JAL-4124 matrix is saved in dataset, with forward references made from alignments
[jalview.git] / src / jalview / xml / binding / jalview / JalviewUserColours.java
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: 2023.09.01 at 02:16:11 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.
22  * 
23  * <p>The following schema fragment specifies the expected content contained within this class.
24  * 
25  * <pre>
26  * <complexType name="JalviewUserColours">
27  *   <complexContent>
28  *     <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
29  *       <sequence>
30  *         <element name="Version" type="{http://www.w3.org/2001/XMLSchema}string" minOccurs="0"/>
31  *         <element name="colour" maxOccurs="unbounded" minOccurs="0">
32  *           <complexType>
33  *             <complexContent>
34  *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
35  *                 <sequence>
36  *                   <element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/>
37  *                 </sequence>
38  *                 <attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" />
39  *                 <attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
40  *                 <attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" />
41  *                 <attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" />
42  *                 <attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" />
43  *                 <attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" />
44  *                 <attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" />
45  *                 <attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" />
46  *                 <attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" />
47  *                 <attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" />
48  *               </restriction>
49  *             </complexContent>
50  *           </complexType>
51  *         </element>
52  *         <element name="filter" maxOccurs="unbounded" minOccurs="0">
53  *           <complexType>
54  *             <complexContent>
55  *               <restriction base="{http://www.w3.org/2001/XMLSchema}anyType">
56  *                 <sequence>
57  *                   <element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/>
58  *                 </sequence>
59  *                 <attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" />
60  *               </restriction>
61  *             </complexContent>
62  *           </complexType>
63  *         </element>
64  *       </sequence>
65  *       <attribute name="schemeName" type="{http://www.w3.org/2001/XMLSchema}string" />
66  *     </restriction>
67  *   </complexContent>
68  * </complexType>
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     @XmlElement(name = "Version", namespace = "")
82     protected String version;
83     @XmlElement(namespace = "")
84     protected List<JalviewUserColours.Colour> colour;
85     @XmlElement(namespace = "")
86     protected List<JalviewUserColours.Filter> filter;
87     @XmlAttribute(name = "schemeName")
88     protected String schemeName;
89
90     /**
91      * Gets the value of the version property.
92      * 
93      * @return
94      *     possible object is
95      *     {@link String }
96      *     
97      */
98     public String getVersion() {
99         return version;
100     }
101
102     /**
103      * Sets the value of the version property.
104      * 
105      * @param value
106      *     allowed object is
107      *     {@link String }
108      *     
109      */
110     public void setVersion(String value) {
111         this.version = value;
112     }
113
114     /**
115      * Gets the value of the colour property.
116      * 
117      * &lt;p&gt;
118      * This accessor method returns a reference to the live list,
119      * not a snapshot. Therefore any modification you make to the
120      * returned list will be present inside the JAXB object.
121      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the colour property.
122      * 
123      * &lt;p&gt;
124      * For example, to add a new item, do as follows:
125      * &lt;pre&gt;
126      *    getColour().add(newItem);
127      * &lt;/pre&gt;
128      * 
129      * 
130      * &lt;p&gt;
131      * Objects of the following type(s) are allowed in the list
132      * {@link JalviewUserColours.Colour }
133      * 
134      * 
135      */
136     public List<JalviewUserColours.Colour> getColour() {
137         if (colour == null) {
138             colour = new ArrayList<JalviewUserColours.Colour>();
139         }
140         return this.colour;
141     }
142
143     /**
144      * Gets the value of the filter property.
145      * 
146      * &lt;p&gt;
147      * This accessor method returns a reference to the live list,
148      * not a snapshot. Therefore any modification you make to the
149      * returned list will be present inside the JAXB object.
150      * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the filter property.
151      * 
152      * &lt;p&gt;
153      * For example, to add a new item, do as follows:
154      * &lt;pre&gt;
155      *    getFilter().add(newItem);
156      * &lt;/pre&gt;
157      * 
158      * 
159      * &lt;p&gt;
160      * Objects of the following type(s) are allowed in the list
161      * {@link JalviewUserColours.Filter }
162      * 
163      * 
164      */
165     public List<JalviewUserColours.Filter> getFilter() {
166         if (filter == null) {
167             filter = new ArrayList<JalviewUserColours.Filter>();
168         }
169         return this.filter;
170     }
171
172     /**
173      * Gets the value of the schemeName property.
174      * 
175      * @return
176      *     possible object is
177      *     {@link String }
178      *     
179      */
180     public String getSchemeName() {
181         return schemeName;
182     }
183
184     /**
185      * Sets the value of the schemeName property.
186      * 
187      * @param value
188      *     allowed object is
189      *     {@link String }
190      *     
191      */
192     public void setSchemeName(String value) {
193         this.schemeName = value;
194     }
195
196
197     /**
198      * &lt;p&gt;Java class for anonymous complex type.
199      * 
200      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
201      * 
202      * &lt;pre&gt;
203      * &amp;lt;complexType&amp;gt;
204      *   &amp;lt;complexContent&amp;gt;
205      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
206      *       &amp;lt;sequence&amp;gt;
207      *         &amp;lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&amp;gt;
208      *       &amp;lt;/sequence&amp;gt;
209      *       &amp;lt;attribute name="Name" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
210      *       &amp;lt;attribute name="RGB" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
211      *       &amp;lt;attribute name="minRGB" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
212      *       &amp;lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&amp;gt;
213      *       &amp;lt;attribute name="threshType" type="{www.jalview.org/colours}ThresholdType" /&amp;gt;
214      *       &amp;lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
215      *       &amp;lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
216      *       &amp;lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&amp;gt;
217      *       &amp;lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
218      *       &amp;lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&amp;gt;
219      *     &amp;lt;/restriction&amp;gt;
220      *   &amp;lt;/complexContent&amp;gt;
221      * &amp;lt;/complexType&amp;gt;
222      * &lt;/pre&gt;
223      * 
224      * 
225      */
226     @XmlAccessorType(XmlAccessType.FIELD)
227     @XmlType(name = "", propOrder = {
228         "attributeName"
229     })
230     public static class Colour {
231
232         @XmlElement(namespace = "")
233         protected List<String> attributeName;
234         @XmlAttribute(name = "Name")
235         protected String name;
236         @XmlAttribute(name = "RGB", required = true)
237         protected String rgb;
238         @XmlAttribute(name = "minRGB")
239         protected String minRGB;
240         @XmlAttribute(name = "noValueColour")
241         protected NoValueColour noValueColour;
242         @XmlAttribute(name = "threshType")
243         protected ThresholdType threshType;
244         @XmlAttribute(name = "threshold")
245         protected Float threshold;
246         @XmlAttribute(name = "max")
247         protected Float max;
248         @XmlAttribute(name = "min")
249         protected Float min;
250         @XmlAttribute(name = "colourByLabel")
251         protected Boolean colourByLabel;
252         @XmlAttribute(name = "autoScale")
253         protected Boolean autoScale;
254
255         /**
256          * Gets the value of the attributeName property.
257          * 
258          * &lt;p&gt;
259          * This accessor method returns a reference to the live list,
260          * not a snapshot. Therefore any modification you make to the
261          * returned list will be present inside the JAXB object.
262          * This is why there is not a &lt;CODE&gt;set&lt;/CODE&gt; method for the attributeName property.
263          * 
264          * &lt;p&gt;
265          * For example, to add a new item, do as follows:
266          * &lt;pre&gt;
267          *    getAttributeName().add(newItem);
268          * &lt;/pre&gt;
269          * 
270          * 
271          * &lt;p&gt;
272          * Objects of the following type(s) are allowed in the list
273          * {@link String }
274          * 
275          * 
276          */
277         public List<String> getAttributeName() {
278             if (attributeName == null) {
279                 attributeName = new ArrayList<String>();
280             }
281             return this.attributeName;
282         }
283
284         /**
285          * Gets the value of the name property.
286          * 
287          * @return
288          *     possible object is
289          *     {@link String }
290          *     
291          */
292         public String getName() {
293             return name;
294         }
295
296         /**
297          * Sets the value of the name property.
298          * 
299          * @param value
300          *     allowed object is
301          *     {@link String }
302          *     
303          */
304         public void setName(String value) {
305             this.name = value;
306         }
307
308         /**
309          * Gets the value of the rgb property.
310          * 
311          * @return
312          *     possible object is
313          *     {@link String }
314          *     
315          */
316         public String getRGB() {
317             return rgb;
318         }
319
320         /**
321          * Sets the value of the rgb property.
322          * 
323          * @param value
324          *     allowed object is
325          *     {@link String }
326          *     
327          */
328         public void setRGB(String value) {
329             this.rgb = value;
330         }
331
332         /**
333          * Gets the value of the minRGB property.
334          * 
335          * @return
336          *     possible object is
337          *     {@link String }
338          *     
339          */
340         public String getMinRGB() {
341             return minRGB;
342         }
343
344         /**
345          * Sets the value of the minRGB property.
346          * 
347          * @param value
348          *     allowed object is
349          *     {@link String }
350          *     
351          */
352         public void setMinRGB(String value) {
353             this.minRGB = value;
354         }
355
356         /**
357          * Gets the value of the noValueColour property.
358          * 
359          * @return
360          *     possible object is
361          *     {@link NoValueColour }
362          *     
363          */
364         public NoValueColour getNoValueColour() {
365             if (noValueColour == null) {
366                 return NoValueColour.MIN;
367             } else {
368                 return noValueColour;
369             }
370         }
371
372         /**
373          * Sets the value of the noValueColour property.
374          * 
375          * @param value
376          *     allowed object is
377          *     {@link NoValueColour }
378          *     
379          */
380         public void setNoValueColour(NoValueColour value) {
381             this.noValueColour = value;
382         }
383
384         /**
385          * Gets the value of the threshType property.
386          * 
387          * @return
388          *     possible object is
389          *     {@link ThresholdType }
390          *     
391          */
392         public ThresholdType getThreshType() {
393             return threshType;
394         }
395
396         /**
397          * Sets the value of the threshType property.
398          * 
399          * @param value
400          *     allowed object is
401          *     {@link ThresholdType }
402          *     
403          */
404         public void setThreshType(ThresholdType value) {
405             this.threshType = value;
406         }
407
408         /**
409          * Gets the value of the threshold property.
410          * 
411          * @return
412          *     possible object is
413          *     {@link Float }
414          *     
415          */
416         public Float getThreshold() {
417             return threshold;
418         }
419
420         /**
421          * Sets the value of the threshold property.
422          * 
423          * @param value
424          *     allowed object is
425          *     {@link Float }
426          *     
427          */
428         public void setThreshold(Float value) {
429             this.threshold = value;
430         }
431
432         /**
433          * Gets the value of the max property.
434          * 
435          * @return
436          *     possible object is
437          *     {@link Float }
438          *     
439          */
440         public Float getMax() {
441             return max;
442         }
443
444         /**
445          * Sets the value of the max property.
446          * 
447          * @param value
448          *     allowed object is
449          *     {@link Float }
450          *     
451          */
452         public void setMax(Float value) {
453             this.max = value;
454         }
455
456         /**
457          * Gets the value of the min property.
458          * 
459          * @return
460          *     possible object is
461          *     {@link Float }
462          *     
463          */
464         public Float getMin() {
465             return min;
466         }
467
468         /**
469          * Sets the value of the min property.
470          * 
471          * @param value
472          *     allowed object is
473          *     {@link Float }
474          *     
475          */
476         public void setMin(Float value) {
477             this.min = value;
478         }
479
480         /**
481          * Gets the value of the colourByLabel property.
482          * 
483          * @return
484          *     possible object is
485          *     {@link Boolean }
486          *     
487          */
488         public Boolean isColourByLabel() {
489             return colourByLabel;
490         }
491
492         /**
493          * Sets the value of the colourByLabel property.
494          * 
495          * @param value
496          *     allowed object is
497          *     {@link Boolean }
498          *     
499          */
500         public void setColourByLabel(Boolean value) {
501             this.colourByLabel = value;
502         }
503
504         /**
505          * Gets the value of the autoScale property.
506          * 
507          * @return
508          *     possible object is
509          *     {@link Boolean }
510          *     
511          */
512         public Boolean isAutoScale() {
513             return autoScale;
514         }
515
516         /**
517          * Sets the value of the autoScale property.
518          * 
519          * @param value
520          *     allowed object is
521          *     {@link Boolean }
522          *     
523          */
524         public void setAutoScale(Boolean value) {
525             this.autoScale = value;
526         }
527
528     }
529
530
531     /**
532      * &lt;p&gt;Java class for anonymous complex type.
533      * 
534      * &lt;p&gt;The following schema fragment specifies the expected content contained within this class.
535      * 
536      * &lt;pre&gt;
537      * &amp;lt;complexType&amp;gt;
538      *   &amp;lt;complexContent&amp;gt;
539      *     &amp;lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&amp;gt;
540      *       &amp;lt;sequence&amp;gt;
541      *         &amp;lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet"/&amp;gt;
542      *       &amp;lt;/sequence&amp;gt;
543      *       &amp;lt;attribute name="featureType" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&amp;gt;
544      *     &amp;lt;/restriction&amp;gt;
545      *   &amp;lt;/complexContent&amp;gt;
546      * &amp;lt;/complexType&amp;gt;
547      * &lt;/pre&gt;
548      * 
549      * 
550      */
551     @XmlAccessorType(XmlAccessType.FIELD)
552     @XmlType(name = "", propOrder = {
553         "matcherSet"
554     })
555     public static class Filter {
556
557         @XmlElement(namespace = "", required = true)
558         protected FeatureMatcherSet matcherSet;
559         @XmlAttribute(name = "featureType", required = true)
560         protected String featureType;
561
562         /**
563          * Gets the value of the matcherSet property.
564          * 
565          * @return
566          *     possible object is
567          *     {@link FeatureMatcherSet }
568          *     
569          */
570         public FeatureMatcherSet getMatcherSet() {
571             return matcherSet;
572         }
573
574         /**
575          * Sets the value of the matcherSet property.
576          * 
577          * @param value
578          *     allowed object is
579          *     {@link FeatureMatcherSet }
580          *     
581          */
582         public void setMatcherSet(FeatureMatcherSet value) {
583             this.matcherSet = value;
584         }
585
586         /**
587          * Gets the value of the featureType property.
588          * 
589          * @return
590          *     possible object is
591          *     {@link String }
592          *     
593          */
594         public String getFeatureType() {
595             return featureType;
596         }
597
598         /**
599          * Sets the value of the featureType property.
600          * 
601          * @param value
602          *     allowed object is
603          *     {@link String }
604          *     
605          */
606         public void setFeatureType(String value) {
607             this.featureType = value;
608         }
609
610     }
611
612 }