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: 2023.11.01 at 07:03:09 PM GMT
9 package jalview.xml.binding.jalview;
11 import java.util.ArrayList;
12 import java.util.List;
13 import javax.xml.bind.annotation.XmlAccessType;
14 import javax.xml.bind.annotation.XmlAccessorType;
15 import javax.xml.bind.annotation.XmlAttribute;
16 import javax.xml.bind.annotation.XmlElement;
17 import javax.xml.bind.annotation.XmlID;
18 import javax.xml.bind.annotation.XmlSchemaType;
19 import javax.xml.bind.annotation.XmlType;
20 import javax.xml.bind.annotation.XmlValue;
21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23 import javax.xml.datatype.XMLGregorianCalendar;
27 * <p>Java class for JalviewModel complex type.
29 * <p>The following schema fragment specifies the expected content contained within this class.
32 * &lt;complexType name="JalviewModel"&gt;
33 * &lt;complexContent&gt;
34 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
35 * &lt;sequence&gt;
36 * &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
37 * &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
38 * &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
39 * &lt;sequence&gt;
40 * &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
41 * &lt;complexType&gt;
42 * &lt;complexContent&gt;
43 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
44 * &lt;sequence&gt;
45 * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
46 * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
47 * &lt;complexType&gt;
48 * &lt;complexContent&gt;
49 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
50 * &lt;sequence&gt;
51 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
52 * &lt;complexType&gt;
53 * &lt;simpleContent&gt;
54 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
55 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
56 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
57 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
58 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
59 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
60 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
61 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
62 * &lt;/extension&gt;
63 * &lt;/simpleContent&gt;
64 * &lt;/complexType&gt;
65 * &lt;/element&gt;
66 * &lt;/sequence&gt;
67 * &lt;/extension&gt;
68 * &lt;/complexContent&gt;
69 * &lt;/complexType&gt;
70 * &lt;/element&gt;
71 * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
72 * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
73 * &lt;complexType&gt;
74 * &lt;complexContent&gt;
75 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
76 * &lt;sequence&gt;
77 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
78 * &lt;complexType&gt;
79 * &lt;complexContent&gt;
80 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
81 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
82 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
83 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
84 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
85 * &lt;/restriction&gt;
86 * &lt;/complexContent&gt;
87 * &lt;/complexType&gt;
88 * &lt;/element&gt;
89 * &lt;/sequence&gt;
90 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
91 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
92 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
93 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
94 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
95 * &lt;/restriction&gt;
96 * &lt;/complexContent&gt;
97 * &lt;/complexType&gt;
98 * &lt;/element&gt;
99 * &lt;/sequence&gt;
100 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
101 * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
102 * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
103 * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
104 * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
105 * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
106 * &lt;/restriction&gt;
107 * &lt;/complexContent&gt;
108 * &lt;/complexType&gt;
109 * &lt;/element&gt;
110 * &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
111 * &lt;complexType&gt;
112 * &lt;complexContent&gt;
113 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
114 * &lt;sequence&gt;
115 * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
116 * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
117 * &lt;/sequence&gt;
118 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
119 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
120 * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
121 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
122 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
123 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
124 * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
125 * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
126 * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
127 * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
128 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
129 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
130 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
131 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
132 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
133 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
134 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
135 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
136 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
137 * &lt;/restriction&gt;
138 * &lt;/complexContent&gt;
139 * &lt;/complexType&gt;
140 * &lt;/element&gt;
141 * &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
142 * &lt;complexType&gt;
143 * &lt;complexContent&gt;
144 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
145 * &lt;sequence&gt;
146 * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
147 * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
148 * &lt;complexType&gt;
149 * &lt;complexContent&gt;
150 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
151 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
152 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
153 * &lt;/restriction&gt;
154 * &lt;/complexContent&gt;
155 * &lt;/complexType&gt;
156 * &lt;/element&gt;
157 * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
158 * &lt;complexType&gt;
159 * &lt;complexContent&gt;
160 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
161 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
162 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
163 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
164 * &lt;/extension&gt;
165 * &lt;/complexContent&gt;
166 * &lt;/complexType&gt;
167 * &lt;/element&gt;
168 * &lt;element name="overview" minOccurs="0"&gt;
169 * &lt;complexType&gt;
170 * &lt;complexContent&gt;
171 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
172 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
173 * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
174 * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
175 * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
176 * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
177 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
178 * &lt;/restriction&gt;
179 * &lt;/complexContent&gt;
180 * &lt;/complexType&gt;
181 * &lt;/element&gt;
182 * &lt;/sequence&gt;
183 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
184 * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
185 * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
186 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
187 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
188 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
189 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
190 * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
191 * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
192 * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
193 * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
194 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
195 * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
196 * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
197 * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
198 * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
199 * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
200 * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
201 * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
202 * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
203 * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
204 * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
205 * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
206 * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
207 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
208 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
209 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
210 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
211 * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
212 * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
213 * &lt;attribute name="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="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
219 * &lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
220 * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
221 * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
222 * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
223 * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
224 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
225 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
226 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
227 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
228 * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
229 * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
230 * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
231 * &lt;/restriction&gt;
232 * &lt;/complexContent&gt;
233 * &lt;/complexType&gt;
234 * &lt;/element&gt;
235 * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
236 * &lt;complexType&gt;
237 * &lt;complexContent&gt;
238 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
239 * &lt;sequence&gt;
240 * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
241 * &lt;/sequence&gt;
242 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
243 * &lt;/restriction&gt;
244 * &lt;/complexContent&gt;
245 * &lt;/complexType&gt;
246 * &lt;/element&gt;
247 * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
248 * &lt;complexType&gt;
249 * &lt;complexContent&gt;
250 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
251 * &lt;sequence minOccurs="0"&gt;
252 * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
253 * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
254 * &lt;/sequence&gt;
255 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
256 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
257 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
258 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
259 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
260 * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
261 * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
262 * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
263 * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
264 * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
265 * &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
266 * &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
267 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
268 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
269 * &lt;/restriction&gt;
270 * &lt;/complexContent&gt;
271 * &lt;/complexType&gt;
272 * &lt;/element&gt;
273 * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
274 * &lt;complexType&gt;
275 * &lt;complexContent&gt;
276 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
277 * &lt;sequence&gt;
278 * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
279 * &lt;complexType&gt;
280 * &lt;complexContent&gt;
281 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
282 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
283 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
284 * &lt;/restriction&gt;
285 * &lt;/complexContent&gt;
286 * &lt;/complexType&gt;
287 * &lt;/element&gt;
288 * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
289 * &lt;complexType&gt;
290 * &lt;complexContent&gt;
291 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
292 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
293 * &lt;/restriction&gt;
294 * &lt;/complexContent&gt;
295 * &lt;/complexType&gt;
296 * &lt;/element&gt;
297 * &lt;element name="seqPointMin"&gt;
298 * &lt;complexType&gt;
299 * &lt;complexContent&gt;
300 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
301 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
302 * &lt;/restriction&gt;
303 * &lt;/complexContent&gt;
304 * &lt;/complexType&gt;
305 * &lt;/element&gt;
306 * &lt;element name="seqPointMax"&gt;
307 * &lt;complexType&gt;
308 * &lt;complexContent&gt;
309 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
310 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
311 * &lt;/restriction&gt;
312 * &lt;/complexContent&gt;
313 * &lt;/complexType&gt;
314 * &lt;/element&gt;
315 * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
316 * &lt;/sequence&gt;
317 * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
318 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
319 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
320 * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
321 * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
322 * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
323 * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
324 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
325 * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
326 * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
327 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
328 * &lt;/restriction&gt;
329 * &lt;/complexContent&gt;
330 * &lt;/complexType&gt;
331 * &lt;/element&gt;
332 * &lt;element name="FeatureSettings" minOccurs="0"&gt;
333 * &lt;complexType&gt;
334 * &lt;complexContent&gt;
335 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
336 * &lt;sequence&gt;
337 * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
338 * &lt;complexType&gt;
339 * &lt;complexContent&gt;
340 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
341 * &lt;sequence&gt;
342 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
343 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
344 * &lt;/sequence&gt;
345 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
346 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
347 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
348 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
349 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
350 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
351 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
352 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
353 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
354 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
355 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
356 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
357 * &lt;/restriction&gt;
358 * &lt;/complexContent&gt;
359 * &lt;/complexType&gt;
360 * &lt;/element&gt;
361 * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
362 * &lt;complexType&gt;
363 * &lt;complexContent&gt;
364 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
365 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
366 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
367 * &lt;/restriction&gt;
368 * &lt;/complexContent&gt;
369 * &lt;/complexType&gt;
370 * &lt;/element&gt;
371 * &lt;/sequence&gt;
372 * &lt;/restriction&gt;
373 * &lt;/complexContent&gt;
374 * &lt;/complexType&gt;
375 * &lt;/element&gt;
376 * &lt;/sequence&gt;
377 * &lt;/sequence&gt;
378 * &lt;/restriction&gt;
379 * &lt;/complexContent&gt;
380 * &lt;/complexType&gt;
385 @XmlAccessorType(XmlAccessType.FIELD)
386 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
398 public class JalviewModel {
400 @XmlElement(required = true)
401 @XmlSchemaType(name = "dateTime")
402 protected XMLGregorianCalendar creationDate;
403 @XmlElement(required = true)
404 protected String version;
405 @XmlElement(required = true)
406 protected VAMSAS vamsasModel;
407 @XmlElement(name = "JSeq")
408 protected List<JalviewModel.JSeq> jSeq;
409 @XmlElement(name = "JGroup")
410 protected List<JalviewModel.JGroup> jGroup;
411 @XmlElement(name = "Viewport")
412 protected List<JalviewModel.Viewport> viewport;
413 @XmlElement(name = "UserColours")
414 protected List<JalviewModel.UserColours> userColours;
415 protected List<JalviewModel.Tree> tree;
416 @XmlElement(name = "PcaViewer")
417 protected List<JalviewModel.PcaViewer> pcaViewer;
418 @XmlElement(name = "FeatureSettings")
419 protected JalviewModel.FeatureSettings featureSettings;
422 * Gets the value of the creationDate property.
426 * {@link XMLGregorianCalendar }
429 public XMLGregorianCalendar getCreationDate() {
434 * Sets the value of the creationDate property.
438 * {@link XMLGregorianCalendar }
441 public void setCreationDate(XMLGregorianCalendar value) {
442 this.creationDate = value;
446 * Gets the value of the version property.
453 public String getVersion() {
458 * Sets the value of the version property.
465 public void setVersion(String value) {
466 this.version = value;
470 * Gets the value of the vamsasModel property.
477 public VAMSAS getVamsasModel() {
482 * Sets the value of the vamsasModel property.
489 public void setVamsasModel(VAMSAS value) {
490 this.vamsasModel = value;
494 * Gets the value of the jSeq property.
497 * This accessor method returns a reference to the live list,
498 * not a snapshot. Therefore any modification you make to the
499 * returned list will be present inside the JAXB object.
500 * This is why there is not a <CODE>set</CODE> method for the jSeq property.
503 * For example, to add a new item, do as follows:
505 * getJSeq().add(newItem);
510 * Objects of the following type(s) are allowed in the list
511 * {@link JalviewModel.JSeq }
515 public List<JalviewModel.JSeq> getJSeq() {
517 jSeq = new ArrayList<JalviewModel.JSeq>();
523 * Gets the value of the jGroup property.
526 * This accessor method returns a reference to the live list,
527 * not a snapshot. Therefore any modification you make to the
528 * returned list will be present inside the JAXB object.
529 * This is why there is not a <CODE>set</CODE> method for the jGroup property.
532 * For example, to add a new item, do as follows:
534 * getJGroup().add(newItem);
539 * Objects of the following type(s) are allowed in the list
540 * {@link JalviewModel.JGroup }
544 public List<JalviewModel.JGroup> getJGroup() {
545 if (jGroup == null) {
546 jGroup = new ArrayList<JalviewModel.JGroup>();
552 * Gets the value of the viewport property.
555 * This accessor method returns a reference to the live list,
556 * not a snapshot. Therefore any modification you make to the
557 * returned list will be present inside the JAXB object.
558 * This is why there is not a <CODE>set</CODE> method for the viewport property.
561 * For example, to add a new item, do as follows:
563 * getViewport().add(newItem);
568 * Objects of the following type(s) are allowed in the list
569 * {@link JalviewModel.Viewport }
573 public List<JalviewModel.Viewport> getViewport() {
574 if (viewport == null) {
575 viewport = new ArrayList<JalviewModel.Viewport>();
577 return this.viewport;
581 * Gets the value of the userColours property.
584 * This accessor method returns a reference to the live list,
585 * not a snapshot. Therefore any modification you make to the
586 * returned list will be present inside the JAXB object.
587 * This is why there is not a <CODE>set</CODE> method for the userColours property.
590 * For example, to add a new item, do as follows:
592 * getUserColours().add(newItem);
597 * Objects of the following type(s) are allowed in the list
598 * {@link JalviewModel.UserColours }
602 public List<JalviewModel.UserColours> getUserColours() {
603 if (userColours == null) {
604 userColours = new ArrayList<JalviewModel.UserColours>();
606 return this.userColours;
610 * Gets the value of the tree property.
613 * This accessor method returns a reference to the live list,
614 * not a snapshot. Therefore any modification you make to the
615 * returned list will be present inside the JAXB object.
616 * This is why there is not a <CODE>set</CODE> method for the tree property.
619 * For example, to add a new item, do as follows:
621 * getTree().add(newItem);
626 * Objects of the following type(s) are allowed in the list
627 * {@link JalviewModel.Tree }
631 public List<JalviewModel.Tree> getTree() {
633 tree = new ArrayList<JalviewModel.Tree>();
639 * Gets the value of the pcaViewer property.
642 * This accessor method returns a reference to the live list,
643 * not a snapshot. Therefore any modification you make to the
644 * returned list will be present inside the JAXB object.
645 * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
648 * For example, to add a new item, do as follows:
650 * getPcaViewer().add(newItem);
655 * Objects of the following type(s) are allowed in the list
656 * {@link JalviewModel.PcaViewer }
660 public List<JalviewModel.PcaViewer> getPcaViewer() {
661 if (pcaViewer == null) {
662 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
664 return this.pcaViewer;
668 * Gets the value of the featureSettings property.
672 * {@link JalviewModel.FeatureSettings }
675 public JalviewModel.FeatureSettings getFeatureSettings() {
676 return featureSettings;
680 * Sets the value of the featureSettings property.
684 * {@link JalviewModel.FeatureSettings }
687 public void setFeatureSettings(JalviewModel.FeatureSettings value) {
688 this.featureSettings = value;
693 * <p>Java class for anonymous complex type.
695 * <p>The following schema fragment specifies the expected content contained within this class.
698 * &lt;complexType&gt;
699 * &lt;complexContent&gt;
700 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
701 * &lt;sequence&gt;
702 * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
703 * &lt;complexType&gt;
704 * &lt;complexContent&gt;
705 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
706 * &lt;sequence&gt;
707 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
708 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
709 * &lt;/sequence&gt;
710 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
711 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
712 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
713 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
714 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
715 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
716 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
717 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
718 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
719 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
720 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
721 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
722 * &lt;/restriction&gt;
723 * &lt;/complexContent&gt;
724 * &lt;/complexType&gt;
725 * &lt;/element&gt;
726 * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
727 * &lt;complexType&gt;
728 * &lt;complexContent&gt;
729 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
730 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
731 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
732 * &lt;/restriction&gt;
733 * &lt;/complexContent&gt;
734 * &lt;/complexType&gt;
735 * &lt;/element&gt;
736 * &lt;/sequence&gt;
737 * &lt;/restriction&gt;
738 * &lt;/complexContent&gt;
739 * &lt;/complexType&gt;
744 @XmlAccessorType(XmlAccessType.FIELD)
745 @XmlType(name = "", propOrder = {
749 public static class FeatureSettings {
751 @XmlElement(namespace = "www.jalview.org")
752 protected List<JalviewModel.FeatureSettings.Setting> setting;
753 @XmlElement(namespace = "www.jalview.org")
754 protected List<JalviewModel.FeatureSettings.Group> group;
757 * Gets the value of the setting property.
760 * This accessor method returns a reference to the live list,
761 * not a snapshot. Therefore any modification you make to the
762 * returned list will be present inside the JAXB object.
763 * This is why there is not a <CODE>set</CODE> method for the setting property.
766 * For example, to add a new item, do as follows:
768 * getSetting().add(newItem);
773 * Objects of the following type(s) are allowed in the list
774 * {@link JalviewModel.FeatureSettings.Setting }
778 public List<JalviewModel.FeatureSettings.Setting> getSetting() {
779 if (setting == null) {
780 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
786 * Gets the value of the group property.
789 * This accessor method returns a reference to the live list,
790 * not a snapshot. Therefore any modification you make to the
791 * returned list will be present inside the JAXB object.
792 * This is why there is not a <CODE>set</CODE> method for the group property.
795 * For example, to add a new item, do as follows:
797 * getGroup().add(newItem);
802 * Objects of the following type(s) are allowed in the list
803 * {@link JalviewModel.FeatureSettings.Group }
807 public List<JalviewModel.FeatureSettings.Group> getGroup() {
809 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
816 * <p>Java class for anonymous complex type.
818 * <p>The following schema fragment specifies the expected content contained within this class.
821 * &lt;complexType&gt;
822 * &lt;complexContent&gt;
823 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
824 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
825 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
826 * &lt;/restriction&gt;
827 * &lt;/complexContent&gt;
828 * &lt;/complexType&gt;
833 @XmlAccessorType(XmlAccessType.FIELD)
835 public static class Group {
837 @XmlAttribute(name = "name", required = true)
838 protected String name;
839 @XmlAttribute(name = "display", required = true)
840 protected boolean display;
843 * Gets the value of the name property.
850 public String getName() {
855 * Sets the value of the name property.
862 public void setName(String value) {
867 * Gets the value of the display property.
870 public boolean isDisplay() {
875 * Sets the value of the display property.
878 public void setDisplay(boolean value) {
879 this.display = value;
886 * <p>Java class for anonymous complex type.
888 * <p>The following schema fragment specifies the expected content contained within this class.
891 * &lt;complexType&gt;
892 * &lt;complexContent&gt;
893 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
894 * &lt;sequence&gt;
895 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
896 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
897 * &lt;/sequence&gt;
898 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
899 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
900 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
901 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
902 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
903 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
904 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
905 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
906 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
907 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
908 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
909 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
910 * &lt;/restriction&gt;
911 * &lt;/complexContent&gt;
912 * &lt;/complexType&gt;
917 @XmlAccessorType(XmlAccessType.FIELD)
918 @XmlType(name = "", propOrder = {
922 public static class Setting {
924 @XmlElement(namespace = "www.jalview.org")
925 protected List<String> attributeName;
926 @XmlElement(namespace = "www.jalview.org")
927 protected FeatureMatcherSet matcherSet;
928 @XmlAttribute(name = "type", required = true)
929 protected String type;
930 @XmlAttribute(name = "colour", required = true)
931 protected int colour;
932 @XmlAttribute(name = "display", required = true)
933 protected boolean display;
934 @XmlAttribute(name = "order")
935 protected Float order;
936 @XmlAttribute(name = "mincolour")
937 protected Integer mincolour;
938 @XmlAttribute(name = "noValueColour")
939 protected NoValueColour noValueColour;
940 @XmlAttribute(name = "threshold")
941 protected Float threshold;
942 @XmlAttribute(name = "threshstate")
943 protected Integer threshstate;
944 @XmlAttribute(name = "max")
946 @XmlAttribute(name = "min")
948 @XmlAttribute(name = "colourByLabel")
949 protected Boolean colourByLabel;
950 @XmlAttribute(name = "autoScale")
951 protected Boolean autoScale;
954 * Gets the value of the attributeName property.
957 * This accessor method returns a reference to the live list,
958 * not a snapshot. Therefore any modification you make to the
959 * returned list will be present inside the JAXB object.
960 * This is why there is not a <CODE>set</CODE> method for the attributeName property.
963 * For example, to add a new item, do as follows:
965 * getAttributeName().add(newItem);
970 * Objects of the following type(s) are allowed in the list
975 public List<String> getAttributeName() {
976 if (attributeName == null) {
977 attributeName = new ArrayList<String>();
979 return this.attributeName;
983 * Gets the value of the matcherSet property.
987 * {@link FeatureMatcherSet }
990 public FeatureMatcherSet getMatcherSet() {
995 * Sets the value of the matcherSet property.
999 * {@link FeatureMatcherSet }
1002 public void setMatcherSet(FeatureMatcherSet value) {
1003 this.matcherSet = value;
1007 * Gets the value of the type property.
1010 * possible object is
1014 public String getType() {
1019 * Sets the value of the type property.
1026 public void setType(String value) {
1031 * Gets the value of the colour property.
1034 public int getColour() {
1039 * Sets the value of the colour property.
1042 public void setColour(int value) {
1043 this.colour = value;
1047 * Gets the value of the display property.
1050 public boolean isDisplay() {
1055 * Sets the value of the display property.
1058 public void setDisplay(boolean value) {
1059 this.display = value;
1063 * Gets the value of the order property.
1066 * possible object is
1070 public Float getOrder() {
1075 * Sets the value of the order property.
1082 public void setOrder(Float value) {
1087 * Gets the value of the mincolour property.
1090 * possible object is
1094 public Integer getMincolour() {
1099 * Sets the value of the mincolour property.
1106 public void setMincolour(Integer value) {
1107 this.mincolour = value;
1111 * Gets the value of the noValueColour property.
1114 * possible object is
1115 * {@link NoValueColour }
1118 public NoValueColour getNoValueColour() {
1119 if (noValueColour == null) {
1120 return NoValueColour.MIN;
1122 return noValueColour;
1127 * Sets the value of the noValueColour property.
1131 * {@link NoValueColour }
1134 public void setNoValueColour(NoValueColour value) {
1135 this.noValueColour = value;
1139 * Gets the value of the threshold property.
1142 * possible object is
1146 public Float getThreshold() {
1151 * Sets the value of the threshold property.
1158 public void setThreshold(Float value) {
1159 this.threshold = value;
1163 * Gets the value of the threshstate property.
1166 * possible object is
1170 public Integer getThreshstate() {
1175 * Sets the value of the threshstate property.
1182 public void setThreshstate(Integer value) {
1183 this.threshstate = value;
1187 * Gets the value of the max property.
1190 * possible object is
1194 public Float getMax() {
1199 * Sets the value of the max property.
1206 public void setMax(Float value) {
1211 * Gets the value of the min property.
1214 * possible object is
1218 public Float getMin() {
1223 * Sets the value of the min property.
1230 public void setMin(Float value) {
1235 * Gets the value of the colourByLabel property.
1238 * possible object is
1242 public Boolean isColourByLabel() {
1243 return colourByLabel;
1247 * Sets the value of the colourByLabel property.
1254 public void setColourByLabel(Boolean value) {
1255 this.colourByLabel = value;
1259 * Gets the value of the autoScale property.
1262 * possible object is
1266 public Boolean isAutoScale() {
1271 * Sets the value of the autoScale property.
1278 public void setAutoScale(Boolean value) {
1279 this.autoScale = value;
1288 * <p>Java class for anonymous complex type.
1290 * <p>The following schema fragment specifies the expected content contained within this class.
1293 * &lt;complexType&gt;
1294 * &lt;complexContent&gt;
1295 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1296 * &lt;sequence&gt;
1297 * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
1298 * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
1299 * &lt;/sequence&gt;
1300 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1301 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1302 * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1303 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1304 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1305 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1306 * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1307 * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1308 * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1309 * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1310 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1311 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1312 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1313 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1314 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1315 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1316 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1317 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1318 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1319 * &lt;/restriction&gt;
1320 * &lt;/complexContent&gt;
1321 * &lt;/complexType&gt;
1326 @XmlAccessorType(XmlAccessType.FIELD)
1327 @XmlType(name = "", propOrder = {
1331 public static class JGroup {
1333 @XmlElement(namespace = "www.jalview.org", required = true)
1334 protected List<String> seq;
1335 @XmlElement(namespace = "www.jalview.org")
1336 protected AnnotationColourScheme annotationColours;
1337 @XmlAttribute(name = "start")
1338 protected Integer start;
1339 @XmlAttribute(name = "end")
1340 protected Integer end;
1341 @XmlAttribute(name = "name")
1342 protected String name;
1343 @XmlAttribute(name = "colour")
1344 protected String colour;
1345 @XmlAttribute(name = "consThreshold")
1346 protected Integer consThreshold;
1347 @XmlAttribute(name = "pidThreshold")
1348 protected Integer pidThreshold;
1349 @XmlAttribute(name = "outlineColour")
1350 protected Integer outlineColour;
1351 @XmlAttribute(name = "displayBoxes")
1352 protected Boolean displayBoxes;
1353 @XmlAttribute(name = "displayText")
1354 protected Boolean displayText;
1355 @XmlAttribute(name = "colourText")
1356 protected Boolean colourText;
1357 @XmlAttribute(name = "textCol1")
1358 protected Integer textCol1;
1359 @XmlAttribute(name = "textCol2")
1360 protected Integer textCol2;
1361 @XmlAttribute(name = "textColThreshold")
1362 protected Integer textColThreshold;
1363 @XmlAttribute(name = "showUnconserved")
1364 protected Boolean showUnconserved;
1365 @XmlAttribute(name = "ignoreGapsinConsensus")
1366 protected Boolean ignoreGapsinConsensus;
1367 @XmlAttribute(name = "showConsensusHistogram")
1368 protected Boolean showConsensusHistogram;
1369 @XmlAttribute(name = "showSequenceLogo")
1370 protected Boolean showSequenceLogo;
1371 @XmlAttribute(name = "normaliseSequenceLogo")
1372 protected Boolean normaliseSequenceLogo;
1373 @XmlAttribute(name = "id")
1374 protected String id;
1377 * Gets the value of the seq property.
1380 * This accessor method returns a reference to the live list,
1381 * not a snapshot. Therefore any modification you make to the
1382 * returned list will be present inside the JAXB object.
1383 * This is why there is not a <CODE>set</CODE> method for the seq property.
1386 * For example, to add a new item, do as follows:
1388 * getSeq().add(newItem);
1393 * Objects of the following type(s) are allowed in the list
1398 public List<String> getSeq() {
1400 seq = new ArrayList<String>();
1406 * Gets the value of the annotationColours property.
1409 * possible object is
1410 * {@link AnnotationColourScheme }
1413 public AnnotationColourScheme getAnnotationColours() {
1414 return annotationColours;
1418 * Sets the value of the annotationColours property.
1422 * {@link AnnotationColourScheme }
1425 public void setAnnotationColours(AnnotationColourScheme value) {
1426 this.annotationColours = value;
1430 * Gets the value of the start property.
1433 * possible object is
1437 public Integer getStart() {
1442 * Sets the value of the start property.
1449 public void setStart(Integer value) {
1454 * Gets the value of the end property.
1457 * possible object is
1461 public Integer getEnd() {
1466 * Sets the value of the end property.
1473 public void setEnd(Integer value) {
1478 * Gets the value of the name property.
1481 * possible object is
1485 public String getName() {
1490 * Sets the value of the name property.
1497 public void setName(String value) {
1502 * Gets the value of the colour property.
1505 * possible object is
1509 public String getColour() {
1514 * Sets the value of the colour property.
1521 public void setColour(String value) {
1522 this.colour = value;
1526 * Gets the value of the consThreshold property.
1529 * possible object is
1533 public Integer getConsThreshold() {
1534 return consThreshold;
1538 * Sets the value of the consThreshold property.
1545 public void setConsThreshold(Integer value) {
1546 this.consThreshold = value;
1550 * Gets the value of the pidThreshold property.
1553 * possible object is
1557 public Integer getPidThreshold() {
1558 return pidThreshold;
1562 * Sets the value of the pidThreshold property.
1569 public void setPidThreshold(Integer value) {
1570 this.pidThreshold = value;
1574 * Gets the value of the outlineColour property.
1577 * possible object is
1581 public Integer getOutlineColour() {
1582 return outlineColour;
1586 * Sets the value of the outlineColour property.
1593 public void setOutlineColour(Integer value) {
1594 this.outlineColour = value;
1598 * Gets the value of the displayBoxes property.
1601 * possible object is
1605 public Boolean isDisplayBoxes() {
1606 return displayBoxes;
1610 * Sets the value of the displayBoxes property.
1617 public void setDisplayBoxes(Boolean value) {
1618 this.displayBoxes = value;
1622 * Gets the value of the displayText property.
1625 * possible object is
1629 public Boolean isDisplayText() {
1634 * Sets the value of the displayText property.
1641 public void setDisplayText(Boolean value) {
1642 this.displayText = value;
1646 * Gets the value of the colourText property.
1649 * possible object is
1653 public Boolean isColourText() {
1658 * Sets the value of the colourText property.
1665 public void setColourText(Boolean value) {
1666 this.colourText = value;
1670 * Gets the value of the textCol1 property.
1673 * possible object is
1677 public Integer getTextCol1() {
1682 * Sets the value of the textCol1 property.
1689 public void setTextCol1(Integer value) {
1690 this.textCol1 = value;
1694 * Gets the value of the textCol2 property.
1697 * possible object is
1701 public Integer getTextCol2() {
1706 * Sets the value of the textCol2 property.
1713 public void setTextCol2(Integer value) {
1714 this.textCol2 = value;
1718 * Gets the value of the textColThreshold property.
1721 * possible object is
1725 public Integer getTextColThreshold() {
1726 return textColThreshold;
1730 * Sets the value of the textColThreshold property.
1737 public void setTextColThreshold(Integer value) {
1738 this.textColThreshold = value;
1742 * Gets the value of the showUnconserved property.
1745 * possible object is
1749 public Boolean isShowUnconserved() {
1750 return showUnconserved;
1754 * Sets the value of the showUnconserved property.
1761 public void setShowUnconserved(Boolean value) {
1762 this.showUnconserved = value;
1766 * Gets the value of the ignoreGapsinConsensus property.
1769 * possible object is
1773 public boolean isIgnoreGapsinConsensus() {
1774 if (ignoreGapsinConsensus == null) {
1777 return ignoreGapsinConsensus;
1782 * Sets the value of the ignoreGapsinConsensus property.
1789 public void setIgnoreGapsinConsensus(Boolean value) {
1790 this.ignoreGapsinConsensus = value;
1794 * Gets the value of the showConsensusHistogram property.
1797 * possible object is
1801 public boolean isShowConsensusHistogram() {
1802 if (showConsensusHistogram == null) {
1805 return showConsensusHistogram;
1810 * Sets the value of the showConsensusHistogram property.
1817 public void setShowConsensusHistogram(Boolean value) {
1818 this.showConsensusHistogram = value;
1822 * Gets the value of the showSequenceLogo property.
1825 * possible object is
1829 public boolean isShowSequenceLogo() {
1830 if (showSequenceLogo == null) {
1833 return showSequenceLogo;
1838 * Sets the value of the showSequenceLogo property.
1845 public void setShowSequenceLogo(Boolean value) {
1846 this.showSequenceLogo = value;
1850 * Gets the value of the normaliseSequenceLogo property.
1853 * possible object is
1857 public boolean isNormaliseSequenceLogo() {
1858 if (normaliseSequenceLogo == null) {
1861 return normaliseSequenceLogo;
1866 * Sets the value of the normaliseSequenceLogo property.
1873 public void setNormaliseSequenceLogo(Boolean value) {
1874 this.normaliseSequenceLogo = value;
1878 * Gets the value of the id property.
1881 * possible object is
1885 public String getId() {
1890 * Sets the value of the id property.
1897 public void setId(String value) {
1905 * <p>Java class for anonymous complex type.
1907 * <p>The following schema fragment specifies the expected content contained within this class.
1910 * &lt;complexType&gt;
1911 * &lt;complexContent&gt;
1912 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1913 * &lt;sequence&gt;
1914 * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
1915 * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
1916 * &lt;complexType&gt;
1917 * &lt;complexContent&gt;
1918 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
1919 * &lt;sequence&gt;
1920 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
1921 * &lt;complexType&gt;
1922 * &lt;simpleContent&gt;
1923 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
1924 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
1925 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1926 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1927 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1928 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1929 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1930 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1931 * &lt;/extension&gt;
1932 * &lt;/simpleContent&gt;
1933 * &lt;/complexType&gt;
1934 * &lt;/element&gt;
1935 * &lt;/sequence&gt;
1936 * &lt;/extension&gt;
1937 * &lt;/complexContent&gt;
1938 * &lt;/complexType&gt;
1939 * &lt;/element&gt;
1940 * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
1941 * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
1942 * &lt;complexType&gt;
1943 * &lt;complexContent&gt;
1944 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1945 * &lt;sequence&gt;
1946 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
1947 * &lt;complexType&gt;
1948 * &lt;complexContent&gt;
1949 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1950 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1951 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1952 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1953 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1954 * &lt;/restriction&gt;
1955 * &lt;/complexContent&gt;
1956 * &lt;/complexType&gt;
1957 * &lt;/element&gt;
1958 * &lt;/sequence&gt;
1959 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
1960 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1961 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1962 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1963 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1964 * &lt;/restriction&gt;
1965 * &lt;/complexContent&gt;
1966 * &lt;/complexType&gt;
1967 * &lt;/element&gt;
1968 * &lt;/sequence&gt;
1969 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1970 * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1971 * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1972 * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1973 * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1974 * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1975 * &lt;/restriction&gt;
1976 * &lt;/complexContent&gt;
1977 * &lt;/complexType&gt;
1982 @XmlAccessorType(XmlAccessType.FIELD)
1983 @XmlType(name = "", propOrder = {
1989 public static class JSeq {
1991 @XmlElement(namespace = "www.jalview.org")
1992 protected List<Feature> features;
1993 @XmlElement(namespace = "www.jalview.org")
1994 protected List<JalviewModel.JSeq.Pdbids> pdbids;
1995 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1996 protected List<Integer> hiddenSequences;
1997 @XmlElement(namespace = "www.jalview.org")
1998 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1999 @XmlAttribute(name = "colour")
2000 protected Integer colour;
2001 @XmlAttribute(name = "start", required = true)
2002 protected int start;
2003 @XmlAttribute(name = "end", required = true)
2005 @XmlAttribute(name = "id", required = true)
2006 protected String id;
2007 @XmlAttribute(name = "hidden")
2008 protected Boolean hidden;
2009 @XmlAttribute(name = "viewreference")
2010 protected Boolean viewreference;
2013 * Gets the value of the features property.
2016 * This accessor method returns a reference to the live list,
2017 * not a snapshot. Therefore any modification you make to the
2018 * returned list will be present inside the JAXB object.
2019 * This is why there is not a <CODE>set</CODE> method for the features property.
2022 * For example, to add a new item, do as follows:
2024 * getFeatures().add(newItem);
2029 * Objects of the following type(s) are allowed in the list
2034 public List<Feature> getFeatures() {
2035 if (features == null) {
2036 features = new ArrayList<Feature>();
2038 return this.features;
2042 * Gets the value of the pdbids property.
2045 * This accessor method returns a reference to the live list,
2046 * not a snapshot. Therefore any modification you make to the
2047 * returned list will be present inside the JAXB object.
2048 * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2051 * For example, to add a new item, do as follows:
2053 * getPdbids().add(newItem);
2058 * Objects of the following type(s) are allowed in the list
2059 * {@link JalviewModel.JSeq.Pdbids }
2063 public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2064 if (pdbids == null) {
2065 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2071 * Gets the value of the hiddenSequences property.
2074 * This accessor method returns a reference to the live list,
2075 * not a snapshot. Therefore any modification you make to the
2076 * returned list will be present inside the JAXB object.
2077 * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2080 * For example, to add a new item, do as follows:
2082 * getHiddenSequences().add(newItem);
2087 * Objects of the following type(s) are allowed in the list
2092 public List<Integer> getHiddenSequences() {
2093 if (hiddenSequences == null) {
2094 hiddenSequences = new ArrayList<Integer>();
2096 return this.hiddenSequences;
2100 * Gets the value of the rnaViewer property.
2103 * This accessor method returns a reference to the live list,
2104 * not a snapshot. Therefore any modification you make to the
2105 * returned list will be present inside the JAXB object.
2106 * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2109 * For example, to add a new item, do as follows:
2111 * getRnaViewer().add(newItem);
2116 * Objects of the following type(s) are allowed in the list
2117 * {@link JalviewModel.JSeq.RnaViewer }
2121 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2122 if (rnaViewer == null) {
2123 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2125 return this.rnaViewer;
2129 * Gets the value of the colour property.
2132 * possible object is
2136 public Integer getColour() {
2141 * Sets the value of the colour property.
2148 public void setColour(Integer value) {
2149 this.colour = value;
2153 * Gets the value of the start property.
2156 public int getStart() {
2161 * Sets the value of the start property.
2164 public void setStart(int value) {
2169 * Gets the value of the end property.
2172 public int getEnd() {
2177 * Sets the value of the end property.
2180 public void setEnd(int value) {
2185 * Gets the value of the id property.
2188 * possible object is
2192 public String getId() {
2197 * Sets the value of the id property.
2204 public void setId(String value) {
2209 * Gets the value of the hidden property.
2212 * possible object is
2216 public Boolean isHidden() {
2221 * Sets the value of the hidden property.
2228 public void setHidden(Boolean value) {
2229 this.hidden = value;
2233 * Gets the value of the viewreference property.
2236 * possible object is
2240 public Boolean isViewreference() {
2241 return viewreference;
2245 * Sets the value of the viewreference property.
2252 public void setViewreference(Boolean value) {
2253 this.viewreference = value;
2258 * <p>Java class for anonymous complex type.
2260 * <p>The following schema fragment specifies the expected content contained within this class.
2263 * &lt;complexType&gt;
2264 * &lt;complexContent&gt;
2265 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
2266 * &lt;sequence&gt;
2267 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
2268 * &lt;complexType&gt;
2269 * &lt;simpleContent&gt;
2270 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2271 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2272 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2273 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2274 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2275 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2276 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2277 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2278 * &lt;/extension&gt;
2279 * &lt;/simpleContent&gt;
2280 * &lt;/complexType&gt;
2281 * &lt;/element&gt;
2282 * &lt;/sequence&gt;
2283 * &lt;/extension&gt;
2284 * &lt;/complexContent&gt;
2285 * &lt;/complexType&gt;
2290 @XmlAccessorType(XmlAccessType.FIELD)
2291 @XmlType(name = "", propOrder = {
2294 public static class Pdbids
2298 @XmlElement(namespace = "www.jalview.org")
2299 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2302 * Gets the value of the structureState property.
2305 * This accessor method returns a reference to the live list,
2306 * not a snapshot. Therefore any modification you make to the
2307 * returned list will be present inside the JAXB object.
2308 * This is why there is not a <CODE>set</CODE> method for the structureState property.
2311 * For example, to add a new item, do as follows:
2313 * getStructureState().add(newItem);
2318 * Objects of the following type(s) are allowed in the list
2319 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2323 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2324 if (structureState == null) {
2325 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2327 return this.structureState;
2332 * <p>Java class for anonymous complex type.
2334 * <p>The following schema fragment specifies the expected content contained within this class.
2337 * &lt;complexType&gt;
2338 * &lt;simpleContent&gt;
2339 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2340 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2341 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2342 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2343 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2344 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2345 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2346 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2347 * &lt;/extension&gt;
2348 * &lt;/simpleContent&gt;
2349 * &lt;/complexType&gt;
2354 @XmlAccessorType(XmlAccessType.FIELD)
2355 @XmlType(name = "", propOrder = {
2358 public static class StructureState {
2361 protected String value;
2362 @XmlAttribute(name = "visible")
2363 protected Boolean visible;
2364 @XmlAttribute(name = "viewId")
2365 protected String viewId;
2366 @XmlAttribute(name = "alignwithAlignPanel")
2367 protected Boolean alignwithAlignPanel;
2368 @XmlAttribute(name = "colourwithAlignPanel")
2369 protected Boolean colourwithAlignPanel;
2370 @XmlAttribute(name = "colourByJmol")
2371 protected Boolean colourByJmol;
2372 @XmlAttribute(name = "type")
2373 protected String type;
2374 @XmlAttribute(name = "width")
2375 protected Integer width;
2376 @XmlAttribute(name = "height")
2377 protected Integer height;
2378 @XmlAttribute(name = "xpos")
2379 protected Integer xpos;
2380 @XmlAttribute(name = "ypos")
2381 protected Integer ypos;
2384 * Gets the value of the value property.
2387 * possible object is
2391 public String getValue() {
2396 * Sets the value of the value property.
2403 public void setValue(String value) {
2408 * Gets the value of the visible property.
2411 * possible object is
2415 public Boolean isVisible() {
2420 * Sets the value of the visible property.
2427 public void setVisible(Boolean value) {
2428 this.visible = value;
2432 * Gets the value of the viewId property.
2435 * possible object is
2439 public String getViewId() {
2444 * Sets the value of the viewId property.
2451 public void setViewId(String value) {
2452 this.viewId = value;
2456 * Gets the value of the alignwithAlignPanel property.
2459 * possible object is
2463 public boolean isAlignwithAlignPanel() {
2464 if (alignwithAlignPanel == null) {
2467 return alignwithAlignPanel;
2472 * Sets the value of the alignwithAlignPanel property.
2479 public void setAlignwithAlignPanel(Boolean value) {
2480 this.alignwithAlignPanel = value;
2484 * Gets the value of the colourwithAlignPanel property.
2487 * possible object is
2491 public boolean isColourwithAlignPanel() {
2492 if (colourwithAlignPanel == null) {
2495 return colourwithAlignPanel;
2500 * Sets the value of the colourwithAlignPanel property.
2507 public void setColourwithAlignPanel(Boolean value) {
2508 this.colourwithAlignPanel = value;
2512 * Gets the value of the colourByJmol property.
2515 * possible object is
2519 public boolean isColourByJmol() {
2520 if (colourByJmol == null) {
2523 return colourByJmol;
2528 * Sets the value of the colourByJmol property.
2535 public void setColourByJmol(Boolean value) {
2536 this.colourByJmol = value;
2540 * Gets the value of the type property.
2543 * possible object is
2547 public String getType() {
2552 * Sets the value of the type property.
2559 public void setType(String value) {
2564 * Gets the value of the width property.
2567 * possible object is
2571 public Integer getWidth() {
2576 * Sets the value of the width property.
2583 public void setWidth(Integer value) {
2588 * Gets the value of the height property.
2591 * possible object is
2595 public Integer getHeight() {
2600 * Sets the value of the height property.
2607 public void setHeight(Integer value) {
2608 this.height = value;
2612 * Gets the value of the xpos property.
2615 * possible object is
2619 public Integer getXpos() {
2624 * Sets the value of the xpos property.
2631 public void setXpos(Integer value) {
2636 * Gets the value of the ypos property.
2639 * possible object is
2643 public Integer getYpos() {
2648 * Sets the value of the ypos property.
2655 public void setYpos(Integer value) {
2665 * <p>Java class for anonymous complex type.
2667 * <p>The following schema fragment specifies the expected content contained within this class.
2670 * &lt;complexType&gt;
2671 * &lt;complexContent&gt;
2672 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2673 * &lt;sequence&gt;
2674 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
2675 * &lt;complexType&gt;
2676 * &lt;complexContent&gt;
2677 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2678 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2679 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2680 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2681 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2682 * &lt;/restriction&gt;
2683 * &lt;/complexContent&gt;
2684 * &lt;/complexType&gt;
2685 * &lt;/element&gt;
2686 * &lt;/sequence&gt;
2687 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2688 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2689 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2690 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2691 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2692 * &lt;/restriction&gt;
2693 * &lt;/complexContent&gt;
2694 * &lt;/complexType&gt;
2699 @XmlAccessorType(XmlAccessType.FIELD)
2700 @XmlType(name = "", propOrder = {
2701 "secondaryStructure"
2703 public static class RnaViewer {
2705 @XmlElement(namespace = "www.jalview.org", required = true)
2706 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2707 @XmlAttribute(name = "title")
2708 protected String title;
2709 @XmlAttribute(name = "viewId")
2710 protected String viewId;
2711 @XmlAttribute(name = "dividerLocation")
2712 protected Integer dividerLocation;
2713 @XmlAttribute(name = "selectedRna")
2714 protected Integer selectedRna;
2715 @XmlAttribute(name = "width")
2716 protected Integer width;
2717 @XmlAttribute(name = "height")
2718 protected Integer height;
2719 @XmlAttribute(name = "xpos")
2720 protected Integer xpos;
2721 @XmlAttribute(name = "ypos")
2722 protected Integer ypos;
2725 * Gets the value of the secondaryStructure property.
2728 * This accessor method returns a reference to the live list,
2729 * not a snapshot. Therefore any modification you make to the
2730 * returned list will be present inside the JAXB object.
2731 * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2734 * For example, to add a new item, do as follows:
2736 * getSecondaryStructure().add(newItem);
2741 * Objects of the following type(s) are allowed in the list
2742 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2746 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2747 if (secondaryStructure == null) {
2748 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2750 return this.secondaryStructure;
2754 * Gets the value of the title property.
2757 * possible object is
2761 public String getTitle() {
2766 * Sets the value of the title property.
2773 public void setTitle(String value) {
2778 * Gets the value of the viewId property.
2781 * possible object is
2785 public String getViewId() {
2790 * Sets the value of the viewId property.
2797 public void setViewId(String value) {
2798 this.viewId = value;
2802 * Gets the value of the dividerLocation property.
2805 * possible object is
2809 public Integer getDividerLocation() {
2810 return dividerLocation;
2814 * Sets the value of the dividerLocation property.
2821 public void setDividerLocation(Integer value) {
2822 this.dividerLocation = value;
2826 * Gets the value of the selectedRna property.
2829 * possible object is
2833 public Integer getSelectedRna() {
2838 * Sets the value of the selectedRna property.
2845 public void setSelectedRna(Integer value) {
2846 this.selectedRna = value;
2850 * Gets the value of the width property.
2853 * possible object is
2857 public Integer getWidth() {
2862 * Sets the value of the width property.
2869 public void setWidth(Integer value) {
2874 * Gets the value of the height property.
2877 * possible object is
2881 public Integer getHeight() {
2886 * Sets the value of the height property.
2893 public void setHeight(Integer value) {
2894 this.height = value;
2898 * Gets the value of the xpos property.
2901 * possible object is
2905 public Integer getXpos() {
2910 * Sets the value of the xpos property.
2917 public void setXpos(Integer value) {
2922 * Gets the value of the ypos property.
2925 * possible object is
2929 public Integer getYpos() {
2934 * Sets the value of the ypos property.
2941 public void setYpos(Integer value) {
2947 * <p>Java class for anonymous complex type.
2949 * <p>The following schema fragment specifies the expected content contained within this class.
2952 * &lt;complexType&gt;
2953 * &lt;complexContent&gt;
2954 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2955 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2956 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2957 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2958 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2959 * &lt;/restriction&gt;
2960 * &lt;/complexContent&gt;
2961 * &lt;/complexType&gt;
2966 @XmlAccessorType(XmlAccessType.FIELD)
2968 public static class SecondaryStructure {
2970 @XmlAttribute(name = "title")
2971 protected String title;
2972 @XmlAttribute(name = "annotationId", required = true)
2973 protected String annotationId;
2974 @XmlAttribute(name = "gapped")
2975 protected Boolean gapped;
2976 @XmlAttribute(name = "viewerState")
2977 protected String viewerState;
2980 * Gets the value of the title property.
2983 * possible object is
2987 public String getTitle() {
2992 * Sets the value of the title property.
2999 public void setTitle(String value) {
3004 * Gets the value of the annotationId property.
3007 * possible object is
3011 public String getAnnotationId() {
3012 return annotationId;
3016 * Sets the value of the annotationId property.
3023 public void setAnnotationId(String value) {
3024 this.annotationId = value;
3028 * Gets the value of the gapped property.
3031 * possible object is
3035 public Boolean isGapped() {
3040 * Sets the value of the gapped property.
3047 public void setGapped(Boolean value) {
3048 this.gapped = value;
3052 * Gets the value of the viewerState property.
3055 * possible object is
3059 public String getViewerState() {
3064 * Sets the value of the viewerState property.
3071 public void setViewerState(String value) {
3072 this.viewerState = value;
3083 * <p>Java class for anonymous complex type.
3085 * <p>The following schema fragment specifies the expected content contained within this class.
3088 * &lt;complexType&gt;
3089 * &lt;complexContent&gt;
3090 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3091 * &lt;sequence&gt;
3092 * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
3093 * &lt;complexType&gt;
3094 * &lt;complexContent&gt;
3095 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3096 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3097 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3098 * &lt;/restriction&gt;
3099 * &lt;/complexContent&gt;
3100 * &lt;/complexType&gt;
3101 * &lt;/element&gt;
3102 * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
3103 * &lt;complexType&gt;
3104 * &lt;complexContent&gt;
3105 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3106 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3107 * &lt;/restriction&gt;
3108 * &lt;/complexContent&gt;
3109 * &lt;/complexType&gt;
3110 * &lt;/element&gt;
3111 * &lt;element name="seqPointMin"&gt;
3112 * &lt;complexType&gt;
3113 * &lt;complexContent&gt;
3114 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3115 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3116 * &lt;/restriction&gt;
3117 * &lt;/complexContent&gt;
3118 * &lt;/complexType&gt;
3119 * &lt;/element&gt;
3120 * &lt;element name="seqPointMax"&gt;
3121 * &lt;complexType&gt;
3122 * &lt;complexContent&gt;
3123 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3124 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3125 * &lt;/restriction&gt;
3126 * &lt;/complexContent&gt;
3127 * &lt;/complexType&gt;
3128 * &lt;/element&gt;
3129 * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
3130 * &lt;/sequence&gt;
3131 * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
3132 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
3133 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3134 * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3135 * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3136 * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3137 * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3138 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3139 * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
3140 * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3141 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3142 * &lt;/restriction&gt;
3143 * &lt;/complexContent&gt;
3144 * &lt;/complexType&gt;
3149 @XmlAccessorType(XmlAccessType.FIELD)
3150 @XmlType(name = "", propOrder = {
3157 public static class PcaViewer {
3159 @XmlElement(namespace = "www.jalview.org", required = true)
3160 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3161 @XmlElement(namespace = "www.jalview.org", required = true)
3162 protected List<JalviewModel.PcaViewer.Axis> axis;
3163 @XmlElement(namespace = "www.jalview.org", required = true)
3164 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3165 @XmlElement(namespace = "www.jalview.org", required = true)
3166 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3167 @XmlElement(namespace = "www.jalview.org", required = true)
3168 protected PcaDataType pcaData;
3169 @XmlAttribute(name = "title")
3170 protected String title;
3171 @XmlAttribute(name = "scoreModelName")
3172 protected String scoreModelName;
3173 @XmlAttribute(name = "xDim")
3174 protected Integer xDim;
3175 @XmlAttribute(name = "yDim")
3176 protected Integer yDim;
3177 @XmlAttribute(name = "zDim")
3178 protected Integer zDim;
3179 @XmlAttribute(name = "bgColour")
3180 protected Integer bgColour;
3181 @XmlAttribute(name = "scaleFactor")
3182 protected Float scaleFactor;
3183 @XmlAttribute(name = "showLabels")
3184 protected Boolean showLabels;
3185 @XmlAttribute(name = "linkToAllViews")
3186 protected Boolean linkToAllViews;
3187 @XmlAttribute(name = "includeGaps")
3188 protected Boolean includeGaps;
3189 @XmlAttribute(name = "matchGaps")
3190 protected Boolean matchGaps;
3191 @XmlAttribute(name = "includeGappedColumns")
3192 protected Boolean includeGappedColumns;
3193 @XmlAttribute(name = "denominateByShortestLength")
3194 protected Boolean denominateByShortestLength;
3195 @XmlAttribute(name = "width")
3196 protected Integer width;
3197 @XmlAttribute(name = "height")
3198 protected Integer height;
3199 @XmlAttribute(name = "xpos")
3200 protected Integer xpos;
3201 @XmlAttribute(name = "ypos")
3202 protected Integer ypos;
3205 * Gets the value of the sequencePoint property.
3208 * This accessor method returns a reference to the live list,
3209 * not a snapshot. Therefore any modification you make to the
3210 * returned list will be present inside the JAXB object.
3211 * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3214 * For example, to add a new item, do as follows:
3216 * getSequencePoint().add(newItem);
3221 * Objects of the following type(s) are allowed in the list
3222 * {@link JalviewModel.PcaViewer.SequencePoint }
3226 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3227 if (sequencePoint == null) {
3228 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3230 return this.sequencePoint;
3234 * Gets the value of the axis property.
3237 * This accessor method returns a reference to the live list,
3238 * not a snapshot. Therefore any modification you make to the
3239 * returned list will be present inside the JAXB object.
3240 * This is why there is not a <CODE>set</CODE> method for the axis property.
3243 * For example, to add a new item, do as follows:
3245 * getAxis().add(newItem);
3250 * Objects of the following type(s) are allowed in the list
3251 * {@link JalviewModel.PcaViewer.Axis }
3255 public List<JalviewModel.PcaViewer.Axis> getAxis() {
3257 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3263 * Gets the value of the seqPointMin property.
3266 * possible object is
3267 * {@link JalviewModel.PcaViewer.SeqPointMin }
3270 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3275 * Sets the value of the seqPointMin property.
3279 * {@link JalviewModel.PcaViewer.SeqPointMin }
3282 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3283 this.seqPointMin = value;
3287 * Gets the value of the seqPointMax property.
3290 * possible object is
3291 * {@link JalviewModel.PcaViewer.SeqPointMax }
3294 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3299 * Sets the value of the seqPointMax property.
3303 * {@link JalviewModel.PcaViewer.SeqPointMax }
3306 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3307 this.seqPointMax = value;
3311 * Gets the value of the pcaData property.
3314 * possible object is
3315 * {@link PcaDataType }
3318 public PcaDataType getPcaData() {
3323 * Sets the value of the pcaData property.
3327 * {@link PcaDataType }
3330 public void setPcaData(PcaDataType value) {
3331 this.pcaData = value;
3335 * Gets the value of the title property.
3338 * possible object is
3342 public String getTitle() {
3347 * Sets the value of the title property.
3354 public void setTitle(String value) {
3359 * Gets the value of the scoreModelName property.
3362 * possible object is
3366 public String getScoreModelName() {
3367 return scoreModelName;
3371 * Sets the value of the scoreModelName property.
3378 public void setScoreModelName(String value) {
3379 this.scoreModelName = value;
3383 * Gets the value of the xDim property.
3386 * possible object is
3390 public Integer getXDim() {
3395 * Sets the value of the xDim property.
3402 public void setXDim(Integer value) {
3407 * Gets the value of the yDim property.
3410 * possible object is
3414 public Integer getYDim() {
3419 * Sets the value of the yDim property.
3426 public void setYDim(Integer value) {
3431 * Gets the value of the zDim property.
3434 * possible object is
3438 public Integer getZDim() {
3443 * Sets the value of the zDim property.
3450 public void setZDim(Integer value) {
3455 * Gets the value of the bgColour property.
3458 * possible object is
3462 public Integer getBgColour() {
3467 * Sets the value of the bgColour property.
3474 public void setBgColour(Integer value) {
3475 this.bgColour = value;
3479 * Gets the value of the scaleFactor property.
3482 * possible object is
3486 public Float getScaleFactor() {
3491 * Sets the value of the scaleFactor property.
3498 public void setScaleFactor(Float value) {
3499 this.scaleFactor = value;
3503 * Gets the value of the showLabels property.
3506 * possible object is
3510 public Boolean isShowLabels() {
3515 * Sets the value of the showLabels property.
3522 public void setShowLabels(Boolean value) {
3523 this.showLabels = value;
3527 * Gets the value of the linkToAllViews property.
3530 * possible object is
3534 public Boolean isLinkToAllViews() {
3535 return linkToAllViews;
3539 * Sets the value of the linkToAllViews property.
3546 public void setLinkToAllViews(Boolean value) {
3547 this.linkToAllViews = value;
3551 * Gets the value of the includeGaps property.
3554 * possible object is
3558 public Boolean isIncludeGaps() {
3563 * Sets the value of the includeGaps property.
3570 public void setIncludeGaps(Boolean value) {
3571 this.includeGaps = value;
3575 * Gets the value of the matchGaps property.
3578 * possible object is
3582 public Boolean isMatchGaps() {
3587 * Sets the value of the matchGaps property.
3594 public void setMatchGaps(Boolean value) {
3595 this.matchGaps = value;
3599 * Gets the value of the includeGappedColumns property.
3602 * possible object is
3606 public Boolean isIncludeGappedColumns() {
3607 return includeGappedColumns;
3611 * Sets the value of the includeGappedColumns property.
3618 public void setIncludeGappedColumns(Boolean value) {
3619 this.includeGappedColumns = value;
3623 * Gets the value of the denominateByShortestLength property.
3626 * possible object is
3630 public Boolean isDenominateByShortestLength() {
3631 return denominateByShortestLength;
3635 * Sets the value of the denominateByShortestLength property.
3642 public void setDenominateByShortestLength(Boolean value) {
3643 this.denominateByShortestLength = value;
3647 * Gets the value of the width property.
3650 * possible object is
3654 public Integer getWidth() {
3659 * Sets the value of the width property.
3666 public void setWidth(Integer value) {
3671 * Gets the value of the height property.
3674 * possible object is
3678 public Integer getHeight() {
3683 * Sets the value of the height property.
3690 public void setHeight(Integer value) {
3691 this.height = value;
3695 * Gets the value of the xpos property.
3698 * possible object is
3702 public Integer getXpos() {
3707 * Sets the value of the xpos property.
3714 public void setXpos(Integer value) {
3719 * Gets the value of the ypos property.
3722 * possible object is
3726 public Integer getYpos() {
3731 * Sets the value of the ypos property.
3738 public void setYpos(Integer value) {
3744 * <p>Java class for anonymous complex type.
3746 * <p>The following schema fragment specifies the expected content contained within this class.
3749 * &lt;complexType&gt;
3750 * &lt;complexContent&gt;
3751 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3752 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3753 * &lt;/restriction&gt;
3754 * &lt;/complexContent&gt;
3755 * &lt;/complexType&gt;
3760 @XmlAccessorType(XmlAccessType.FIELD)
3762 public static class Axis {
3764 @XmlAttribute(name = "xPos")
3765 protected Float xPos;
3766 @XmlAttribute(name = "yPos")
3767 protected Float yPos;
3768 @XmlAttribute(name = "zPos")
3769 protected Float zPos;
3772 * Gets the value of the xPos property.
3775 * possible object is
3779 public Float getXPos() {
3784 * Sets the value of the xPos property.
3791 public void setXPos(Float value) {
3796 * Gets the value of the yPos property.
3799 * possible object is
3803 public Float getYPos() {
3808 * Sets the value of the yPos property.
3815 public void setYPos(Float value) {
3820 * Gets the value of the zPos property.
3823 * possible object is
3827 public Float getZPos() {
3832 * Sets the value of the zPos property.
3839 public void setZPos(Float value) {
3847 * <p>Java class for anonymous complex type.
3849 * <p>The following schema fragment specifies the expected content contained within this class.
3852 * &lt;complexType&gt;
3853 * &lt;complexContent&gt;
3854 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3855 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3856 * &lt;/restriction&gt;
3857 * &lt;/complexContent&gt;
3858 * &lt;/complexType&gt;
3863 @XmlAccessorType(XmlAccessType.FIELD)
3865 public static class SeqPointMax {
3867 @XmlAttribute(name = "xPos")
3868 protected Float xPos;
3869 @XmlAttribute(name = "yPos")
3870 protected Float yPos;
3871 @XmlAttribute(name = "zPos")
3872 protected Float zPos;
3875 * Gets the value of the xPos property.
3878 * possible object is
3882 public Float getXPos() {
3887 * Sets the value of the xPos property.
3894 public void setXPos(Float value) {
3899 * Gets the value of the yPos property.
3902 * possible object is
3906 public Float getYPos() {
3911 * Sets the value of the yPos property.
3918 public void setYPos(Float value) {
3923 * Gets the value of the zPos property.
3926 * possible object is
3930 public Float getZPos() {
3935 * Sets the value of the zPos property.
3942 public void setZPos(Float value) {
3950 * <p>Java class for anonymous complex type.
3952 * <p>The following schema fragment specifies the expected content contained within this class.
3955 * &lt;complexType&gt;
3956 * &lt;complexContent&gt;
3957 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3958 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3959 * &lt;/restriction&gt;
3960 * &lt;/complexContent&gt;
3961 * &lt;/complexType&gt;
3966 @XmlAccessorType(XmlAccessType.FIELD)
3968 public static class SeqPointMin {
3970 @XmlAttribute(name = "xPos")
3971 protected Float xPos;
3972 @XmlAttribute(name = "yPos")
3973 protected Float yPos;
3974 @XmlAttribute(name = "zPos")
3975 protected Float zPos;
3978 * Gets the value of the xPos property.
3981 * possible object is
3985 public Float getXPos() {
3990 * Sets the value of the xPos property.
3997 public void setXPos(Float value) {
4002 * Gets the value of the yPos property.
4005 * possible object is
4009 public Float getYPos() {
4014 * Sets the value of the yPos property.
4021 public void setYPos(Float value) {
4026 * Gets the value of the zPos property.
4029 * possible object is
4033 public Float getZPos() {
4038 * Sets the value of the zPos property.
4045 public void setZPos(Float value) {
4053 * <p>Java class for anonymous complex type.
4055 * <p>The following schema fragment specifies the expected content contained within this class.
4058 * &lt;complexType&gt;
4059 * &lt;complexContent&gt;
4060 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4061 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
4062 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4063 * &lt;/restriction&gt;
4064 * &lt;/complexContent&gt;
4065 * &lt;/complexType&gt;
4070 @XmlAccessorType(XmlAccessType.FIELD)
4072 public static class SequencePoint {
4074 @XmlAttribute(name = "sequenceRef")
4075 protected String sequenceRef;
4076 @XmlAttribute(name = "xPos")
4077 protected Float xPos;
4078 @XmlAttribute(name = "yPos")
4079 protected Float yPos;
4080 @XmlAttribute(name = "zPos")
4081 protected Float zPos;
4084 * Gets the value of the sequenceRef property.
4087 * possible object is
4091 public String getSequenceRef() {
4096 * Sets the value of the sequenceRef property.
4103 public void setSequenceRef(String value) {
4104 this.sequenceRef = value;
4108 * Gets the value of the xPos property.
4111 * possible object is
4115 public Float getXPos() {
4120 * Sets the value of the xPos property.
4127 public void setXPos(Float value) {
4132 * Gets the value of the yPos property.
4135 * possible object is
4139 public Float getYPos() {
4144 * Sets the value of the yPos property.
4151 public void setYPos(Float value) {
4156 * Gets the value of the zPos property.
4159 * possible object is
4163 public Float getZPos() {
4168 * Sets the value of the zPos property.
4175 public void setZPos(Float value) {
4185 * <p>Java class for anonymous complex type.
4187 * <p>The following schema fragment specifies the expected content contained within this class.
4190 * &lt;complexType&gt;
4191 * &lt;complexContent&gt;
4192 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4193 * &lt;sequence minOccurs="0"&gt;
4194 * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4195 * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4196 * &lt;/sequence&gt;
4197 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4198 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4199 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4200 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4201 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
4202 * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4203 * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4204 * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4205 * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4206 * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4207 * &lt;attribute name="columnWise" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4208 * &lt;attribute name="columnReference" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4209 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4210 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4211 * &lt;/restriction&gt;
4212 * &lt;/complexContent&gt;
4213 * &lt;/complexType&gt;
4218 @XmlAccessorType(XmlAccessType.FIELD)
4219 @XmlType(name = "", propOrder = {
4223 public static class Tree {
4225 @XmlElement(namespace = "www.jalview.org")
4226 protected String title;
4227 @XmlElement(namespace = "www.jalview.org")
4228 protected String newick;
4229 @XmlAttribute(name = "fontName")
4230 protected String fontName;
4231 @XmlAttribute(name = "fontSize")
4232 protected Integer fontSize;
4233 @XmlAttribute(name = "fontStyle")
4234 protected Integer fontStyle;
4235 @XmlAttribute(name = "threshold")
4236 protected Float threshold;
4237 @XmlAttribute(name = "showBootstrap")
4238 protected Boolean showBootstrap;
4239 @XmlAttribute(name = "showDistances")
4240 protected Boolean showDistances;
4241 @XmlAttribute(name = "markUnlinked")
4242 protected Boolean markUnlinked;
4243 @XmlAttribute(name = "fitToWindow")
4244 protected Boolean fitToWindow;
4245 @XmlAttribute(name = "currentTree")
4246 protected Boolean currentTree;
4247 @XmlAttribute(name = "columnWise")
4248 protected Boolean columnWise;
4249 @XmlAttribute(name = "columnReference")
4250 protected String columnReference;
4251 @XmlAttribute(name = "id")
4252 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4254 @XmlSchemaType(name = "ID")
4255 protected String id;
4256 @XmlAttribute(name = "linkToAllViews")
4257 protected Boolean linkToAllViews;
4258 @XmlAttribute(name = "width")
4259 protected Integer width;
4260 @XmlAttribute(name = "height")
4261 protected Integer height;
4262 @XmlAttribute(name = "xpos")
4263 protected Integer xpos;
4264 @XmlAttribute(name = "ypos")
4265 protected Integer ypos;
4268 * Gets the value of the title property.
4271 * possible object is
4275 public String getTitle() {
4280 * Sets the value of the title property.
4287 public void setTitle(String value) {
4292 * Gets the value of the newick property.
4295 * possible object is
4299 public String getNewick() {
4304 * Sets the value of the newick property.
4311 public void setNewick(String value) {
4312 this.newick = value;
4316 * Gets the value of the fontName property.
4319 * possible object is
4323 public String getFontName() {
4328 * Sets the value of the fontName property.
4335 public void setFontName(String value) {
4336 this.fontName = value;
4340 * Gets the value of the fontSize property.
4343 * possible object is
4347 public Integer getFontSize() {
4352 * Sets the value of the fontSize property.
4359 public void setFontSize(Integer value) {
4360 this.fontSize = value;
4364 * Gets the value of the fontStyle property.
4367 * possible object is
4371 public Integer getFontStyle() {
4376 * Sets the value of the fontStyle property.
4383 public void setFontStyle(Integer value) {
4384 this.fontStyle = value;
4388 * Gets the value of the threshold property.
4391 * possible object is
4395 public Float getThreshold() {
4400 * Sets the value of the threshold property.
4407 public void setThreshold(Float value) {
4408 this.threshold = value;
4412 * Gets the value of the showBootstrap property.
4415 * possible object is
4419 public Boolean isShowBootstrap() {
4420 return showBootstrap;
4424 * Sets the value of the showBootstrap property.
4431 public void setShowBootstrap(Boolean value) {
4432 this.showBootstrap = value;
4436 * Gets the value of the showDistances property.
4439 * possible object is
4443 public Boolean isShowDistances() {
4444 return showDistances;
4448 * Sets the value of the showDistances property.
4455 public void setShowDistances(Boolean value) {
4456 this.showDistances = value;
4460 * Gets the value of the markUnlinked property.
4463 * possible object is
4467 public Boolean isMarkUnlinked() {
4468 return markUnlinked;
4472 * Sets the value of the markUnlinked property.
4479 public void setMarkUnlinked(Boolean value) {
4480 this.markUnlinked = value;
4484 * Gets the value of the fitToWindow property.
4487 * possible object is
4491 public Boolean isFitToWindow() {
4496 * Sets the value of the fitToWindow property.
4503 public void setFitToWindow(Boolean value) {
4504 this.fitToWindow = value;
4508 * Gets the value of the currentTree property.
4511 * possible object is
4515 public Boolean isCurrentTree() {
4520 * Sets the value of the currentTree property.
4527 public void setCurrentTree(Boolean value) {
4528 this.currentTree = value;
4532 * Gets the value of the columnWise property.
4535 * possible object is
4539 public boolean isColumnWise() {
4540 if (columnWise == null) {
4548 * Sets the value of the columnWise property.
4555 public void setColumnWise(Boolean value) {
4556 this.columnWise = value;
4560 * Gets the value of the columnReference property.
4563 * possible object is
4567 public String getColumnReference() {
4568 return columnReference;
4572 * Sets the value of the columnReference property.
4579 public void setColumnReference(String value) {
4580 this.columnReference = value;
4584 * Gets the value of the id property.
4587 * possible object is
4591 public String getId() {
4596 * Sets the value of the id property.
4603 public void setId(String value) {
4608 * Gets the value of the linkToAllViews property.
4611 * possible object is
4615 public boolean isLinkToAllViews() {
4616 if (linkToAllViews == null) {
4619 return linkToAllViews;
4624 * Sets the value of the linkToAllViews property.
4631 public void setLinkToAllViews(Boolean value) {
4632 this.linkToAllViews = value;
4636 * Gets the value of the width property.
4639 * possible object is
4643 public Integer getWidth() {
4648 * Sets the value of the width property.
4655 public void setWidth(Integer value) {
4660 * Gets the value of the height property.
4663 * possible object is
4667 public Integer getHeight() {
4672 * Sets the value of the height property.
4679 public void setHeight(Integer value) {
4680 this.height = value;
4684 * Gets the value of the xpos property.
4687 * possible object is
4691 public Integer getXpos() {
4696 * Sets the value of the xpos property.
4703 public void setXpos(Integer value) {
4708 * Gets the value of the ypos property.
4711 * possible object is
4715 public Integer getYpos() {
4720 * Sets the value of the ypos property.
4727 public void setYpos(Integer value) {
4735 * <p>Java class for anonymous complex type.
4737 * <p>The following schema fragment specifies the expected content contained within this class.
4740 * &lt;complexType&gt;
4741 * &lt;complexContent&gt;
4742 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4743 * &lt;sequence&gt;
4744 * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
4745 * &lt;/sequence&gt;
4746 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4747 * &lt;/restriction&gt;
4748 * &lt;/complexContent&gt;
4749 * &lt;/complexType&gt;
4754 @XmlAccessorType(XmlAccessType.FIELD)
4755 @XmlType(name = "", propOrder = {
4758 public static class UserColours {
4760 @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4761 protected JalviewUserColours userColourScheme;
4762 @XmlAttribute(name = "id")
4763 protected String id;
4766 * Gets the value of the userColourScheme property.
4769 * possible object is
4770 * {@link JalviewUserColours }
4773 public JalviewUserColours getUserColourScheme() {
4774 return userColourScheme;
4778 * Sets the value of the userColourScheme property.
4782 * {@link JalviewUserColours }
4785 public void setUserColourScheme(JalviewUserColours value) {
4786 this.userColourScheme = value;
4790 * Gets the value of the id property.
4793 * possible object is
4797 public String getId() {
4802 * Sets the value of the id property.
4809 public void setId(String value) {
4817 * <p>Java class for anonymous complex type.
4819 * <p>The following schema fragment specifies the expected content contained within this class.
4822 * &lt;complexType&gt;
4823 * &lt;complexContent&gt;
4824 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4825 * &lt;sequence&gt;
4826 * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
4827 * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
4828 * &lt;complexType&gt;
4829 * &lt;complexContent&gt;
4830 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4831 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4832 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4833 * &lt;/restriction&gt;
4834 * &lt;/complexContent&gt;
4835 * &lt;/complexType&gt;
4836 * &lt;/element&gt;
4837 * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
4838 * &lt;complexType&gt;
4839 * &lt;complexContent&gt;
4840 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
4841 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4842 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4843 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4844 * &lt;/extension&gt;
4845 * &lt;/complexContent&gt;
4846 * &lt;/complexType&gt;
4847 * &lt;/element&gt;
4848 * &lt;element name="overview" minOccurs="0"&gt;
4849 * &lt;complexType&gt;
4850 * &lt;complexContent&gt;
4851 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4852 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4853 * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4854 * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4855 * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4856 * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4857 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4858 * &lt;/restriction&gt;
4859 * &lt;/complexContent&gt;
4860 * &lt;/complexType&gt;
4861 * &lt;/element&gt;
4862 * &lt;/sequence&gt;
4863 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4864 * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4865 * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4866 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4867 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4868 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4869 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4870 * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4871 * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4872 * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4873 * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4874 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4875 * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4876 * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4877 * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4878 * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4879 * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4880 * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4881 * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4882 * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4883 * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4884 * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4885 * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4886 * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4887 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4888 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4889 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4890 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4891 * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4892 * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4893 * &lt;attribute name="charWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4894 * &lt;attribute name="charHeight" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4895 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4896 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4897 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4898 * &lt;attribute name="idWidth" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4899 * &lt;attribute name="idWidthManuallyAdjusted" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4900 * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4901 * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4902 * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4903 * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4904 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4905 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4906 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4907 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4908 * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4909 * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4910 * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4911 * &lt;/restriction&gt;
4912 * &lt;/complexContent&gt;
4913 * &lt;/complexType&gt;
4918 @XmlAccessorType(XmlAccessType.FIELD)
4919 @XmlType(name = "", propOrder = {
4920 "annotationColours",
4925 public static class Viewport {
4927 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4928 protected AnnotationColourScheme annotationColours;
4929 @XmlElement(namespace = "www.jalview.org")
4930 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4931 @XmlElement(namespace = "www.jalview.org")
4932 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4933 @XmlElement(namespace = "www.jalview.org")
4934 protected JalviewModel.Viewport.Overview overview;
4935 @XmlAttribute(name = "conservationSelected")
4936 protected Boolean conservationSelected;
4937 @XmlAttribute(name = "pidSelected")
4938 protected Boolean pidSelected;
4939 @XmlAttribute(name = "bgColour")
4940 protected String bgColour;
4941 @XmlAttribute(name = "consThreshold")
4942 protected Integer consThreshold;
4943 @XmlAttribute(name = "pidThreshold")
4944 protected Integer pidThreshold;
4945 @XmlAttribute(name = "title")
4946 protected String title;
4947 @XmlAttribute(name = "showFullId")
4948 protected Boolean showFullId;
4949 @XmlAttribute(name = "rightAlignIds")
4950 protected Boolean rightAlignIds;
4951 @XmlAttribute(name = "showText")
4952 protected Boolean showText;
4953 @XmlAttribute(name = "showColourText")
4954 protected Boolean showColourText;
4955 @XmlAttribute(name = "showUnconserved")
4956 protected Boolean showUnconserved;
4957 @XmlAttribute(name = "showBoxes")
4958 protected Boolean showBoxes;
4959 @XmlAttribute(name = "wrapAlignment")
4960 protected Boolean wrapAlignment;
4961 @XmlAttribute(name = "renderGaps")
4962 protected Boolean renderGaps;
4963 @XmlAttribute(name = "showSequenceFeatures")
4964 protected Boolean showSequenceFeatures;
4965 @XmlAttribute(name = "showNPfeatureTooltip")
4966 protected Boolean showNPfeatureTooltip;
4967 @XmlAttribute(name = "showDbRefTooltip")
4968 protected Boolean showDbRefTooltip;
4969 @XmlAttribute(name = "followHighlight")
4970 protected Boolean followHighlight;
4971 @XmlAttribute(name = "followSelection")
4972 protected Boolean followSelection;
4973 @XmlAttribute(name = "showAnnotation")
4974 protected Boolean showAnnotation;
4975 @XmlAttribute(name = "centreColumnLabels")
4976 protected Boolean centreColumnLabels;
4977 @XmlAttribute(name = "showGroupConservation")
4978 protected Boolean showGroupConservation;
4979 @XmlAttribute(name = "showGroupConsensus")
4980 protected Boolean showGroupConsensus;
4981 @XmlAttribute(name = "showConsensusHistogram")
4982 protected Boolean showConsensusHistogram;
4983 @XmlAttribute(name = "showSequenceLogo")
4984 protected Boolean showSequenceLogo;
4985 @XmlAttribute(name = "normaliseSequenceLogo")
4986 protected Boolean normaliseSequenceLogo;
4987 @XmlAttribute(name = "ignoreGapsinConsensus")
4988 protected Boolean ignoreGapsinConsensus;
4989 @XmlAttribute(name = "startRes")
4990 protected Integer startRes;
4991 @XmlAttribute(name = "startSeq")
4992 protected Integer startSeq;
4993 @XmlAttribute(name = "charWidth")
4994 protected Integer charWidth;
4995 @XmlAttribute(name = "charHeight")
4996 protected Integer charHeight;
4997 @XmlAttribute(name = "fontName")
4998 protected String fontName;
4999 @XmlAttribute(name = "fontSize")
5000 protected Integer fontSize;
5001 @XmlAttribute(name = "fontStyle")
5002 protected Integer fontStyle;
5003 @XmlAttribute(name = "idWidth")
5004 protected Integer idWidth;
5005 @XmlAttribute(name = "idWidthManuallyAdjusted")
5006 protected Boolean idWidthManuallyAdjusted;
5007 @XmlAttribute(name = "scaleProteinAsCdna")
5008 protected Boolean scaleProteinAsCdna;
5009 @XmlAttribute(name = "viewName")
5010 protected String viewName;
5011 @XmlAttribute(name = "sequenceSetId")
5012 protected String sequenceSetId;
5013 @XmlAttribute(name = "gatheredViews")
5014 protected Boolean gatheredViews;
5015 @XmlAttribute(name = "textCol1")
5016 protected Integer textCol1;
5017 @XmlAttribute(name = "textCol2")
5018 protected Integer textCol2;
5019 @XmlAttribute(name = "textColThreshold")
5020 protected Integer textColThreshold;
5021 @XmlAttribute(name = "id")
5022 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
5024 @XmlSchemaType(name = "ID")
5025 protected String id;
5026 @XmlAttribute(name = "complementId")
5027 protected String complementId;
5028 @XmlAttribute(name = "showComplementFeatures")
5029 protected Boolean showComplementFeatures;
5030 @XmlAttribute(name = "showComplementFeaturesOnTop")
5031 protected Boolean showComplementFeaturesOnTop;
5032 @XmlAttribute(name = "width")
5033 protected Integer width;
5034 @XmlAttribute(name = "height")
5035 protected Integer height;
5036 @XmlAttribute(name = "xpos")
5037 protected Integer xpos;
5038 @XmlAttribute(name = "ypos")
5039 protected Integer ypos;
5042 * Gets the value of the annotationColours property.
5045 * possible object is
5046 * {@link AnnotationColourScheme }
5049 public AnnotationColourScheme getAnnotationColours() {
5050 return annotationColours;
5054 * Sets the value of the annotationColours property.
5058 * {@link AnnotationColourScheme }
5061 public void setAnnotationColours(AnnotationColourScheme value) {
5062 this.annotationColours = value;
5066 * Gets the value of the hiddenColumns property.
5069 * This accessor method returns a reference to the live list,
5070 * not a snapshot. Therefore any modification you make to the
5071 * returned list will be present inside the JAXB object.
5072 * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
5075 * For example, to add a new item, do as follows:
5077 * getHiddenColumns().add(newItem);
5082 * Objects of the following type(s) are allowed in the list
5083 * {@link JalviewModel.Viewport.HiddenColumns }
5087 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5088 if (hiddenColumns == null) {
5089 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5091 return this.hiddenColumns;
5095 * Gets the value of the calcIdParam property.
5098 * This accessor method returns a reference to the live list,
5099 * not a snapshot. Therefore any modification you make to the
5100 * returned list will be present inside the JAXB object.
5101 * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5104 * For example, to add a new item, do as follows:
5106 * getCalcIdParam().add(newItem);
5111 * Objects of the following type(s) are allowed in the list
5112 * {@link JalviewModel.Viewport.CalcIdParam }
5116 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5117 if (calcIdParam == null) {
5118 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5120 return this.calcIdParam;
5124 * Gets the value of the overview property.
5127 * possible object is
5128 * {@link JalviewModel.Viewport.Overview }
5131 public JalviewModel.Viewport.Overview getOverview() {
5136 * Sets the value of the overview property.
5140 * {@link JalviewModel.Viewport.Overview }
5143 public void setOverview(JalviewModel.Viewport.Overview value) {
5144 this.overview = value;
5148 * Gets the value of the conservationSelected property.
5151 * possible object is
5155 public Boolean isConservationSelected() {
5156 return conservationSelected;
5160 * Sets the value of the conservationSelected property.
5167 public void setConservationSelected(Boolean value) {
5168 this.conservationSelected = value;
5172 * Gets the value of the pidSelected property.
5175 * possible object is
5179 public Boolean isPidSelected() {
5184 * Sets the value of the pidSelected property.
5191 public void setPidSelected(Boolean value) {
5192 this.pidSelected = value;
5196 * Gets the value of the bgColour property.
5199 * possible object is
5203 public String getBgColour() {
5208 * Sets the value of the bgColour property.
5215 public void setBgColour(String value) {
5216 this.bgColour = value;
5220 * Gets the value of the consThreshold property.
5223 * possible object is
5227 public Integer getConsThreshold() {
5228 return consThreshold;
5232 * Sets the value of the consThreshold property.
5239 public void setConsThreshold(Integer value) {
5240 this.consThreshold = value;
5244 * Gets the value of the pidThreshold property.
5247 * possible object is
5251 public Integer getPidThreshold() {
5252 return pidThreshold;
5256 * Sets the value of the pidThreshold property.
5263 public void setPidThreshold(Integer value) {
5264 this.pidThreshold = value;
5268 * Gets the value of the title property.
5271 * possible object is
5275 public String getTitle() {
5280 * Sets the value of the title property.
5287 public void setTitle(String value) {
5292 * Gets the value of the showFullId property.
5295 * possible object is
5299 public Boolean isShowFullId() {
5304 * Sets the value of the showFullId property.
5311 public void setShowFullId(Boolean value) {
5312 this.showFullId = value;
5316 * Gets the value of the rightAlignIds property.
5319 * possible object is
5323 public Boolean isRightAlignIds() {
5324 return rightAlignIds;
5328 * Sets the value of the rightAlignIds property.
5335 public void setRightAlignIds(Boolean value) {
5336 this.rightAlignIds = value;
5340 * Gets the value of the showText property.
5343 * possible object is
5347 public Boolean isShowText() {
5352 * Sets the value of the showText property.
5359 public void setShowText(Boolean value) {
5360 this.showText = value;
5364 * Gets the value of the showColourText property.
5367 * possible object is
5371 public Boolean isShowColourText() {
5372 return showColourText;
5376 * Sets the value of the showColourText property.
5383 public void setShowColourText(Boolean value) {
5384 this.showColourText = value;
5388 * Gets the value of the showUnconserved property.
5391 * possible object is
5395 public boolean isShowUnconserved() {
5396 if (showUnconserved == null) {
5399 return showUnconserved;
5404 * Sets the value of the showUnconserved property.
5411 public void setShowUnconserved(Boolean value) {
5412 this.showUnconserved = value;
5416 * Gets the value of the showBoxes property.
5419 * possible object is
5423 public Boolean isShowBoxes() {
5428 * Sets the value of the showBoxes property.
5435 public void setShowBoxes(Boolean value) {
5436 this.showBoxes = value;
5440 * Gets the value of the wrapAlignment property.
5443 * possible object is
5447 public Boolean isWrapAlignment() {
5448 return wrapAlignment;
5452 * Sets the value of the wrapAlignment property.
5459 public void setWrapAlignment(Boolean value) {
5460 this.wrapAlignment = value;
5464 * Gets the value of the renderGaps property.
5467 * possible object is
5471 public Boolean isRenderGaps() {
5476 * Sets the value of the renderGaps property.
5483 public void setRenderGaps(Boolean value) {
5484 this.renderGaps = value;
5488 * Gets the value of the showSequenceFeatures property.
5491 * possible object is
5495 public Boolean isShowSequenceFeatures() {
5496 return showSequenceFeatures;
5500 * Sets the value of the showSequenceFeatures property.
5507 public void setShowSequenceFeatures(Boolean value) {
5508 this.showSequenceFeatures = value;
5512 * Gets the value of the showNPfeatureTooltip property.
5515 * possible object is
5519 public Boolean isShowNPfeatureTooltip() {
5520 return showNPfeatureTooltip;
5524 * Sets the value of the showNPfeatureTooltip property.
5531 public void setShowNPfeatureTooltip(Boolean value) {
5532 this.showNPfeatureTooltip = value;
5536 * Gets the value of the showDbRefTooltip property.
5539 * possible object is
5543 public Boolean isShowDbRefTooltip() {
5544 return showDbRefTooltip;
5548 * Sets the value of the showDbRefTooltip property.
5555 public void setShowDbRefTooltip(Boolean value) {
5556 this.showDbRefTooltip = value;
5560 * Gets the value of the followHighlight property.
5563 * possible object is
5567 public boolean isFollowHighlight() {
5568 if (followHighlight == null) {
5571 return followHighlight;
5576 * Sets the value of the followHighlight property.
5583 public void setFollowHighlight(Boolean value) {
5584 this.followHighlight = value;
5588 * Gets the value of the followSelection property.
5591 * possible object is
5595 public boolean isFollowSelection() {
5596 if (followSelection == null) {
5599 return followSelection;
5604 * Sets the value of the followSelection property.
5611 public void setFollowSelection(Boolean value) {
5612 this.followSelection = value;
5616 * Gets the value of the showAnnotation property.
5619 * possible object is
5623 public Boolean isShowAnnotation() {
5624 return showAnnotation;
5628 * Sets the value of the showAnnotation property.
5635 public void setShowAnnotation(Boolean value) {
5636 this.showAnnotation = value;
5640 * Gets the value of the centreColumnLabels property.
5643 * possible object is
5647 public boolean isCentreColumnLabels() {
5648 if (centreColumnLabels == null) {
5651 return centreColumnLabels;
5656 * Sets the value of the centreColumnLabels property.
5663 public void setCentreColumnLabels(Boolean value) {
5664 this.centreColumnLabels = value;
5668 * Gets the value of the showGroupConservation property.
5671 * possible object is
5675 public boolean isShowGroupConservation() {
5676 if (showGroupConservation == null) {
5679 return showGroupConservation;
5684 * Sets the value of the showGroupConservation property.
5691 public void setShowGroupConservation(Boolean value) {
5692 this.showGroupConservation = value;
5696 * Gets the value of the showGroupConsensus property.
5699 * possible object is
5703 public boolean isShowGroupConsensus() {
5704 if (showGroupConsensus == null) {
5707 return showGroupConsensus;
5712 * Sets the value of the showGroupConsensus property.
5719 public void setShowGroupConsensus(Boolean value) {
5720 this.showGroupConsensus = value;
5724 * Gets the value of the showConsensusHistogram property.
5727 * possible object is
5731 public boolean isShowConsensusHistogram() {
5732 if (showConsensusHistogram == null) {
5735 return showConsensusHistogram;
5740 * Sets the value of the showConsensusHistogram property.
5747 public void setShowConsensusHistogram(Boolean value) {
5748 this.showConsensusHistogram = value;
5752 * Gets the value of the showSequenceLogo property.
5755 * possible object is
5759 public boolean isShowSequenceLogo() {
5760 if (showSequenceLogo == null) {
5763 return showSequenceLogo;
5768 * Sets the value of the showSequenceLogo property.
5775 public void setShowSequenceLogo(Boolean value) {
5776 this.showSequenceLogo = value;
5780 * Gets the value of the normaliseSequenceLogo property.
5783 * possible object is
5787 public boolean isNormaliseSequenceLogo() {
5788 if (normaliseSequenceLogo == null) {
5791 return normaliseSequenceLogo;
5796 * Sets the value of the normaliseSequenceLogo property.
5803 public void setNormaliseSequenceLogo(Boolean value) {
5804 this.normaliseSequenceLogo = value;
5808 * Gets the value of the ignoreGapsinConsensus property.
5811 * possible object is
5815 public boolean isIgnoreGapsinConsensus() {
5816 if (ignoreGapsinConsensus == null) {
5819 return ignoreGapsinConsensus;
5824 * Sets the value of the ignoreGapsinConsensus property.
5831 public void setIgnoreGapsinConsensus(Boolean value) {
5832 this.ignoreGapsinConsensus = value;
5836 * Gets the value of the startRes property.
5839 * possible object is
5843 public Integer getStartRes() {
5848 * Sets the value of the startRes property.
5855 public void setStartRes(Integer value) {
5856 this.startRes = value;
5860 * Gets the value of the startSeq property.
5863 * possible object is
5867 public Integer getStartSeq() {
5872 * Sets the value of the startSeq property.
5879 public void setStartSeq(Integer value) {
5880 this.startSeq = value;
5884 * Gets the value of the charWidth property.
5887 * possible object is
5891 public Integer getCharWidth() {
5896 * Sets the value of the charWidth property.
5903 public void setCharWidth(Integer value) {
5904 this.charWidth = value;
5908 * Gets the value of the charHeight property.
5911 * possible object is
5915 public Integer getCharHeight() {
5920 * Sets the value of the charHeight property.
5927 public void setCharHeight(Integer value) {
5928 this.charHeight = value;
5932 * Gets the value of the fontName property.
5935 * possible object is
5939 public String getFontName() {
5944 * Sets the value of the fontName property.
5951 public void setFontName(String value) {
5952 this.fontName = value;
5956 * Gets the value of the fontSize property.
5959 * possible object is
5963 public Integer getFontSize() {
5968 * Sets the value of the fontSize property.
5975 public void setFontSize(Integer value) {
5976 this.fontSize = value;
5980 * Gets the value of the fontStyle property.
5983 * possible object is
5987 public Integer getFontStyle() {
5992 * Sets the value of the fontStyle property.
5999 public void setFontStyle(Integer value) {
6000 this.fontStyle = value;
6004 * Gets the value of the idWidth property.
6007 * possible object is
6011 public Integer getIdWidth() {
6016 * Sets the value of the idWidth property.
6023 public void setIdWidth(Integer value) {
6024 this.idWidth = value;
6028 * Gets the value of the idWidthManuallyAdjusted property.
6031 * possible object is
6035 public Boolean isIdWidthManuallyAdjusted() {
6036 return idWidthManuallyAdjusted;
6040 * Sets the value of the idWidthManuallyAdjusted property.
6047 public void setIdWidthManuallyAdjusted(Boolean value) {
6048 this.idWidthManuallyAdjusted = value;
6052 * Gets the value of the scaleProteinAsCdna property.
6055 * possible object is
6059 public boolean isScaleProteinAsCdna() {
6060 if (scaleProteinAsCdna == null) {
6063 return scaleProteinAsCdna;
6068 * Sets the value of the scaleProteinAsCdna property.
6075 public void setScaleProteinAsCdna(Boolean value) {
6076 this.scaleProteinAsCdna = value;
6080 * Gets the value of the viewName property.
6083 * possible object is
6087 public String getViewName() {
6092 * Sets the value of the viewName property.
6099 public void setViewName(String value) {
6100 this.viewName = value;
6104 * Gets the value of the sequenceSetId property.
6107 * possible object is
6111 public String getSequenceSetId() {
6112 return sequenceSetId;
6116 * Sets the value of the sequenceSetId property.
6123 public void setSequenceSetId(String value) {
6124 this.sequenceSetId = value;
6128 * Gets the value of the gatheredViews property.
6131 * possible object is
6135 public Boolean isGatheredViews() {
6136 return gatheredViews;
6140 * Sets the value of the gatheredViews property.
6147 public void setGatheredViews(Boolean value) {
6148 this.gatheredViews = value;
6152 * Gets the value of the textCol1 property.
6155 * possible object is
6159 public Integer getTextCol1() {
6164 * Sets the value of the textCol1 property.
6171 public void setTextCol1(Integer value) {
6172 this.textCol1 = value;
6176 * Gets the value of the textCol2 property.
6179 * possible object is
6183 public Integer getTextCol2() {
6188 * Sets the value of the textCol2 property.
6195 public void setTextCol2(Integer value) {
6196 this.textCol2 = value;
6200 * Gets the value of the textColThreshold property.
6203 * possible object is
6207 public Integer getTextColThreshold() {
6208 return textColThreshold;
6212 * Sets the value of the textColThreshold property.
6219 public void setTextColThreshold(Integer value) {
6220 this.textColThreshold = value;
6224 * Gets the value of the id property.
6227 * possible object is
6231 public String getId() {
6236 * Sets the value of the id property.
6243 public void setId(String value) {
6248 * Gets the value of the complementId property.
6251 * possible object is
6255 public String getComplementId() {
6256 return complementId;
6260 * Sets the value of the complementId property.
6267 public void setComplementId(String value) {
6268 this.complementId = value;
6272 * Gets the value of the showComplementFeatures property.
6275 * possible object is
6279 public boolean isShowComplementFeatures() {
6280 if (showComplementFeatures == null) {
6283 return showComplementFeatures;
6288 * Sets the value of the showComplementFeatures property.
6295 public void setShowComplementFeatures(Boolean value) {
6296 this.showComplementFeatures = value;
6300 * Gets the value of the showComplementFeaturesOnTop property.
6303 * possible object is
6307 public boolean isShowComplementFeaturesOnTop() {
6308 if (showComplementFeaturesOnTop == null) {
6311 return showComplementFeaturesOnTop;
6316 * Sets the value of the showComplementFeaturesOnTop property.
6323 public void setShowComplementFeaturesOnTop(Boolean value) {
6324 this.showComplementFeaturesOnTop = value;
6328 * Gets the value of the width property.
6331 * possible object is
6335 public Integer getWidth() {
6340 * Sets the value of the width property.
6347 public void setWidth(Integer value) {
6352 * Gets the value of the height property.
6355 * possible object is
6359 public Integer getHeight() {
6364 * Sets the value of the height property.
6371 public void setHeight(Integer value) {
6372 this.height = value;
6376 * Gets the value of the xpos property.
6379 * possible object is
6383 public Integer getXpos() {
6388 * Sets the value of the xpos property.
6395 public void setXpos(Integer value) {
6400 * Gets the value of the ypos property.
6403 * possible object is
6407 public Integer getYpos() {
6412 * Sets the value of the ypos property.
6419 public void setYpos(Integer value) {
6425 * <p>Java class for anonymous complex type.
6427 * <p>The following schema fragment specifies the expected content contained within this class.
6430 * &lt;complexType&gt;
6431 * &lt;complexContent&gt;
6432 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
6433 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
6434 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
6435 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
6436 * &lt;/extension&gt;
6437 * &lt;/complexContent&gt;
6438 * &lt;/complexType&gt;
6443 @XmlAccessorType(XmlAccessType.FIELD)
6445 public static class CalcIdParam
6446 extends WebServiceParameterSet
6449 @XmlAttribute(name = "calcId", required = true)
6450 protected String calcId;
6451 @XmlAttribute(name = "needsUpdate")
6452 protected Boolean needsUpdate;
6453 @XmlAttribute(name = "autoUpdate", required = true)
6454 protected boolean autoUpdate;
6457 * Gets the value of the calcId property.
6460 * possible object is
6464 public String getCalcId() {
6469 * Sets the value of the calcId property.
6476 public void setCalcId(String value) {
6477 this.calcId = value;
6481 * Gets the value of the needsUpdate property.
6484 * possible object is
6488 public boolean isNeedsUpdate() {
6489 if (needsUpdate == null) {
6497 * Sets the value of the needsUpdate property.
6504 public void setNeedsUpdate(Boolean value) {
6505 this.needsUpdate = value;
6509 * Gets the value of the autoUpdate property.
6512 public boolean isAutoUpdate() {
6517 * Sets the value of the autoUpdate property.
6520 public void setAutoUpdate(boolean value) {
6521 this.autoUpdate = value;
6528 * <p>Java class for anonymous complex type.
6530 * <p>The following schema fragment specifies the expected content contained within this class.
6533 * &lt;complexType&gt;
6534 * &lt;complexContent&gt;
6535 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
6536 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6537 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6538 * &lt;/restriction&gt;
6539 * &lt;/complexContent&gt;
6540 * &lt;/complexType&gt;
6545 @XmlAccessorType(XmlAccessType.FIELD)
6547 public static class HiddenColumns {
6549 @XmlAttribute(name = "start")
6550 protected Integer start;
6551 @XmlAttribute(name = "end")
6552 protected Integer end;
6555 * Gets the value of the start property.
6558 * possible object is
6562 public Integer getStart() {
6567 * Sets the value of the start property.
6574 public void setStart(Integer value) {
6579 * Gets the value of the end property.
6582 * possible object is
6586 public Integer getEnd() {
6591 * Sets the value of the end property.
6598 public void setEnd(Integer value) {
6606 * <p>Java class for anonymous complex type.
6608 * <p>The following schema fragment specifies the expected content contained within this class.
6611 * &lt;complexType&gt;
6612 * &lt;complexContent&gt;
6613 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
6614 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
6615 * &lt;attribute name="showHidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
6616 * &lt;attribute name="residueColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6617 * &lt;attribute name="gapColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6618 * &lt;attribute name="hiddenColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6619 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
6620 * &lt;/restriction&gt;
6621 * &lt;/complexContent&gt;
6622 * &lt;/complexType&gt;
6627 @XmlAccessorType(XmlAccessType.FIELD)
6629 public static class Overview {
6631 @XmlAttribute(name = "showHidden")
6632 protected Boolean showHidden;
6633 @XmlAttribute(name = "residueColour")
6634 protected Integer residueColour;
6635 @XmlAttribute(name = "gapColour")
6636 protected Integer gapColour;
6637 @XmlAttribute(name = "hiddenColour")
6638 protected Integer hiddenColour;
6639 @XmlAttribute(name = "title")
6640 protected String title;
6641 @XmlAttribute(name = "width")
6642 protected Integer width;
6643 @XmlAttribute(name = "height")
6644 protected Integer height;
6645 @XmlAttribute(name = "xpos")
6646 protected Integer xpos;
6647 @XmlAttribute(name = "ypos")
6648 protected Integer ypos;
6651 * Gets the value of the showHidden property.
6654 * possible object is
6658 public Boolean isShowHidden() {
6663 * Sets the value of the showHidden property.
6670 public void setShowHidden(Boolean value) {
6671 this.showHidden = value;
6675 * Gets the value of the residueColour property.
6678 * possible object is
6682 public Integer getResidueColour() {
6683 return residueColour;
6687 * Sets the value of the residueColour property.
6694 public void setResidueColour(Integer value) {
6695 this.residueColour = value;
6699 * Gets the value of the gapColour property.
6702 * possible object is
6706 public Integer getGapColour() {
6711 * Sets the value of the gapColour property.
6718 public void setGapColour(Integer value) {
6719 this.gapColour = value;
6723 * Gets the value of the hiddenColour property.
6726 * possible object is
6730 public Integer getHiddenColour() {
6731 return hiddenColour;
6735 * Sets the value of the hiddenColour property.
6742 public void setHiddenColour(Integer value) {
6743 this.hiddenColour = value;
6747 * Gets the value of the title property.
6750 * possible object is
6754 public String getTitle() {
6759 * Sets the value of the title property.
6766 public void setTitle(String value) {
6771 * Gets the value of the width property.
6774 * possible object is
6778 public Integer getWidth() {
6783 * Sets the value of the width property.
6790 public void setWidth(Integer value) {
6795 * Gets the value of the height property.
6798 * possible object is
6802 public Integer getHeight() {
6807 * Sets the value of the height property.
6814 public void setHeight(Integer value) {
6815 this.height = value;
6819 * Gets the value of the xpos property.
6822 * possible object is
6826 public Integer getXpos() {
6831 * Sets the value of the xpos property.
6838 public void setXpos(Integer value) {
6843 * Gets the value of the ypos property.
6846 * possible object is
6850 public Integer getYpos() {
6855 * Sets the value of the ypos property.
6862 public void setYpos(Integer value) {