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Coverage Report

  1. Project Clover database Thu Nov 27 2025 17:21:41 GMT
  2. Package jalview.xml.binding.jalview

File JalviewUserColours.java

 

Coverage histogram

../../../../img/srcFileCovDistChart9.png
13% of files have more coverage

Code metrics

8
39
31
3
637
168
35
0.9
1.26
10.33
1.13

Classes

Class Line # Actions
JalviewUserColours 79 10 8
0.770%
JalviewUserColours.Colour 241 25 23
0.9696%
JalviewUserColours.Filter 580 4 4
1.0100%
 

Contributing tests

This file is covered by 1 test. .

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.XmlType;
18   
19   
20    /**
21    * <p>Java class for JalviewUserColours complex type</p>.
22    *
23    * <p>The following schema fragment specifies the expected content contained within this class.</p>
24    *
25    * <pre>
26    * &lt;complexType name="JalviewUserColours"&gt;
27    * &lt;complexContent&gt;
28    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
29    * &lt;sequence&gt;
30    * &lt;element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/&gt;
31    * &lt;element name="colour" 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 name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
37    * &lt;/sequence&gt;
38    * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
39    * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
40    * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
41    * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
42    * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
43    * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
44    * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
45    * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
46    * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
47    * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
48    * &lt;/restriction&gt;
49    * &lt;/complexContent&gt;
50    * &lt;/complexType&gt;
51    * &lt;/element&gt;
52    * &lt;element name="filter" maxOccurs="unbounded" minOccurs="0"&gt;
53    * &lt;complexType&gt;
54    * &lt;complexContent&gt;
55    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
56    * &lt;sequence&gt;
57    * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
58    * &lt;/sequence&gt;
59    * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
60    * &lt;/restriction&gt;
61    * &lt;/complexContent&gt;
62    * &lt;/complexType&gt;
63    * &lt;/element&gt;
64    * &lt;/sequence&gt;
65    * &lt;attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
66    * &lt;/restriction&gt;
67    * &lt;/complexContent&gt;
68    * &lt;/complexType&gt;
69    * </pre>
70    *
71    *
72    */
73    @XmlAccessorType(XmlAccessType.FIELD)
74    @XmlType(name = "JalviewUserColours", namespace = "www.jalview.org/colours", propOrder = {
75    "version",
76    "colour",
77    "filter"
78    })
 
79    public class JalviewUserColours {
80   
81    /**
82    * Jalview colour scheme document version.
83    *
84    */
85    @XmlElement(name = "Version", namespace = "")
86    protected String version;
87    @XmlElement(namespace = "")
88    protected List<JalviewUserColours.Colour> colour;
89    @XmlElement(namespace = "")
90    protected List<JalviewUserColours.Filter> filter;
91    @XmlAttribute(name = "schemeName")
92    protected String schemeName;
93   
94    /**
95    * Jalview colour scheme document version.
96    *
97    * @return
98    * possible object is
99    * {@link String }
100    *
101    */
 
102  0 toggle public String getVersion() {
103  0 return version;
104    }
105   
106    /**
107    * Sets the value of the version property.
108    *
109    * @param value
110    * allowed object is
111    * {@link String }
112    *
113    * @see #getVersion()
114    */
 
115  0 toggle public void setVersion(String value) {
116  0 this.version = value;
117    }
118   
119    /**
120    * Gets the value of the colour property.
121    *
122    * <p>This accessor method returns a reference to the live list,
123    * not a snapshot. Therefore any modification you make to the
124    * returned list will be present inside the JAXB object.
125    * This is why there is not a <CODE>set</CODE> method for the colour property.</p>
126    *
127    * <p>
128    * For example, to add a new item, do as follows:
129    * </p>
130    * <pre>
131    * getColour().add(newItem);
132    * </pre>
133    *
134    *
135    * <p>
136    * Objects of the following type(s) are allowed in the list
137    * {@link JalviewUserColours.Colour }
138    * </p>
139    *
140    *
141    * @return
142    * The value of the colour property.
143    */
 
144  16 toggle public List<JalviewUserColours.Colour> getColour() {
145  16 if (colour == null) {
146  1 colour = new ArrayList<JalviewUserColours.Colour>();
147    }
148  16 return this.colour;
149    }
150   
151    /**
152    * Gets the value of the filter property.
153    *
154    * <p>This accessor method returns a reference to the live list,
155    * not a snapshot. Therefore any modification you make to the
156    * returned list will be present inside the JAXB object.
157    * This is why there is not a <CODE>set</CODE> method for the filter property.</p>
158    *
159    * <p>
160    * For example, to add a new item, do as follows:
161    * </p>
162    * <pre>
163    * getFilter().add(newItem);
164    * </pre>
165    *
166    *
167    * <p>
168    * Objects of the following type(s) are allowed in the list
169    * {@link JalviewUserColours.Filter }
170    * </p>
171    *
172    *
173    * @return
174    * The value of the filter property.
175    */
 
176  10 toggle public List<JalviewUserColours.Filter> getFilter() {
177  10 if (filter == null) {
178  1 filter = new ArrayList<JalviewUserColours.Filter>();
179    }
180  10 return this.filter;
181    }
182   
183    /**
184    * Gets the value of the schemeName property.
185    *
186    * @return
187    * possible object is
188    * {@link String }
189    *
190    */
 
191  0 toggle public String getSchemeName() {
192  0 return schemeName;
193    }
194   
195    /**
196    * Sets the value of the schemeName property.
197    *
198    * @param value
199    * allowed object is
200    * {@link String }
201    *
202    */
 
203  1 toggle public void setSchemeName(String value) {
204  1 this.schemeName = value;
205    }
206   
207   
208    /**
209    * <p>Java class for anonymous complex type</p>.
210    *
211    * <p>The following schema fragment specifies the expected content contained within this class.</p>
212    *
213    * <pre>
214    * &lt;complexType&gt;
215    * &lt;complexContent&gt;
216    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
217    * &lt;sequence&gt;
218    * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
219    * &lt;/sequence&gt;
220    * &lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
221    * &lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
222    * &lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
223    * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
224    * &lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&gt;
225    * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
226    * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
227    * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
228    * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
229    * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
230    * &lt;/restriction&gt;
231    * &lt;/complexContent&gt;
232    * &lt;/complexType&gt;
233    * </pre>
234    *
235    *
236    */
237    @XmlAccessorType(XmlAccessType.FIELD)
238    @XmlType(name = "", propOrder = {
239    "attributeName"
240    })
 
241    public static class Colour {
242   
243    /**
244    * name of feature attribute to colour by, or attribute and sub-attribute
245    *
246    */
247    @XmlElement(namespace = "")
248    protected List<String> attributeName;
249    /**
250    * Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme
251    *
252    */
253    @XmlAttribute(name = "Name")
254    protected String name;
255    @XmlAttribute(name = "RGB", required = true)
256    protected String rgb;
257    @XmlAttribute(name = "minRGB")
258    protected String minRGB;
259    @XmlAttribute(name = "noValueColour")
260    protected NoValueColour noValueColour;
261    @XmlAttribute(name = "threshType")
262    protected ThresholdType threshType;
263    @XmlAttribute(name = "threshold")
264    protected Float threshold;
265    @XmlAttribute(name = "max")
266    protected Float max;
267    @XmlAttribute(name = "min")
268    protected Float min;
269    @XmlAttribute(name = "colourByLabel")
270    protected Boolean colourByLabel;
271    @XmlAttribute(name = "autoScale")
272    protected Boolean autoScale;
273   
274    /**
275    * name of feature attribute to colour by, or attribute and sub-attribute
276    *
277    * Gets the value of the attributeName property.
278    *
279    * <p>This accessor method returns a reference to the live list,
280    * not a snapshot. Therefore any modification you make to the
281    * returned list will be present inside the JAXB object.
282    * This is why there is not a <CODE>set</CODE> method for the attributeName property.</p>
283    *
284    * <p>
285    * For example, to add a new item, do as follows:
286    * </p>
287    * <pre>
288    * getAttributeName().add(newItem);
289    * </pre>
290    *
291    *
292    * <p>
293    * Objects of the following type(s) are allowed in the list
294    * {@link String }
295    * </p>
296    *
297    *
298    * @return
299    * The value of the attributeName property.
300    */
 
301  7 toggle public List<String> getAttributeName() {
302  7 if (attributeName == null) {
303  4 attributeName = new ArrayList<String>();
304    }
305  7 return this.attributeName;
306    }
307   
308    /**
309    * Single letter residue code for an alignment colour scheme, or feature type for a feature colour scheme
310    *
311    * @return
312    * possible object is
313    * {@link String }
314    *
315    */
 
316  10 toggle public String getName() {
317  10 return name;
318    }
319   
320    /**
321    * Sets the value of the name property.
322    *
323    * @param value
324    * allowed object is
325    * {@link String }
326    *
327    * @see #getName()
328    */
 
329  5 toggle public void setName(String value) {
330  5 this.name = value;
331    }
332   
333    /**
334    * Gets the value of the rgb property.
335    *
336    * @return
337    * possible object is
338    * {@link String }
339    *
340    */
 
341  5 toggle public String getRGB() {
342  5 return rgb;
343    }
344   
345    /**
346    * Sets the value of the rgb property.
347    *
348    * @param value
349    * allowed object is
350    * {@link String }
351    *
352    */
 
353  5 toggle public void setRGB(String value) {
354  5 this.rgb = value;
355    }
356   
357    /**
358    * Gets the value of the minRGB property.
359    *
360    * @return
361    * possible object is
362    * {@link String }
363    *
364    */
 
365  4 toggle public String getMinRGB() {
366  4 return minRGB;
367    }
368   
369    /**
370    * Sets the value of the minRGB property.
371    *
372    * @param value
373    * allowed object is
374    * {@link String }
375    *
376    */
 
377  4 toggle public void setMinRGB(String value) {
378  4 this.minRGB = value;
379    }
380   
381    /**
382    * Gets the value of the noValueColour property.
383    *
384    * @return
385    * possible object is
386    * {@link NoValueColour }
387    *
388    */
 
389  4 toggle public NoValueColour getNoValueColour() {
390  4 if (noValueColour == null) {
391  0 return NoValueColour.MIN;
392    } else {
393  4 return noValueColour;
394    }
395    }
396   
397    /**
398    * Sets the value of the noValueColour property.
399    *
400    * @param value
401    * allowed object is
402    * {@link NoValueColour }
403    *
404    */
 
405  4 toggle public void setNoValueColour(NoValueColour value) {
406  4 this.noValueColour = value;
407    }
408   
409    /**
410    * Gets the value of the threshType property.
411    *
412    * @return
413    * possible object is
414    * {@link ThresholdType }
415    *
416    */
 
417  4 toggle public ThresholdType getThreshType() {
418  4 return threshType;
419    }
420   
421    /**
422    * Sets the value of the threshType property.
423    *
424    * @param value
425    * allowed object is
426    * {@link ThresholdType }
427    *
428    */
 
429  4 toggle public void setThreshType(ThresholdType value) {
430  4 this.threshType = value;
431    }
432   
433    /**
434    * Gets the value of the threshold property.
435    *
436    * @return
437    * possible object is
438    * {@link Float }
439    *
440    */
 
441  8 toggle public Float getThreshold() {
442  8 return threshold;
443    }
444   
445    /**
446    * Sets the value of the threshold property.
447    *
448    * @param value
449    * allowed object is
450    * {@link Float }
451    *
452    */
 
453  4 toggle public void setThreshold(Float value) {
454  4 this.threshold = value;
455    }
456   
457    /**
458    * Gets the value of the max property.
459    *
460    * @return
461    * possible object is
462    * {@link Float }
463    *
464    */
 
465  9 toggle public Float getMax() {
466  9 return max;
467    }
468   
469    /**
470    * Sets the value of the max property.
471    *
472    * @param value
473    * allowed object is
474    * {@link Float }
475    *
476    */
 
477  4 toggle public void setMax(Float value) {
478  4 this.max = value;
479    }
480   
481    /**
482    * Gets the value of the min property.
483    *
484    * @return
485    * possible object is
486    * {@link Float }
487    *
488    */
 
489  4 toggle public Float getMin() {
490  4 return min;
491    }
492   
493    /**
494    * Sets the value of the min property.
495    *
496    * @param value
497    * allowed object is
498    * {@link Float }
499    *
500    */
 
501  4 toggle public void setMin(Float value) {
502  4 this.min = value;
503    }
504   
505    /**
506    * Gets the value of the colourByLabel property.
507    *
508    * @return
509    * possible object is
510    * {@link Boolean }
511    *
512    */
 
513  8 toggle public Boolean isColourByLabel() {
514  8 return colourByLabel;
515    }
516   
517    /**
518    * Sets the value of the colourByLabel property.
519    *
520    * @param value
521    * allowed object is
522    * {@link Boolean }
523    *
524    */
 
525  4 toggle public void setColourByLabel(Boolean value) {
526  4 this.colourByLabel = value;
527    }
528   
529    /**
530    * Gets the value of the autoScale property.
531    *
532    * @return
533    * possible object is
534    * {@link Boolean }
535    *
536    */
 
537  8 toggle public Boolean isAutoScale() {
538  8 return autoScale;
539    }
540   
541    /**
542    * Sets the value of the autoScale property.
543    *
544    * @param value
545    * allowed object is
546    * {@link Boolean }
547    *
548    */
 
549  4 toggle public void setAutoScale(Boolean value) {
550  4 this.autoScale = value;
551    }
552   
553    }
554   
555   
556    /**
557    * <p>Java class for anonymous complex type</p>.
558    *
559    * <p>The following schema fragment specifies the expected content contained within this class.</p>
560    *
561    * <pre>
562    * &lt;complexType&gt;
563    * &lt;complexContent&gt;
564    * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
565    * &lt;sequence&gt;
566    * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&gt;
567    * &lt;/sequence&gt;
568    * &lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
569    * &lt;/restriction&gt;
570    * &lt;/complexContent&gt;
571    * &lt;/complexType&gt;
572    * </pre>
573    *
574    *
575    */
576    @XmlAccessorType(XmlAccessType.FIELD)
577    @XmlType(name = "", propOrder = {
578    "matcherSet"
579    })
 
580    public static class Filter {
581   
582    @XmlElement(namespace = "", required = true)
583    protected FeatureMatcherSet matcherSet;
584    @XmlAttribute(name = "featureType", required = true)
585    protected String featureType;
586   
587    /**
588    * Gets the value of the matcherSet property.
589    *
590    * @return
591    * possible object is
592    * {@link FeatureMatcherSet }
593    *
594    */
 
595  3 toggle public FeatureMatcherSet getMatcherSet() {
596  3 return matcherSet;
597    }
598   
599    /**
600    * Sets the value of the matcherSet property.
601    *
602    * @param value
603    * allowed object is
604    * {@link FeatureMatcherSet }
605    *
606    */
 
607  3 toggle public void setMatcherSet(FeatureMatcherSet value) {
608  3 this.matcherSet = value;
609    }
610   
611    /**
612    * Gets the value of the featureType property.
613    *
614    * @return
615    * possible object is
616    * {@link String }
617    *
618    */
 
619  3 toggle public String getFeatureType() {
620  3 return featureType;
621    }
622   
623    /**
624    * Sets the value of the featureType property.
625    *
626    * @param value
627    * allowed object is
628    * {@link String }
629    *
630    */
 
631  3 toggle public void setFeatureType(String value) {
632  3 this.featureType = value;
633    }
634   
635    }
636   
637    }