAlignment property.
624    *
625    * @return
626    * possible object is
627    * {@link Boolean }
628    *
629    */
 
630  516 toggle public boolean isBelowAlignment() {
631  516 if (belowAlignment == null) {
632  144 return true;
633    } else {
634  372 return belowAlignment;
635    }
636    }
637   
638    /**
639    * Sets the value of the belowAlignment property.
640    *
641    * @param value
642    * allowed object is
643    * {@link Boolean }
644    *
645    */
 
646  357 toggle public void setBelowAlignment(Boolean value) {
647  357 this.belowAlignment = value;
648    }
649   
650    /**
651    * Gets the value of the calcId property.
652    *
653    * @return
654    * possible object is
655    * {@link String }
656    *
657    */
 
658  516 toggle public String getCalcId() {
659  516 return calcId;
660    }
661   
662    /**
663    * Sets the value of the calcId property.
664    *
665    * @param value
666    * allowed object is
667    * {@link String }
668    *
669    */
 
670  333 toggle public void setCalcId(String value) {
671  333 this.calcId = value;
672    }
673   
674   
675    /**
676    * <p>Java class for anonymous complex type.
677    *
678    * <p>The following schema fragment specifies the expected content contained within this class.
679    *
680    * <pre>
681    * &lt;complexType>
682    * &lt;complexContent>
683    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
684    * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" />
685    * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}string" />
686    * &lt;/restriction>
687    * &lt;/complexContent>
688    * &lt;/complexType>
689    * </pre>
690    *
691    *
692    */
693    @XmlAccessorType(XmlAccessType.FIELD)
694    @XmlType(name = "")
 
695    public static class Property {
696   
697    @XmlAttribute(name = "name")
698    protected String name;
699    @XmlAttribute(name = "value")
700    protected String value;
701   
702    /**
703    * Gets the value of the name property.
704    *
705    * @return
706    * possible object is
707    * {@link String }
708    *
709    */
 
710  0 toggle public String getName() {
711  0 return name;
712    }
713   
714    /**
715    * Sets the value of the name property.
716    *
717    * @param value
718    * allowed object is
719    * {@link String }
720    *
721    */
 
722  0 toggle public void setName(String value) {
723  0 this.name = value;
724    }
725   
726    /**
727    * Gets the value of the value property.
728    *
729    * @return
730    * possible object is
731    * {@link String }
732    *
733    */
 
734  0 toggle public String getValue() {
735  0 return value;
736    }
737   
738    /**
739    * Sets the value of the value property.
740    *
741    * @param value
742    * allowed object is
743    * {@link String }
744    *
745    */
 
746  0 toggle public void setValue(String value) {
747  0 this.value = value;
748    }
749   
750    }
751   
752   
753    /**
754    * <p>Java class for anonymous complex type.
755    *
756    * <p>The following schema fragment specifies the expected content contained within this class.
757    *
758    * <pre>
759    * &lt;complexType>
760    * &lt;complexContent>
761    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
762    * &lt;attribute name="label" type="{http://www.w3.org/2001/XMLSchema}string" />
763    * &lt;attribute name="value" type="{http://www.w3.org/2001/XMLSchema}float" />
764    * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" />
765    * &lt;/restriction>
766    * &lt;/complexContent>
767    * &lt;/complexType>
768    * </pre>
769    *
770    *
771    */
772    @XmlAccessorType(XmlAccessType.FIELD)
773    @XmlType(name = "")
 
774    public static class ThresholdLine {
775   
776    @XmlAttribute(name = "label")
777    protected String label;
778    @XmlAttribute(name = "value")
779    protected Float value;
780    @XmlAttribute(name = "colour")
781    protected Integer colour;
782   
783    /**
784    * Gets the value of the label property.
785    *
786    * @return
787    * possible object is
788    * {@link String }
789    *
790    */
 
791  30 toggle public String getLabel() {
792  30 return label;
793    }
794   
795    /**
796    * Sets the value of the label property.
797    *
798    * @param value
799    * allowed object is
800    * {@link String }
801    *
802    */
 
803  30 toggle public void setLabel(String value) {
804  30 this.label = value;
805    }
806   
807    /**
808    * Gets the value of the value property.
809    *
810    * @return
811    * possible object is
812    * {@link Float }
813    *
814    */
 
815  30 toggle public Float getValue() {
816  30 return value;
817    }
818   
819    /**
820    * Sets the value of the value property.
821    *
822    * @param value
823    * allowed object is
824    * {@link Float }
825    *
826    */
 
827  30 toggle public void setValue(Float value) {
828  30 this.value = value;
829    }
830   
831    /**
832    * Gets the value of the colour property.
833    *
834    * @return
835    * possible object is
836    * {@link Integer }
837    *
838    */
 
839  30 toggle public Integer getColour() {
840  30 return colour;
841    }
842   
843    /**
844    * Sets the value of the colour property.
845    *
846    * @param value
847    * allowed object is
848    * {@link Integer }
849    *
850    */
 
851  30 toggle public void setColour(Integer value) {
852  30 this.colour = value;
853    }
854   
855    }
856   
857    }
  • Report generated by OpenClover v 4.4.1 on Thu Aug 13 2020 12:06:48 BST using coverage data from Thu Aug 13 2020 12:06:40 BST.
  • OpenClover is free and open-source software.