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: 2022.02.07 at 04:44:47 PM GMT
9 package jalview.xml.binding.jalview;
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.XmlID;
18 import javax.xml.bind.annotation.XmlSchemaType;
19 import javax.xml.bind.annotation.XmlType;
20 import javax.xml.bind.annotation.XmlValue;
21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23 import javax.xml.datatype.XMLGregorianCalendar;
27 * <p>Java class for JalviewModel complex type.
29 * <p>The following schema fragment specifies the expected content contained within this class.
32 * &lt;complexType name="JalviewModel"&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="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
37 * &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
38 * &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
39 * &lt;sequence&gt;
40 * &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
41 * &lt;complexType&gt;
42 * &lt;complexContent&gt;
43 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
44 * &lt;sequence&gt;
45 * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
46 * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
47 * &lt;complexType&gt;
48 * &lt;complexContent&gt;
49 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
50 * &lt;sequence&gt;
51 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
52 * &lt;complexType&gt;
53 * &lt;simpleContent&gt;
54 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
55 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
56 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
57 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
58 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
59 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
60 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
61 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
62 * &lt;/extension&gt;
63 * &lt;/simpleContent&gt;
64 * &lt;/complexType&gt;
65 * &lt;/element&gt;
66 * &lt;/sequence&gt;
67 * &lt;/extension&gt;
68 * &lt;/complexContent&gt;
69 * &lt;/complexType&gt;
70 * &lt;/element&gt;
71 * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
72 * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
73 * &lt;complexType&gt;
74 * &lt;complexContent&gt;
75 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
76 * &lt;sequence&gt;
77 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
78 * &lt;complexType&gt;
79 * &lt;complexContent&gt;
80 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
81 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
82 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
83 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
84 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
85 * &lt;/restriction&gt;
86 * &lt;/complexContent&gt;
87 * &lt;/complexType&gt;
88 * &lt;/element&gt;
89 * &lt;/sequence&gt;
90 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
91 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
92 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
93 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
94 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
95 * &lt;/restriction&gt;
96 * &lt;/complexContent&gt;
97 * &lt;/complexType&gt;
98 * &lt;/element&gt;
99 * &lt;/sequence&gt;
100 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
101 * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
102 * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
103 * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
104 * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
105 * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
106 * &lt;/restriction&gt;
107 * &lt;/complexContent&gt;
108 * &lt;/complexType&gt;
109 * &lt;/element&gt;
110 * &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
111 * &lt;complexType&gt;
112 * &lt;complexContent&gt;
113 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
114 * &lt;sequence&gt;
115 * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
116 * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
117 * &lt;/sequence&gt;
118 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
119 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
120 * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
121 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
122 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
123 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
124 * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
125 * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
126 * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
127 * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
128 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
129 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
130 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
131 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
132 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
133 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
134 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
135 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
136 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
137 * &lt;/restriction&gt;
138 * &lt;/complexContent&gt;
139 * &lt;/complexType&gt;
140 * &lt;/element&gt;
141 * &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
142 * &lt;complexType&gt;
143 * &lt;complexContent&gt;
144 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
145 * &lt;sequence&gt;
146 * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
147 * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
148 * &lt;complexType&gt;
149 * &lt;complexContent&gt;
150 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
151 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
152 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
153 * &lt;/restriction&gt;
154 * &lt;/complexContent&gt;
155 * &lt;/complexType&gt;
156 * &lt;/element&gt;
157 * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
158 * &lt;complexType&gt;
159 * &lt;complexContent&gt;
160 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
161 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
162 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
163 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
164 * &lt;/extension&gt;
165 * &lt;/complexContent&gt;
166 * &lt;/complexType&gt;
167 * &lt;/element&gt;
168 * &lt;element name="overview" minOccurs="0"&gt;
169 * &lt;complexType&gt;
170 * &lt;complexContent&gt;
171 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
172 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
173 * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
174 * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
175 * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
176 * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
177 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
178 * &lt;/restriction&gt;
179 * &lt;/complexContent&gt;
180 * &lt;/complexType&gt;
181 * &lt;/element&gt;
182 * &lt;/sequence&gt;
183 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
184 * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
185 * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
186 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
187 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
188 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
189 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
190 * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
191 * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
192 * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
193 * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
194 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
195 * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
196 * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
197 * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
198 * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
199 * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
200 * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
201 * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
202 * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
203 * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
204 * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
205 * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
206 * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
207 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
208 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
209 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
210 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
211 * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
212 * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
213 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
214 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
215 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
216 * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
217 * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
218 * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
219 * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
220 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
221 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
222 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
223 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
224 * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
225 * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
226 * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
227 * &lt;/restriction&gt;
228 * &lt;/complexContent&gt;
229 * &lt;/complexType&gt;
230 * &lt;/element&gt;
231 * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
232 * &lt;complexType&gt;
233 * &lt;complexContent&gt;
234 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
235 * &lt;sequence&gt;
236 * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
237 * &lt;/sequence&gt;
238 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
239 * &lt;/restriction&gt;
240 * &lt;/complexContent&gt;
241 * &lt;/complexType&gt;
242 * &lt;/element&gt;
243 * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
244 * &lt;complexType&gt;
245 * &lt;complexContent&gt;
246 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
247 * &lt;sequence minOccurs="0"&gt;
248 * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
249 * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
250 * &lt;/sequence&gt;
251 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
252 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
253 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
254 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
255 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
256 * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
257 * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
258 * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
259 * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
260 * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
261 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
262 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
263 * &lt;/restriction&gt;
264 * &lt;/complexContent&gt;
265 * &lt;/complexType&gt;
266 * &lt;/element&gt;
267 * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
268 * &lt;complexType&gt;
269 * &lt;complexContent&gt;
270 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
271 * &lt;sequence&gt;
272 * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
273 * &lt;complexType&gt;
274 * &lt;complexContent&gt;
275 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
276 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
277 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
278 * &lt;/restriction&gt;
279 * &lt;/complexContent&gt;
280 * &lt;/complexType&gt;
281 * &lt;/element&gt;
282 * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
283 * &lt;complexType&gt;
284 * &lt;complexContent&gt;
285 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
286 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
287 * &lt;/restriction&gt;
288 * &lt;/complexContent&gt;
289 * &lt;/complexType&gt;
290 * &lt;/element&gt;
291 * &lt;element name="seqPointMin"&gt;
292 * &lt;complexType&gt;
293 * &lt;complexContent&gt;
294 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
295 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
296 * &lt;/restriction&gt;
297 * &lt;/complexContent&gt;
298 * &lt;/complexType&gt;
299 * &lt;/element&gt;
300 * &lt;element name="seqPointMax"&gt;
301 * &lt;complexType&gt;
302 * &lt;complexContent&gt;
303 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
304 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
305 * &lt;/restriction&gt;
306 * &lt;/complexContent&gt;
307 * &lt;/complexType&gt;
308 * &lt;/element&gt;
309 * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
310 * &lt;/sequence&gt;
311 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
312 * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
313 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
314 * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
315 * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
316 * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
317 * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
318 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
319 * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
320 * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
321 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
322 * &lt;/restriction&gt;
323 * &lt;/complexContent&gt;
324 * &lt;/complexType&gt;
325 * &lt;/element&gt;
326 * &lt;element name="FeatureSettings" minOccurs="0"&gt;
327 * &lt;complexType&gt;
328 * &lt;complexContent&gt;
329 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
330 * &lt;sequence&gt;
331 * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
332 * &lt;complexType&gt;
333 * &lt;complexContent&gt;
334 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
335 * &lt;sequence&gt;
336 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
337 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
338 * &lt;/sequence&gt;
339 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
340 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
341 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
342 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
343 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
344 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
345 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
346 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
347 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
348 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
349 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
350 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
351 * &lt;/restriction&gt;
352 * &lt;/complexContent&gt;
353 * &lt;/complexType&gt;
354 * &lt;/element&gt;
355 * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
356 * &lt;complexType&gt;
357 * &lt;complexContent&gt;
358 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
359 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
360 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
361 * &lt;/restriction&gt;
362 * &lt;/complexContent&gt;
363 * &lt;/complexType&gt;
364 * &lt;/element&gt;
365 * &lt;/sequence&gt;
366 * &lt;/restriction&gt;
367 * &lt;/complexContent&gt;
368 * &lt;/complexType&gt;
369 * &lt;/element&gt;
370 * &lt;/sequence&gt;
371 * &lt;/sequence&gt;
372 * &lt;/restriction&gt;
373 * &lt;/complexContent&gt;
374 * &lt;/complexType&gt;
379 @XmlAccessorType(XmlAccessType.FIELD)
380 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
392 public class JalviewModel {
394 @XmlElement(required = true)
395 @XmlSchemaType(name = "dateTime")
396 protected XMLGregorianCalendar creationDate;
397 @XmlElement(required = true)
398 protected String version;
399 @XmlElement(required = true)
400 protected VAMSAS vamsasModel;
401 @XmlElement(name = "JSeq")
402 protected List<JalviewModel.JSeq> jSeq;
403 @XmlElement(name = "JGroup")
404 protected List<JalviewModel.JGroup> jGroup;
405 @XmlElement(name = "Viewport")
406 protected List<JalviewModel.Viewport> viewport;
407 @XmlElement(name = "UserColours")
408 protected List<JalviewModel.UserColours> userColours;
409 protected List<JalviewModel.Tree> tree;
410 @XmlElement(name = "PcaViewer")
411 protected List<JalviewModel.PcaViewer> pcaViewer;
412 @XmlElement(name = "FeatureSettings")
413 protected JalviewModel.FeatureSettings featureSettings;
416 * Gets the value of the creationDate property.
420 * {@link XMLGregorianCalendar }
423 public XMLGregorianCalendar getCreationDate() {
428 * Sets the value of the creationDate property.
432 * {@link XMLGregorianCalendar }
435 public void setCreationDate(XMLGregorianCalendar value) {
436 this.creationDate = value;
440 * Gets the value of the version property.
447 public String getVersion() {
452 * Sets the value of the version property.
459 public void setVersion(String value) {
460 this.version = value;
464 * Gets the value of the vamsasModel property.
471 public VAMSAS getVamsasModel() {
476 * Sets the value of the vamsasModel property.
483 public void setVamsasModel(VAMSAS value) {
484 this.vamsasModel = value;
488 * Gets the value of the jSeq property.
491 * This accessor method returns a reference to the live list,
492 * not a snapshot. Therefore any modification you make to the
493 * returned list will be present inside the JAXB object.
494 * This is why there is not a <CODE>set</CODE> method for the jSeq property.
497 * For example, to add a new item, do as follows:
499 * getJSeq().add(newItem);
504 * Objects of the following type(s) are allowed in the list
505 * {@link JalviewModel.JSeq }
509 public List<JalviewModel.JSeq> getJSeq() {
511 jSeq = new ArrayList<JalviewModel.JSeq>();
517 * Gets the value of the jGroup property.
520 * This accessor method returns a reference to the live list,
521 * not a snapshot. Therefore any modification you make to the
522 * returned list will be present inside the JAXB object.
523 * This is why there is not a <CODE>set</CODE> method for the jGroup property.
526 * For example, to add a new item, do as follows:
528 * getJGroup().add(newItem);
533 * Objects of the following type(s) are allowed in the list
534 * {@link JalviewModel.JGroup }
538 public List<JalviewModel.JGroup> getJGroup() {
539 if (jGroup == null) {
540 jGroup = new ArrayList<JalviewModel.JGroup>();
546 * Gets the value of the viewport property.
549 * This accessor method returns a reference to the live list,
550 * not a snapshot. Therefore any modification you make to the
551 * returned list will be present inside the JAXB object.
552 * This is why there is not a <CODE>set</CODE> method for the viewport property.
555 * For example, to add a new item, do as follows:
557 * getViewport().add(newItem);
562 * Objects of the following type(s) are allowed in the list
563 * {@link JalviewModel.Viewport }
567 public List<JalviewModel.Viewport> getViewport() {
568 if (viewport == null) {
569 viewport = new ArrayList<JalviewModel.Viewport>();
571 return this.viewport;
575 * Gets the value of the userColours property.
578 * This accessor method returns a reference to the live list,
579 * not a snapshot. Therefore any modification you make to the
580 * returned list will be present inside the JAXB object.
581 * This is why there is not a <CODE>set</CODE> method for the userColours property.
584 * For example, to add a new item, do as follows:
586 * getUserColours().add(newItem);
591 * Objects of the following type(s) are allowed in the list
592 * {@link JalviewModel.UserColours }
596 public List<JalviewModel.UserColours> getUserColours() {
597 if (userColours == null) {
598 userColours = new ArrayList<JalviewModel.UserColours>();
600 return this.userColours;
604 * Gets the value of the tree property.
607 * This accessor method returns a reference to the live list,
608 * not a snapshot. Therefore any modification you make to the
609 * returned list will be present inside the JAXB object.
610 * This is why there is not a <CODE>set</CODE> method for the tree property.
613 * For example, to add a new item, do as follows:
615 * getTree().add(newItem);
620 * Objects of the following type(s) are allowed in the list
621 * {@link JalviewModel.Tree }
625 public List<JalviewModel.Tree> getTree() {
627 tree = new ArrayList<JalviewModel.Tree>();
633 * Gets the value of the pcaViewer property.
636 * This accessor method returns a reference to the live list,
637 * not a snapshot. Therefore any modification you make to the
638 * returned list will be present inside the JAXB object.
639 * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
642 * For example, to add a new item, do as follows:
644 * getPcaViewer().add(newItem);
649 * Objects of the following type(s) are allowed in the list
650 * {@link JalviewModel.PcaViewer }
654 public List<JalviewModel.PcaViewer> getPcaViewer() {
655 if (pcaViewer == null) {
656 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
658 return this.pcaViewer;
662 * Gets the value of the featureSettings property.
666 * {@link JalviewModel.FeatureSettings }
669 public JalviewModel.FeatureSettings getFeatureSettings() {
670 return featureSettings;
674 * Sets the value of the featureSettings property.
678 * {@link JalviewModel.FeatureSettings }
681 public void setFeatureSettings(JalviewModel.FeatureSettings value) {
682 this.featureSettings = value;
687 * <p>Java class for anonymous complex type.
689 * <p>The following schema fragment specifies the expected content contained within this class.
692 * &lt;complexType&gt;
693 * &lt;complexContent&gt;
694 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
695 * &lt;sequence&gt;
696 * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
697 * &lt;complexType&gt;
698 * &lt;complexContent&gt;
699 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
700 * &lt;sequence&gt;
701 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
702 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
703 * &lt;/sequence&gt;
704 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
705 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
706 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
707 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
708 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
709 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
710 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
711 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
712 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
713 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
714 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
715 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
716 * &lt;/restriction&gt;
717 * &lt;/complexContent&gt;
718 * &lt;/complexType&gt;
719 * &lt;/element&gt;
720 * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
721 * &lt;complexType&gt;
722 * &lt;complexContent&gt;
723 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
724 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
725 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
726 * &lt;/restriction&gt;
727 * &lt;/complexContent&gt;
728 * &lt;/complexType&gt;
729 * &lt;/element&gt;
730 * &lt;/sequence&gt;
731 * &lt;/restriction&gt;
732 * &lt;/complexContent&gt;
733 * &lt;/complexType&gt;
738 @XmlAccessorType(XmlAccessType.FIELD)
739 @XmlType(name = "", propOrder = {
743 public static class FeatureSettings {
745 @XmlElement(namespace = "www.jalview.org")
746 protected List<JalviewModel.FeatureSettings.Setting> setting;
747 @XmlElement(namespace = "www.jalview.org")
748 protected List<JalviewModel.FeatureSettings.Group> group;
751 * Gets the value of the setting property.
754 * This accessor method returns a reference to the live list,
755 * not a snapshot. Therefore any modification you make to the
756 * returned list will be present inside the JAXB object.
757 * This is why there is not a <CODE>set</CODE> method for the setting property.
760 * For example, to add a new item, do as follows:
762 * getSetting().add(newItem);
767 * Objects of the following type(s) are allowed in the list
768 * {@link JalviewModel.FeatureSettings.Setting }
772 public List<JalviewModel.FeatureSettings.Setting> getSetting() {
773 if (setting == null) {
774 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
780 * Gets the value of the group property.
783 * This accessor method returns a reference to the live list,
784 * not a snapshot. Therefore any modification you make to the
785 * returned list will be present inside the JAXB object.
786 * This is why there is not a <CODE>set</CODE> method for the group property.
789 * For example, to add a new item, do as follows:
791 * getGroup().add(newItem);
796 * Objects of the following type(s) are allowed in the list
797 * {@link JalviewModel.FeatureSettings.Group }
801 public List<JalviewModel.FeatureSettings.Group> getGroup() {
803 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
810 * <p>Java class for anonymous complex type.
812 * <p>The following schema fragment specifies the expected content contained within this class.
815 * &lt;complexType&gt;
816 * &lt;complexContent&gt;
817 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
818 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
819 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
820 * &lt;/restriction&gt;
821 * &lt;/complexContent&gt;
822 * &lt;/complexType&gt;
827 @XmlAccessorType(XmlAccessType.FIELD)
829 public static class Group {
831 @XmlAttribute(name = "name", required = true)
832 protected String name;
833 @XmlAttribute(name = "display", required = true)
834 protected boolean display;
837 * Gets the value of the name property.
844 public String getName() {
849 * Sets the value of the name property.
856 public void setName(String value) {
861 * Gets the value of the display property.
864 public boolean isDisplay() {
869 * Sets the value of the display property.
872 public void setDisplay(boolean value) {
873 this.display = value;
880 * <p>Java class for anonymous complex type.
882 * <p>The following schema fragment specifies the expected content contained within this class.
885 * &lt;complexType&gt;
886 * &lt;complexContent&gt;
887 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
888 * &lt;sequence&gt;
889 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
890 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
891 * &lt;/sequence&gt;
892 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
893 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
894 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
895 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
896 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
897 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
898 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
899 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
900 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
901 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
902 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
903 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
904 * &lt;/restriction&gt;
905 * &lt;/complexContent&gt;
906 * &lt;/complexType&gt;
911 @XmlAccessorType(XmlAccessType.FIELD)
912 @XmlType(name = "", propOrder = {
916 public static class Setting {
918 @XmlElement(namespace = "www.jalview.org")
919 protected List<String> attributeName;
920 @XmlElement(namespace = "www.jalview.org")
921 protected FeatureMatcherSet matcherSet;
922 @XmlAttribute(name = "type", required = true)
923 protected String type;
924 @XmlAttribute(name = "colour", required = true)
925 protected int colour;
926 @XmlAttribute(name = "display", required = true)
927 protected boolean display;
928 @XmlAttribute(name = "order")
929 protected Float order;
930 @XmlAttribute(name = "mincolour")
931 protected Integer mincolour;
932 @XmlAttribute(name = "noValueColour")
933 protected NoValueColour noValueColour;
934 @XmlAttribute(name = "threshold")
935 protected Float threshold;
936 @XmlAttribute(name = "threshstate")
937 protected Integer threshstate;
938 @XmlAttribute(name = "max")
940 @XmlAttribute(name = "min")
942 @XmlAttribute(name = "colourByLabel")
943 protected Boolean colourByLabel;
944 @XmlAttribute(name = "autoScale")
945 protected Boolean autoScale;
948 * Gets the value of the attributeName property.
951 * This accessor method returns a reference to the live list,
952 * not a snapshot. Therefore any modification you make to the
953 * returned list will be present inside the JAXB object.
954 * This is why there is not a <CODE>set</CODE> method for the attributeName property.
957 * For example, to add a new item, do as follows:
959 * getAttributeName().add(newItem);
964 * Objects of the following type(s) are allowed in the list
969 public List<String> getAttributeName() {
970 if (attributeName == null) {
971 attributeName = new ArrayList<String>();
973 return this.attributeName;
977 * Gets the value of the matcherSet property.
981 * {@link FeatureMatcherSet }
984 public FeatureMatcherSet getMatcherSet() {
989 * Sets the value of the matcherSet property.
993 * {@link FeatureMatcherSet }
996 public void setMatcherSet(FeatureMatcherSet value) {
997 this.matcherSet = value;
1001 * Gets the value of the type property.
1004 * possible object is
1008 public String getType() {
1013 * Sets the value of the type property.
1020 public void setType(String value) {
1025 * Gets the value of the colour property.
1028 public int getColour() {
1033 * Sets the value of the colour property.
1036 public void setColour(int value) {
1037 this.colour = value;
1041 * Gets the value of the display property.
1044 public boolean isDisplay() {
1049 * Sets the value of the display property.
1052 public void setDisplay(boolean value) {
1053 this.display = value;
1057 * Gets the value of the order property.
1060 * possible object is
1064 public Float getOrder() {
1069 * Sets the value of the order property.
1076 public void setOrder(Float value) {
1081 * Gets the value of the mincolour property.
1084 * possible object is
1088 public Integer getMincolour() {
1093 * Sets the value of the mincolour property.
1100 public void setMincolour(Integer value) {
1101 this.mincolour = value;
1105 * Gets the value of the noValueColour property.
1108 * possible object is
1109 * {@link NoValueColour }
1112 public NoValueColour getNoValueColour() {
1113 if (noValueColour == null) {
1114 return NoValueColour.MIN;
1116 return noValueColour;
1121 * Sets the value of the noValueColour property.
1125 * {@link NoValueColour }
1128 public void setNoValueColour(NoValueColour value) {
1129 this.noValueColour = value;
1133 * Gets the value of the threshold property.
1136 * possible object is
1140 public Float getThreshold() {
1145 * Sets the value of the threshold property.
1152 public void setThreshold(Float value) {
1153 this.threshold = value;
1157 * Gets the value of the threshstate property.
1160 * possible object is
1164 public Integer getThreshstate() {
1169 * Sets the value of the threshstate property.
1176 public void setThreshstate(Integer value) {
1177 this.threshstate = value;
1181 * Gets the value of the max property.
1184 * possible object is
1188 public Float getMax() {
1193 * Sets the value of the max property.
1200 public void setMax(Float value) {
1205 * Gets the value of the min property.
1208 * possible object is
1212 public Float getMin() {
1217 * Sets the value of the min property.
1224 public void setMin(Float value) {
1229 * Gets the value of the colourByLabel property.
1232 * possible object is
1236 public Boolean isColourByLabel() {
1237 return colourByLabel;
1241 * Sets the value of the colourByLabel property.
1248 public void setColourByLabel(Boolean value) {
1249 this.colourByLabel = value;
1253 * Gets the value of the autoScale property.
1256 * possible object is
1260 public Boolean isAutoScale() {
1265 * Sets the value of the autoScale property.
1272 public void setAutoScale(Boolean value) {
1273 this.autoScale = value;
1282 * <p>Java class for anonymous complex type.
1284 * <p>The following schema fragment specifies the expected content contained within this class.
1287 * &lt;complexType&gt;
1288 * &lt;complexContent&gt;
1289 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1290 * &lt;sequence&gt;
1291 * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
1292 * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
1293 * &lt;/sequence&gt;
1294 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1295 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1296 * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1297 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1298 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1299 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1300 * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1301 * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1302 * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1303 * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1304 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1305 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1306 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1307 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1308 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1309 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1310 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1311 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1312 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1313 * &lt;/restriction&gt;
1314 * &lt;/complexContent&gt;
1315 * &lt;/complexType&gt;
1320 @XmlAccessorType(XmlAccessType.FIELD)
1321 @XmlType(name = "", propOrder = {
1325 public static class JGroup {
1327 @XmlElement(namespace = "www.jalview.org", required = true)
1328 protected List<String> seq;
1329 @XmlElement(namespace = "www.jalview.org")
1330 protected AnnotationColourScheme annotationColours;
1331 @XmlAttribute(name = "start")
1332 protected Integer start;
1333 @XmlAttribute(name = "end")
1334 protected Integer end;
1335 @XmlAttribute(name = "name")
1336 protected String name;
1337 @XmlAttribute(name = "colour")
1338 protected String colour;
1339 @XmlAttribute(name = "consThreshold")
1340 protected Integer consThreshold;
1341 @XmlAttribute(name = "pidThreshold")
1342 protected Integer pidThreshold;
1343 @XmlAttribute(name = "outlineColour")
1344 protected Integer outlineColour;
1345 @XmlAttribute(name = "displayBoxes")
1346 protected Boolean displayBoxes;
1347 @XmlAttribute(name = "displayText")
1348 protected Boolean displayText;
1349 @XmlAttribute(name = "colourText")
1350 protected Boolean colourText;
1351 @XmlAttribute(name = "textCol1")
1352 protected Integer textCol1;
1353 @XmlAttribute(name = "textCol2")
1354 protected Integer textCol2;
1355 @XmlAttribute(name = "textColThreshold")
1356 protected Integer textColThreshold;
1357 @XmlAttribute(name = "showUnconserved")
1358 protected Boolean showUnconserved;
1359 @XmlAttribute(name = "ignoreGapsinConsensus")
1360 protected Boolean ignoreGapsinConsensus;
1361 @XmlAttribute(name = "showConsensusHistogram")
1362 protected Boolean showConsensusHistogram;
1363 @XmlAttribute(name = "showSequenceLogo")
1364 protected Boolean showSequenceLogo;
1365 @XmlAttribute(name = "normaliseSequenceLogo")
1366 protected Boolean normaliseSequenceLogo;
1367 @XmlAttribute(name = "id")
1368 protected String id;
1371 * Gets the value of the seq property.
1374 * This accessor method returns a reference to the live list,
1375 * not a snapshot. Therefore any modification you make to the
1376 * returned list will be present inside the JAXB object.
1377 * This is why there is not a <CODE>set</CODE> method for the seq property.
1380 * For example, to add a new item, do as follows:
1382 * getSeq().add(newItem);
1387 * Objects of the following type(s) are allowed in the list
1392 public List<String> getSeq() {
1394 seq = new ArrayList<String>();
1400 * Gets the value of the annotationColours property.
1403 * possible object is
1404 * {@link AnnotationColourScheme }
1407 public AnnotationColourScheme getAnnotationColours() {
1408 return annotationColours;
1412 * Sets the value of the annotationColours property.
1416 * {@link AnnotationColourScheme }
1419 public void setAnnotationColours(AnnotationColourScheme value) {
1420 this.annotationColours = value;
1424 * Gets the value of the start property.
1427 * possible object is
1431 public Integer getStart() {
1436 * Sets the value of the start property.
1443 public void setStart(Integer value) {
1448 * Gets the value of the end property.
1451 * possible object is
1455 public Integer getEnd() {
1460 * Sets the value of the end property.
1467 public void setEnd(Integer value) {
1472 * Gets the value of the name property.
1475 * possible object is
1479 public String getName() {
1484 * Sets the value of the name property.
1491 public void setName(String value) {
1496 * Gets the value of the colour property.
1499 * possible object is
1503 public String getColour() {
1508 * Sets the value of the colour property.
1515 public void setColour(String value) {
1516 this.colour = value;
1520 * Gets the value of the consThreshold property.
1523 * possible object is
1527 public Integer getConsThreshold() {
1528 return consThreshold;
1532 * Sets the value of the consThreshold property.
1539 public void setConsThreshold(Integer value) {
1540 this.consThreshold = value;
1544 * Gets the value of the pidThreshold property.
1547 * possible object is
1551 public Integer getPidThreshold() {
1552 return pidThreshold;
1556 * Sets the value of the pidThreshold property.
1563 public void setPidThreshold(Integer value) {
1564 this.pidThreshold = value;
1568 * Gets the value of the outlineColour property.
1571 * possible object is
1575 public Integer getOutlineColour() {
1576 return outlineColour;
1580 * Sets the value of the outlineColour property.
1587 public void setOutlineColour(Integer value) {
1588 this.outlineColour = value;
1592 * Gets the value of the displayBoxes property.
1595 * possible object is
1599 public Boolean isDisplayBoxes() {
1600 return displayBoxes;
1604 * Sets the value of the displayBoxes property.
1611 public void setDisplayBoxes(Boolean value) {
1612 this.displayBoxes = value;
1616 * Gets the value of the displayText property.
1619 * possible object is
1623 public Boolean isDisplayText() {
1628 * Sets the value of the displayText property.
1635 public void setDisplayText(Boolean value) {
1636 this.displayText = value;
1640 * Gets the value of the colourText property.
1643 * possible object is
1647 public Boolean isColourText() {
1652 * Sets the value of the colourText property.
1659 public void setColourText(Boolean value) {
1660 this.colourText = value;
1664 * Gets the value of the textCol1 property.
1667 * possible object is
1671 public Integer getTextCol1() {
1676 * Sets the value of the textCol1 property.
1683 public void setTextCol1(Integer value) {
1684 this.textCol1 = value;
1688 * Gets the value of the textCol2 property.
1691 * possible object is
1695 public Integer getTextCol2() {
1700 * Sets the value of the textCol2 property.
1707 public void setTextCol2(Integer value) {
1708 this.textCol2 = value;
1712 * Gets the value of the textColThreshold property.
1715 * possible object is
1719 public Integer getTextColThreshold() {
1720 return textColThreshold;
1724 * Sets the value of the textColThreshold property.
1731 public void setTextColThreshold(Integer value) {
1732 this.textColThreshold = value;
1736 * Gets the value of the showUnconserved property.
1739 * possible object is
1743 public Boolean isShowUnconserved() {
1744 return showUnconserved;
1748 * Sets the value of the showUnconserved property.
1755 public void setShowUnconserved(Boolean value) {
1756 this.showUnconserved = value;
1760 * Gets the value of the ignoreGapsinConsensus property.
1763 * possible object is
1767 public boolean isIgnoreGapsinConsensus() {
1768 if (ignoreGapsinConsensus == null) {
1771 return ignoreGapsinConsensus;
1776 * Sets the value of the ignoreGapsinConsensus property.
1783 public void setIgnoreGapsinConsensus(Boolean value) {
1784 this.ignoreGapsinConsensus = value;
1788 * Gets the value of the showConsensusHistogram property.
1791 * possible object is
1795 public boolean isShowConsensusHistogram() {
1796 if (showConsensusHistogram == null) {
1799 return showConsensusHistogram;
1804 * Sets the value of the showConsensusHistogram property.
1811 public void setShowConsensusHistogram(Boolean value) {
1812 this.showConsensusHistogram = value;
1816 * Gets the value of the showSequenceLogo property.
1819 * possible object is
1823 public boolean isShowSequenceLogo() {
1824 if (showSequenceLogo == null) {
1827 return showSequenceLogo;
1832 * Sets the value of the showSequenceLogo property.
1839 public void setShowSequenceLogo(Boolean value) {
1840 this.showSequenceLogo = value;
1844 * Gets the value of the normaliseSequenceLogo property.
1847 * possible object is
1851 public boolean isNormaliseSequenceLogo() {
1852 if (normaliseSequenceLogo == null) {
1855 return normaliseSequenceLogo;
1860 * Sets the value of the normaliseSequenceLogo property.
1867 public void setNormaliseSequenceLogo(Boolean value) {
1868 this.normaliseSequenceLogo = value;
1872 * Gets the value of the id property.
1875 * possible object is
1879 public String getId() {
1884 * Sets the value of the id property.
1891 public void setId(String value) {
1899 * <p>Java class for anonymous complex type.
1901 * <p>The following schema fragment specifies the expected content contained within this class.
1904 * &lt;complexType&gt;
1905 * &lt;complexContent&gt;
1906 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1907 * &lt;sequence&gt;
1908 * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
1909 * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
1910 * &lt;complexType&gt;
1911 * &lt;complexContent&gt;
1912 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
1913 * &lt;sequence&gt;
1914 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
1915 * &lt;complexType&gt;
1916 * &lt;simpleContent&gt;
1917 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
1918 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
1919 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1920 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1921 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1922 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1923 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1924 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1925 * &lt;/extension&gt;
1926 * &lt;/simpleContent&gt;
1927 * &lt;/complexType&gt;
1928 * &lt;/element&gt;
1929 * &lt;/sequence&gt;
1930 * &lt;/extension&gt;
1931 * &lt;/complexContent&gt;
1932 * &lt;/complexType&gt;
1933 * &lt;/element&gt;
1934 * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
1935 * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
1936 * &lt;complexType&gt;
1937 * &lt;complexContent&gt;
1938 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1939 * &lt;sequence&gt;
1940 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
1941 * &lt;complexType&gt;
1942 * &lt;complexContent&gt;
1943 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1944 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1945 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1946 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1947 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1948 * &lt;/restriction&gt;
1949 * &lt;/complexContent&gt;
1950 * &lt;/complexType&gt;
1951 * &lt;/element&gt;
1952 * &lt;/sequence&gt;
1953 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
1954 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1955 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1956 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1957 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1958 * &lt;/restriction&gt;
1959 * &lt;/complexContent&gt;
1960 * &lt;/complexType&gt;
1961 * &lt;/element&gt;
1962 * &lt;/sequence&gt;
1963 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1964 * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1965 * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1966 * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1967 * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1968 * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1969 * &lt;/restriction&gt;
1970 * &lt;/complexContent&gt;
1971 * &lt;/complexType&gt;
1976 @XmlAccessorType(XmlAccessType.FIELD)
1977 @XmlType(name = "", propOrder = {
1983 public static class JSeq {
1985 @XmlElement(namespace = "www.jalview.org")
1986 protected List<Feature> features;
1987 @XmlElement(namespace = "www.jalview.org")
1988 protected List<JalviewModel.JSeq.Pdbids> pdbids;
1989 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1990 protected List<Integer> hiddenSequences;
1991 @XmlElement(namespace = "www.jalview.org")
1992 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1993 @XmlAttribute(name = "colour")
1994 protected Integer colour;
1995 @XmlAttribute(name = "start", required = true)
1996 protected int start;
1997 @XmlAttribute(name = "end", required = true)
1999 @XmlAttribute(name = "id", required = true)
2000 protected String id;
2001 @XmlAttribute(name = "hidden")
2002 protected Boolean hidden;
2003 @XmlAttribute(name = "viewreference")
2004 protected Boolean viewreference;
2007 * Gets the value of the features property.
2010 * This accessor method returns a reference to the live list,
2011 * not a snapshot. Therefore any modification you make to the
2012 * returned list will be present inside the JAXB object.
2013 * This is why there is not a <CODE>set</CODE> method for the features property.
2016 * For example, to add a new item, do as follows:
2018 * getFeatures().add(newItem);
2023 * Objects of the following type(s) are allowed in the list
2028 public List<Feature> getFeatures() {
2029 if (features == null) {
2030 features = new ArrayList<Feature>();
2032 return this.features;
2036 * Gets the value of the pdbids property.
2039 * This accessor method returns a reference to the live list,
2040 * not a snapshot. Therefore any modification you make to the
2041 * returned list will be present inside the JAXB object.
2042 * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2045 * For example, to add a new item, do as follows:
2047 * getPdbids().add(newItem);
2052 * Objects of the following type(s) are allowed in the list
2053 * {@link JalviewModel.JSeq.Pdbids }
2057 public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2058 if (pdbids == null) {
2059 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2065 * Gets the value of the hiddenSequences property.
2068 * This accessor method returns a reference to the live list,
2069 * not a snapshot. Therefore any modification you make to the
2070 * returned list will be present inside the JAXB object.
2071 * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2074 * For example, to add a new item, do as follows:
2076 * getHiddenSequences().add(newItem);
2081 * Objects of the following type(s) are allowed in the list
2086 public List<Integer> getHiddenSequences() {
2087 if (hiddenSequences == null) {
2088 hiddenSequences = new ArrayList<Integer>();
2090 return this.hiddenSequences;
2094 * Gets the value of the rnaViewer property.
2097 * This accessor method returns a reference to the live list,
2098 * not a snapshot. Therefore any modification you make to the
2099 * returned list will be present inside the JAXB object.
2100 * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2103 * For example, to add a new item, do as follows:
2105 * getRnaViewer().add(newItem);
2110 * Objects of the following type(s) are allowed in the list
2111 * {@link JalviewModel.JSeq.RnaViewer }
2115 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2116 if (rnaViewer == null) {
2117 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2119 return this.rnaViewer;
2123 * Gets the value of the colour property.
2126 * possible object is
2130 public Integer getColour() {
2135 * Sets the value of the colour property.
2142 public void setColour(Integer value) {
2143 this.colour = value;
2147 * Gets the value of the start property.
2150 public int getStart() {
2155 * Sets the value of the start property.
2158 public void setStart(int value) {
2163 * Gets the value of the end property.
2166 public int getEnd() {
2171 * Sets the value of the end property.
2174 public void setEnd(int value) {
2179 * Gets the value of the id property.
2182 * possible object is
2186 public String getId() {
2191 * Sets the value of the id property.
2198 public void setId(String value) {
2203 * Gets the value of the hidden property.
2206 * possible object is
2210 public Boolean isHidden() {
2215 * Sets the value of the hidden property.
2222 public void setHidden(Boolean value) {
2223 this.hidden = value;
2227 * Gets the value of the viewreference property.
2230 * possible object is
2234 public Boolean isViewreference() {
2235 return viewreference;
2239 * Sets the value of the viewreference property.
2246 public void setViewreference(Boolean value) {
2247 this.viewreference = value;
2252 * <p>Java class for anonymous complex type.
2254 * <p>The following schema fragment specifies the expected content contained within this class.
2257 * &lt;complexType&gt;
2258 * &lt;complexContent&gt;
2259 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
2260 * &lt;sequence&gt;
2261 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
2262 * &lt;complexType&gt;
2263 * &lt;simpleContent&gt;
2264 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2265 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2266 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2267 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2268 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2269 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2270 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2271 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2272 * &lt;/extension&gt;
2273 * &lt;/simpleContent&gt;
2274 * &lt;/complexType&gt;
2275 * &lt;/element&gt;
2276 * &lt;/sequence&gt;
2277 * &lt;/extension&gt;
2278 * &lt;/complexContent&gt;
2279 * &lt;/complexType&gt;
2284 @XmlAccessorType(XmlAccessType.FIELD)
2285 @XmlType(name = "", propOrder = {
2288 public static class Pdbids
2292 @XmlElement(namespace = "www.jalview.org")
2293 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2296 * Gets the value of the structureState property.
2299 * This accessor method returns a reference to the live list,
2300 * not a snapshot. Therefore any modification you make to the
2301 * returned list will be present inside the JAXB object.
2302 * This is why there is not a <CODE>set</CODE> method for the structureState property.
2305 * For example, to add a new item, do as follows:
2307 * getStructureState().add(newItem);
2312 * Objects of the following type(s) are allowed in the list
2313 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2317 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2318 if (structureState == null) {
2319 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2321 return this.structureState;
2326 * <p>Java class for anonymous complex type.
2328 * <p>The following schema fragment specifies the expected content contained within this class.
2331 * &lt;complexType&gt;
2332 * &lt;simpleContent&gt;
2333 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2334 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2335 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2336 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2337 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2338 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2339 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2340 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2341 * &lt;/extension&gt;
2342 * &lt;/simpleContent&gt;
2343 * &lt;/complexType&gt;
2348 @XmlAccessorType(XmlAccessType.FIELD)
2349 @XmlType(name = "", propOrder = {
2352 public static class StructureState {
2355 protected String value;
2356 @XmlAttribute(name = "visible")
2357 protected Boolean visible;
2358 @XmlAttribute(name = "viewId")
2359 protected String viewId;
2360 @XmlAttribute(name = "alignwithAlignPanel")
2361 protected Boolean alignwithAlignPanel;
2362 @XmlAttribute(name = "colourwithAlignPanel")
2363 protected Boolean colourwithAlignPanel;
2364 @XmlAttribute(name = "colourByJmol")
2365 protected Boolean colourByJmol;
2366 @XmlAttribute(name = "type")
2367 protected String type;
2368 @XmlAttribute(name = "width")
2369 protected Integer width;
2370 @XmlAttribute(name = "height")
2371 protected Integer height;
2372 @XmlAttribute(name = "xpos")
2373 protected Integer xpos;
2374 @XmlAttribute(name = "ypos")
2375 protected Integer ypos;
2378 * Gets the value of the value property.
2381 * possible object is
2385 public String getValue() {
2390 * Sets the value of the value property.
2397 public void setValue(String value) {
2402 * Gets the value of the visible property.
2405 * possible object is
2409 public Boolean isVisible() {
2414 * Sets the value of the visible property.
2421 public void setVisible(Boolean value) {
2422 this.visible = value;
2426 * Gets the value of the viewId property.
2429 * possible object is
2433 public String getViewId() {
2438 * Sets the value of the viewId property.
2445 public void setViewId(String value) {
2446 this.viewId = value;
2450 * Gets the value of the alignwithAlignPanel property.
2453 * possible object is
2457 public boolean isAlignwithAlignPanel() {
2458 if (alignwithAlignPanel == null) {
2461 return alignwithAlignPanel;
2466 * Sets the value of the alignwithAlignPanel property.
2473 public void setAlignwithAlignPanel(Boolean value) {
2474 this.alignwithAlignPanel = value;
2478 * Gets the value of the colourwithAlignPanel property.
2481 * possible object is
2485 public boolean isColourwithAlignPanel() {
2486 if (colourwithAlignPanel == null) {
2489 return colourwithAlignPanel;
2494 * Sets the value of the colourwithAlignPanel property.
2501 public void setColourwithAlignPanel(Boolean value) {
2502 this.colourwithAlignPanel = value;
2506 * Gets the value of the colourByJmol property.
2509 * possible object is
2513 public boolean isColourByJmol() {
2514 if (colourByJmol == null) {
2517 return colourByJmol;
2522 * Sets the value of the colourByJmol property.
2529 public void setColourByJmol(Boolean value) {
2530 this.colourByJmol = value;
2534 * Gets the value of the type property.
2537 * possible object is
2541 public String getType() {
2546 * Sets the value of the type property.
2553 public void setType(String value) {
2558 * Gets the value of the width property.
2561 * possible object is
2565 public Integer getWidth() {
2570 * Sets the value of the width property.
2577 public void setWidth(Integer value) {
2582 * Gets the value of the height property.
2585 * possible object is
2589 public Integer getHeight() {
2594 * Sets the value of the height property.
2601 public void setHeight(Integer value) {
2602 this.height = value;
2606 * Gets the value of the xpos property.
2609 * possible object is
2613 public Integer getXpos() {
2618 * Sets the value of the xpos property.
2625 public void setXpos(Integer value) {
2630 * Gets the value of the ypos property.
2633 * possible object is
2637 public Integer getYpos() {
2642 * Sets the value of the ypos property.
2649 public void setYpos(Integer value) {
2659 * <p>Java class for anonymous complex type.
2661 * <p>The following schema fragment specifies the expected content contained within this class.
2664 * &lt;complexType&gt;
2665 * &lt;complexContent&gt;
2666 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2667 * &lt;sequence&gt;
2668 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
2669 * &lt;complexType&gt;
2670 * &lt;complexContent&gt;
2671 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2672 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2673 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2674 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2675 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2676 * &lt;/restriction&gt;
2677 * &lt;/complexContent&gt;
2678 * &lt;/complexType&gt;
2679 * &lt;/element&gt;
2680 * &lt;/sequence&gt;
2681 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2682 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2683 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2684 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2685 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2686 * &lt;/restriction&gt;
2687 * &lt;/complexContent&gt;
2688 * &lt;/complexType&gt;
2693 @XmlAccessorType(XmlAccessType.FIELD)
2694 @XmlType(name = "", propOrder = {
2695 "secondaryStructure"
2697 public static class RnaViewer {
2699 @XmlElement(namespace = "www.jalview.org", required = true)
2700 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2701 @XmlAttribute(name = "title")
2702 protected String title;
2703 @XmlAttribute(name = "viewId")
2704 protected String viewId;
2705 @XmlAttribute(name = "dividerLocation")
2706 protected Integer dividerLocation;
2707 @XmlAttribute(name = "selectedRna")
2708 protected Integer selectedRna;
2709 @XmlAttribute(name = "width")
2710 protected Integer width;
2711 @XmlAttribute(name = "height")
2712 protected Integer height;
2713 @XmlAttribute(name = "xpos")
2714 protected Integer xpos;
2715 @XmlAttribute(name = "ypos")
2716 protected Integer ypos;
2719 * Gets the value of the secondaryStructure property.
2722 * This accessor method returns a reference to the live list,
2723 * not a snapshot. Therefore any modification you make to the
2724 * returned list will be present inside the JAXB object.
2725 * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2728 * For example, to add a new item, do as follows:
2730 * getSecondaryStructure().add(newItem);
2735 * Objects of the following type(s) are allowed in the list
2736 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2740 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2741 if (secondaryStructure == null) {
2742 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2744 return this.secondaryStructure;
2748 * Gets the value of the title property.
2751 * possible object is
2755 public String getTitle() {
2760 * Sets the value of the title property.
2767 public void setTitle(String value) {
2772 * Gets the value of the viewId property.
2775 * possible object is
2779 public String getViewId() {
2784 * Sets the value of the viewId property.
2791 public void setViewId(String value) {
2792 this.viewId = value;
2796 * Gets the value of the dividerLocation property.
2799 * possible object is
2803 public Integer getDividerLocation() {
2804 return dividerLocation;
2808 * Sets the value of the dividerLocation property.
2815 public void setDividerLocation(Integer value) {
2816 this.dividerLocation = value;
2820 * Gets the value of the selectedRna property.
2823 * possible object is
2827 public Integer getSelectedRna() {
2832 * Sets the value of the selectedRna property.
2839 public void setSelectedRna(Integer value) {
2840 this.selectedRna = value;
2844 * Gets the value of the width property.
2847 * possible object is
2851 public Integer getWidth() {
2856 * Sets the value of the width property.
2863 public void setWidth(Integer value) {
2868 * Gets the value of the height property.
2871 * possible object is
2875 public Integer getHeight() {
2880 * Sets the value of the height property.
2887 public void setHeight(Integer value) {
2888 this.height = value;
2892 * Gets the value of the xpos property.
2895 * possible object is
2899 public Integer getXpos() {
2904 * Sets the value of the xpos property.
2911 public void setXpos(Integer value) {
2916 * Gets the value of the ypos property.
2919 * possible object is
2923 public Integer getYpos() {
2928 * Sets the value of the ypos property.
2935 public void setYpos(Integer value) {
2941 * <p>Java class for anonymous complex type.
2943 * <p>The following schema fragment specifies the expected content contained within this class.
2946 * &lt;complexType&gt;
2947 * &lt;complexContent&gt;
2948 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2949 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2950 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2951 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2952 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2953 * &lt;/restriction&gt;
2954 * &lt;/complexContent&gt;
2955 * &lt;/complexType&gt;
2960 @XmlAccessorType(XmlAccessType.FIELD)
2962 public static class SecondaryStructure {
2964 @XmlAttribute(name = "title")
2965 protected String title;
2966 @XmlAttribute(name = "annotationId", required = true)
2967 protected String annotationId;
2968 @XmlAttribute(name = "gapped")
2969 protected Boolean gapped;
2970 @XmlAttribute(name = "viewerState")
2971 protected String viewerState;
2974 * Gets the value of the title property.
2977 * possible object is
2981 public String getTitle() {
2986 * Sets the value of the title property.
2993 public void setTitle(String value) {
2998 * Gets the value of the annotationId property.
3001 * possible object is
3005 public String getAnnotationId() {
3006 return annotationId;
3010 * Sets the value of the annotationId property.
3017 public void setAnnotationId(String value) {
3018 this.annotationId = value;
3022 * Gets the value of the gapped property.
3025 * possible object is
3029 public Boolean isGapped() {
3034 * Sets the value of the gapped property.
3041 public void setGapped(Boolean value) {
3042 this.gapped = value;
3046 * Gets the value of the viewerState property.
3049 * possible object is
3053 public String getViewerState() {
3058 * Sets the value of the viewerState property.
3065 public void setViewerState(String value) {
3066 this.viewerState = value;
3077 * <p>Java class for anonymous complex type.
3079 * <p>The following schema fragment specifies the expected content contained within this class.
3082 * &lt;complexType&gt;
3083 * &lt;complexContent&gt;
3084 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3085 * &lt;sequence&gt;
3086 * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
3087 * &lt;complexType&gt;
3088 * &lt;complexContent&gt;
3089 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3090 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3091 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3092 * &lt;/restriction&gt;
3093 * &lt;/complexContent&gt;
3094 * &lt;/complexType&gt;
3095 * &lt;/element&gt;
3096 * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
3097 * &lt;complexType&gt;
3098 * &lt;complexContent&gt;
3099 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3100 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3101 * &lt;/restriction&gt;
3102 * &lt;/complexContent&gt;
3103 * &lt;/complexType&gt;
3104 * &lt;/element&gt;
3105 * &lt;element name="seqPointMin"&gt;
3106 * &lt;complexType&gt;
3107 * &lt;complexContent&gt;
3108 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3109 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3110 * &lt;/restriction&gt;
3111 * &lt;/complexContent&gt;
3112 * &lt;/complexType&gt;
3113 * &lt;/element&gt;
3114 * &lt;element name="seqPointMax"&gt;
3115 * &lt;complexType&gt;
3116 * &lt;complexContent&gt;
3117 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3118 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3119 * &lt;/restriction&gt;
3120 * &lt;/complexContent&gt;
3121 * &lt;/complexType&gt;
3122 * &lt;/element&gt;
3123 * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
3124 * &lt;/sequence&gt;
3125 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
3126 * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
3127 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3128 * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3129 * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3130 * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3131 * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3132 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3133 * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
3134 * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3135 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3136 * &lt;/restriction&gt;
3137 * &lt;/complexContent&gt;
3138 * &lt;/complexType&gt;
3143 @XmlAccessorType(XmlAccessType.FIELD)
3144 @XmlType(name = "", propOrder = {
3151 public static class PcaViewer {
3153 @XmlElement(namespace = "www.jalview.org", required = true)
3154 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3155 @XmlElement(namespace = "www.jalview.org", required = true)
3156 protected List<JalviewModel.PcaViewer.Axis> axis;
3157 @XmlElement(namespace = "www.jalview.org", required = true)
3158 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3159 @XmlElement(namespace = "www.jalview.org", required = true)
3160 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3161 @XmlElement(namespace = "www.jalview.org", required = true)
3162 protected PcaDataType pcaData;
3163 @XmlAttribute(name = "title")
3164 protected String title;
3165 @XmlAttribute(name = "scoreModelName")
3166 protected String scoreModelName;
3167 @XmlAttribute(name = "xDim")
3168 protected Integer xDim;
3169 @XmlAttribute(name = "yDim")
3170 protected Integer yDim;
3171 @XmlAttribute(name = "zDim")
3172 protected Integer zDim;
3173 @XmlAttribute(name = "bgColour")
3174 protected Integer bgColour;
3175 @XmlAttribute(name = "scaleFactor")
3176 protected Float scaleFactor;
3177 @XmlAttribute(name = "showLabels")
3178 protected Boolean showLabels;
3179 @XmlAttribute(name = "linkToAllViews")
3180 protected Boolean linkToAllViews;
3181 @XmlAttribute(name = "width")
3182 protected Integer width;
3183 @XmlAttribute(name = "height")
3184 protected Integer height;
3185 @XmlAttribute(name = "xpos")
3186 protected Integer xpos;
3187 @XmlAttribute(name = "ypos")
3188 protected Integer ypos;
3189 @XmlAttribute(name = "includeGaps")
3190 protected Boolean includeGaps;
3191 @XmlAttribute(name = "matchGaps")
3192 protected Boolean matchGaps;
3193 @XmlAttribute(name = "includeGappedColumns")
3194 protected Boolean includeGappedColumns;
3195 @XmlAttribute(name = "denominateByShortestLength")
3196 protected Boolean denominateByShortestLength;
3199 * Gets the value of the sequencePoint property.
3202 * This accessor method returns a reference to the live list,
3203 * not a snapshot. Therefore any modification you make to the
3204 * returned list will be present inside the JAXB object.
3205 * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3208 * For example, to add a new item, do as follows:
3210 * getSequencePoint().add(newItem);
3215 * Objects of the following type(s) are allowed in the list
3216 * {@link JalviewModel.PcaViewer.SequencePoint }
3220 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3221 if (sequencePoint == null) {
3222 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3224 return this.sequencePoint;
3228 * Gets the value of the axis property.
3231 * This accessor method returns a reference to the live list,
3232 * not a snapshot. Therefore any modification you make to the
3233 * returned list will be present inside the JAXB object.
3234 * This is why there is not a <CODE>set</CODE> method for the axis property.
3237 * For example, to add a new item, do as follows:
3239 * getAxis().add(newItem);
3244 * Objects of the following type(s) are allowed in the list
3245 * {@link JalviewModel.PcaViewer.Axis }
3249 public List<JalviewModel.PcaViewer.Axis> getAxis() {
3251 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3257 * Gets the value of the seqPointMin property.
3260 * possible object is
3261 * {@link JalviewModel.PcaViewer.SeqPointMin }
3264 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3269 * Sets the value of the seqPointMin property.
3273 * {@link JalviewModel.PcaViewer.SeqPointMin }
3276 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3277 this.seqPointMin = value;
3281 * Gets the value of the seqPointMax property.
3284 * possible object is
3285 * {@link JalviewModel.PcaViewer.SeqPointMax }
3288 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3293 * Sets the value of the seqPointMax property.
3297 * {@link JalviewModel.PcaViewer.SeqPointMax }
3300 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3301 this.seqPointMax = value;
3305 * Gets the value of the pcaData property.
3308 * possible object is
3309 * {@link PcaDataType }
3312 public PcaDataType getPcaData() {
3317 * Sets the value of the pcaData property.
3321 * {@link PcaDataType }
3324 public void setPcaData(PcaDataType value) {
3325 this.pcaData = value;
3329 * Gets the value of the title property.
3332 * possible object is
3336 public String getTitle() {
3341 * Sets the value of the title property.
3348 public void setTitle(String value) {
3353 * Gets the value of the scoreModelName property.
3356 * possible object is
3360 public String getScoreModelName() {
3361 return scoreModelName;
3365 * Sets the value of the scoreModelName property.
3372 public void setScoreModelName(String value) {
3373 this.scoreModelName = value;
3377 * Gets the value of the xDim property.
3380 * possible object is
3384 public Integer getXDim() {
3389 * Sets the value of the xDim property.
3396 public void setXDim(Integer value) {
3401 * Gets the value of the yDim property.
3404 * possible object is
3408 public Integer getYDim() {
3413 * Sets the value of the yDim property.
3420 public void setYDim(Integer value) {
3425 * Gets the value of the zDim property.
3428 * possible object is
3432 public Integer getZDim() {
3437 * Sets the value of the zDim property.
3444 public void setZDim(Integer value) {
3449 * Gets the value of the bgColour property.
3452 * possible object is
3456 public Integer getBgColour() {
3461 * Sets the value of the bgColour property.
3468 public void setBgColour(Integer value) {
3469 this.bgColour = value;
3473 * Gets the value of the scaleFactor property.
3476 * possible object is
3480 public Float getScaleFactor() {
3485 * Sets the value of the scaleFactor property.
3492 public void setScaleFactor(Float value) {
3493 this.scaleFactor = value;
3497 * Gets the value of the showLabels property.
3500 * possible object is
3504 public Boolean isShowLabels() {
3509 * Sets the value of the showLabels property.
3516 public void setShowLabels(Boolean value) {
3517 this.showLabels = value;
3521 * Gets the value of the linkToAllViews property.
3524 * possible object is
3528 public Boolean isLinkToAllViews() {
3529 return linkToAllViews;
3533 * Sets the value of the linkToAllViews property.
3540 public void setLinkToAllViews(Boolean value) {
3541 this.linkToAllViews = value;
3545 * Gets the value of the width property.
3548 * possible object is
3552 public Integer getWidth() {
3557 * Sets the value of the width property.
3564 public void setWidth(Integer value) {
3569 * Gets the value of the height property.
3572 * possible object is
3576 public Integer getHeight() {
3581 * Sets the value of the height property.
3588 public void setHeight(Integer value) {
3589 this.height = value;
3593 * Gets the value of the xpos property.
3596 * possible object is
3600 public Integer getXpos() {
3605 * Sets the value of the xpos property.
3612 public void setXpos(Integer value) {
3617 * Gets the value of the ypos property.
3620 * possible object is
3624 public Integer getYpos() {
3629 * Sets the value of the ypos property.
3636 public void setYpos(Integer value) {
3641 * Gets the value of the includeGaps property.
3644 * possible object is
3648 public Boolean isIncludeGaps() {
3653 * Sets the value of the includeGaps property.
3660 public void setIncludeGaps(Boolean value) {
3661 this.includeGaps = value;
3665 * Gets the value of the matchGaps property.
3668 * possible object is
3672 public Boolean isMatchGaps() {
3677 * Sets the value of the matchGaps property.
3684 public void setMatchGaps(Boolean value) {
3685 this.matchGaps = value;
3689 * Gets the value of the includeGappedColumns property.
3692 * possible object is
3696 public Boolean isIncludeGappedColumns() {
3697 return includeGappedColumns;
3701 * Sets the value of the includeGappedColumns property.
3708 public void setIncludeGappedColumns(Boolean value) {
3709 this.includeGappedColumns = value;
3713 * Gets the value of the denominateByShortestLength property.
3716 * possible object is
3720 public Boolean isDenominateByShortestLength() {
3721 return denominateByShortestLength;
3725 * Sets the value of the denominateByShortestLength property.
3732 public void setDenominateByShortestLength(Boolean value) {
3733 this.denominateByShortestLength = value;
3738 * <p>Java class for anonymous complex type.
3740 * <p>The following schema fragment specifies the expected content contained within this class.
3743 * &lt;complexType&gt;
3744 * &lt;complexContent&gt;
3745 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3746 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3747 * &lt;/restriction&gt;
3748 * &lt;/complexContent&gt;
3749 * &lt;/complexType&gt;
3754 @XmlAccessorType(XmlAccessType.FIELD)
3756 public static class Axis {
3758 @XmlAttribute(name = "xPos")
3759 protected Float xPos;
3760 @XmlAttribute(name = "yPos")
3761 protected Float yPos;
3762 @XmlAttribute(name = "zPos")
3763 protected Float zPos;
3766 * Gets the value of the xPos property.
3769 * possible object is
3773 public Float getXPos() {
3778 * Sets the value of the xPos property.
3785 public void setXPos(Float value) {
3790 * Gets the value of the yPos property.
3793 * possible object is
3797 public Float getYPos() {
3802 * Sets the value of the yPos property.
3809 public void setYPos(Float value) {
3814 * Gets the value of the zPos property.
3817 * possible object is
3821 public Float getZPos() {
3826 * Sets the value of the zPos property.
3833 public void setZPos(Float value) {
3841 * <p>Java class for anonymous complex type.
3843 * <p>The following schema fragment specifies the expected content contained within this class.
3846 * &lt;complexType&gt;
3847 * &lt;complexContent&gt;
3848 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3849 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3850 * &lt;/restriction&gt;
3851 * &lt;/complexContent&gt;
3852 * &lt;/complexType&gt;
3857 @XmlAccessorType(XmlAccessType.FIELD)
3859 public static class SeqPointMax {
3861 @XmlAttribute(name = "xPos")
3862 protected Float xPos;
3863 @XmlAttribute(name = "yPos")
3864 protected Float yPos;
3865 @XmlAttribute(name = "zPos")
3866 protected Float zPos;
3869 * Gets the value of the xPos property.
3872 * possible object is
3876 public Float getXPos() {
3881 * Sets the value of the xPos property.
3888 public void setXPos(Float value) {
3893 * Gets the value of the yPos property.
3896 * possible object is
3900 public Float getYPos() {
3905 * Sets the value of the yPos property.
3912 public void setYPos(Float value) {
3917 * Gets the value of the zPos property.
3920 * possible object is
3924 public Float getZPos() {
3929 * Sets the value of the zPos property.
3936 public void setZPos(Float value) {
3944 * <p>Java class for anonymous complex type.
3946 * <p>The following schema fragment specifies the expected content contained within this class.
3949 * &lt;complexType&gt;
3950 * &lt;complexContent&gt;
3951 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3952 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3953 * &lt;/restriction&gt;
3954 * &lt;/complexContent&gt;
3955 * &lt;/complexType&gt;
3960 @XmlAccessorType(XmlAccessType.FIELD)
3962 public static class SeqPointMin {
3964 @XmlAttribute(name = "xPos")
3965 protected Float xPos;
3966 @XmlAttribute(name = "yPos")
3967 protected Float yPos;
3968 @XmlAttribute(name = "zPos")
3969 protected Float zPos;
3972 * Gets the value of the xPos property.
3975 * possible object is
3979 public Float getXPos() {
3984 * Sets the value of the xPos property.
3991 public void setXPos(Float value) {
3996 * Gets the value of the yPos property.
3999 * possible object is
4003 public Float getYPos() {
4008 * Sets the value of the yPos property.
4015 public void setYPos(Float value) {
4020 * Gets the value of the zPos property.
4023 * possible object is
4027 public Float getZPos() {
4032 * Sets the value of the zPos property.
4039 public void setZPos(Float value) {
4047 * <p>Java class for anonymous complex type.
4049 * <p>The following schema fragment specifies the expected content contained within this class.
4052 * &lt;complexType&gt;
4053 * &lt;complexContent&gt;
4054 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4055 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
4056 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4057 * &lt;/restriction&gt;
4058 * &lt;/complexContent&gt;
4059 * &lt;/complexType&gt;
4064 @XmlAccessorType(XmlAccessType.FIELD)
4066 public static class SequencePoint {
4068 @XmlAttribute(name = "sequenceRef")
4069 protected String sequenceRef;
4070 @XmlAttribute(name = "xPos")
4071 protected Float xPos;
4072 @XmlAttribute(name = "yPos")
4073 protected Float yPos;
4074 @XmlAttribute(name = "zPos")
4075 protected Float zPos;
4078 * Gets the value of the sequenceRef property.
4081 * possible object is
4085 public String getSequenceRef() {
4090 * Sets the value of the sequenceRef property.
4097 public void setSequenceRef(String value) {
4098 this.sequenceRef = value;
4102 * Gets the value of the xPos property.
4105 * possible object is
4109 public Float getXPos() {
4114 * Sets the value of the xPos property.
4121 public void setXPos(Float value) {
4126 * Gets the value of the yPos property.
4129 * possible object is
4133 public Float getYPos() {
4138 * Sets the value of the yPos property.
4145 public void setYPos(Float value) {
4150 * Gets the value of the zPos property.
4153 * possible object is
4157 public Float getZPos() {
4162 * Sets the value of the zPos property.
4169 public void setZPos(Float value) {
4179 * <p>Java class for anonymous complex type.
4181 * <p>The following schema fragment specifies the expected content contained within this class.
4184 * &lt;complexType&gt;
4185 * &lt;complexContent&gt;
4186 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4187 * &lt;sequence minOccurs="0"&gt;
4188 * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4189 * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4190 * &lt;/sequence&gt;
4191 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4192 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4193 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4194 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4195 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
4196 * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4197 * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4198 * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4199 * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4200 * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4201 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4202 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4203 * &lt;/restriction&gt;
4204 * &lt;/complexContent&gt;
4205 * &lt;/complexType&gt;
4210 @XmlAccessorType(XmlAccessType.FIELD)
4211 @XmlType(name = "", propOrder = {
4215 public static class Tree {
4217 @XmlElement(namespace = "www.jalview.org")
4218 protected String title;
4219 @XmlElement(namespace = "www.jalview.org")
4220 protected String newick;
4221 @XmlAttribute(name = "fontName")
4222 protected String fontName;
4223 @XmlAttribute(name = "fontSize")
4224 protected Integer fontSize;
4225 @XmlAttribute(name = "fontStyle")
4226 protected Integer fontStyle;
4227 @XmlAttribute(name = "threshold")
4228 protected Float threshold;
4229 @XmlAttribute(name = "showBootstrap")
4230 protected Boolean showBootstrap;
4231 @XmlAttribute(name = "showDistances")
4232 protected Boolean showDistances;
4233 @XmlAttribute(name = "markUnlinked")
4234 protected Boolean markUnlinked;
4235 @XmlAttribute(name = "fitToWindow")
4236 protected Boolean fitToWindow;
4237 @XmlAttribute(name = "currentTree")
4238 protected Boolean currentTree;
4239 @XmlAttribute(name = "id")
4240 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4242 @XmlSchemaType(name = "ID")
4243 protected String id;
4244 @XmlAttribute(name = "linkToAllViews")
4245 protected Boolean linkToAllViews;
4246 @XmlAttribute(name = "width")
4247 protected Integer width;
4248 @XmlAttribute(name = "height")
4249 protected Integer height;
4250 @XmlAttribute(name = "xpos")
4251 protected Integer xpos;
4252 @XmlAttribute(name = "ypos")
4253 protected Integer ypos;
4256 * Gets the value of the title property.
4259 * possible object is
4263 public String getTitle() {
4268 * Sets the value of the title property.
4275 public void setTitle(String value) {
4280 * Gets the value of the newick property.
4283 * possible object is
4287 public String getNewick() {
4292 * Sets the value of the newick property.
4299 public void setNewick(String value) {
4300 this.newick = value;
4304 * Gets the value of the fontName property.
4307 * possible object is
4311 public String getFontName() {
4316 * Sets the value of the fontName property.
4323 public void setFontName(String value) {
4324 this.fontName = value;
4328 * Gets the value of the fontSize property.
4331 * possible object is
4335 public Integer getFontSize() {
4340 * Sets the value of the fontSize property.
4347 public void setFontSize(Integer value) {
4348 this.fontSize = value;
4352 * Gets the value of the fontStyle property.
4355 * possible object is
4359 public Integer getFontStyle() {
4364 * Sets the value of the fontStyle property.
4371 public void setFontStyle(Integer value) {
4372 this.fontStyle = value;
4376 * Gets the value of the threshold property.
4379 * possible object is
4383 public Float getThreshold() {
4388 * Sets the value of the threshold property.
4395 public void setThreshold(Float value) {
4396 this.threshold = value;
4400 * Gets the value of the showBootstrap property.
4403 * possible object is
4407 public Boolean isShowBootstrap() {
4408 return showBootstrap;
4412 * Sets the value of the showBootstrap property.
4419 public void setShowBootstrap(Boolean value) {
4420 this.showBootstrap = value;
4424 * Gets the value of the showDistances property.
4427 * possible object is
4431 public Boolean isShowDistances() {
4432 return showDistances;
4436 * Sets the value of the showDistances property.
4443 public void setShowDistances(Boolean value) {
4444 this.showDistances = value;
4448 * Gets the value of the markUnlinked property.
4451 * possible object is
4455 public Boolean isMarkUnlinked() {
4456 return markUnlinked;
4460 * Sets the value of the markUnlinked property.
4467 public void setMarkUnlinked(Boolean value) {
4468 this.markUnlinked = value;
4472 * Gets the value of the fitToWindow property.
4475 * possible object is
4479 public Boolean isFitToWindow() {
4484 * Sets the value of the fitToWindow property.
4491 public void setFitToWindow(Boolean value) {
4492 this.fitToWindow = value;
4496 * Gets the value of the currentTree property.
4499 * possible object is
4503 public Boolean isCurrentTree() {
4508 * Sets the value of the currentTree property.
4515 public void setCurrentTree(Boolean value) {
4516 this.currentTree = value;
4520 * Gets the value of the id property.
4523 * possible object is
4527 public String getId() {
4532 * Sets the value of the id property.
4539 public void setId(String value) {
4544 * Gets the value of the linkToAllViews property.
4547 * possible object is
4551 public boolean isLinkToAllViews() {
4552 if (linkToAllViews == null) {
4555 return linkToAllViews;
4560 * Sets the value of the linkToAllViews property.
4567 public void setLinkToAllViews(Boolean value) {
4568 this.linkToAllViews = value;
4572 * Gets the value of the width property.
4575 * possible object is
4579 public Integer getWidth() {
4584 * Sets the value of the width property.
4591 public void setWidth(Integer value) {
4596 * Gets the value of the height property.
4599 * possible object is
4603 public Integer getHeight() {
4608 * Sets the value of the height property.
4615 public void setHeight(Integer value) {
4616 this.height = value;
4620 * Gets the value of the xpos property.
4623 * possible object is
4627 public Integer getXpos() {
4632 * Sets the value of the xpos property.
4639 public void setXpos(Integer value) {
4644 * Gets the value of the ypos property.
4647 * possible object is
4651 public Integer getYpos() {
4656 * Sets the value of the ypos property.
4663 public void setYpos(Integer value) {
4671 * <p>Java class for anonymous complex type.
4673 * <p>The following schema fragment specifies the expected content contained within this class.
4676 * &lt;complexType&gt;
4677 * &lt;complexContent&gt;
4678 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4679 * &lt;sequence&gt;
4680 * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
4681 * &lt;/sequence&gt;
4682 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4683 * &lt;/restriction&gt;
4684 * &lt;/complexContent&gt;
4685 * &lt;/complexType&gt;
4690 @XmlAccessorType(XmlAccessType.FIELD)
4691 @XmlType(name = "", propOrder = {
4694 public static class UserColours {
4696 @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4697 protected JalviewUserColours userColourScheme;
4698 @XmlAttribute(name = "id")
4699 protected String id;
4702 * Gets the value of the userColourScheme property.
4705 * possible object is
4706 * {@link JalviewUserColours }
4709 public JalviewUserColours getUserColourScheme() {
4710 return userColourScheme;
4714 * Sets the value of the userColourScheme property.
4718 * {@link JalviewUserColours }
4721 public void setUserColourScheme(JalviewUserColours value) {
4722 this.userColourScheme = value;
4726 * Gets the value of the id property.
4729 * possible object is
4733 public String getId() {
4738 * Sets the value of the id property.
4745 public void setId(String value) {
4753 * <p>Java class for anonymous complex type.
4755 * <p>The following schema fragment specifies the expected content contained within this class.
4758 * &lt;complexType&gt;
4759 * &lt;complexContent&gt;
4760 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4761 * &lt;sequence&gt;
4762 * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
4763 * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
4764 * &lt;complexType&gt;
4765 * &lt;complexContent&gt;
4766 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4767 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4768 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4769 * &lt;/restriction&gt;
4770 * &lt;/complexContent&gt;
4771 * &lt;/complexType&gt;
4772 * &lt;/element&gt;
4773 * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
4774 * &lt;complexType&gt;
4775 * &lt;complexContent&gt;
4776 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
4777 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4778 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4779 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4780 * &lt;/extension&gt;
4781 * &lt;/complexContent&gt;
4782 * &lt;/complexType&gt;
4783 * &lt;/element&gt;
4784 * &lt;element name="overview" minOccurs="0"&gt;
4785 * &lt;complexType&gt;
4786 * &lt;complexContent&gt;
4787 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4788 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4789 * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4790 * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4791 * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4792 * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4793 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4794 * &lt;/restriction&gt;
4795 * &lt;/complexContent&gt;
4796 * &lt;/complexType&gt;
4797 * &lt;/element&gt;
4798 * &lt;/sequence&gt;
4799 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4800 * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4801 * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4802 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4803 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4804 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4805 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4806 * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4807 * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4808 * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4809 * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4810 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4811 * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4812 * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4813 * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4814 * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4815 * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4816 * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4817 * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4818 * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4819 * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4820 * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4821 * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4822 * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4823 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4824 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4825 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4826 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4827 * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4828 * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4829 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4830 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4831 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4832 * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4833 * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4834 * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4835 * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4836 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4837 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4838 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4839 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4840 * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4841 * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4842 * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4843 * &lt;/restriction&gt;
4844 * &lt;/complexContent&gt;
4845 * &lt;/complexType&gt;
4850 @XmlAccessorType(XmlAccessType.FIELD)
4851 @XmlType(name = "", propOrder = {
4852 "annotationColours",
4857 public static class Viewport {
4859 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4860 protected AnnotationColourScheme annotationColours;
4861 @XmlElement(namespace = "www.jalview.org")
4862 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4863 @XmlElement(namespace = "www.jalview.org")
4864 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4865 @XmlElement(namespace = "www.jalview.org")
4866 protected JalviewModel.Viewport.Overview overview;
4867 @XmlAttribute(name = "conservationSelected")
4868 protected Boolean conservationSelected;
4869 @XmlAttribute(name = "pidSelected")
4870 protected Boolean pidSelected;
4871 @XmlAttribute(name = "bgColour")
4872 protected String bgColour;
4873 @XmlAttribute(name = "consThreshold")
4874 protected Integer consThreshold;
4875 @XmlAttribute(name = "pidThreshold")
4876 protected Integer pidThreshold;
4877 @XmlAttribute(name = "title")
4878 protected String title;
4879 @XmlAttribute(name = "showFullId")
4880 protected Boolean showFullId;
4881 @XmlAttribute(name = "rightAlignIds")
4882 protected Boolean rightAlignIds;
4883 @XmlAttribute(name = "showText")
4884 protected Boolean showText;
4885 @XmlAttribute(name = "showColourText")
4886 protected Boolean showColourText;
4887 @XmlAttribute(name = "showUnconserved")
4888 protected Boolean showUnconserved;
4889 @XmlAttribute(name = "showBoxes")
4890 protected Boolean showBoxes;
4891 @XmlAttribute(name = "wrapAlignment")
4892 protected Boolean wrapAlignment;
4893 @XmlAttribute(name = "renderGaps")
4894 protected Boolean renderGaps;
4895 @XmlAttribute(name = "showSequenceFeatures")
4896 protected Boolean showSequenceFeatures;
4897 @XmlAttribute(name = "showNPfeatureTooltip")
4898 protected Boolean showNPfeatureTooltip;
4899 @XmlAttribute(name = "showDbRefTooltip")
4900 protected Boolean showDbRefTooltip;
4901 @XmlAttribute(name = "followHighlight")
4902 protected Boolean followHighlight;
4903 @XmlAttribute(name = "followSelection")
4904 protected Boolean followSelection;
4905 @XmlAttribute(name = "showAnnotation")
4906 protected Boolean showAnnotation;
4907 @XmlAttribute(name = "centreColumnLabels")
4908 protected Boolean centreColumnLabels;
4909 @XmlAttribute(name = "showGroupConservation")
4910 protected Boolean showGroupConservation;
4911 @XmlAttribute(name = "showGroupConsensus")
4912 protected Boolean showGroupConsensus;
4913 @XmlAttribute(name = "showConsensusHistogram")
4914 protected Boolean showConsensusHistogram;
4915 @XmlAttribute(name = "showSequenceLogo")
4916 protected Boolean showSequenceLogo;
4917 @XmlAttribute(name = "normaliseSequenceLogo")
4918 protected Boolean normaliseSequenceLogo;
4919 @XmlAttribute(name = "ignoreGapsinConsensus")
4920 protected Boolean ignoreGapsinConsensus;
4921 @XmlAttribute(name = "startRes")
4922 protected Integer startRes;
4923 @XmlAttribute(name = "startSeq")
4924 protected Integer startSeq;
4925 @XmlAttribute(name = "fontName")
4926 protected String fontName;
4927 @XmlAttribute(name = "fontSize")
4928 protected Integer fontSize;
4929 @XmlAttribute(name = "fontStyle")
4930 protected Integer fontStyle;
4931 @XmlAttribute(name = "scaleProteinAsCdna")
4932 protected Boolean scaleProteinAsCdna;
4933 @XmlAttribute(name = "viewName")
4934 protected String viewName;
4935 @XmlAttribute(name = "sequenceSetId")
4936 protected String sequenceSetId;
4937 @XmlAttribute(name = "gatheredViews")
4938 protected Boolean gatheredViews;
4939 @XmlAttribute(name = "textCol1")
4940 protected Integer textCol1;
4941 @XmlAttribute(name = "textCol2")
4942 protected Integer textCol2;
4943 @XmlAttribute(name = "textColThreshold")
4944 protected Integer textColThreshold;
4945 @XmlAttribute(name = "id")
4946 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4948 @XmlSchemaType(name = "ID")
4949 protected String id;
4950 @XmlAttribute(name = "complementId")
4951 protected String complementId;
4952 @XmlAttribute(name = "showComplementFeatures")
4953 protected Boolean showComplementFeatures;
4954 @XmlAttribute(name = "showComplementFeaturesOnTop")
4955 protected Boolean showComplementFeaturesOnTop;
4956 @XmlAttribute(name = "width")
4957 protected Integer width;
4958 @XmlAttribute(name = "height")
4959 protected Integer height;
4960 @XmlAttribute(name = "xpos")
4961 protected Integer xpos;
4962 @XmlAttribute(name = "ypos")
4963 protected Integer ypos;
4966 * Gets the value of the annotationColours property.
4969 * possible object is
4970 * {@link AnnotationColourScheme }
4973 public AnnotationColourScheme getAnnotationColours() {
4974 return annotationColours;
4978 * Sets the value of the annotationColours property.
4982 * {@link AnnotationColourScheme }
4985 public void setAnnotationColours(AnnotationColourScheme value) {
4986 this.annotationColours = value;
4990 * Gets the value of the hiddenColumns property.
4993 * This accessor method returns a reference to the live list,
4994 * not a snapshot. Therefore any modification you make to the
4995 * returned list will be present inside the JAXB object.
4996 * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4999 * For example, to add a new item, do as follows:
5001 * getHiddenColumns().add(newItem);
5006 * Objects of the following type(s) are allowed in the list
5007 * {@link JalviewModel.Viewport.HiddenColumns }
5011 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5012 if (hiddenColumns == null) {
5013 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5015 return this.hiddenColumns;
5019 * Gets the value of the calcIdParam property.
5022 * This accessor method returns a reference to the live list,
5023 * not a snapshot. Therefore any modification you make to the
5024 * returned list will be present inside the JAXB object.
5025 * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5028 * For example, to add a new item, do as follows:
5030 * getCalcIdParam().add(newItem);
5035 * Objects of the following type(s) are allowed in the list
5036 * {@link JalviewModel.Viewport.CalcIdParam }
5040 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5041 if (calcIdParam == null) {
5042 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5044 return this.calcIdParam;
5048 * Gets the value of the overview property.
5051 * possible object is
5052 * {@link JalviewModel.Viewport.Overview }
5055 public JalviewModel.Viewport.Overview getOverview() {
5060 * Sets the value of the overview property.
5064 * {@link JalviewModel.Viewport.Overview }
5067 public void setOverview(JalviewModel.Viewport.Overview value) {
5068 this.overview = value;
5072 * Gets the value of the conservationSelected property.
5075 * possible object is
5079 public Boolean isConservationSelected() {
5080 return conservationSelected;
5084 * Sets the value of the conservationSelected property.
5091 public void setConservationSelected(Boolean value) {
5092 this.conservationSelected = value;
5096 * Gets the value of the pidSelected property.
5099 * possible object is
5103 public Boolean isPidSelected() {
5108 * Sets the value of the pidSelected property.
5115 public void setPidSelected(Boolean value) {
5116 this.pidSelected = value;
5120 * Gets the value of the bgColour property.
5123 * possible object is
5127 public String getBgColour() {
5132 * Sets the value of the bgColour property.
5139 public void setBgColour(String value) {
5140 this.bgColour = value;
5144 * Gets the value of the consThreshold property.
5147 * possible object is
5151 public Integer getConsThreshold() {
5152 return consThreshold;
5156 * Sets the value of the consThreshold property.
5163 public void setConsThreshold(Integer value) {
5164 this.consThreshold = value;
5168 * Gets the value of the pidThreshold property.
5171 * possible object is
5175 public Integer getPidThreshold() {
5176 return pidThreshold;
5180 * Sets the value of the pidThreshold property.
5187 public void setPidThreshold(Integer value) {
5188 this.pidThreshold = value;
5192 * Gets the value of the title property.
5195 * possible object is
5199 public String getTitle() {
5204 * Sets the value of the title property.
5211 public void setTitle(String value) {
5216 * Gets the value of the showFullId property.
5219 * possible object is
5223 public Boolean isShowFullId() {
5228 * Sets the value of the showFullId property.
5235 public void setShowFullId(Boolean value) {
5236 this.showFullId = value;
5240 * Gets the value of the rightAlignIds property.
5243 * possible object is
5247 public Boolean isRightAlignIds() {
5248 return rightAlignIds;
5252 * Sets the value of the rightAlignIds property.
5259 public void setRightAlignIds(Boolean value) {
5260 this.rightAlignIds = value;
5264 * Gets the value of the showText property.
5267 * possible object is
5271 public Boolean isShowText() {
5276 * Sets the value of the showText property.
5283 public void setShowText(Boolean value) {
5284 this.showText = value;
5288 * Gets the value of the showColourText property.
5291 * possible object is
5295 public Boolean isShowColourText() {
5296 return showColourText;
5300 * Sets the value of the showColourText property.
5307 public void setShowColourText(Boolean value) {
5308 this.showColourText = value;
5312 * Gets the value of the showUnconserved property.
5315 * possible object is
5319 public boolean isShowUnconserved() {
5320 if (showUnconserved == null) {
5323 return showUnconserved;
5328 * Sets the value of the showUnconserved property.
5335 public void setShowUnconserved(Boolean value) {
5336 this.showUnconserved = value;
5340 * Gets the value of the showBoxes property.
5343 * possible object is
5347 public Boolean isShowBoxes() {
5352 * Sets the value of the showBoxes property.
5359 public void setShowBoxes(Boolean value) {
5360 this.showBoxes = value;
5364 * Gets the value of the wrapAlignment property.
5367 * possible object is
5371 public Boolean isWrapAlignment() {
5372 return wrapAlignment;
5376 * Sets the value of the wrapAlignment property.
5383 public void setWrapAlignment(Boolean value) {
5384 this.wrapAlignment = value;
5388 * Gets the value of the renderGaps property.
5391 * possible object is
5395 public Boolean isRenderGaps() {
5400 * Sets the value of the renderGaps property.
5407 public void setRenderGaps(Boolean value) {
5408 this.renderGaps = value;
5412 * Gets the value of the showSequenceFeatures property.
5415 * possible object is
5419 public Boolean isShowSequenceFeatures() {
5420 return showSequenceFeatures;
5424 * Sets the value of the showSequenceFeatures property.
5431 public void setShowSequenceFeatures(Boolean value) {
5432 this.showSequenceFeatures = value;
5436 * Gets the value of the showNPfeatureTooltip property.
5439 * possible object is
5443 public Boolean isShowNPfeatureTooltip() {
5444 return showNPfeatureTooltip;
5448 * Sets the value of the showNPfeatureTooltip property.
5455 public void setShowNPfeatureTooltip(Boolean value) {
5456 this.showNPfeatureTooltip = value;
5460 * Gets the value of the showDbRefTooltip property.
5463 * possible object is
5467 public Boolean isShowDbRefTooltip() {
5468 return showDbRefTooltip;
5472 * Sets the value of the showDbRefTooltip property.
5479 public void setShowDbRefTooltip(Boolean value) {
5480 this.showDbRefTooltip = value;
5484 * Gets the value of the followHighlight property.
5487 * possible object is
5491 public boolean isFollowHighlight() {
5492 if (followHighlight == null) {
5495 return followHighlight;
5500 * Sets the value of the followHighlight property.
5507 public void setFollowHighlight(Boolean value) {
5508 this.followHighlight = value;
5512 * Gets the value of the followSelection property.
5515 * possible object is
5519 public boolean isFollowSelection() {
5520 if (followSelection == null) {
5523 return followSelection;
5528 * Sets the value of the followSelection property.
5535 public void setFollowSelection(Boolean value) {
5536 this.followSelection = value;
5540 * Gets the value of the showAnnotation property.
5543 * possible object is
5547 public Boolean isShowAnnotation() {
5548 return showAnnotation;
5552 * Sets the value of the showAnnotation property.
5559 public void setShowAnnotation(Boolean value) {
5560 this.showAnnotation = value;
5564 * Gets the value of the centreColumnLabels property.
5567 * possible object is
5571 public boolean isCentreColumnLabels() {
5572 if (centreColumnLabels == null) {
5575 return centreColumnLabels;
5580 * Sets the value of the centreColumnLabels property.
5587 public void setCentreColumnLabels(Boolean value) {
5588 this.centreColumnLabels = value;
5592 * Gets the value of the showGroupConservation property.
5595 * possible object is
5599 public boolean isShowGroupConservation() {
5600 if (showGroupConservation == null) {
5603 return showGroupConservation;
5608 * Sets the value of the showGroupConservation property.
5615 public void setShowGroupConservation(Boolean value) {
5616 this.showGroupConservation = value;
5620 * Gets the value of the showGroupConsensus property.
5623 * possible object is
5627 public boolean isShowGroupConsensus() {
5628 if (showGroupConsensus == null) {
5631 return showGroupConsensus;
5636 * Sets the value of the showGroupConsensus property.
5643 public void setShowGroupConsensus(Boolean value) {
5644 this.showGroupConsensus = value;
5648 * Gets the value of the showConsensusHistogram property.
5651 * possible object is
5655 public boolean isShowConsensusHistogram() {
5656 if (showConsensusHistogram == null) {
5659 return showConsensusHistogram;
5664 * Sets the value of the showConsensusHistogram property.
5671 public void setShowConsensusHistogram(Boolean value) {
5672 this.showConsensusHistogram = value;
5676 * Gets the value of the showSequenceLogo property.
5679 * possible object is
5683 public boolean isShowSequenceLogo() {
5684 if (showSequenceLogo == null) {
5687 return showSequenceLogo;
5692 * Sets the value of the showSequenceLogo property.
5699 public void setShowSequenceLogo(Boolean value) {
5700 this.showSequenceLogo = value;
5704 * Gets the value of the normaliseSequenceLogo property.
5707 * possible object is
5711 public boolean isNormaliseSequenceLogo() {
5712 if (normaliseSequenceLogo == null) {
5715 return normaliseSequenceLogo;
5720 * Sets the value of the normaliseSequenceLogo property.
5727 public void setNormaliseSequenceLogo(Boolean value) {
5728 this.normaliseSequenceLogo = value;
5732 * Gets the value of the ignoreGapsinConsensus property.
5735 * possible object is
5739 public boolean isIgnoreGapsinConsensus() {
5740 if (ignoreGapsinConsensus == null) {
5743 return ignoreGapsinConsensus;
5748 * Sets the value of the ignoreGapsinConsensus property.
5755 public void setIgnoreGapsinConsensus(Boolean value) {
5756 this.ignoreGapsinConsensus = value;
5760 * Gets the value of the startRes property.
5763 * possible object is
5767 public Integer getStartRes() {
5772 * Sets the value of the startRes property.
5779 public void setStartRes(Integer value) {
5780 this.startRes = value;
5784 * Gets the value of the startSeq property.
5787 * possible object is
5791 public Integer getStartSeq() {
5796 * Sets the value of the startSeq property.
5803 public void setStartSeq(Integer value) {
5804 this.startSeq = value;
5808 * Gets the value of the fontName property.
5811 * possible object is
5815 public String getFontName() {
5820 * Sets the value of the fontName property.
5827 public void setFontName(String value) {
5828 this.fontName = value;
5832 * Gets the value of the fontSize property.
5835 * possible object is
5839 public Integer getFontSize() {
5844 * Sets the value of the fontSize property.
5851 public void setFontSize(Integer value) {
5852 this.fontSize = value;
5856 * Gets the value of the fontStyle property.
5859 * possible object is
5863 public Integer getFontStyle() {
5868 * Sets the value of the fontStyle property.
5875 public void setFontStyle(Integer value) {
5876 this.fontStyle = value;
5880 * Gets the value of the scaleProteinAsCdna property.
5883 * possible object is
5887 public boolean isScaleProteinAsCdna() {
5888 if (scaleProteinAsCdna == null) {
5891 return scaleProteinAsCdna;
5896 * Sets the value of the scaleProteinAsCdna property.
5903 public void setScaleProteinAsCdna(Boolean value) {
5904 this.scaleProteinAsCdna = value;
5908 * Gets the value of the viewName property.
5911 * possible object is
5915 public String getViewName() {
5920 * Sets the value of the viewName property.
5927 public void setViewName(String value) {
5928 this.viewName = value;
5932 * Gets the value of the sequenceSetId property.
5935 * possible object is
5939 public String getSequenceSetId() {
5940 return sequenceSetId;
5944 * Sets the value of the sequenceSetId property.
5951 public void setSequenceSetId(String value) {
5952 this.sequenceSetId = value;
5956 * Gets the value of the gatheredViews property.
5959 * possible object is
5963 public Boolean isGatheredViews() {
5964 return gatheredViews;
5968 * Sets the value of the gatheredViews property.
5975 public void setGatheredViews(Boolean value) {
5976 this.gatheredViews = value;
5980 * Gets the value of the textCol1 property.
5983 * possible object is
5987 public Integer getTextCol1() {
5992 * Sets the value of the textCol1 property.
5999 public void setTextCol1(Integer value) {
6000 this.textCol1 = value;
6004 * Gets the value of the textCol2 property.
6007 * possible object is
6011 public Integer getTextCol2() {
6016 * Sets the value of the textCol2 property.
6023 public void setTextCol2(Integer value) {
6024 this.textCol2 = value;
6028 * Gets the value of the textColThreshold property.
6031 * possible object is
6035 public Integer getTextColThreshold() {
6036 return textColThreshold;
6040 * Sets the value of the textColThreshold property.
6047 public void setTextColThreshold(Integer value) {
6048 this.textColThreshold = value;
6052 * Gets the value of the id property.
6055 * possible object is
6059 public String getId() {
6064 * Sets the value of the id property.
6071 public void setId(String value) {
6076 * Gets the value of the complementId property.
6079 * possible object is
6083 public String getComplementId() {
6084 return complementId;
6088 * Sets the value of the complementId property.
6095 public void setComplementId(String value) {
6096 this.complementId = value;
6100 * Gets the value of the showComplementFeatures property.
6103 * possible object is
6107 public boolean isShowComplementFeatures() {
6108 if (showComplementFeatures == null) {
6111 return showComplementFeatures;
6116 * Sets the value of the showComplementFeatures property.
6123 public void setShowComplementFeatures(Boolean value) {
6124 this.showComplementFeatures = value;
6128 * Gets the value of the showComplementFeaturesOnTop property.
6131 * possible object is
6135 public boolean isShowComplementFeaturesOnTop() {
6136 if (showComplementFeaturesOnTop == null) {
6139 return showComplementFeaturesOnTop;
6144 * Sets the value of the showComplementFeaturesOnTop property.
6151 public void setShowComplementFeaturesOnTop(Boolean value) {
6152 this.showComplementFeaturesOnTop = value;
6156 * Gets the value of the width property.
6159 * possible object is
6163 public Integer getWidth() {
6168 * Sets the value of the width property.
6175 public void setWidth(Integer value) {
6180 * Gets the value of the height property.
6183 * possible object is
6187 public Integer getHeight() {
6192 * Sets the value of the height property.
6199 public void setHeight(Integer value) {
6200 this.height = value;
6204 * Gets the value of the xpos property.
6207 * possible object is
6211 public Integer getXpos() {
6216 * Sets the value of the xpos property.
6223 public void setXpos(Integer value) {
6228 * Gets the value of the ypos property.
6231 * possible object is
6235 public Integer getYpos() {
6240 * Sets the value of the ypos property.
6247 public void setYpos(Integer value) {
6253 * <p>Java class for anonymous complex type.
6255 * <p>The following schema fragment specifies the expected content contained within this class.
6258 * &lt;complexType&gt;
6259 * &lt;complexContent&gt;
6260 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
6261 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
6262 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
6263 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
6264 * &lt;/extension&gt;
6265 * &lt;/complexContent&gt;
6266 * &lt;/complexType&gt;
6271 @XmlAccessorType(XmlAccessType.FIELD)
6273 public static class CalcIdParam
6274 extends WebServiceParameterSet
6277 @XmlAttribute(name = "calcId", required = true)
6278 protected String calcId;
6279 @XmlAttribute(name = "needsUpdate")
6280 protected Boolean needsUpdate;
6281 @XmlAttribute(name = "autoUpdate", required = true)
6282 protected boolean autoUpdate;
6285 * Gets the value of the calcId property.
6288 * possible object is
6292 public String getCalcId() {
6297 * Sets the value of the calcId property.
6304 public void setCalcId(String value) {
6305 this.calcId = value;
6309 * Gets the value of the needsUpdate property.
6312 * possible object is
6316 public boolean isNeedsUpdate() {
6317 if (needsUpdate == null) {
6325 * Sets the value of the needsUpdate property.
6332 public void setNeedsUpdate(Boolean value) {
6333 this.needsUpdate = value;
6337 * Gets the value of the autoUpdate property.
6340 public boolean isAutoUpdate() {
6345 * Sets the value of the autoUpdate property.
6348 public void setAutoUpdate(boolean value) {
6349 this.autoUpdate = value;
6356 * <p>Java class for anonymous complex type.
6358 * <p>The following schema fragment specifies the expected content contained within this class.
6361 * &lt;complexType&gt;
6362 * &lt;complexContent&gt;
6363 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
6364 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6365 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6366 * &lt;/restriction&gt;
6367 * &lt;/complexContent&gt;
6368 * &lt;/complexType&gt;
6373 @XmlAccessorType(XmlAccessType.FIELD)
6375 public static class HiddenColumns {
6377 @XmlAttribute(name = "start")
6378 protected Integer start;
6379 @XmlAttribute(name = "end")
6380 protected Integer end;
6383 * Gets the value of the start property.
6386 * possible object is
6390 public Integer getStart() {
6395 * Sets the value of the start property.
6402 public void setStart(Integer value) {
6407 * Gets the value of the end property.
6410 * possible object is
6414 public Integer getEnd() {
6419 * Sets the value of the end property.
6426 public void setEnd(Integer value) {
6434 * <p>Java class for anonymous complex type.
6436 * <p>The following schema fragment specifies the expected content contained within this class.
6439 * &lt;complexType&gt;
6440 * &lt;complexContent&gt;
6441 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
6442 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
6443 * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
6444 * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6445 * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6446 * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6447 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
6448 * &lt;/restriction&gt;
6449 * &lt;/complexContent&gt;
6450 * &lt;/complexType&gt;
6455 @XmlAccessorType(XmlAccessType.FIELD)
6457 public static class Overview {
6459 @XmlAttribute(name = "showHidden")
6460 protected Boolean showHidden;
6461 @XmlAttribute(name = "residueColour")
6462 protected Integer residueColour;
6463 @XmlAttribute(name = "gapColour")
6464 protected Integer gapColour;
6465 @XmlAttribute(name = "hiddenColour")
6466 protected Integer hiddenColour;
6467 @XmlAttribute(name = "title")
6468 protected String title;
6469 @XmlAttribute(name = "width")
6470 protected Integer width;
6471 @XmlAttribute(name = "height")
6472 protected Integer height;
6473 @XmlAttribute(name = "xpos")
6474 protected Integer xpos;
6475 @XmlAttribute(name = "ypos")
6476 protected Integer ypos;
6479 * Gets the value of the showHidden property.
6482 * possible object is
6486 public Boolean isShowHidden() {
6491 * Sets the value of the showHidden property.
6498 public void setShowHidden(Boolean value) {
6499 this.showHidden = value;
6503 * Gets the value of the residueColour property.
6506 * possible object is
6510 public Integer getResidueColour() {
6511 return residueColour;
6515 * Sets the value of the residueColour property.
6522 public void setResidueColour(Integer value) {
6523 this.residueColour = value;
6527 * Gets the value of the gapColour property.
6530 * possible object is
6534 public Integer getGapColour() {
6539 * Sets the value of the gapColour property.
6546 public void setGapColour(Integer value) {
6547 this.gapColour = value;
6551 * Gets the value of the hiddenColour property.
6554 * possible object is
6558 public Integer getHiddenColour() {
6559 return hiddenColour;
6563 * Sets the value of the hiddenColour property.
6570 public void setHiddenColour(Integer value) {
6571 this.hiddenColour = value;
6575 * Gets the value of the title property.
6578 * possible object is
6582 public String getTitle() {
6587 * Sets the value of the title property.
6594 public void setTitle(String value) {
6599 * Gets the value of the width property.
6602 * possible object is
6606 public Integer getWidth() {
6611 * Sets the value of the width property.
6618 public void setWidth(Integer value) {
6623 * Gets the value of the height property.
6626 * possible object is
6630 public Integer getHeight() {
6635 * Sets the value of the height property.
6642 public void setHeight(Integer value) {
6643 this.height = value;
6647 * Gets the value of the xpos property.
6650 * possible object is
6654 public Integer getXpos() {
6659 * Sets the value of the xpos property.
6666 public void setXpos(Integer value) {
6671 * Gets the value of the ypos property.
6674 * possible object is
6678 public Integer getYpos() {
6683 * Sets the value of the ypos property.
6690 public void setYpos(Integer value) {