2 // This file was generated by the Eclipse Implementation of JAXB, v2.3.3
3 // See https://eclipse-ee4j.github.io/jaxb-ri
4 // Any modifications to this file will be lost upon recompilation of the source schema.
5 // Generated on: 2023.09.01 at 02:16:11 PM BST
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="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
214 * &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
215 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
216 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
217 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
218 * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
219 * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
220 * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
221 * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
222 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
223 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
224 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
225 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
226 * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
227 * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
228 * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
229 * &lt;/restriction&gt;
230 * &lt;/complexContent&gt;
231 * &lt;/complexType&gt;
232 * &lt;/element&gt;
233 * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
234 * &lt;complexType&gt;
235 * &lt;complexContent&gt;
236 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
237 * &lt;sequence&gt;
238 * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
239 * &lt;/sequence&gt;
240 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
241 * &lt;/restriction&gt;
242 * &lt;/complexContent&gt;
243 * &lt;/complexType&gt;
244 * &lt;/element&gt;
245 * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
246 * &lt;complexType&gt;
247 * &lt;complexContent&gt;
248 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
249 * &lt;sequence minOccurs="0"&gt;
250 * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
251 * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
252 * &lt;/sequence&gt;
253 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
254 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
255 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
256 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
257 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
258 * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
259 * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
260 * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
261 * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
262 * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
263 * &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
264 * &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
265 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
266 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
267 * &lt;/restriction&gt;
268 * &lt;/complexContent&gt;
269 * &lt;/complexType&gt;
270 * &lt;/element&gt;
271 * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
272 * &lt;complexType&gt;
273 * &lt;complexContent&gt;
274 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
275 * &lt;sequence&gt;
276 * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
277 * &lt;complexType&gt;
278 * &lt;complexContent&gt;
279 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
280 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
281 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
282 * &lt;/restriction&gt;
283 * &lt;/complexContent&gt;
284 * &lt;/complexType&gt;
285 * &lt;/element&gt;
286 * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
287 * &lt;complexType&gt;
288 * &lt;complexContent&gt;
289 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
290 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
291 * &lt;/restriction&gt;
292 * &lt;/complexContent&gt;
293 * &lt;/complexType&gt;
294 * &lt;/element&gt;
295 * &lt;element name="seqPointMin"&gt;
296 * &lt;complexType&gt;
297 * &lt;complexContent&gt;
298 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
299 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
300 * &lt;/restriction&gt;
301 * &lt;/complexContent&gt;
302 * &lt;/complexType&gt;
303 * &lt;/element&gt;
304 * &lt;element name="seqPointMax"&gt;
305 * &lt;complexType&gt;
306 * &lt;complexContent&gt;
307 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
308 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
309 * &lt;/restriction&gt;
310 * &lt;/complexContent&gt;
311 * &lt;/complexType&gt;
312 * &lt;/element&gt;
313 * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
314 * &lt;/sequence&gt;
315 * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
316 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
317 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
318 * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
319 * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
320 * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
321 * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
322 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
323 * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
324 * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
325 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
326 * &lt;/restriction&gt;
327 * &lt;/complexContent&gt;
328 * &lt;/complexType&gt;
329 * &lt;/element&gt;
330 * &lt;element name="FeatureSettings" minOccurs="0"&gt;
331 * &lt;complexType&gt;
332 * &lt;complexContent&gt;
333 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
334 * &lt;sequence&gt;
335 * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
336 * &lt;complexType&gt;
337 * &lt;complexContent&gt;
338 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
339 * &lt;sequence&gt;
340 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
341 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
342 * &lt;/sequence&gt;
343 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
344 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
345 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
346 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
347 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
348 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
349 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
350 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
351 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
352 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
353 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
354 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
355 * &lt;/restriction&gt;
356 * &lt;/complexContent&gt;
357 * &lt;/complexType&gt;
358 * &lt;/element&gt;
359 * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
360 * &lt;complexType&gt;
361 * &lt;complexContent&gt;
362 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
363 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
364 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
365 * &lt;/restriction&gt;
366 * &lt;/complexContent&gt;
367 * &lt;/complexType&gt;
368 * &lt;/element&gt;
369 * &lt;/sequence&gt;
370 * &lt;/restriction&gt;
371 * &lt;/complexContent&gt;
372 * &lt;/complexType&gt;
373 * &lt;/element&gt;
374 * &lt;/sequence&gt;
375 * &lt;/sequence&gt;
376 * &lt;/restriction&gt;
377 * &lt;/complexContent&gt;
378 * &lt;/complexType&gt;
383 @XmlAccessorType(XmlAccessType.FIELD)
384 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
396 public class JalviewModel {
398 @XmlElement(required = true)
399 @XmlSchemaType(name = "dateTime")
400 protected XMLGregorianCalendar creationDate;
401 @XmlElement(required = true)
402 protected String version;
403 @XmlElement(required = true)
404 protected VAMSAS vamsasModel;
405 @XmlElement(name = "JSeq")
406 protected List<JalviewModel.JSeq> jSeq;
407 @XmlElement(name = "JGroup")
408 protected List<JalviewModel.JGroup> jGroup;
409 @XmlElement(name = "Viewport")
410 protected List<JalviewModel.Viewport> viewport;
411 @XmlElement(name = "UserColours")
412 protected List<JalviewModel.UserColours> userColours;
413 protected List<JalviewModel.Tree> tree;
414 @XmlElement(name = "PcaViewer")
415 protected List<JalviewModel.PcaViewer> pcaViewer;
416 @XmlElement(name = "FeatureSettings")
417 protected JalviewModel.FeatureSettings featureSettings;
420 * Gets the value of the creationDate property.
424 * {@link XMLGregorianCalendar }
427 public XMLGregorianCalendar getCreationDate() {
432 * Sets the value of the creationDate property.
436 * {@link XMLGregorianCalendar }
439 public void setCreationDate(XMLGregorianCalendar value) {
440 this.creationDate = value;
444 * Gets the value of the version property.
451 public String getVersion() {
456 * Sets the value of the version property.
463 public void setVersion(String value) {
464 this.version = value;
468 * Gets the value of the vamsasModel property.
475 public VAMSAS getVamsasModel() {
480 * Sets the value of the vamsasModel property.
487 public void setVamsasModel(VAMSAS value) {
488 this.vamsasModel = value;
492 * Gets the value of the jSeq property.
495 * This accessor method returns a reference to the live list,
496 * not a snapshot. Therefore any modification you make to the
497 * returned list will be present inside the JAXB object.
498 * This is why there is not a <CODE>set</CODE> method for the jSeq property.
501 * For example, to add a new item, do as follows:
503 * getJSeq().add(newItem);
508 * Objects of the following type(s) are allowed in the list
509 * {@link JalviewModel.JSeq }
513 public List<JalviewModel.JSeq> getJSeq() {
515 jSeq = new ArrayList<JalviewModel.JSeq>();
521 * Gets the value of the jGroup property.
524 * This accessor method returns a reference to the live list,
525 * not a snapshot. Therefore any modification you make to the
526 * returned list will be present inside the JAXB object.
527 * This is why there is not a <CODE>set</CODE> method for the jGroup property.
530 * For example, to add a new item, do as follows:
532 * getJGroup().add(newItem);
537 * Objects of the following type(s) are allowed in the list
538 * {@link JalviewModel.JGroup }
542 public List<JalviewModel.JGroup> getJGroup() {
543 if (jGroup == null) {
544 jGroup = new ArrayList<JalviewModel.JGroup>();
550 * Gets the value of the viewport property.
553 * This accessor method returns a reference to the live list,
554 * not a snapshot. Therefore any modification you make to the
555 * returned list will be present inside the JAXB object.
556 * This is why there is not a <CODE>set</CODE> method for the viewport property.
559 * For example, to add a new item, do as follows:
561 * getViewport().add(newItem);
566 * Objects of the following type(s) are allowed in the list
567 * {@link JalviewModel.Viewport }
571 public List<JalviewModel.Viewport> getViewport() {
572 if (viewport == null) {
573 viewport = new ArrayList<JalviewModel.Viewport>();
575 return this.viewport;
579 * Gets the value of the userColours property.
582 * This accessor method returns a reference to the live list,
583 * not a snapshot. Therefore any modification you make to the
584 * returned list will be present inside the JAXB object.
585 * This is why there is not a <CODE>set</CODE> method for the userColours property.
588 * For example, to add a new item, do as follows:
590 * getUserColours().add(newItem);
595 * Objects of the following type(s) are allowed in the list
596 * {@link JalviewModel.UserColours }
600 public List<JalviewModel.UserColours> getUserColours() {
601 if (userColours == null) {
602 userColours = new ArrayList<JalviewModel.UserColours>();
604 return this.userColours;
608 * Gets the value of the tree property.
611 * This accessor method returns a reference to the live list,
612 * not a snapshot. Therefore any modification you make to the
613 * returned list will be present inside the JAXB object.
614 * This is why there is not a <CODE>set</CODE> method for the tree property.
617 * For example, to add a new item, do as follows:
619 * getTree().add(newItem);
624 * Objects of the following type(s) are allowed in the list
625 * {@link JalviewModel.Tree }
629 public List<JalviewModel.Tree> getTree() {
631 tree = new ArrayList<JalviewModel.Tree>();
637 * Gets the value of the pcaViewer property.
640 * This accessor method returns a reference to the live list,
641 * not a snapshot. Therefore any modification you make to the
642 * returned list will be present inside the JAXB object.
643 * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
646 * For example, to add a new item, do as follows:
648 * getPcaViewer().add(newItem);
653 * Objects of the following type(s) are allowed in the list
654 * {@link JalviewModel.PcaViewer }
658 public List<JalviewModel.PcaViewer> getPcaViewer() {
659 if (pcaViewer == null) {
660 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
662 return this.pcaViewer;
666 * Gets the value of the featureSettings property.
670 * {@link JalviewModel.FeatureSettings }
673 public JalviewModel.FeatureSettings getFeatureSettings() {
674 return featureSettings;
678 * Sets the value of the featureSettings property.
682 * {@link JalviewModel.FeatureSettings }
685 public void setFeatureSettings(JalviewModel.FeatureSettings value) {
686 this.featureSettings = value;
691 * <p>Java class for anonymous complex type.
693 * <p>The following schema fragment specifies the expected content contained within this class.
696 * &lt;complexType&gt;
697 * &lt;complexContent&gt;
698 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
699 * &lt;sequence&gt;
700 * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
701 * &lt;complexType&gt;
702 * &lt;complexContent&gt;
703 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
704 * &lt;sequence&gt;
705 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
706 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
707 * &lt;/sequence&gt;
708 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
709 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
710 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
711 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
712 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
713 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
714 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
715 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
716 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
717 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
718 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
719 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
720 * &lt;/restriction&gt;
721 * &lt;/complexContent&gt;
722 * &lt;/complexType&gt;
723 * &lt;/element&gt;
724 * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
725 * &lt;complexType&gt;
726 * &lt;complexContent&gt;
727 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
728 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
729 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
730 * &lt;/restriction&gt;
731 * &lt;/complexContent&gt;
732 * &lt;/complexType&gt;
733 * &lt;/element&gt;
734 * &lt;/sequence&gt;
735 * &lt;/restriction&gt;
736 * &lt;/complexContent&gt;
737 * &lt;/complexType&gt;
742 @XmlAccessorType(XmlAccessType.FIELD)
743 @XmlType(name = "", propOrder = {
747 public static class FeatureSettings {
749 @XmlElement(namespace = "www.jalview.org")
750 protected List<JalviewModel.FeatureSettings.Setting> setting;
751 @XmlElement(namespace = "www.jalview.org")
752 protected List<JalviewModel.FeatureSettings.Group> group;
755 * Gets the value of the setting property.
758 * This accessor method returns a reference to the live list,
759 * not a snapshot. Therefore any modification you make to the
760 * returned list will be present inside the JAXB object.
761 * This is why there is not a <CODE>set</CODE> method for the setting property.
764 * For example, to add a new item, do as follows:
766 * getSetting().add(newItem);
771 * Objects of the following type(s) are allowed in the list
772 * {@link JalviewModel.FeatureSettings.Setting }
776 public List<JalviewModel.FeatureSettings.Setting> getSetting() {
777 if (setting == null) {
778 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
784 * Gets the value of the group property.
787 * This accessor method returns a reference to the live list,
788 * not a snapshot. Therefore any modification you make to the
789 * returned list will be present inside the JAXB object.
790 * This is why there is not a <CODE>set</CODE> method for the group property.
793 * For example, to add a new item, do as follows:
795 * getGroup().add(newItem);
800 * Objects of the following type(s) are allowed in the list
801 * {@link JalviewModel.FeatureSettings.Group }
805 public List<JalviewModel.FeatureSettings.Group> getGroup() {
807 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
814 * <p>Java class for anonymous complex type.
816 * <p>The following schema fragment specifies the expected content contained within this class.
819 * &lt;complexType&gt;
820 * &lt;complexContent&gt;
821 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
822 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
823 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
824 * &lt;/restriction&gt;
825 * &lt;/complexContent&gt;
826 * &lt;/complexType&gt;
831 @XmlAccessorType(XmlAccessType.FIELD)
833 public static class Group {
835 @XmlAttribute(name = "name", required = true)
836 protected String name;
837 @XmlAttribute(name = "display", required = true)
838 protected boolean display;
841 * Gets the value of the name property.
848 public String getName() {
853 * Sets the value of the name property.
860 public void setName(String value) {
865 * Gets the value of the display property.
868 public boolean isDisplay() {
873 * Sets the value of the display property.
876 public void setDisplay(boolean value) {
877 this.display = value;
884 * <p>Java class for anonymous complex type.
886 * <p>The following schema fragment specifies the expected content contained within this class.
889 * &lt;complexType&gt;
890 * &lt;complexContent&gt;
891 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
892 * &lt;sequence&gt;
893 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
894 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
895 * &lt;/sequence&gt;
896 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
897 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
898 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
899 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
900 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
901 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
902 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
903 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
904 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
905 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
906 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
907 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
908 * &lt;/restriction&gt;
909 * &lt;/complexContent&gt;
910 * &lt;/complexType&gt;
915 @XmlAccessorType(XmlAccessType.FIELD)
916 @XmlType(name = "", propOrder = {
920 public static class Setting {
922 @XmlElement(namespace = "www.jalview.org")
923 protected List<String> attributeName;
924 @XmlElement(namespace = "www.jalview.org")
925 protected FeatureMatcherSet matcherSet;
926 @XmlAttribute(name = "type", required = true)
927 protected String type;
928 @XmlAttribute(name = "colour", required = true)
929 protected int colour;
930 @XmlAttribute(name = "display", required = true)
931 protected boolean display;
932 @XmlAttribute(name = "order")
933 protected Float order;
934 @XmlAttribute(name = "mincolour")
935 protected Integer mincolour;
936 @XmlAttribute(name = "noValueColour")
937 protected NoValueColour noValueColour;
938 @XmlAttribute(name = "threshold")
939 protected Float threshold;
940 @XmlAttribute(name = "threshstate")
941 protected Integer threshstate;
942 @XmlAttribute(name = "max")
944 @XmlAttribute(name = "min")
946 @XmlAttribute(name = "colourByLabel")
947 protected Boolean colourByLabel;
948 @XmlAttribute(name = "autoScale")
949 protected Boolean autoScale;
952 * Gets the value of the attributeName property.
955 * This accessor method returns a reference to the live list,
956 * not a snapshot. Therefore any modification you make to the
957 * returned list will be present inside the JAXB object.
958 * This is why there is not a <CODE>set</CODE> method for the attributeName property.
961 * For example, to add a new item, do as follows:
963 * getAttributeName().add(newItem);
968 * Objects of the following type(s) are allowed in the list
973 public List<String> getAttributeName() {
974 if (attributeName == null) {
975 attributeName = new ArrayList<String>();
977 return this.attributeName;
981 * Gets the value of the matcherSet property.
985 * {@link FeatureMatcherSet }
988 public FeatureMatcherSet getMatcherSet() {
993 * Sets the value of the matcherSet property.
997 * {@link FeatureMatcherSet }
1000 public void setMatcherSet(FeatureMatcherSet value) {
1001 this.matcherSet = value;
1005 * Gets the value of the type property.
1008 * possible object is
1012 public String getType() {
1017 * Sets the value of the type property.
1024 public void setType(String value) {
1029 * Gets the value of the colour property.
1032 public int getColour() {
1037 * Sets the value of the colour property.
1040 public void setColour(int value) {
1041 this.colour = value;
1045 * Gets the value of the display property.
1048 public boolean isDisplay() {
1053 * Sets the value of the display property.
1056 public void setDisplay(boolean value) {
1057 this.display = value;
1061 * Gets the value of the order property.
1064 * possible object is
1068 public Float getOrder() {
1073 * Sets the value of the order property.
1080 public void setOrder(Float value) {
1085 * Gets the value of the mincolour property.
1088 * possible object is
1092 public Integer getMincolour() {
1097 * Sets the value of the mincolour property.
1104 public void setMincolour(Integer value) {
1105 this.mincolour = value;
1109 * Gets the value of the noValueColour property.
1112 * possible object is
1113 * {@link NoValueColour }
1116 public NoValueColour getNoValueColour() {
1117 if (noValueColour == null) {
1118 return NoValueColour.MIN;
1120 return noValueColour;
1125 * Sets the value of the noValueColour property.
1129 * {@link NoValueColour }
1132 public void setNoValueColour(NoValueColour value) {
1133 this.noValueColour = value;
1137 * Gets the value of the threshold property.
1140 * possible object is
1144 public Float getThreshold() {
1149 * Sets the value of the threshold property.
1156 public void setThreshold(Float value) {
1157 this.threshold = value;
1161 * Gets the value of the threshstate property.
1164 * possible object is
1168 public Integer getThreshstate() {
1173 * Sets the value of the threshstate property.
1180 public void setThreshstate(Integer value) {
1181 this.threshstate = value;
1185 * Gets the value of the max property.
1188 * possible object is
1192 public Float getMax() {
1197 * Sets the value of the max property.
1204 public void setMax(Float value) {
1209 * Gets the value of the min property.
1212 * possible object is
1216 public Float getMin() {
1221 * Sets the value of the min property.
1228 public void setMin(Float value) {
1233 * Gets the value of the colourByLabel property.
1236 * possible object is
1240 public Boolean isColourByLabel() {
1241 return colourByLabel;
1245 * Sets the value of the colourByLabel property.
1252 public void setColourByLabel(Boolean value) {
1253 this.colourByLabel = value;
1257 * Gets the value of the autoScale property.
1260 * possible object is
1264 public Boolean isAutoScale() {
1269 * Sets the value of the autoScale property.
1276 public void setAutoScale(Boolean value) {
1277 this.autoScale = value;
1286 * <p>Java class for anonymous complex type.
1288 * <p>The following schema fragment specifies the expected content contained within this class.
1291 * &lt;complexType&gt;
1292 * &lt;complexContent&gt;
1293 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1294 * &lt;sequence&gt;
1295 * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
1296 * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
1297 * &lt;/sequence&gt;
1298 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1299 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1300 * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1301 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1302 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1303 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1304 * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1305 * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1306 * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1307 * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1308 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1309 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1310 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1311 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1312 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1313 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1314 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1315 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1316 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1317 * &lt;/restriction&gt;
1318 * &lt;/complexContent&gt;
1319 * &lt;/complexType&gt;
1324 @XmlAccessorType(XmlAccessType.FIELD)
1325 @XmlType(name = "", propOrder = {
1329 public static class JGroup {
1331 @XmlElement(namespace = "www.jalview.org", required = true)
1332 protected List<String> seq;
1333 @XmlElement(namespace = "www.jalview.org")
1334 protected AnnotationColourScheme annotationColours;
1335 @XmlAttribute(name = "start")
1336 protected Integer start;
1337 @XmlAttribute(name = "end")
1338 protected Integer end;
1339 @XmlAttribute(name = "name")
1340 protected String name;
1341 @XmlAttribute(name = "colour")
1342 protected String colour;
1343 @XmlAttribute(name = "consThreshold")
1344 protected Integer consThreshold;
1345 @XmlAttribute(name = "pidThreshold")
1346 protected Integer pidThreshold;
1347 @XmlAttribute(name = "outlineColour")
1348 protected Integer outlineColour;
1349 @XmlAttribute(name = "displayBoxes")
1350 protected Boolean displayBoxes;
1351 @XmlAttribute(name = "displayText")
1352 protected Boolean displayText;
1353 @XmlAttribute(name = "colourText")
1354 protected Boolean colourText;
1355 @XmlAttribute(name = "textCol1")
1356 protected Integer textCol1;
1357 @XmlAttribute(name = "textCol2")
1358 protected Integer textCol2;
1359 @XmlAttribute(name = "textColThreshold")
1360 protected Integer textColThreshold;
1361 @XmlAttribute(name = "showUnconserved")
1362 protected Boolean showUnconserved;
1363 @XmlAttribute(name = "ignoreGapsinConsensus")
1364 protected Boolean ignoreGapsinConsensus;
1365 @XmlAttribute(name = "showConsensusHistogram")
1366 protected Boolean showConsensusHistogram;
1367 @XmlAttribute(name = "showSequenceLogo")
1368 protected Boolean showSequenceLogo;
1369 @XmlAttribute(name = "normaliseSequenceLogo")
1370 protected Boolean normaliseSequenceLogo;
1371 @XmlAttribute(name = "id")
1372 protected String id;
1375 * Gets the value of the seq property.
1378 * This accessor method returns a reference to the live list,
1379 * not a snapshot. Therefore any modification you make to the
1380 * returned list will be present inside the JAXB object.
1381 * This is why there is not a <CODE>set</CODE> method for the seq property.
1384 * For example, to add a new item, do as follows:
1386 * getSeq().add(newItem);
1391 * Objects of the following type(s) are allowed in the list
1396 public List<String> getSeq() {
1398 seq = new ArrayList<String>();
1404 * Gets the value of the annotationColours property.
1407 * possible object is
1408 * {@link AnnotationColourScheme }
1411 public AnnotationColourScheme getAnnotationColours() {
1412 return annotationColours;
1416 * Sets the value of the annotationColours property.
1420 * {@link AnnotationColourScheme }
1423 public void setAnnotationColours(AnnotationColourScheme value) {
1424 this.annotationColours = value;
1428 * Gets the value of the start property.
1431 * possible object is
1435 public Integer getStart() {
1440 * Sets the value of the start property.
1447 public void setStart(Integer value) {
1452 * Gets the value of the end property.
1455 * possible object is
1459 public Integer getEnd() {
1464 * Sets the value of the end property.
1471 public void setEnd(Integer value) {
1476 * Gets the value of the name property.
1479 * possible object is
1483 public String getName() {
1488 * Sets the value of the name property.
1495 public void setName(String value) {
1500 * Gets the value of the colour property.
1503 * possible object is
1507 public String getColour() {
1512 * Sets the value of the colour property.
1519 public void setColour(String value) {
1520 this.colour = value;
1524 * Gets the value of the consThreshold property.
1527 * possible object is
1531 public Integer getConsThreshold() {
1532 return consThreshold;
1536 * Sets the value of the consThreshold property.
1543 public void setConsThreshold(Integer value) {
1544 this.consThreshold = value;
1548 * Gets the value of the pidThreshold property.
1551 * possible object is
1555 public Integer getPidThreshold() {
1556 return pidThreshold;
1560 * Sets the value of the pidThreshold property.
1567 public void setPidThreshold(Integer value) {
1568 this.pidThreshold = value;
1572 * Gets the value of the outlineColour property.
1575 * possible object is
1579 public Integer getOutlineColour() {
1580 return outlineColour;
1584 * Sets the value of the outlineColour property.
1591 public void setOutlineColour(Integer value) {
1592 this.outlineColour = value;
1596 * Gets the value of the displayBoxes property.
1599 * possible object is
1603 public Boolean isDisplayBoxes() {
1604 return displayBoxes;
1608 * Sets the value of the displayBoxes property.
1615 public void setDisplayBoxes(Boolean value) {
1616 this.displayBoxes = value;
1620 * Gets the value of the displayText property.
1623 * possible object is
1627 public Boolean isDisplayText() {
1632 * Sets the value of the displayText property.
1639 public void setDisplayText(Boolean value) {
1640 this.displayText = value;
1644 * Gets the value of the colourText property.
1647 * possible object is
1651 public Boolean isColourText() {
1656 * Sets the value of the colourText property.
1663 public void setColourText(Boolean value) {
1664 this.colourText = value;
1668 * Gets the value of the textCol1 property.
1671 * possible object is
1675 public Integer getTextCol1() {
1680 * Sets the value of the textCol1 property.
1687 public void setTextCol1(Integer value) {
1688 this.textCol1 = value;
1692 * Gets the value of the textCol2 property.
1695 * possible object is
1699 public Integer getTextCol2() {
1704 * Sets the value of the textCol2 property.
1711 public void setTextCol2(Integer value) {
1712 this.textCol2 = value;
1716 * Gets the value of the textColThreshold property.
1719 * possible object is
1723 public Integer getTextColThreshold() {
1724 return textColThreshold;
1728 * Sets the value of the textColThreshold property.
1735 public void setTextColThreshold(Integer value) {
1736 this.textColThreshold = value;
1740 * Gets the value of the showUnconserved property.
1743 * possible object is
1747 public Boolean isShowUnconserved() {
1748 return showUnconserved;
1752 * Sets the value of the showUnconserved property.
1759 public void setShowUnconserved(Boolean value) {
1760 this.showUnconserved = value;
1764 * Gets the value of the ignoreGapsinConsensus property.
1767 * possible object is
1771 public boolean isIgnoreGapsinConsensus() {
1772 if (ignoreGapsinConsensus == null) {
1775 return ignoreGapsinConsensus;
1780 * Sets the value of the ignoreGapsinConsensus property.
1787 public void setIgnoreGapsinConsensus(Boolean value) {
1788 this.ignoreGapsinConsensus = value;
1792 * Gets the value of the showConsensusHistogram property.
1795 * possible object is
1799 public boolean isShowConsensusHistogram() {
1800 if (showConsensusHistogram == null) {
1803 return showConsensusHistogram;
1808 * Sets the value of the showConsensusHistogram property.
1815 public void setShowConsensusHistogram(Boolean value) {
1816 this.showConsensusHistogram = value;
1820 * Gets the value of the showSequenceLogo property.
1823 * possible object is
1827 public boolean isShowSequenceLogo() {
1828 if (showSequenceLogo == null) {
1831 return showSequenceLogo;
1836 * Sets the value of the showSequenceLogo property.
1843 public void setShowSequenceLogo(Boolean value) {
1844 this.showSequenceLogo = value;
1848 * Gets the value of the normaliseSequenceLogo property.
1851 * possible object is
1855 public boolean isNormaliseSequenceLogo() {
1856 if (normaliseSequenceLogo == null) {
1859 return normaliseSequenceLogo;
1864 * Sets the value of the normaliseSequenceLogo property.
1871 public void setNormaliseSequenceLogo(Boolean value) {
1872 this.normaliseSequenceLogo = value;
1876 * Gets the value of the id property.
1879 * possible object is
1883 public String getId() {
1888 * Sets the value of the id property.
1895 public void setId(String value) {
1903 * <p>Java class for anonymous complex type.
1905 * <p>The following schema fragment specifies the expected content contained within this class.
1908 * &lt;complexType&gt;
1909 * &lt;complexContent&gt;
1910 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1911 * &lt;sequence&gt;
1912 * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
1913 * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
1914 * &lt;complexType&gt;
1915 * &lt;complexContent&gt;
1916 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
1917 * &lt;sequence&gt;
1918 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
1919 * &lt;complexType&gt;
1920 * &lt;simpleContent&gt;
1921 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
1922 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
1923 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1924 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1925 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1926 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1927 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1928 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1929 * &lt;/extension&gt;
1930 * &lt;/simpleContent&gt;
1931 * &lt;/complexType&gt;
1932 * &lt;/element&gt;
1933 * &lt;/sequence&gt;
1934 * &lt;/extension&gt;
1935 * &lt;/complexContent&gt;
1936 * &lt;/complexType&gt;
1937 * &lt;/element&gt;
1938 * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
1939 * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
1940 * &lt;complexType&gt;
1941 * &lt;complexContent&gt;
1942 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1943 * &lt;sequence&gt;
1944 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
1945 * &lt;complexType&gt;
1946 * &lt;complexContent&gt;
1947 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1948 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1949 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1950 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1951 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1952 * &lt;/restriction&gt;
1953 * &lt;/complexContent&gt;
1954 * &lt;/complexType&gt;
1955 * &lt;/element&gt;
1956 * &lt;/sequence&gt;
1957 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
1958 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1959 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1960 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1961 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1962 * &lt;/restriction&gt;
1963 * &lt;/complexContent&gt;
1964 * &lt;/complexType&gt;
1965 * &lt;/element&gt;
1966 * &lt;/sequence&gt;
1967 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1968 * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1969 * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1970 * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1971 * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1972 * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1973 * &lt;/restriction&gt;
1974 * &lt;/complexContent&gt;
1975 * &lt;/complexType&gt;
1980 @XmlAccessorType(XmlAccessType.FIELD)
1981 @XmlType(name = "", propOrder = {
1987 public static class JSeq {
1989 @XmlElement(namespace = "www.jalview.org")
1990 protected List<Feature> features;
1991 @XmlElement(namespace = "www.jalview.org")
1992 protected List<JalviewModel.JSeq.Pdbids> pdbids;
1993 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1994 protected List<Integer> hiddenSequences;
1995 @XmlElement(namespace = "www.jalview.org")
1996 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1997 @XmlAttribute(name = "colour")
1998 protected Integer colour;
1999 @XmlAttribute(name = "start", required = true)
2000 protected int start;
2001 @XmlAttribute(name = "end", required = true)
2003 @XmlAttribute(name = "id", required = true)
2004 protected String id;
2005 @XmlAttribute(name = "hidden")
2006 protected Boolean hidden;
2007 @XmlAttribute(name = "viewreference")
2008 protected Boolean viewreference;
2011 * Gets the value of the features property.
2014 * This accessor method returns a reference to the live list,
2015 * not a snapshot. Therefore any modification you make to the
2016 * returned list will be present inside the JAXB object.
2017 * This is why there is not a <CODE>set</CODE> method for the features property.
2020 * For example, to add a new item, do as follows:
2022 * getFeatures().add(newItem);
2027 * Objects of the following type(s) are allowed in the list
2032 public List<Feature> getFeatures() {
2033 if (features == null) {
2034 features = new ArrayList<Feature>();
2036 return this.features;
2040 * Gets the value of the pdbids property.
2043 * This accessor method returns a reference to the live list,
2044 * not a snapshot. Therefore any modification you make to the
2045 * returned list will be present inside the JAXB object.
2046 * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2049 * For example, to add a new item, do as follows:
2051 * getPdbids().add(newItem);
2056 * Objects of the following type(s) are allowed in the list
2057 * {@link JalviewModel.JSeq.Pdbids }
2061 public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2062 if (pdbids == null) {
2063 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2069 * Gets the value of the hiddenSequences property.
2072 * This accessor method returns a reference to the live list,
2073 * not a snapshot. Therefore any modification you make to the
2074 * returned list will be present inside the JAXB object.
2075 * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2078 * For example, to add a new item, do as follows:
2080 * getHiddenSequences().add(newItem);
2085 * Objects of the following type(s) are allowed in the list
2090 public List<Integer> getHiddenSequences() {
2091 if (hiddenSequences == null) {
2092 hiddenSequences = new ArrayList<Integer>();
2094 return this.hiddenSequences;
2098 * Gets the value of the rnaViewer property.
2101 * This accessor method returns a reference to the live list,
2102 * not a snapshot. Therefore any modification you make to the
2103 * returned list will be present inside the JAXB object.
2104 * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2107 * For example, to add a new item, do as follows:
2109 * getRnaViewer().add(newItem);
2114 * Objects of the following type(s) are allowed in the list
2115 * {@link JalviewModel.JSeq.RnaViewer }
2119 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2120 if (rnaViewer == null) {
2121 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2123 return this.rnaViewer;
2127 * Gets the value of the colour property.
2130 * possible object is
2134 public Integer getColour() {
2139 * Sets the value of the colour property.
2146 public void setColour(Integer value) {
2147 this.colour = value;
2151 * Gets the value of the start property.
2154 public int getStart() {
2159 * Sets the value of the start property.
2162 public void setStart(int value) {
2167 * Gets the value of the end property.
2170 public int getEnd() {
2175 * Sets the value of the end property.
2178 public void setEnd(int value) {
2183 * Gets the value of the id property.
2186 * possible object is
2190 public String getId() {
2195 * Sets the value of the id property.
2202 public void setId(String value) {
2207 * Gets the value of the hidden property.
2210 * possible object is
2214 public Boolean isHidden() {
2219 * Sets the value of the hidden property.
2226 public void setHidden(Boolean value) {
2227 this.hidden = value;
2231 * Gets the value of the viewreference property.
2234 * possible object is
2238 public Boolean isViewreference() {
2239 return viewreference;
2243 * Sets the value of the viewreference property.
2250 public void setViewreference(Boolean value) {
2251 this.viewreference = value;
2256 * <p>Java class for anonymous complex type.
2258 * <p>The following schema fragment specifies the expected content contained within this class.
2261 * &lt;complexType&gt;
2262 * &lt;complexContent&gt;
2263 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
2264 * &lt;sequence&gt;
2265 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
2266 * &lt;complexType&gt;
2267 * &lt;simpleContent&gt;
2268 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2269 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2270 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2271 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2272 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2273 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2274 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2275 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2276 * &lt;/extension&gt;
2277 * &lt;/simpleContent&gt;
2278 * &lt;/complexType&gt;
2279 * &lt;/element&gt;
2280 * &lt;/sequence&gt;
2281 * &lt;/extension&gt;
2282 * &lt;/complexContent&gt;
2283 * &lt;/complexType&gt;
2288 @XmlAccessorType(XmlAccessType.FIELD)
2289 @XmlType(name = "", propOrder = {
2292 public static class Pdbids
2296 @XmlElement(namespace = "www.jalview.org")
2297 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2300 * Gets the value of the structureState property.
2303 * This accessor method returns a reference to the live list,
2304 * not a snapshot. Therefore any modification you make to the
2305 * returned list will be present inside the JAXB object.
2306 * This is why there is not a <CODE>set</CODE> method for the structureState property.
2309 * For example, to add a new item, do as follows:
2311 * getStructureState().add(newItem);
2316 * Objects of the following type(s) are allowed in the list
2317 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2321 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2322 if (structureState == null) {
2323 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2325 return this.structureState;
2330 * <p>Java class for anonymous complex type.
2332 * <p>The following schema fragment specifies the expected content contained within this class.
2335 * &lt;complexType&gt;
2336 * &lt;simpleContent&gt;
2337 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2338 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2339 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2340 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2341 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2342 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2343 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2344 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2345 * &lt;/extension&gt;
2346 * &lt;/simpleContent&gt;
2347 * &lt;/complexType&gt;
2352 @XmlAccessorType(XmlAccessType.FIELD)
2353 @XmlType(name = "", propOrder = {
2356 public static class StructureState {
2359 protected String value;
2360 @XmlAttribute(name = "visible")
2361 protected Boolean visible;
2362 @XmlAttribute(name = "viewId")
2363 protected String viewId;
2364 @XmlAttribute(name = "alignwithAlignPanel")
2365 protected Boolean alignwithAlignPanel;
2366 @XmlAttribute(name = "colourwithAlignPanel")
2367 protected Boolean colourwithAlignPanel;
2368 @XmlAttribute(name = "colourByJmol")
2369 protected Boolean colourByJmol;
2370 @XmlAttribute(name = "type")
2371 protected String type;
2372 @XmlAttribute(name = "width")
2373 protected Integer width;
2374 @XmlAttribute(name = "height")
2375 protected Integer height;
2376 @XmlAttribute(name = "xpos")
2377 protected Integer xpos;
2378 @XmlAttribute(name = "ypos")
2379 protected Integer ypos;
2382 * Gets the value of the value property.
2385 * possible object is
2389 public String getValue() {
2394 * Sets the value of the value property.
2401 public void setValue(String value) {
2406 * Gets the value of the visible property.
2409 * possible object is
2413 public Boolean isVisible() {
2418 * Sets the value of the visible property.
2425 public void setVisible(Boolean value) {
2426 this.visible = value;
2430 * Gets the value of the viewId property.
2433 * possible object is
2437 public String getViewId() {
2442 * Sets the value of the viewId property.
2449 public void setViewId(String value) {
2450 this.viewId = value;
2454 * Gets the value of the alignwithAlignPanel property.
2457 * possible object is
2461 public boolean isAlignwithAlignPanel() {
2462 if (alignwithAlignPanel == null) {
2465 return alignwithAlignPanel;
2470 * Sets the value of the alignwithAlignPanel property.
2477 public void setAlignwithAlignPanel(Boolean value) {
2478 this.alignwithAlignPanel = value;
2482 * Gets the value of the colourwithAlignPanel property.
2485 * possible object is
2489 public boolean isColourwithAlignPanel() {
2490 if (colourwithAlignPanel == null) {
2493 return colourwithAlignPanel;
2498 * Sets the value of the colourwithAlignPanel property.
2505 public void setColourwithAlignPanel(Boolean value) {
2506 this.colourwithAlignPanel = value;
2510 * Gets the value of the colourByJmol property.
2513 * possible object is
2517 public boolean isColourByJmol() {
2518 if (colourByJmol == null) {
2521 return colourByJmol;
2526 * Sets the value of the colourByJmol property.
2533 public void setColourByJmol(Boolean value) {
2534 this.colourByJmol = value;
2538 * Gets the value of the type property.
2541 * possible object is
2545 public String getType() {
2550 * Sets the value of the type property.
2557 public void setType(String value) {
2562 * Gets the value of the width property.
2565 * possible object is
2569 public Integer getWidth() {
2574 * Sets the value of the width property.
2581 public void setWidth(Integer value) {
2586 * Gets the value of the height property.
2589 * possible object is
2593 public Integer getHeight() {
2598 * Sets the value of the height property.
2605 public void setHeight(Integer value) {
2606 this.height = value;
2610 * Gets the value of the xpos property.
2613 * possible object is
2617 public Integer getXpos() {
2622 * Sets the value of the xpos property.
2629 public void setXpos(Integer value) {
2634 * Gets the value of the ypos property.
2637 * possible object is
2641 public Integer getYpos() {
2646 * Sets the value of the ypos property.
2653 public void setYpos(Integer value) {
2663 * <p>Java class for anonymous complex type.
2665 * <p>The following schema fragment specifies the expected content contained within this class.
2668 * &lt;complexType&gt;
2669 * &lt;complexContent&gt;
2670 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2671 * &lt;sequence&gt;
2672 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
2673 * &lt;complexType&gt;
2674 * &lt;complexContent&gt;
2675 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2676 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2677 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2678 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2679 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2680 * &lt;/restriction&gt;
2681 * &lt;/complexContent&gt;
2682 * &lt;/complexType&gt;
2683 * &lt;/element&gt;
2684 * &lt;/sequence&gt;
2685 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2686 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2687 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2688 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2689 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2690 * &lt;/restriction&gt;
2691 * &lt;/complexContent&gt;
2692 * &lt;/complexType&gt;
2697 @XmlAccessorType(XmlAccessType.FIELD)
2698 @XmlType(name = "", propOrder = {
2699 "secondaryStructure"
2701 public static class RnaViewer {
2703 @XmlElement(namespace = "www.jalview.org", required = true)
2704 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2705 @XmlAttribute(name = "title")
2706 protected String title;
2707 @XmlAttribute(name = "viewId")
2708 protected String viewId;
2709 @XmlAttribute(name = "dividerLocation")
2710 protected Integer dividerLocation;
2711 @XmlAttribute(name = "selectedRna")
2712 protected Integer selectedRna;
2713 @XmlAttribute(name = "width")
2714 protected Integer width;
2715 @XmlAttribute(name = "height")
2716 protected Integer height;
2717 @XmlAttribute(name = "xpos")
2718 protected Integer xpos;
2719 @XmlAttribute(name = "ypos")
2720 protected Integer ypos;
2723 * Gets the value of the secondaryStructure property.
2726 * This accessor method returns a reference to the live list,
2727 * not a snapshot. Therefore any modification you make to the
2728 * returned list will be present inside the JAXB object.
2729 * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2732 * For example, to add a new item, do as follows:
2734 * getSecondaryStructure().add(newItem);
2739 * Objects of the following type(s) are allowed in the list
2740 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2744 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2745 if (secondaryStructure == null) {
2746 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2748 return this.secondaryStructure;
2752 * Gets the value of the title property.
2755 * possible object is
2759 public String getTitle() {
2764 * Sets the value of the title property.
2771 public void setTitle(String value) {
2776 * Gets the value of the viewId property.
2779 * possible object is
2783 public String getViewId() {
2788 * Sets the value of the viewId property.
2795 public void setViewId(String value) {
2796 this.viewId = value;
2800 * Gets the value of the dividerLocation property.
2803 * possible object is
2807 public Integer getDividerLocation() {
2808 return dividerLocation;
2812 * Sets the value of the dividerLocation property.
2819 public void setDividerLocation(Integer value) {
2820 this.dividerLocation = value;
2824 * Gets the value of the selectedRna property.
2827 * possible object is
2831 public Integer getSelectedRna() {
2836 * Sets the value of the selectedRna property.
2843 public void setSelectedRna(Integer value) {
2844 this.selectedRna = value;
2848 * Gets the value of the width property.
2851 * possible object is
2855 public Integer getWidth() {
2860 * Sets the value of the width property.
2867 public void setWidth(Integer value) {
2872 * Gets the value of the height property.
2875 * possible object is
2879 public Integer getHeight() {
2884 * Sets the value of the height property.
2891 public void setHeight(Integer value) {
2892 this.height = value;
2896 * Gets the value of the xpos property.
2899 * possible object is
2903 public Integer getXpos() {
2908 * Sets the value of the xpos property.
2915 public void setXpos(Integer value) {
2920 * Gets the value of the ypos property.
2923 * possible object is
2927 public Integer getYpos() {
2932 * Sets the value of the ypos property.
2939 public void setYpos(Integer value) {
2945 * <p>Java class for anonymous complex type.
2947 * <p>The following schema fragment specifies the expected content contained within this class.
2950 * &lt;complexType&gt;
2951 * &lt;complexContent&gt;
2952 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2953 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2954 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2955 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2956 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2957 * &lt;/restriction&gt;
2958 * &lt;/complexContent&gt;
2959 * &lt;/complexType&gt;
2964 @XmlAccessorType(XmlAccessType.FIELD)
2966 public static class SecondaryStructure {
2968 @XmlAttribute(name = "title")
2969 protected String title;
2970 @XmlAttribute(name = "annotationId", required = true)
2971 protected String annotationId;
2972 @XmlAttribute(name = "gapped")
2973 protected Boolean gapped;
2974 @XmlAttribute(name = "viewerState")
2975 protected String viewerState;
2978 * Gets the value of the title property.
2981 * possible object is
2985 public String getTitle() {
2990 * Sets the value of the title property.
2997 public void setTitle(String value) {
3002 * Gets the value of the annotationId property.
3005 * possible object is
3009 public String getAnnotationId() {
3010 return annotationId;
3014 * Sets the value of the annotationId property.
3021 public void setAnnotationId(String value) {
3022 this.annotationId = value;
3026 * Gets the value of the gapped property.
3029 * possible object is
3033 public Boolean isGapped() {
3038 * Sets the value of the gapped property.
3045 public void setGapped(Boolean value) {
3046 this.gapped = value;
3050 * Gets the value of the viewerState property.
3053 * possible object is
3057 public String getViewerState() {
3062 * Sets the value of the viewerState property.
3069 public void setViewerState(String value) {
3070 this.viewerState = value;
3081 * <p>Java class for anonymous complex type.
3083 * <p>The following schema fragment specifies the expected content contained within this class.
3086 * &lt;complexType&gt;
3087 * &lt;complexContent&gt;
3088 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3089 * &lt;sequence&gt;
3090 * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
3091 * &lt;complexType&gt;
3092 * &lt;complexContent&gt;
3093 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3094 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3095 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3096 * &lt;/restriction&gt;
3097 * &lt;/complexContent&gt;
3098 * &lt;/complexType&gt;
3099 * &lt;/element&gt;
3100 * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
3101 * &lt;complexType&gt;
3102 * &lt;complexContent&gt;
3103 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3104 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3105 * &lt;/restriction&gt;
3106 * &lt;/complexContent&gt;
3107 * &lt;/complexType&gt;
3108 * &lt;/element&gt;
3109 * &lt;element name="seqPointMin"&gt;
3110 * &lt;complexType&gt;
3111 * &lt;complexContent&gt;
3112 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3113 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3114 * &lt;/restriction&gt;
3115 * &lt;/complexContent&gt;
3116 * &lt;/complexType&gt;
3117 * &lt;/element&gt;
3118 * &lt;element name="seqPointMax"&gt;
3119 * &lt;complexType&gt;
3120 * &lt;complexContent&gt;
3121 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3122 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3123 * &lt;/restriction&gt;
3124 * &lt;/complexContent&gt;
3125 * &lt;/complexType&gt;
3126 * &lt;/element&gt;
3127 * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
3128 * &lt;/sequence&gt;
3129 * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
3130 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
3131 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3132 * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3133 * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3134 * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3135 * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3136 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3137 * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
3138 * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3139 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3140 * &lt;/restriction&gt;
3141 * &lt;/complexContent&gt;
3142 * &lt;/complexType&gt;
3147 @XmlAccessorType(XmlAccessType.FIELD)
3148 @XmlType(name = "", propOrder = {
3155 public static class PcaViewer {
3157 @XmlElement(namespace = "www.jalview.org", required = true)
3158 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3159 @XmlElement(namespace = "www.jalview.org", required = true)
3160 protected List<JalviewModel.PcaViewer.Axis> axis;
3161 @XmlElement(namespace = "www.jalview.org", required = true)
3162 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3163 @XmlElement(namespace = "www.jalview.org", required = true)
3164 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3165 @XmlElement(namespace = "www.jalview.org", required = true)
3166 protected PcaDataType pcaData;
3167 @XmlAttribute(name = "title")
3168 protected String title;
3169 @XmlAttribute(name = "scoreModelName")
3170 protected String scoreModelName;
3171 @XmlAttribute(name = "xDim")
3172 protected Integer xDim;
3173 @XmlAttribute(name = "yDim")
3174 protected Integer yDim;
3175 @XmlAttribute(name = "zDim")
3176 protected Integer zDim;
3177 @XmlAttribute(name = "bgColour")
3178 protected Integer bgColour;
3179 @XmlAttribute(name = "scaleFactor")
3180 protected Float scaleFactor;
3181 @XmlAttribute(name = "showLabels")
3182 protected Boolean showLabels;
3183 @XmlAttribute(name = "linkToAllViews")
3184 protected Boolean linkToAllViews;
3185 @XmlAttribute(name = "includeGaps")
3186 protected Boolean includeGaps;
3187 @XmlAttribute(name = "matchGaps")
3188 protected Boolean matchGaps;
3189 @XmlAttribute(name = "includeGappedColumns")
3190 protected Boolean includeGappedColumns;
3191 @XmlAttribute(name = "denominateByShortestLength")
3192 protected Boolean denominateByShortestLength;
3193 @XmlAttribute(name = "width")
3194 protected Integer width;
3195 @XmlAttribute(name = "height")
3196 protected Integer height;
3197 @XmlAttribute(name = "xpos")
3198 protected Integer xpos;
3199 @XmlAttribute(name = "ypos")
3200 protected Integer ypos;
3203 * Gets the value of the sequencePoint property.
3206 * This accessor method returns a reference to the live list,
3207 * not a snapshot. Therefore any modification you make to the
3208 * returned list will be present inside the JAXB object.
3209 * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3212 * For example, to add a new item, do as follows:
3214 * getSequencePoint().add(newItem);
3219 * Objects of the following type(s) are allowed in the list
3220 * {@link JalviewModel.PcaViewer.SequencePoint }
3224 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3225 if (sequencePoint == null) {
3226 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3228 return this.sequencePoint;
3232 * Gets the value of the axis property.
3235 * This accessor method returns a reference to the live list,
3236 * not a snapshot. Therefore any modification you make to the
3237 * returned list will be present inside the JAXB object.
3238 * This is why there is not a <CODE>set</CODE> method for the axis property.
3241 * For example, to add a new item, do as follows:
3243 * getAxis().add(newItem);
3248 * Objects of the following type(s) are allowed in the list
3249 * {@link JalviewModel.PcaViewer.Axis }
3253 public List<JalviewModel.PcaViewer.Axis> getAxis() {
3255 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3261 * Gets the value of the seqPointMin property.
3264 * possible object is
3265 * {@link JalviewModel.PcaViewer.SeqPointMin }
3268 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3273 * Sets the value of the seqPointMin property.
3277 * {@link JalviewModel.PcaViewer.SeqPointMin }
3280 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3281 this.seqPointMin = value;
3285 * Gets the value of the seqPointMax property.
3288 * possible object is
3289 * {@link JalviewModel.PcaViewer.SeqPointMax }
3292 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3297 * Sets the value of the seqPointMax property.
3301 * {@link JalviewModel.PcaViewer.SeqPointMax }
3304 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3305 this.seqPointMax = value;
3309 * Gets the value of the pcaData property.
3312 * possible object is
3313 * {@link PcaDataType }
3316 public PcaDataType getPcaData() {
3321 * Sets the value of the pcaData property.
3325 * {@link PcaDataType }
3328 public void setPcaData(PcaDataType value) {
3329 this.pcaData = value;
3333 * Gets the value of the title property.
3336 * possible object is
3340 public String getTitle() {
3345 * Sets the value of the title property.
3352 public void setTitle(String value) {
3357 * Gets the value of the scoreModelName property.
3360 * possible object is
3364 public String getScoreModelName() {
3365 return scoreModelName;
3369 * Sets the value of the scoreModelName property.
3376 public void setScoreModelName(String value) {
3377 this.scoreModelName = value;
3381 * Gets the value of the xDim property.
3384 * possible object is
3388 public Integer getXDim() {
3393 * Sets the value of the xDim property.
3400 public void setXDim(Integer value) {
3405 * Gets the value of the yDim property.
3408 * possible object is
3412 public Integer getYDim() {
3417 * Sets the value of the yDim property.
3424 public void setYDim(Integer value) {
3429 * Gets the value of the zDim property.
3432 * possible object is
3436 public Integer getZDim() {
3441 * Sets the value of the zDim property.
3448 public void setZDim(Integer value) {
3453 * Gets the value of the bgColour property.
3456 * possible object is
3460 public Integer getBgColour() {
3465 * Sets the value of the bgColour property.
3472 public void setBgColour(Integer value) {
3473 this.bgColour = value;
3477 * Gets the value of the scaleFactor property.
3480 * possible object is
3484 public Float getScaleFactor() {
3489 * Sets the value of the scaleFactor property.
3496 public void setScaleFactor(Float value) {
3497 this.scaleFactor = value;
3501 * Gets the value of the showLabels property.
3504 * possible object is
3508 public Boolean isShowLabels() {
3513 * Sets the value of the showLabels property.
3520 public void setShowLabels(Boolean value) {
3521 this.showLabels = value;
3525 * Gets the value of the linkToAllViews property.
3528 * possible object is
3532 public Boolean isLinkToAllViews() {
3533 return linkToAllViews;
3537 * Sets the value of the linkToAllViews property.
3544 public void setLinkToAllViews(Boolean value) {
3545 this.linkToAllViews = value;
3549 * Gets the value of the includeGaps property.
3552 * possible object is
3556 public Boolean isIncludeGaps() {
3561 * Sets the value of the includeGaps property.
3568 public void setIncludeGaps(Boolean value) {
3569 this.includeGaps = value;
3573 * Gets the value of the matchGaps property.
3576 * possible object is
3580 public Boolean isMatchGaps() {
3585 * Sets the value of the matchGaps property.
3592 public void setMatchGaps(Boolean value) {
3593 this.matchGaps = value;
3597 * Gets the value of the includeGappedColumns property.
3600 * possible object is
3604 public Boolean isIncludeGappedColumns() {
3605 return includeGappedColumns;
3609 * Sets the value of the includeGappedColumns property.
3616 public void setIncludeGappedColumns(Boolean value) {
3617 this.includeGappedColumns = value;
3621 * Gets the value of the denominateByShortestLength property.
3624 * possible object is
3628 public Boolean isDenominateByShortestLength() {
3629 return denominateByShortestLength;
3633 * Sets the value of the denominateByShortestLength property.
3640 public void setDenominateByShortestLength(Boolean value) {
3641 this.denominateByShortestLength = value;
3645 * Gets the value of the width property.
3648 * possible object is
3652 public Integer getWidth() {
3657 * Sets the value of the width property.
3664 public void setWidth(Integer value) {
3669 * Gets the value of the height property.
3672 * possible object is
3676 public Integer getHeight() {
3681 * Sets the value of the height property.
3688 public void setHeight(Integer value) {
3689 this.height = value;
3693 * Gets the value of the xpos property.
3696 * possible object is
3700 public Integer getXpos() {
3705 * Sets the value of the xpos property.
3712 public void setXpos(Integer value) {
3717 * Gets the value of the ypos property.
3720 * possible object is
3724 public Integer getYpos() {
3729 * Sets the value of the ypos property.
3736 public void setYpos(Integer value) {
3742 * <p>Java class for anonymous complex type.
3744 * <p>The following schema fragment specifies the expected content contained within this class.
3747 * &lt;complexType&gt;
3748 * &lt;complexContent&gt;
3749 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3750 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3751 * &lt;/restriction&gt;
3752 * &lt;/complexContent&gt;
3753 * &lt;/complexType&gt;
3758 @XmlAccessorType(XmlAccessType.FIELD)
3760 public static class Axis {
3762 @XmlAttribute(name = "xPos")
3763 protected Float xPos;
3764 @XmlAttribute(name = "yPos")
3765 protected Float yPos;
3766 @XmlAttribute(name = "zPos")
3767 protected Float zPos;
3770 * Gets the value of the xPos property.
3773 * possible object is
3777 public Float getXPos() {
3782 * Sets the value of the xPos property.
3789 public void setXPos(Float value) {
3794 * Gets the value of the yPos property.
3797 * possible object is
3801 public Float getYPos() {
3806 * Sets the value of the yPos property.
3813 public void setYPos(Float value) {
3818 * Gets the value of the zPos property.
3821 * possible object is
3825 public Float getZPos() {
3830 * Sets the value of the zPos property.
3837 public void setZPos(Float value) {
3845 * <p>Java class for anonymous complex type.
3847 * <p>The following schema fragment specifies the expected content contained within this class.
3850 * &lt;complexType&gt;
3851 * &lt;complexContent&gt;
3852 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3853 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3854 * &lt;/restriction&gt;
3855 * &lt;/complexContent&gt;
3856 * &lt;/complexType&gt;
3861 @XmlAccessorType(XmlAccessType.FIELD)
3863 public static class SeqPointMax {
3865 @XmlAttribute(name = "xPos")
3866 protected Float xPos;
3867 @XmlAttribute(name = "yPos")
3868 protected Float yPos;
3869 @XmlAttribute(name = "zPos")
3870 protected Float zPos;
3873 * Gets the value of the xPos property.
3876 * possible object is
3880 public Float getXPos() {
3885 * Sets the value of the xPos property.
3892 public void setXPos(Float value) {
3897 * Gets the value of the yPos property.
3900 * possible object is
3904 public Float getYPos() {
3909 * Sets the value of the yPos property.
3916 public void setYPos(Float value) {
3921 * Gets the value of the zPos property.
3924 * possible object is
3928 public Float getZPos() {
3933 * Sets the value of the zPos property.
3940 public void setZPos(Float value) {
3948 * <p>Java class for anonymous complex type.
3950 * <p>The following schema fragment specifies the expected content contained within this class.
3953 * &lt;complexType&gt;
3954 * &lt;complexContent&gt;
3955 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3956 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3957 * &lt;/restriction&gt;
3958 * &lt;/complexContent&gt;
3959 * &lt;/complexType&gt;
3964 @XmlAccessorType(XmlAccessType.FIELD)
3966 public static class SeqPointMin {
3968 @XmlAttribute(name = "xPos")
3969 protected Float xPos;
3970 @XmlAttribute(name = "yPos")
3971 protected Float yPos;
3972 @XmlAttribute(name = "zPos")
3973 protected Float zPos;
3976 * Gets the value of the xPos property.
3979 * possible object is
3983 public Float getXPos() {
3988 * Sets the value of the xPos property.
3995 public void setXPos(Float value) {
4000 * Gets the value of the yPos property.
4003 * possible object is
4007 public Float getYPos() {
4012 * Sets the value of the yPos property.
4019 public void setYPos(Float value) {
4024 * Gets the value of the zPos property.
4027 * possible object is
4031 public Float getZPos() {
4036 * Sets the value of the zPos property.
4043 public void setZPos(Float value) {
4051 * <p>Java class for anonymous complex type.
4053 * <p>The following schema fragment specifies the expected content contained within this class.
4056 * &lt;complexType&gt;
4057 * &lt;complexContent&gt;
4058 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4059 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
4060 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4061 * &lt;/restriction&gt;
4062 * &lt;/complexContent&gt;
4063 * &lt;/complexType&gt;
4068 @XmlAccessorType(XmlAccessType.FIELD)
4070 public static class SequencePoint {
4072 @XmlAttribute(name = "sequenceRef")
4073 protected String sequenceRef;
4074 @XmlAttribute(name = "xPos")
4075 protected Float xPos;
4076 @XmlAttribute(name = "yPos")
4077 protected Float yPos;
4078 @XmlAttribute(name = "zPos")
4079 protected Float zPos;
4082 * Gets the value of the sequenceRef property.
4085 * possible object is
4089 public String getSequenceRef() {
4094 * Sets the value of the sequenceRef property.
4101 public void setSequenceRef(String value) {
4102 this.sequenceRef = value;
4106 * Gets the value of the xPos property.
4109 * possible object is
4113 public Float getXPos() {
4118 * Sets the value of the xPos property.
4125 public void setXPos(Float value) {
4130 * Gets the value of the yPos property.
4133 * possible object is
4137 public Float getYPos() {
4142 * Sets the value of the yPos property.
4149 public void setYPos(Float value) {
4154 * Gets the value of the zPos property.
4157 * possible object is
4161 public Float getZPos() {
4166 * Sets the value of the zPos property.
4173 public void setZPos(Float value) {
4183 * <p>Java class for anonymous complex type.
4185 * <p>The following schema fragment specifies the expected content contained within this class.
4188 * &lt;complexType&gt;
4189 * &lt;complexContent&gt;
4190 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4191 * &lt;sequence minOccurs="0"&gt;
4192 * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4193 * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4194 * &lt;/sequence&gt;
4195 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4196 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4197 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4198 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4199 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
4200 * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4201 * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4202 * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4203 * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4204 * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4205 * &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4206 * &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4207 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4208 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4209 * &lt;/restriction&gt;
4210 * &lt;/complexContent&gt;
4211 * &lt;/complexType&gt;
4216 @XmlAccessorType(XmlAccessType.FIELD)
4217 @XmlType(name = "", propOrder = {
4221 public static class Tree {
4223 @XmlElement(namespace = "www.jalview.org")
4224 protected String title;
4225 @XmlElement(namespace = "www.jalview.org")
4226 protected String newick;
4227 @XmlAttribute(name = "fontName")
4228 protected String fontName;
4229 @XmlAttribute(name = "fontSize")
4230 protected Integer fontSize;
4231 @XmlAttribute(name = "fontStyle")
4232 protected Integer fontStyle;
4233 @XmlAttribute(name = "threshold")
4234 protected Float threshold;
4235 @XmlAttribute(name = "showBootstrap")
4236 protected Boolean showBootstrap;
4237 @XmlAttribute(name = "showDistances")
4238 protected Boolean showDistances;
4239 @XmlAttribute(name = "markUnlinked")
4240 protected Boolean markUnlinked;
4241 @XmlAttribute(name = "fitToWindow")
4242 protected Boolean fitToWindow;
4243 @XmlAttribute(name = "currentTree")
4244 protected Boolean currentTree;
4245 @XmlAttribute(name = "columnWise")
4246 protected Boolean columnWise;
4247 @XmlAttribute(name = "columnReference")
4248 protected String columnReference;
4249 @XmlAttribute(name = "id")
4250 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4252 @XmlSchemaType(name = "ID")
4253 protected String id;
4254 @XmlAttribute(name = "linkToAllViews")
4255 protected Boolean linkToAllViews;
4256 @XmlAttribute(name = "width")
4257 protected Integer width;
4258 @XmlAttribute(name = "height")
4259 protected Integer height;
4260 @XmlAttribute(name = "xpos")
4261 protected Integer xpos;
4262 @XmlAttribute(name = "ypos")
4263 protected Integer ypos;
4266 * Gets the value of the title property.
4269 * possible object is
4273 public String getTitle() {
4278 * Sets the value of the title property.
4285 public void setTitle(String value) {
4290 * Gets the value of the newick property.
4293 * possible object is
4297 public String getNewick() {
4302 * Sets the value of the newick property.
4309 public void setNewick(String value) {
4310 this.newick = value;
4314 * Gets the value of the fontName property.
4317 * possible object is
4321 public String getFontName() {
4326 * Sets the value of the fontName property.
4333 public void setFontName(String value) {
4334 this.fontName = value;
4338 * Gets the value of the fontSize property.
4341 * possible object is
4345 public Integer getFontSize() {
4350 * Sets the value of the fontSize property.
4357 public void setFontSize(Integer value) {
4358 this.fontSize = value;
4362 * Gets the value of the fontStyle property.
4365 * possible object is
4369 public Integer getFontStyle() {
4374 * Sets the value of the fontStyle property.
4381 public void setFontStyle(Integer value) {
4382 this.fontStyle = value;
4386 * Gets the value of the threshold property.
4389 * possible object is
4393 public Float getThreshold() {
4398 * Sets the value of the threshold property.
4405 public void setThreshold(Float value) {
4406 this.threshold = value;
4410 * Gets the value of the showBootstrap property.
4413 * possible object is
4417 public Boolean isShowBootstrap() {
4418 return showBootstrap;
4422 * Sets the value of the showBootstrap property.
4429 public void setShowBootstrap(Boolean value) {
4430 this.showBootstrap = value;
4434 * Gets the value of the showDistances property.
4437 * possible object is
4441 public Boolean isShowDistances() {
4442 return showDistances;
4446 * Sets the value of the showDistances property.
4453 public void setShowDistances(Boolean value) {
4454 this.showDistances = value;
4458 * Gets the value of the markUnlinked property.
4461 * possible object is
4465 public Boolean isMarkUnlinked() {
4466 return markUnlinked;
4470 * Sets the value of the markUnlinked property.
4477 public void setMarkUnlinked(Boolean value) {
4478 this.markUnlinked = value;
4482 * Gets the value of the fitToWindow property.
4485 * possible object is
4489 public Boolean isFitToWindow() {
4494 * Sets the value of the fitToWindow property.
4501 public void setFitToWindow(Boolean value) {
4502 this.fitToWindow = value;
4506 * Gets the value of the currentTree property.
4509 * possible object is
4513 public Boolean isCurrentTree() {
4518 * Sets the value of the currentTree property.
4525 public void setCurrentTree(Boolean value) {
4526 this.currentTree = value;
4530 * Gets the value of the columnWise property.
4533 * possible object is
4537 public boolean isColumnWise() {
4538 if (columnWise == null) {
4546 * Sets the value of the columnWise property.
4553 public void setColumnWise(Boolean value) {
4554 this.columnWise = value;
4558 * Gets the value of the columnReference property.
4561 * possible object is
4565 public String getColumnReference() {
4566 return columnReference;
4570 * Sets the value of the columnReference property.
4577 public void setColumnReference(String value) {
4578 this.columnReference = value;
4582 * Gets the value of the id property.
4585 * possible object is
4589 public String getId() {
4594 * Sets the value of the id property.
4601 public void setId(String value) {
4606 * Gets the value of the linkToAllViews property.
4609 * possible object is
4613 public boolean isLinkToAllViews() {
4614 if (linkToAllViews == null) {
4617 return linkToAllViews;
4622 * Sets the value of the linkToAllViews property.
4629 public void setLinkToAllViews(Boolean value) {
4630 this.linkToAllViews = value;
4634 * Gets the value of the width property.
4637 * possible object is
4641 public Integer getWidth() {
4646 * Sets the value of the width property.
4653 public void setWidth(Integer value) {
4658 * Gets the value of the height property.
4661 * possible object is
4665 public Integer getHeight() {
4670 * Sets the value of the height property.
4677 public void setHeight(Integer value) {
4678 this.height = value;
4682 * Gets the value of the xpos property.
4685 * possible object is
4689 public Integer getXpos() {
4694 * Sets the value of the xpos property.
4701 public void setXpos(Integer value) {
4706 * Gets the value of the ypos property.
4709 * possible object is
4713 public Integer getYpos() {
4718 * Sets the value of the ypos property.
4725 public void setYpos(Integer value) {
4733 * <p>Java class for anonymous complex type.
4735 * <p>The following schema fragment specifies the expected content contained within this class.
4738 * &lt;complexType&gt;
4739 * &lt;complexContent&gt;
4740 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4741 * &lt;sequence&gt;
4742 * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
4743 * &lt;/sequence&gt;
4744 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4745 * &lt;/restriction&gt;
4746 * &lt;/complexContent&gt;
4747 * &lt;/complexType&gt;
4752 @XmlAccessorType(XmlAccessType.FIELD)
4753 @XmlType(name = "", propOrder = {
4756 public static class UserColours {
4758 @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4759 protected JalviewUserColours userColourScheme;
4760 @XmlAttribute(name = "id")
4761 protected String id;
4764 * Gets the value of the userColourScheme property.
4767 * possible object is
4768 * {@link JalviewUserColours }
4771 public JalviewUserColours getUserColourScheme() {
4772 return userColourScheme;
4776 * Sets the value of the userColourScheme property.
4780 * {@link JalviewUserColours }
4783 public void setUserColourScheme(JalviewUserColours value) {
4784 this.userColourScheme = value;
4788 * Gets the value of the id property.
4791 * possible object is
4795 public String getId() {
4800 * Sets the value of the id property.
4807 public void setId(String value) {
4815 * <p>Java class for anonymous complex type.
4817 * <p>The following schema fragment specifies the expected content contained within this class.
4820 * &lt;complexType&gt;
4821 * &lt;complexContent&gt;
4822 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4823 * &lt;sequence&gt;
4824 * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
4825 * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
4826 * &lt;complexType&gt;
4827 * &lt;complexContent&gt;
4828 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4829 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4830 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4831 * &lt;/restriction&gt;
4832 * &lt;/complexContent&gt;
4833 * &lt;/complexType&gt;
4834 * &lt;/element&gt;
4835 * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
4836 * &lt;complexType&gt;
4837 * &lt;complexContent&gt;
4838 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
4839 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4840 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4841 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4842 * &lt;/extension&gt;
4843 * &lt;/complexContent&gt;
4844 * &lt;/complexType&gt;
4845 * &lt;/element&gt;
4846 * &lt;element name="overview" minOccurs="0"&gt;
4847 * &lt;complexType&gt;
4848 * &lt;complexContent&gt;
4849 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4850 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4851 * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4852 * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4853 * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4854 * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4855 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4856 * &lt;/restriction&gt;
4857 * &lt;/complexContent&gt;
4858 * &lt;/complexType&gt;
4859 * &lt;/element&gt;
4860 * &lt;/sequence&gt;
4861 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4862 * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4863 * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4864 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4865 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4866 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4867 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4868 * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4869 * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4870 * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4871 * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4872 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4873 * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4874 * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4875 * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4876 * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4877 * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4878 * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4879 * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4880 * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4881 * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4882 * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4883 * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4884 * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4885 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4886 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4887 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4888 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4889 * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4890 * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4891 * &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4892 * &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4893 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4894 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4895 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4896 * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4897 * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4898 * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4899 * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4900 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4901 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4902 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4903 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4904 * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4905 * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4906 * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4907 * &lt;/restriction&gt;
4908 * &lt;/complexContent&gt;
4909 * &lt;/complexType&gt;
4914 @XmlAccessorType(XmlAccessType.FIELD)
4915 @XmlType(name = "", propOrder = {
4916 "annotationColours",
4921 public static class Viewport {
4923 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4924 protected AnnotationColourScheme annotationColours;
4925 @XmlElement(namespace = "www.jalview.org")
4926 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4927 @XmlElement(namespace = "www.jalview.org")
4928 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4929 @XmlElement(namespace = "www.jalview.org")
4930 protected JalviewModel.Viewport.Overview overview;
4931 @XmlAttribute(name = "conservationSelected")
4932 protected Boolean conservationSelected;
4933 @XmlAttribute(name = "pidSelected")
4934 protected Boolean pidSelected;
4935 @XmlAttribute(name = "bgColour")
4936 protected String bgColour;
4937 @XmlAttribute(name = "consThreshold")
4938 protected Integer consThreshold;
4939 @XmlAttribute(name = "pidThreshold")
4940 protected Integer pidThreshold;
4941 @XmlAttribute(name = "title")
4942 protected String title;
4943 @XmlAttribute(name = "showFullId")
4944 protected Boolean showFullId;
4945 @XmlAttribute(name = "rightAlignIds")
4946 protected Boolean rightAlignIds;
4947 @XmlAttribute(name = "showText")
4948 protected Boolean showText;
4949 @XmlAttribute(name = "showColourText")
4950 protected Boolean showColourText;
4951 @XmlAttribute(name = "showUnconserved")
4952 protected Boolean showUnconserved;
4953 @XmlAttribute(name = "showBoxes")
4954 protected Boolean showBoxes;
4955 @XmlAttribute(name = "wrapAlignment")
4956 protected Boolean wrapAlignment;
4957 @XmlAttribute(name = "renderGaps")
4958 protected Boolean renderGaps;
4959 @XmlAttribute(name = "showSequenceFeatures")
4960 protected Boolean showSequenceFeatures;
4961 @XmlAttribute(name = "showNPfeatureTooltip")
4962 protected Boolean showNPfeatureTooltip;
4963 @XmlAttribute(name = "showDbRefTooltip")
4964 protected Boolean showDbRefTooltip;
4965 @XmlAttribute(name = "followHighlight")
4966 protected Boolean followHighlight;
4967 @XmlAttribute(name = "followSelection")
4968 protected Boolean followSelection;
4969 @XmlAttribute(name = "showAnnotation")
4970 protected Boolean showAnnotation;
4971 @XmlAttribute(name = "centreColumnLabels")
4972 protected Boolean centreColumnLabels;
4973 @XmlAttribute(name = "showGroupConservation")
4974 protected Boolean showGroupConservation;
4975 @XmlAttribute(name = "showGroupConsensus")
4976 protected Boolean showGroupConsensus;
4977 @XmlAttribute(name = "showConsensusHistogram")
4978 protected Boolean showConsensusHistogram;
4979 @XmlAttribute(name = "showSequenceLogo")
4980 protected Boolean showSequenceLogo;
4981 @XmlAttribute(name = "normaliseSequenceLogo")
4982 protected Boolean normaliseSequenceLogo;
4983 @XmlAttribute(name = "ignoreGapsinConsensus")
4984 protected Boolean ignoreGapsinConsensus;
4985 @XmlAttribute(name = "startRes")
4986 protected Integer startRes;
4987 @XmlAttribute(name = "startSeq")
4988 protected Integer startSeq;
4989 @XmlAttribute(name = "charWidth")
4990 protected Integer charWidth;
4991 @XmlAttribute(name = "charHeight")
4992 protected Integer charHeight;
4993 @XmlAttribute(name = "fontName")
4994 protected String fontName;
4995 @XmlAttribute(name = "fontSize")
4996 protected Integer fontSize;
4997 @XmlAttribute(name = "fontStyle")
4998 protected Integer fontStyle;
4999 @XmlAttribute(name = "scaleProteinAsCdna")
5000 protected Boolean scaleProteinAsCdna;
5001 @XmlAttribute(name = "viewName")
5002 protected String viewName;
5003 @XmlAttribute(name = "sequenceSetId")
5004 protected String sequenceSetId;
5005 @XmlAttribute(name = "gatheredViews")
5006 protected Boolean gatheredViews;
5007 @XmlAttribute(name = "textCol1")
5008 protected Integer textCol1;
5009 @XmlAttribute(name = "textCol2")
5010 protected Integer textCol2;
5011 @XmlAttribute(name = "textColThreshold")
5012 protected Integer textColThreshold;
5013 @XmlAttribute(name = "id")
5014 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5016 @XmlSchemaType(name = "ID")
5017 protected String id;
5018 @XmlAttribute(name = "complementId")
5019 protected String complementId;
5020 @XmlAttribute(name = "showComplementFeatures")
5021 protected Boolean showComplementFeatures;
5022 @XmlAttribute(name = "showComplementFeaturesOnTop")
5023 protected Boolean showComplementFeaturesOnTop;
5024 @XmlAttribute(name = "width")
5025 protected Integer width;
5026 @XmlAttribute(name = "height")
5027 protected Integer height;
5028 @XmlAttribute(name = "xpos")
5029 protected Integer xpos;
5030 @XmlAttribute(name = "ypos")
5031 protected Integer ypos;
5034 * Gets the value of the annotationColours property.
5037 * possible object is
5038 * {@link AnnotationColourScheme }
5041 public AnnotationColourScheme getAnnotationColours() {
5042 return annotationColours;
5046 * Sets the value of the annotationColours property.
5050 * {@link AnnotationColourScheme }
5053 public void setAnnotationColours(AnnotationColourScheme value) {
5054 this.annotationColours = value;
5058 * Gets the value of the hiddenColumns property.
5061 * This accessor method returns a reference to the live list,
5062 * not a snapshot. Therefore any modification you make to the
5063 * returned list will be present inside the JAXB object.
5064 * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
5067 * For example, to add a new item, do as follows:
5069 * getHiddenColumns().add(newItem);
5074 * Objects of the following type(s) are allowed in the list
5075 * {@link JalviewModel.Viewport.HiddenColumns }
5079 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5080 if (hiddenColumns == null) {
5081 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5083 return this.hiddenColumns;
5087 * Gets the value of the calcIdParam property.
5090 * This accessor method returns a reference to the live list,
5091 * not a snapshot. Therefore any modification you make to the
5092 * returned list will be present inside the JAXB object.
5093 * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5096 * For example, to add a new item, do as follows:
5098 * getCalcIdParam().add(newItem);
5103 * Objects of the following type(s) are allowed in the list
5104 * {@link JalviewModel.Viewport.CalcIdParam }
5108 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5109 if (calcIdParam == null) {
5110 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5112 return this.calcIdParam;
5116 * Gets the value of the overview property.
5119 * possible object is
5120 * {@link JalviewModel.Viewport.Overview }
5123 public JalviewModel.Viewport.Overview getOverview() {
5128 * Sets the value of the overview property.
5132 * {@link JalviewModel.Viewport.Overview }
5135 public void setOverview(JalviewModel.Viewport.Overview value) {
5136 this.overview = value;
5140 * Gets the value of the conservationSelected property.
5143 * possible object is
5147 public Boolean isConservationSelected() {
5148 return conservationSelected;
5152 * Sets the value of the conservationSelected property.
5159 public void setConservationSelected(Boolean value) {
5160 this.conservationSelected = value;
5164 * Gets the value of the pidSelected property.
5167 * possible object is
5171 public Boolean isPidSelected() {
5176 * Sets the value of the pidSelected property.
5183 public void setPidSelected(Boolean value) {
5184 this.pidSelected = value;
5188 * Gets the value of the bgColour property.
5191 * possible object is
5195 public String getBgColour() {
5200 * Sets the value of the bgColour property.
5207 public void setBgColour(String value) {
5208 this.bgColour = value;
5212 * Gets the value of the consThreshold property.
5215 * possible object is
5219 public Integer getConsThreshold() {
5220 return consThreshold;
5224 * Sets the value of the consThreshold property.
5231 public void setConsThreshold(Integer value) {
5232 this.consThreshold = value;
5236 * Gets the value of the pidThreshold property.
5239 * possible object is
5243 public Integer getPidThreshold() {
5244 return pidThreshold;
5248 * Sets the value of the pidThreshold property.
5255 public void setPidThreshold(Integer value) {
5256 this.pidThreshold = value;
5260 * Gets the value of the title property.
5263 * possible object is
5267 public String getTitle() {
5272 * Sets the value of the title property.
5279 public void setTitle(String value) {
5284 * Gets the value of the showFullId property.
5287 * possible object is
5291 public Boolean isShowFullId() {
5296 * Sets the value of the showFullId property.
5303 public void setShowFullId(Boolean value) {
5304 this.showFullId = value;
5308 * Gets the value of the rightAlignIds property.
5311 * possible object is
5315 public Boolean isRightAlignIds() {
5316 return rightAlignIds;
5320 * Sets the value of the rightAlignIds property.
5327 public void setRightAlignIds(Boolean value) {
5328 this.rightAlignIds = value;
5332 * Gets the value of the showText property.
5335 * possible object is
5339 public Boolean isShowText() {
5344 * Sets the value of the showText property.
5351 public void setShowText(Boolean value) {
5352 this.showText = value;
5356 * Gets the value of the showColourText property.
5359 * possible object is
5363 public Boolean isShowColourText() {
5364 return showColourText;
5368 * Sets the value of the showColourText property.
5375 public void setShowColourText(Boolean value) {
5376 this.showColourText = value;
5380 * Gets the value of the showUnconserved property.
5383 * possible object is
5387 public boolean isShowUnconserved() {
5388 if (showUnconserved == null) {
5391 return showUnconserved;
5396 * Sets the value of the showUnconserved property.
5403 public void setShowUnconserved(Boolean value) {
5404 this.showUnconserved = value;
5408 * Gets the value of the showBoxes property.
5411 * possible object is
5415 public Boolean isShowBoxes() {
5420 * Sets the value of the showBoxes property.
5427 public void setShowBoxes(Boolean value) {
5428 this.showBoxes = value;
5432 * Gets the value of the wrapAlignment property.
5435 * possible object is
5439 public Boolean isWrapAlignment() {
5440 return wrapAlignment;
5444 * Sets the value of the wrapAlignment property.
5451 public void setWrapAlignment(Boolean value) {
5452 this.wrapAlignment = value;
5456 * Gets the value of the renderGaps property.
5459 * possible object is
5463 public Boolean isRenderGaps() {
5468 * Sets the value of the renderGaps property.
5475 public void setRenderGaps(Boolean value) {
5476 this.renderGaps = value;
5480 * Gets the value of the showSequenceFeatures property.
5483 * possible object is
5487 public Boolean isShowSequenceFeatures() {
5488 return showSequenceFeatures;
5492 * Sets the value of the showSequenceFeatures property.
5499 public void setShowSequenceFeatures(Boolean value) {
5500 this.showSequenceFeatures = value;
5504 * Gets the value of the showNPfeatureTooltip property.
5507 * possible object is
5511 public Boolean isShowNPfeatureTooltip() {
5512 return showNPfeatureTooltip;
5516 * Sets the value of the showNPfeatureTooltip property.
5523 public void setShowNPfeatureTooltip(Boolean value) {
5524 this.showNPfeatureTooltip = value;
5528 * Gets the value of the showDbRefTooltip property.
5531 * possible object is
5535 public Boolean isShowDbRefTooltip() {
5536 return showDbRefTooltip;
5540 * Sets the value of the showDbRefTooltip property.
5547 public void setShowDbRefTooltip(Boolean value) {
5548 this.showDbRefTooltip = value;
5552 * Gets the value of the followHighlight property.
5555 * possible object is
5559 public boolean isFollowHighlight() {
5560 if (followHighlight == null) {
5563 return followHighlight;
5568 * Sets the value of the followHighlight property.
5575 public void setFollowHighlight(Boolean value) {
5576 this.followHighlight = value;
5580 * Gets the value of the followSelection property.
5583 * possible object is
5587 public boolean isFollowSelection() {
5588 if (followSelection == null) {
5591 return followSelection;
5596 * Sets the value of the followSelection property.
5603 public void setFollowSelection(Boolean value) {
5604 this.followSelection = value;
5608 * Gets the value of the showAnnotation property.
5611 * possible object is
5615 public Boolean isShowAnnotation() {
5616 return showAnnotation;
5620 * Sets the value of the showAnnotation property.
5627 public void setShowAnnotation(Boolean value) {
5628 this.showAnnotation = value;
5632 * Gets the value of the centreColumnLabels property.
5635 * possible object is
5639 public boolean isCentreColumnLabels() {
5640 if (centreColumnLabels == null) {
5643 return centreColumnLabels;
5648 * Sets the value of the centreColumnLabels property.
5655 public void setCentreColumnLabels(Boolean value) {
5656 this.centreColumnLabels = value;
5660 * Gets the value of the showGroupConservation property.
5663 * possible object is
5667 public boolean isShowGroupConservation() {
5668 if (showGroupConservation == null) {
5671 return showGroupConservation;
5676 * Sets the value of the showGroupConservation property.
5683 public void setShowGroupConservation(Boolean value) {
5684 this.showGroupConservation = value;
5688 * Gets the value of the showGroupConsensus property.
5691 * possible object is
5695 public boolean isShowGroupConsensus() {
5696 if (showGroupConsensus == null) {
5699 return showGroupConsensus;
5704 * Sets the value of the showGroupConsensus property.
5711 public void setShowGroupConsensus(Boolean value) {
5712 this.showGroupConsensus = value;
5716 * Gets the value of the showConsensusHistogram property.
5719 * possible object is
5723 public boolean isShowConsensusHistogram() {
5724 if (showConsensusHistogram == null) {
5727 return showConsensusHistogram;
5732 * Sets the value of the showConsensusHistogram property.
5739 public void setShowConsensusHistogram(Boolean value) {
5740 this.showConsensusHistogram = value;
5744 * Gets the value of the showSequenceLogo property.
5747 * possible object is
5751 public boolean isShowSequenceLogo() {
5752 if (showSequenceLogo == null) {
5755 return showSequenceLogo;
5760 * Sets the value of the showSequenceLogo property.
5767 public void setShowSequenceLogo(Boolean value) {
5768 this.showSequenceLogo = value;
5772 * Gets the value of the normaliseSequenceLogo property.
5775 * possible object is
5779 public boolean isNormaliseSequenceLogo() {
5780 if (normaliseSequenceLogo == null) {
5783 return normaliseSequenceLogo;
5788 * Sets the value of the normaliseSequenceLogo property.
5795 public void setNormaliseSequenceLogo(Boolean value) {
5796 this.normaliseSequenceLogo = value;
5800 * Gets the value of the ignoreGapsinConsensus property.
5803 * possible object is
5807 public boolean isIgnoreGapsinConsensus() {
5808 if (ignoreGapsinConsensus == null) {
5811 return ignoreGapsinConsensus;
5816 * Sets the value of the ignoreGapsinConsensus property.
5823 public void setIgnoreGapsinConsensus(Boolean value) {
5824 this.ignoreGapsinConsensus = value;
5828 * Gets the value of the startRes property.
5831 * possible object is
5835 public Integer getStartRes() {
5840 * Sets the value of the startRes property.
5847 public void setStartRes(Integer value) {
5848 this.startRes = value;
5852 * Gets the value of the startSeq property.
5855 * possible object is
5859 public Integer getStartSeq() {
5864 * Sets the value of the startSeq property.
5871 public void setStartSeq(Integer value) {
5872 this.startSeq = value;
5876 * Gets the value of the charWidth property.
5879 * possible object is
5883 public Integer getCharWidth() {
5888 * Sets the value of the charWidth property.
5895 public void setCharWidth(Integer value) {
5896 this.charWidth = value;
5900 * Gets the value of the charHeight property.
5903 * possible object is
5907 public Integer getCharHeight() {
5912 * Sets the value of the charHeight property.
5919 public void setCharHeight(Integer value) {
5920 this.charHeight = value;
5924 * Gets the value of the fontName property.
5927 * possible object is
5931 public String getFontName() {
5936 * Sets the value of the fontName property.
5943 public void setFontName(String value) {
5944 this.fontName = value;
5948 * Gets the value of the fontSize property.
5951 * possible object is
5955 public Integer getFontSize() {
5960 * Sets the value of the fontSize property.
5967 public void setFontSize(Integer value) {
5968 this.fontSize = value;
5972 * Gets the value of the fontStyle property.
5975 * possible object is
5979 public Integer getFontStyle() {
5984 * Sets the value of the fontStyle property.
5991 public void setFontStyle(Integer value) {
5992 this.fontStyle = value;
5996 * Gets the value of the scaleProteinAsCdna property.
5999 * possible object is
6003 public boolean isScaleProteinAsCdna() {
6004 if (scaleProteinAsCdna == null) {
6007 return scaleProteinAsCdna;
6012 * Sets the value of the scaleProteinAsCdna property.
6019 public void setScaleProteinAsCdna(Boolean value) {
6020 this.scaleProteinAsCdna = value;
6024 * Gets the value of the viewName property.
6027 * possible object is
6031 public String getViewName() {
6036 * Sets the value of the viewName property.
6043 public void setViewName(String value) {
6044 this.viewName = value;
6048 * Gets the value of the sequenceSetId property.
6051 * possible object is
6055 public String getSequenceSetId() {
6056 return sequenceSetId;
6060 * Sets the value of the sequenceSetId property.
6067 public void setSequenceSetId(String value) {
6068 this.sequenceSetId = value;
6072 * Gets the value of the gatheredViews property.
6075 * possible object is
6079 public Boolean isGatheredViews() {
6080 return gatheredViews;
6084 * Sets the value of the gatheredViews property.
6091 public void setGatheredViews(Boolean value) {
6092 this.gatheredViews = value;
6096 * Gets the value of the textCol1 property.
6099 * possible object is
6103 public Integer getTextCol1() {
6108 * Sets the value of the textCol1 property.
6115 public void setTextCol1(Integer value) {
6116 this.textCol1 = value;
6120 * Gets the value of the textCol2 property.
6123 * possible object is
6127 public Integer getTextCol2() {
6132 * Sets the value of the textCol2 property.
6139 public void setTextCol2(Integer value) {
6140 this.textCol2 = value;
6144 * Gets the value of the textColThreshold property.
6147 * possible object is
6151 public Integer getTextColThreshold() {
6152 return textColThreshold;
6156 * Sets the value of the textColThreshold property.
6163 public void setTextColThreshold(Integer value) {
6164 this.textColThreshold = value;
6168 * Gets the value of the id property.
6171 * possible object is
6175 public String getId() {
6180 * Sets the value of the id property.
6187 public void setId(String value) {
6192 * Gets the value of the complementId property.
6195 * possible object is
6199 public String getComplementId() {
6200 return complementId;
6204 * Sets the value of the complementId property.
6211 public void setComplementId(String value) {
6212 this.complementId = value;
6216 * Gets the value of the showComplementFeatures property.
6219 * possible object is
6223 public boolean isShowComplementFeatures() {
6224 if (showComplementFeatures == null) {
6227 return showComplementFeatures;
6232 * Sets the value of the showComplementFeatures property.
6239 public void setShowComplementFeatures(Boolean value) {
6240 this.showComplementFeatures = value;
6244 * Gets the value of the showComplementFeaturesOnTop property.
6247 * possible object is
6251 public boolean isShowComplementFeaturesOnTop() {
6252 if (showComplementFeaturesOnTop == null) {
6255 return showComplementFeaturesOnTop;
6260 * Sets the value of the showComplementFeaturesOnTop property.
6267 public void setShowComplementFeaturesOnTop(Boolean value) {
6268 this.showComplementFeaturesOnTop = value;
6272 * Gets the value of the width property.
6275 * possible object is
6279 public Integer getWidth() {
6284 * Sets the value of the width property.
6291 public void setWidth(Integer value) {
6296 * Gets the value of the height property.
6299 * possible object is
6303 public Integer getHeight() {
6308 * Sets the value of the height property.
6315 public void setHeight(Integer value) {
6316 this.height = value;
6320 * Gets the value of the xpos property.
6323 * possible object is
6327 public Integer getXpos() {
6332 * Sets the value of the xpos property.
6339 public void setXpos(Integer value) {
6344 * Gets the value of the ypos property.
6347 * possible object is
6351 public Integer getYpos() {
6356 * Sets the value of the ypos property.
6363 public void setYpos(Integer value) {
6369 * <p>Java class for anonymous complex type.
6371 * <p>The following schema fragment specifies the expected content contained within this class.
6374 * &lt;complexType&gt;
6375 * &lt;complexContent&gt;
6376 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
6377 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
6378 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
6379 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
6380 * &lt;/extension&gt;
6381 * &lt;/complexContent&gt;
6382 * &lt;/complexType&gt;
6387 @XmlAccessorType(XmlAccessType.FIELD)
6389 public static class CalcIdParam
6390 extends WebServiceParameterSet
6393 @XmlAttribute(name = "calcId", required = true)
6394 protected String calcId;
6395 @XmlAttribute(name = "needsUpdate")
6396 protected Boolean needsUpdate;
6397 @XmlAttribute(name = "autoUpdate", required = true)
6398 protected boolean autoUpdate;
6401 * Gets the value of the calcId property.
6404 * possible object is
6408 public String getCalcId() {
6413 * Sets the value of the calcId property.
6420 public void setCalcId(String value) {
6421 this.calcId = value;
6425 * Gets the value of the needsUpdate property.
6428 * possible object is
6432 public boolean isNeedsUpdate() {
6433 if (needsUpdate == null) {
6441 * Sets the value of the needsUpdate property.
6448 public void setNeedsUpdate(Boolean value) {
6449 this.needsUpdate = value;
6453 * Gets the value of the autoUpdate property.
6456 public boolean isAutoUpdate() {
6461 * Sets the value of the autoUpdate property.
6464 public void setAutoUpdate(boolean value) {
6465 this.autoUpdate = value;
6472 * <p>Java class for anonymous complex type.
6474 * <p>The following schema fragment specifies the expected content contained within this class.
6477 * &lt;complexType&gt;
6478 * &lt;complexContent&gt;
6479 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
6480 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6481 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6482 * &lt;/restriction&gt;
6483 * &lt;/complexContent&gt;
6484 * &lt;/complexType&gt;
6489 @XmlAccessorType(XmlAccessType.FIELD)
6491 public static class HiddenColumns {
6493 @XmlAttribute(name = "start")
6494 protected Integer start;
6495 @XmlAttribute(name = "end")
6496 protected Integer end;
6499 * Gets the value of the start property.
6502 * possible object is
6506 public Integer getStart() {
6511 * Sets the value of the start property.
6518 public void setStart(Integer value) {
6523 * Gets the value of the end property.
6526 * possible object is
6530 public Integer getEnd() {
6535 * Sets the value of the end property.
6542 public void setEnd(Integer value) {
6550 * <p>Java class for anonymous complex type.
6552 * <p>The following schema fragment specifies the expected content contained within this class.
6555 * &lt;complexType&gt;
6556 * &lt;complexContent&gt;
6557 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
6558 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
6559 * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
6560 * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6561 * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6562 * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6563 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
6564 * &lt;/restriction&gt;
6565 * &lt;/complexContent&gt;
6566 * &lt;/complexType&gt;
6571 @XmlAccessorType(XmlAccessType.FIELD)
6573 public static class Overview {
6575 @XmlAttribute(name = "showHidden")
6576 protected Boolean showHidden;
6577 @XmlAttribute(name = "residueColour")
6578 protected Integer residueColour;
6579 @XmlAttribute(name = "gapColour")
6580 protected Integer gapColour;
6581 @XmlAttribute(name = "hiddenColour")
6582 protected Integer hiddenColour;
6583 @XmlAttribute(name = "title")
6584 protected String title;
6585 @XmlAttribute(name = "width")
6586 protected Integer width;
6587 @XmlAttribute(name = "height")
6588 protected Integer height;
6589 @XmlAttribute(name = "xpos")
6590 protected Integer xpos;
6591 @XmlAttribute(name = "ypos")
6592 protected Integer ypos;
6595 * Gets the value of the showHidden property.
6598 * possible object is
6602 public Boolean isShowHidden() {
6607 * Sets the value of the showHidden property.
6614 public void setShowHidden(Boolean value) {
6615 this.showHidden = value;
6619 * Gets the value of the residueColour property.
6622 * possible object is
6626 public Integer getResidueColour() {
6627 return residueColour;
6631 * Sets the value of the residueColour property.
6638 public void setResidueColour(Integer value) {
6639 this.residueColour = value;
6643 * Gets the value of the gapColour property.
6646 * possible object is
6650 public Integer getGapColour() {
6655 * Sets the value of the gapColour property.
6662 public void setGapColour(Integer value) {
6663 this.gapColour = value;
6667 * Gets the value of the hiddenColour property.
6670 * possible object is
6674 public Integer getHiddenColour() {
6675 return hiddenColour;
6679 * Sets the value of the hiddenColour property.
6686 public void setHiddenColour(Integer value) {
6687 this.hiddenColour = value;
6691 * Gets the value of the title property.
6694 * possible object is
6698 public String getTitle() {
6703 * Sets the value of the title property.
6710 public void setTitle(String value) {
6715 * Gets the value of the width property.
6718 * possible object is
6722 public Integer getWidth() {
6727 * Sets the value of the width property.
6734 public void setWidth(Integer value) {
6739 * Gets the value of the height property.
6742 * possible object is
6746 public Integer getHeight() {
6751 * Sets the value of the height property.
6758 public void setHeight(Integer value) {
6759 this.height = value;
6763 * Gets the value of the xpos property.
6766 * possible object is
6770 public Integer getXpos() {
6775 * Sets the value of the xpos property.
6782 public void setXpos(Integer value) {
6787 * Gets the value of the ypos property.
6790 * possible object is
6794 public Integer getYpos() {
6799 * Sets the value of the ypos property.
6806 public void setYpos(Integer value) {