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: 2021.08.30 at 11:05:22 AM BST
9 package jalview.xml.binding.jalview;
11 import java.util.ArrayList;
12 import java.util.List;
13 import javax.xml.bind.annotation.XmlAccessType;
14 import javax.xml.bind.annotation.XmlAccessorType;
15 import javax.xml.bind.annotation.XmlAttribute;
16 import javax.xml.bind.annotation.XmlElement;
17 import javax.xml.bind.annotation.XmlID;
18 import javax.xml.bind.annotation.XmlSchemaType;
19 import javax.xml.bind.annotation.XmlType;
20 import javax.xml.bind.annotation.XmlValue;
21 import javax.xml.bind.annotation.adapters.CollapsedStringAdapter;
22 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
23 import javax.xml.datatype.XMLGregorianCalendar;
27 * <p>Java class for JalviewModel complex type.
29 * <p>The following schema fragment specifies the expected content contained within this class.
32 * &lt;complexType name="JalviewModel"&gt;
33 * &lt;complexContent&gt;
34 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
35 * &lt;sequence&gt;
36 * &lt;element name="creationDate" type="{http://www.w3.org/2001/XMLSchema}dateTime"/&gt;
37 * &lt;element name="version" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
38 * &lt;element name="vamsasModel" type="{www.vamsas.ac.uk/jalview/version2}VAMSAS"/&gt;
39 * &lt;sequence&gt;
40 * &lt;element name="JSeq" maxOccurs="unbounded" minOccurs="0"&gt;
41 * &lt;complexType&gt;
42 * &lt;complexContent&gt;
43 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
44 * &lt;sequence&gt;
45 * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
46 * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
47 * &lt;complexType&gt;
48 * &lt;complexContent&gt;
49 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
50 * &lt;sequence&gt;
51 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
52 * &lt;complexType&gt;
53 * &lt;simpleContent&gt;
54 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
55 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
56 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
57 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
58 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
59 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
60 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
61 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
62 * &lt;/extension&gt;
63 * &lt;/simpleContent&gt;
64 * &lt;/complexType&gt;
65 * &lt;/element&gt;
66 * &lt;/sequence&gt;
67 * &lt;/extension&gt;
68 * &lt;/complexContent&gt;
69 * &lt;/complexType&gt;
70 * &lt;/element&gt;
71 * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
72 * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
73 * &lt;complexType&gt;
74 * &lt;complexContent&gt;
75 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
76 * &lt;sequence&gt;
77 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
78 * &lt;complexType&gt;
79 * &lt;complexContent&gt;
80 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
81 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
82 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
83 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
84 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
85 * &lt;/restriction&gt;
86 * &lt;/complexContent&gt;
87 * &lt;/complexType&gt;
88 * &lt;/element&gt;
89 * &lt;/sequence&gt;
90 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
91 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
92 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
93 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
94 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
95 * &lt;/restriction&gt;
96 * &lt;/complexContent&gt;
97 * &lt;/complexType&gt;
98 * &lt;/element&gt;
99 * &lt;/sequence&gt;
100 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
101 * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
102 * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
103 * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
104 * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
105 * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
106 * &lt;/restriction&gt;
107 * &lt;/complexContent&gt;
108 * &lt;/complexType&gt;
109 * &lt;/element&gt;
110 * &lt;element name="JGroup" maxOccurs="unbounded" minOccurs="0"&gt;
111 * &lt;complexType&gt;
112 * &lt;complexContent&gt;
113 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
114 * &lt;sequence&gt;
115 * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
116 * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
117 * &lt;/sequence&gt;
118 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
119 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
120 * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
121 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
122 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
123 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
124 * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
125 * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
126 * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
127 * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
128 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
129 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
130 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
131 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
132 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
133 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
134 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
135 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
136 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
137 * &lt;/restriction&gt;
138 * &lt;/complexContent&gt;
139 * &lt;/complexType&gt;
140 * &lt;/element&gt;
141 * &lt;element name="Viewport" maxOccurs="unbounded" minOccurs="0"&gt;
142 * &lt;complexType&gt;
143 * &lt;complexContent&gt;
144 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
145 * &lt;sequence&gt;
146 * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
147 * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
148 * &lt;complexType&gt;
149 * &lt;complexContent&gt;
150 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
151 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
152 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
153 * &lt;/restriction&gt;
154 * &lt;/complexContent&gt;
155 * &lt;/complexType&gt;
156 * &lt;/element&gt;
157 * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
158 * &lt;complexType&gt;
159 * &lt;complexContent&gt;
160 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
161 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
162 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
163 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
164 * &lt;/extension&gt;
165 * &lt;/complexContent&gt;
166 * &lt;/complexType&gt;
167 * &lt;/element&gt;
168 * &lt;/sequence&gt;
169 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
170 * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
171 * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
172 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
173 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
174 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
175 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
176 * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
177 * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
178 * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
179 * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
180 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
181 * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
182 * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
183 * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
184 * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
185 * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
186 * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
187 * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
188 * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
189 * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
190 * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
191 * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
192 * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
193 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
194 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
195 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
196 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
197 * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
198 * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
199 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
200 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
201 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
202 * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
203 * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
204 * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
205 * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
206 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
207 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
208 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
209 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
210 * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
211 * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
212 * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
213 * &lt;/restriction&gt;
214 * &lt;/complexContent&gt;
215 * &lt;/complexType&gt;
216 * &lt;/element&gt;
217 * &lt;element name="UserColours" maxOccurs="unbounded" minOccurs="0"&gt;
218 * &lt;complexType&gt;
219 * &lt;complexContent&gt;
220 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
221 * &lt;sequence&gt;
222 * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
223 * &lt;/sequence&gt;
224 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
225 * &lt;/restriction&gt;
226 * &lt;/complexContent&gt;
227 * &lt;/complexType&gt;
228 * &lt;/element&gt;
229 * &lt;element name="tree" maxOccurs="unbounded" minOccurs="0"&gt;
230 * &lt;complexType&gt;
231 * &lt;complexContent&gt;
232 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
233 * &lt;sequence minOccurs="0"&gt;
234 * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
235 * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
236 * &lt;/sequence&gt;
237 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
238 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
239 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
240 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
241 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
242 * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
243 * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
244 * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
245 * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
246 * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
247 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
248 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
249 * &lt;/restriction&gt;
250 * &lt;/complexContent&gt;
251 * &lt;/complexType&gt;
252 * &lt;/element&gt;
253 * &lt;element name="PcaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
254 * &lt;complexType&gt;
255 * &lt;complexContent&gt;
256 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
257 * &lt;sequence&gt;
258 * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
259 * &lt;complexType&gt;
260 * &lt;complexContent&gt;
261 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
262 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
263 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
264 * &lt;/restriction&gt;
265 * &lt;/complexContent&gt;
266 * &lt;/complexType&gt;
267 * &lt;/element&gt;
268 * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
269 * &lt;complexType&gt;
270 * &lt;complexContent&gt;
271 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
272 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
273 * &lt;/restriction&gt;
274 * &lt;/complexContent&gt;
275 * &lt;/complexType&gt;
276 * &lt;/element&gt;
277 * &lt;element name="seqPointMin"&gt;
278 * &lt;complexType&gt;
279 * &lt;complexContent&gt;
280 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
281 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
282 * &lt;/restriction&gt;
283 * &lt;/complexContent&gt;
284 * &lt;/complexType&gt;
285 * &lt;/element&gt;
286 * &lt;element name="seqPointMax"&gt;
287 * &lt;complexType&gt;
288 * &lt;complexContent&gt;
289 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
290 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
291 * &lt;/restriction&gt;
292 * &lt;/complexContent&gt;
293 * &lt;/complexType&gt;
294 * &lt;/element&gt;
295 * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
296 * &lt;/sequence&gt;
297 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
298 * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
299 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
300 * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
301 * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
302 * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
303 * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
304 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
305 * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
306 * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
307 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
308 * &lt;/restriction&gt;
309 * &lt;/complexContent&gt;
310 * &lt;/complexType&gt;
311 * &lt;/element&gt;
312 * &lt;element name="FeatureSettings" minOccurs="0"&gt;
313 * &lt;complexType&gt;
314 * &lt;complexContent&gt;
315 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
316 * &lt;sequence&gt;
317 * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
318 * &lt;complexType&gt;
319 * &lt;complexContent&gt;
320 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
321 * &lt;sequence&gt;
322 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
323 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
324 * &lt;/sequence&gt;
325 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
326 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
327 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
328 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
329 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
330 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
331 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
332 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
333 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
334 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
335 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
336 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
337 * &lt;/restriction&gt;
338 * &lt;/complexContent&gt;
339 * &lt;/complexType&gt;
340 * &lt;/element&gt;
341 * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
342 * &lt;complexType&gt;
343 * &lt;complexContent&gt;
344 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
345 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
346 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
347 * &lt;/restriction&gt;
348 * &lt;/complexContent&gt;
349 * &lt;/complexType&gt;
350 * &lt;/element&gt;
351 * &lt;/sequence&gt;
352 * &lt;/restriction&gt;
353 * &lt;/complexContent&gt;
354 * &lt;/complexType&gt;
355 * &lt;/element&gt;
356 * &lt;/sequence&gt;
357 * &lt;/sequence&gt;
358 * &lt;/restriction&gt;
359 * &lt;/complexContent&gt;
360 * &lt;/complexType&gt;
365 @XmlAccessorType(XmlAccessType.FIELD)
366 @XmlType(name = "JalviewModel", namespace = "www.jalview.org", propOrder = {
378 public class JalviewModel {
380 @XmlElement(required = true)
381 @XmlSchemaType(name = "dateTime")
382 protected XMLGregorianCalendar creationDate;
383 @XmlElement(required = true)
384 protected String version;
385 @XmlElement(required = true)
386 protected VAMSAS vamsasModel;
387 @XmlElement(name = "JSeq")
388 protected List<JalviewModel.JSeq> jSeq;
389 @XmlElement(name = "JGroup")
390 protected List<JalviewModel.JGroup> jGroup;
391 @XmlElement(name = "Viewport")
392 protected List<JalviewModel.Viewport> viewport;
393 @XmlElement(name = "UserColours")
394 protected List<JalviewModel.UserColours> userColours;
395 protected List<JalviewModel.Tree> tree;
396 @XmlElement(name = "PcaViewer")
397 protected List<JalviewModel.PcaViewer> pcaViewer;
398 @XmlElement(name = "FeatureSettings")
399 protected JalviewModel.FeatureSettings featureSettings;
402 * Gets the value of the creationDate property.
406 * {@link XMLGregorianCalendar }
409 public XMLGregorianCalendar getCreationDate() {
414 * Sets the value of the creationDate property.
418 * {@link XMLGregorianCalendar }
421 public void setCreationDate(XMLGregorianCalendar value) {
422 this.creationDate = value;
426 * Gets the value of the version property.
433 public String getVersion() {
438 * Sets the value of the version property.
445 public void setVersion(String value) {
446 this.version = value;
450 * Gets the value of the vamsasModel property.
457 public VAMSAS getVamsasModel() {
462 * Sets the value of the vamsasModel property.
469 public void setVamsasModel(VAMSAS value) {
470 this.vamsasModel = value;
474 * Gets the value of the jSeq property.
477 * This accessor method returns a reference to the live list,
478 * not a snapshot. Therefore any modification you make to the
479 * returned list will be present inside the JAXB object.
480 * This is why there is not a <CODE>set</CODE> method for the jSeq property.
483 * For example, to add a new item, do as follows:
485 * getJSeq().add(newItem);
490 * Objects of the following type(s) are allowed in the list
491 * {@link JalviewModel.JSeq }
495 public List<JalviewModel.JSeq> getJSeq() {
497 jSeq = new ArrayList<JalviewModel.JSeq>();
503 * Gets the value of the jGroup property.
506 * This accessor method returns a reference to the live list,
507 * not a snapshot. Therefore any modification you make to the
508 * returned list will be present inside the JAXB object.
509 * This is why there is not a <CODE>set</CODE> method for the jGroup property.
512 * For example, to add a new item, do as follows:
514 * getJGroup().add(newItem);
519 * Objects of the following type(s) are allowed in the list
520 * {@link JalviewModel.JGroup }
524 public List<JalviewModel.JGroup> getJGroup() {
525 if (jGroup == null) {
526 jGroup = new ArrayList<JalviewModel.JGroup>();
532 * Gets the value of the viewport property.
535 * This accessor method returns a reference to the live list,
536 * not a snapshot. Therefore any modification you make to the
537 * returned list will be present inside the JAXB object.
538 * This is why there is not a <CODE>set</CODE> method for the viewport property.
541 * For example, to add a new item, do as follows:
543 * getViewport().add(newItem);
548 * Objects of the following type(s) are allowed in the list
549 * {@link JalviewModel.Viewport }
553 public List<JalviewModel.Viewport> getViewport() {
554 if (viewport == null) {
555 viewport = new ArrayList<JalviewModel.Viewport>();
557 return this.viewport;
561 * Gets the value of the userColours property.
564 * This accessor method returns a reference to the live list,
565 * not a snapshot. Therefore any modification you make to the
566 * returned list will be present inside the JAXB object.
567 * This is why there is not a <CODE>set</CODE> method for the userColours property.
570 * For example, to add a new item, do as follows:
572 * getUserColours().add(newItem);
577 * Objects of the following type(s) are allowed in the list
578 * {@link JalviewModel.UserColours }
582 public List<JalviewModel.UserColours> getUserColours() {
583 if (userColours == null) {
584 userColours = new ArrayList<JalviewModel.UserColours>();
586 return this.userColours;
590 * Gets the value of the tree property.
593 * This accessor method returns a reference to the live list,
594 * not a snapshot. Therefore any modification you make to the
595 * returned list will be present inside the JAXB object.
596 * This is why there is not a <CODE>set</CODE> method for the tree property.
599 * For example, to add a new item, do as follows:
601 * getTree().add(newItem);
606 * Objects of the following type(s) are allowed in the list
607 * {@link JalviewModel.Tree }
611 public List<JalviewModel.Tree> getTree() {
613 tree = new ArrayList<JalviewModel.Tree>();
619 * Gets the value of the pcaViewer property.
622 * This accessor method returns a reference to the live list,
623 * not a snapshot. Therefore any modification you make to the
624 * returned list will be present inside the JAXB object.
625 * This is why there is not a <CODE>set</CODE> method for the pcaViewer property.
628 * For example, to add a new item, do as follows:
630 * getPcaViewer().add(newItem);
635 * Objects of the following type(s) are allowed in the list
636 * {@link JalviewModel.PcaViewer }
640 public List<JalviewModel.PcaViewer> getPcaViewer() {
641 if (pcaViewer == null) {
642 pcaViewer = new ArrayList<JalviewModel.PcaViewer>();
644 return this.pcaViewer;
648 * Gets the value of the featureSettings property.
652 * {@link JalviewModel.FeatureSettings }
655 public JalviewModel.FeatureSettings getFeatureSettings() {
656 return featureSettings;
660 * Sets the value of the featureSettings property.
664 * {@link JalviewModel.FeatureSettings }
667 public void setFeatureSettings(JalviewModel.FeatureSettings value) {
668 this.featureSettings = value;
673 * <p>Java class for anonymous complex type.
675 * <p>The following schema fragment specifies the expected content contained within this class.
678 * &lt;complexType&gt;
679 * &lt;complexContent&gt;
680 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
681 * &lt;sequence&gt;
682 * &lt;element name="setting" maxOccurs="unbounded" minOccurs="0"&gt;
683 * &lt;complexType&gt;
684 * &lt;complexContent&gt;
685 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
686 * &lt;sequence&gt;
687 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
688 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
689 * &lt;/sequence&gt;
690 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
691 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
692 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
693 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
694 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
695 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
696 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
697 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
698 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
699 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
700 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
701 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
702 * &lt;/restriction&gt;
703 * &lt;/complexContent&gt;
704 * &lt;/complexType&gt;
705 * &lt;/element&gt;
706 * &lt;element name="group" maxOccurs="unbounded" minOccurs="0"&gt;
707 * &lt;complexType&gt;
708 * &lt;complexContent&gt;
709 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
710 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
711 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
712 * &lt;/restriction&gt;
713 * &lt;/complexContent&gt;
714 * &lt;/complexType&gt;
715 * &lt;/element&gt;
716 * &lt;/sequence&gt;
717 * &lt;/restriction&gt;
718 * &lt;/complexContent&gt;
719 * &lt;/complexType&gt;
724 @XmlAccessorType(XmlAccessType.FIELD)
725 @XmlType(name = "", propOrder = {
729 public static class FeatureSettings {
731 @XmlElement(namespace = "www.jalview.org")
732 protected List<JalviewModel.FeatureSettings.Setting> setting;
733 @XmlElement(namespace = "www.jalview.org")
734 protected List<JalviewModel.FeatureSettings.Group> group;
737 * Gets the value of the setting property.
740 * This accessor method returns a reference to the live list,
741 * not a snapshot. Therefore any modification you make to the
742 * returned list will be present inside the JAXB object.
743 * This is why there is not a <CODE>set</CODE> method for the setting property.
746 * For example, to add a new item, do as follows:
748 * getSetting().add(newItem);
753 * Objects of the following type(s) are allowed in the list
754 * {@link JalviewModel.FeatureSettings.Setting }
758 public List<JalviewModel.FeatureSettings.Setting> getSetting() {
759 if (setting == null) {
760 setting = new ArrayList<JalviewModel.FeatureSettings.Setting>();
766 * Gets the value of the group property.
769 * This accessor method returns a reference to the live list,
770 * not a snapshot. Therefore any modification you make to the
771 * returned list will be present inside the JAXB object.
772 * This is why there is not a <CODE>set</CODE> method for the group property.
775 * For example, to add a new item, do as follows:
777 * getGroup().add(newItem);
782 * Objects of the following type(s) are allowed in the list
783 * {@link JalviewModel.FeatureSettings.Group }
787 public List<JalviewModel.FeatureSettings.Group> getGroup() {
789 group = new ArrayList<JalviewModel.FeatureSettings.Group>();
796 * <p>Java class for anonymous complex type.
798 * <p>The following schema fragment specifies the expected content contained within this class.
801 * &lt;complexType&gt;
802 * &lt;complexContent&gt;
803 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
804 * &lt;attribute name="name" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
805 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
806 * &lt;/restriction&gt;
807 * &lt;/complexContent&gt;
808 * &lt;/complexType&gt;
813 @XmlAccessorType(XmlAccessType.FIELD)
815 public static class Group {
817 @XmlAttribute(name = "name", required = true)
818 protected String name;
819 @XmlAttribute(name = "display", required = true)
820 protected boolean display;
823 * Gets the value of the name property.
830 public String getName() {
835 * Sets the value of the name property.
842 public void setName(String value) {
847 * Gets the value of the display property.
850 public boolean isDisplay() {
855 * Sets the value of the display property.
858 public void setDisplay(boolean value) {
859 this.display = value;
866 * <p>Java class for anonymous complex type.
868 * <p>The following schema fragment specifies the expected content contained within this class.
871 * &lt;complexType&gt;
872 * &lt;complexContent&gt;
873 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
874 * &lt;sequence&gt;
875 * &lt;element name="attributeName" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="2" minOccurs="0"/&gt;
876 * &lt;element name="matcherSet" type="{www.jalview.org/colours}FeatureMatcherSet" minOccurs="0"/&gt;
877 * &lt;/sequence&gt;
878 * &lt;attribute name="type" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
879 * &lt;attribute name="colour" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
880 * &lt;attribute name="display" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
881 * &lt;attribute name="order" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
882 * &lt;attribute name="mincolour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
883 * &lt;attribute name="noValueColour" type="{www.jalview.org/colours}NoValueColour" default="Min" /&gt;
884 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
885 * &lt;attribute name="threshstate" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
886 * &lt;attribute name="max" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
887 * &lt;attribute name="min" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
888 * &lt;attribute name="colourByLabel" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
889 * &lt;attribute name="autoScale" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
890 * &lt;/restriction&gt;
891 * &lt;/complexContent&gt;
892 * &lt;/complexType&gt;
897 @XmlAccessorType(XmlAccessType.FIELD)
898 @XmlType(name = "", propOrder = {
902 public static class Setting {
904 @XmlElement(namespace = "www.jalview.org")
905 protected List<String> attributeName;
906 @XmlElement(namespace = "www.jalview.org")
907 protected FeatureMatcherSet matcherSet;
908 @XmlAttribute(name = "type", required = true)
909 protected String type;
910 @XmlAttribute(name = "colour", required = true)
911 protected int colour;
912 @XmlAttribute(name = "display", required = true)
913 protected boolean display;
914 @XmlAttribute(name = "order")
915 protected Float order;
916 @XmlAttribute(name = "mincolour")
917 protected Integer mincolour;
918 @XmlAttribute(name = "noValueColour")
919 protected NoValueColour noValueColour;
920 @XmlAttribute(name = "threshold")
921 protected Float threshold;
922 @XmlAttribute(name = "threshstate")
923 protected Integer threshstate;
924 @XmlAttribute(name = "max")
926 @XmlAttribute(name = "min")
928 @XmlAttribute(name = "colourByLabel")
929 protected Boolean colourByLabel;
930 @XmlAttribute(name = "autoScale")
931 protected Boolean autoScale;
934 * Gets the value of the attributeName property.
937 * This accessor method returns a reference to the live list,
938 * not a snapshot. Therefore any modification you make to the
939 * returned list will be present inside the JAXB object.
940 * This is why there is not a <CODE>set</CODE> method for the attributeName property.
943 * For example, to add a new item, do as follows:
945 * getAttributeName().add(newItem);
950 * Objects of the following type(s) are allowed in the list
955 public List<String> getAttributeName() {
956 if (attributeName == null) {
957 attributeName = new ArrayList<String>();
959 return this.attributeName;
963 * Gets the value of the matcherSet property.
967 * {@link FeatureMatcherSet }
970 public FeatureMatcherSet getMatcherSet() {
975 * Sets the value of the matcherSet property.
979 * {@link FeatureMatcherSet }
982 public void setMatcherSet(FeatureMatcherSet value) {
983 this.matcherSet = value;
987 * Gets the value of the type property.
994 public String getType() {
999 * Sets the value of the type property.
1006 public void setType(String value) {
1011 * Gets the value of the colour property.
1014 public int getColour() {
1019 * Sets the value of the colour property.
1022 public void setColour(int value) {
1023 this.colour = value;
1027 * Gets the value of the display property.
1030 public boolean isDisplay() {
1035 * Sets the value of the display property.
1038 public void setDisplay(boolean value) {
1039 this.display = value;
1043 * Gets the value of the order property.
1046 * possible object is
1050 public Float getOrder() {
1055 * Sets the value of the order property.
1062 public void setOrder(Float value) {
1067 * Gets the value of the mincolour property.
1070 * possible object is
1074 public Integer getMincolour() {
1079 * Sets the value of the mincolour property.
1086 public void setMincolour(Integer value) {
1087 this.mincolour = value;
1091 * Gets the value of the noValueColour property.
1094 * possible object is
1095 * {@link NoValueColour }
1098 public NoValueColour getNoValueColour() {
1099 if (noValueColour == null) {
1100 return NoValueColour.MIN;
1102 return noValueColour;
1107 * Sets the value of the noValueColour property.
1111 * {@link NoValueColour }
1114 public void setNoValueColour(NoValueColour value) {
1115 this.noValueColour = value;
1119 * Gets the value of the threshold property.
1122 * possible object is
1126 public Float getThreshold() {
1131 * Sets the value of the threshold property.
1138 public void setThreshold(Float value) {
1139 this.threshold = value;
1143 * Gets the value of the threshstate property.
1146 * possible object is
1150 public Integer getThreshstate() {
1155 * Sets the value of the threshstate property.
1162 public void setThreshstate(Integer value) {
1163 this.threshstate = value;
1167 * Gets the value of the max property.
1170 * possible object is
1174 public Float getMax() {
1179 * Sets the value of the max property.
1186 public void setMax(Float value) {
1191 * Gets the value of the min property.
1194 * possible object is
1198 public Float getMin() {
1203 * Sets the value of the min property.
1210 public void setMin(Float value) {
1215 * Gets the value of the colourByLabel property.
1218 * possible object is
1222 public Boolean isColourByLabel() {
1223 return colourByLabel;
1227 * Sets the value of the colourByLabel property.
1234 public void setColourByLabel(Boolean value) {
1235 this.colourByLabel = value;
1239 * Gets the value of the autoScale property.
1242 * possible object is
1246 public Boolean isAutoScale() {
1251 * Sets the value of the autoScale property.
1258 public void setAutoScale(Boolean value) {
1259 this.autoScale = value;
1268 * <p>Java class for anonymous complex type.
1270 * <p>The following schema fragment specifies the expected content contained within this class.
1273 * &lt;complexType&gt;
1274 * &lt;complexContent&gt;
1275 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1276 * &lt;sequence&gt;
1277 * &lt;element name="seq" type="{http://www.w3.org/2001/XMLSchema}string" maxOccurs="unbounded"/&gt;
1278 * &lt;element name="annotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
1279 * &lt;/sequence&gt;
1280 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1281 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1282 * &lt;attribute name="name" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1283 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1284 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1285 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1286 * &lt;attribute name="outlineColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1287 * &lt;attribute name="displayBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1288 * &lt;attribute name="displayText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1289 * &lt;attribute name="colourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1290 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1291 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1292 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1293 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1294 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1295 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1296 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1297 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1298 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1299 * &lt;/restriction&gt;
1300 * &lt;/complexContent&gt;
1301 * &lt;/complexType&gt;
1306 @XmlAccessorType(XmlAccessType.FIELD)
1307 @XmlType(name = "", propOrder = {
1311 public static class JGroup {
1313 @XmlElement(namespace = "www.jalview.org", required = true)
1314 protected List<String> seq;
1315 @XmlElement(namespace = "www.jalview.org")
1316 protected AnnotationColourScheme annotationColours;
1317 @XmlAttribute(name = "start")
1318 protected Integer start;
1319 @XmlAttribute(name = "end")
1320 protected Integer end;
1321 @XmlAttribute(name = "name")
1322 protected String name;
1323 @XmlAttribute(name = "colour")
1324 protected String colour;
1325 @XmlAttribute(name = "consThreshold")
1326 protected Integer consThreshold;
1327 @XmlAttribute(name = "pidThreshold")
1328 protected Integer pidThreshold;
1329 @XmlAttribute(name = "outlineColour")
1330 protected Integer outlineColour;
1331 @XmlAttribute(name = "displayBoxes")
1332 protected Boolean displayBoxes;
1333 @XmlAttribute(name = "displayText")
1334 protected Boolean displayText;
1335 @XmlAttribute(name = "colourText")
1336 protected Boolean colourText;
1337 @XmlAttribute(name = "textCol1")
1338 protected Integer textCol1;
1339 @XmlAttribute(name = "textCol2")
1340 protected Integer textCol2;
1341 @XmlAttribute(name = "textColThreshold")
1342 protected Integer textColThreshold;
1343 @XmlAttribute(name = "showUnconserved")
1344 protected Boolean showUnconserved;
1345 @XmlAttribute(name = "ignoreGapsinConsensus")
1346 protected Boolean ignoreGapsinConsensus;
1347 @XmlAttribute(name = "showConsensusHistogram")
1348 protected Boolean showConsensusHistogram;
1349 @XmlAttribute(name = "showSequenceLogo")
1350 protected Boolean showSequenceLogo;
1351 @XmlAttribute(name = "normaliseSequenceLogo")
1352 protected Boolean normaliseSequenceLogo;
1353 @XmlAttribute(name = "id")
1354 protected String id;
1357 * Gets the value of the seq property.
1360 * This accessor method returns a reference to the live list,
1361 * not a snapshot. Therefore any modification you make to the
1362 * returned list will be present inside the JAXB object.
1363 * This is why there is not a <CODE>set</CODE> method for the seq property.
1366 * For example, to add a new item, do as follows:
1368 * getSeq().add(newItem);
1373 * Objects of the following type(s) are allowed in the list
1378 public List<String> getSeq() {
1380 seq = new ArrayList<String>();
1386 * Gets the value of the annotationColours property.
1389 * possible object is
1390 * {@link AnnotationColourScheme }
1393 public AnnotationColourScheme getAnnotationColours() {
1394 return annotationColours;
1398 * Sets the value of the annotationColours property.
1402 * {@link AnnotationColourScheme }
1405 public void setAnnotationColours(AnnotationColourScheme value) {
1406 this.annotationColours = value;
1410 * Gets the value of the start property.
1413 * possible object is
1417 public Integer getStart() {
1422 * Sets the value of the start property.
1429 public void setStart(Integer value) {
1434 * Gets the value of the end property.
1437 * possible object is
1441 public Integer getEnd() {
1446 * Sets the value of the end property.
1453 public void setEnd(Integer value) {
1458 * Gets the value of the name property.
1461 * possible object is
1465 public String getName() {
1470 * Sets the value of the name property.
1477 public void setName(String value) {
1482 * Gets the value of the colour property.
1485 * possible object is
1489 public String getColour() {
1494 * Sets the value of the colour property.
1501 public void setColour(String value) {
1502 this.colour = value;
1506 * Gets the value of the consThreshold property.
1509 * possible object is
1513 public Integer getConsThreshold() {
1514 return consThreshold;
1518 * Sets the value of the consThreshold property.
1525 public void setConsThreshold(Integer value) {
1526 this.consThreshold = value;
1530 * Gets the value of the pidThreshold property.
1533 * possible object is
1537 public Integer getPidThreshold() {
1538 return pidThreshold;
1542 * Sets the value of the pidThreshold property.
1549 public void setPidThreshold(Integer value) {
1550 this.pidThreshold = value;
1554 * Gets the value of the outlineColour property.
1557 * possible object is
1561 public Integer getOutlineColour() {
1562 return outlineColour;
1566 * Sets the value of the outlineColour property.
1573 public void setOutlineColour(Integer value) {
1574 this.outlineColour = value;
1578 * Gets the value of the displayBoxes property.
1581 * possible object is
1585 public Boolean isDisplayBoxes() {
1586 return displayBoxes;
1590 * Sets the value of the displayBoxes property.
1597 public void setDisplayBoxes(Boolean value) {
1598 this.displayBoxes = value;
1602 * Gets the value of the displayText property.
1605 * possible object is
1609 public Boolean isDisplayText() {
1614 * Sets the value of the displayText property.
1621 public void setDisplayText(Boolean value) {
1622 this.displayText = value;
1626 * Gets the value of the colourText property.
1629 * possible object is
1633 public Boolean isColourText() {
1638 * Sets the value of the colourText property.
1645 public void setColourText(Boolean value) {
1646 this.colourText = value;
1650 * Gets the value of the textCol1 property.
1653 * possible object is
1657 public Integer getTextCol1() {
1662 * Sets the value of the textCol1 property.
1669 public void setTextCol1(Integer value) {
1670 this.textCol1 = value;
1674 * Gets the value of the textCol2 property.
1677 * possible object is
1681 public Integer getTextCol2() {
1686 * Sets the value of the textCol2 property.
1693 public void setTextCol2(Integer value) {
1694 this.textCol2 = value;
1698 * Gets the value of the textColThreshold property.
1701 * possible object is
1705 public Integer getTextColThreshold() {
1706 return textColThreshold;
1710 * Sets the value of the textColThreshold property.
1717 public void setTextColThreshold(Integer value) {
1718 this.textColThreshold = value;
1722 * Gets the value of the showUnconserved property.
1725 * possible object is
1729 public Boolean isShowUnconserved() {
1730 return showUnconserved;
1734 * Sets the value of the showUnconserved property.
1741 public void setShowUnconserved(Boolean value) {
1742 this.showUnconserved = value;
1746 * Gets the value of the ignoreGapsinConsensus property.
1749 * possible object is
1753 public boolean isIgnoreGapsinConsensus() {
1754 if (ignoreGapsinConsensus == null) {
1757 return ignoreGapsinConsensus;
1762 * Sets the value of the ignoreGapsinConsensus property.
1769 public void setIgnoreGapsinConsensus(Boolean value) {
1770 this.ignoreGapsinConsensus = value;
1774 * Gets the value of the showConsensusHistogram property.
1777 * possible object is
1781 public boolean isShowConsensusHistogram() {
1782 if (showConsensusHistogram == null) {
1785 return showConsensusHistogram;
1790 * Sets the value of the showConsensusHistogram property.
1797 public void setShowConsensusHistogram(Boolean value) {
1798 this.showConsensusHistogram = value;
1802 * Gets the value of the showSequenceLogo property.
1805 * possible object is
1809 public boolean isShowSequenceLogo() {
1810 if (showSequenceLogo == null) {
1813 return showSequenceLogo;
1818 * Sets the value of the showSequenceLogo property.
1825 public void setShowSequenceLogo(Boolean value) {
1826 this.showSequenceLogo = value;
1830 * Gets the value of the normaliseSequenceLogo property.
1833 * possible object is
1837 public boolean isNormaliseSequenceLogo() {
1838 if (normaliseSequenceLogo == null) {
1841 return normaliseSequenceLogo;
1846 * Sets the value of the normaliseSequenceLogo property.
1853 public void setNormaliseSequenceLogo(Boolean value) {
1854 this.normaliseSequenceLogo = value;
1858 * Gets the value of the id property.
1861 * possible object is
1865 public String getId() {
1870 * Sets the value of the id property.
1877 public void setId(String value) {
1885 * <p>Java class for anonymous complex type.
1887 * <p>The following schema fragment specifies the expected content contained within this class.
1890 * &lt;complexType&gt;
1891 * &lt;complexContent&gt;
1892 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1893 * &lt;sequence&gt;
1894 * &lt;element name="features" type="{www.jalview.org}feature" maxOccurs="unbounded" minOccurs="0"/&gt;
1895 * &lt;element name="pdbids" maxOccurs="unbounded" minOccurs="0"&gt;
1896 * &lt;complexType&gt;
1897 * &lt;complexContent&gt;
1898 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
1899 * &lt;sequence&gt;
1900 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
1901 * &lt;complexType&gt;
1902 * &lt;simpleContent&gt;
1903 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
1904 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
1905 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1906 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1907 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1908 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
1909 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
1910 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1911 * &lt;/extension&gt;
1912 * &lt;/simpleContent&gt;
1913 * &lt;/complexType&gt;
1914 * &lt;/element&gt;
1915 * &lt;/sequence&gt;
1916 * &lt;/extension&gt;
1917 * &lt;/complexContent&gt;
1918 * &lt;/complexType&gt;
1919 * &lt;/element&gt;
1920 * &lt;element name="hiddenSequences" type="{http://www.w3.org/2001/XMLSchema}int" maxOccurs="unbounded" minOccurs="0"/&gt;
1921 * &lt;element name="rnaViewer" maxOccurs="unbounded" minOccurs="0"&gt;
1922 * &lt;complexType&gt;
1923 * &lt;complexContent&gt;
1924 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1925 * &lt;sequence&gt;
1926 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
1927 * &lt;complexType&gt;
1928 * &lt;complexContent&gt;
1929 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
1930 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1931 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1932 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1933 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1934 * &lt;/restriction&gt;
1935 * &lt;/complexContent&gt;
1936 * &lt;/complexType&gt;
1937 * &lt;/element&gt;
1938 * &lt;/sequence&gt;
1939 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
1940 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1941 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1942 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1943 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1944 * &lt;/restriction&gt;
1945 * &lt;/complexContent&gt;
1946 * &lt;/complexType&gt;
1947 * &lt;/element&gt;
1948 * &lt;/sequence&gt;
1949 * &lt;attribute name="colour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1950 * &lt;attribute name="start" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1951 * &lt;attribute name="end" use="required" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
1952 * &lt;attribute name="id" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
1953 * &lt;attribute name="hidden" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1954 * &lt;attribute name="viewreference" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
1955 * &lt;/restriction&gt;
1956 * &lt;/complexContent&gt;
1957 * &lt;/complexType&gt;
1962 @XmlAccessorType(XmlAccessType.FIELD)
1963 @XmlType(name = "", propOrder = {
1970 public static class JSeq {
1972 @XmlElement(namespace = "www.jalview.org")
1973 protected List<Feature> features;
1974 @XmlElement(namespace = "www.jalview.org")
1975 protected List<JalviewModel.JSeq.Pdbids> pdbids;
1976 @XmlElement(namespace = "www.jalview.org", type = Integer.class)
1977 protected List<Integer> hiddenSequences;
1978 @XmlElement(namespace = "www.jalview.org")
1979 protected List<JalviewModel.JSeq.RnaViewer> rnaViewer;
1980 @XmlElement(namespace = "www.jalview.org")
1981 protected String hmmerProfile;
1982 @XmlAttribute(name = "colour")
1983 protected Integer colour;
1984 @XmlAttribute(name = "start", required = true)
1985 protected int start;
1986 @XmlAttribute(name = "end", required = true)
1988 @XmlAttribute(name = "id", required = true)
1989 protected String id;
1990 @XmlAttribute(name = "hidden")
1991 protected Boolean hidden;
1992 @XmlAttribute(name = "viewreference")
1993 protected Boolean viewreference;
1996 * Gets the value of the features property.
1999 * This accessor method returns a reference to the live list,
2000 * not a snapshot. Therefore any modification you make to the
2001 * returned list will be present inside the JAXB object.
2002 * This is why there is not a <CODE>set</CODE> method for the features property.
2005 * For example, to add a new item, do as follows:
2007 * getFeatures().add(newItem);
2012 * Objects of the following type(s) are allowed in the list
2017 public List<Feature> getFeatures() {
2018 if (features == null) {
2019 features = new ArrayList<Feature>();
2021 return this.features;
2025 * Gets the value of the pdbids property.
2028 * This accessor method returns a reference to the live list,
2029 * not a snapshot. Therefore any modification you make to the
2030 * returned list will be present inside the JAXB object.
2031 * This is why there is not a <CODE>set</CODE> method for the pdbids property.
2034 * For example, to add a new item, do as follows:
2036 * getPdbids().add(newItem);
2041 * Objects of the following type(s) are allowed in the list
2042 * {@link JalviewModel.JSeq.Pdbids }
2046 public List<JalviewModel.JSeq.Pdbids> getPdbids() {
2047 if (pdbids == null) {
2048 pdbids = new ArrayList<JalviewModel.JSeq.Pdbids>();
2054 * Gets the value of the hiddenSequences property.
2057 * This accessor method returns a reference to the live list,
2058 * not a snapshot. Therefore any modification you make to the
2059 * returned list will be present inside the JAXB object.
2060 * This is why there is not a <CODE>set</CODE> method for the hiddenSequences property.
2063 * For example, to add a new item, do as follows:
2065 * getHiddenSequences().add(newItem);
2070 * Objects of the following type(s) are allowed in the list
2075 public List<Integer> getHiddenSequences() {
2076 if (hiddenSequences == null) {
2077 hiddenSequences = new ArrayList<Integer>();
2079 return this.hiddenSequences;
2083 * Gets the value of the rnaViewer property.
2086 * This accessor method returns a reference to the live list,
2087 * not a snapshot. Therefore any modification you make to the
2088 * returned list will be present inside the JAXB object.
2089 * This is why there is not a <CODE>set</CODE> method for the rnaViewer property.
2092 * For example, to add a new item, do as follows:
2094 * getRnaViewer().add(newItem);
2099 * Objects of the following type(s) are allowed in the list
2100 * {@link JalviewModel.JSeq.RnaViewer }
2104 public List<JalviewModel.JSeq.RnaViewer> getRnaViewer() {
2105 if (rnaViewer == null) {
2106 rnaViewer = new ArrayList<JalviewModel.JSeq.RnaViewer>();
2108 return this.rnaViewer;
2112 * Gets the value of the hmmerProfile property.
2115 * possible object is
2119 public String getHmmerProfile() {
2120 return hmmerProfile;
2124 * Sets the value of the hmmerProfile property.
2131 public void setHmmerProfile(String value) {
2132 this.hmmerProfile = value;
2136 * Gets the value of the colour property.
2139 * possible object is
2143 public Integer getColour() {
2148 * Sets the value of the colour property.
2155 public void setColour(Integer value) {
2156 this.colour = value;
2160 * Gets the value of the start property.
2163 public int getStart() {
2168 * Sets the value of the start property.
2171 public void setStart(int value) {
2176 * Gets the value of the end property.
2179 public int getEnd() {
2184 * Sets the value of the end property.
2187 public void setEnd(int value) {
2192 * Gets the value of the id property.
2195 * possible object is
2199 public String getId() {
2204 * Sets the value of the id property.
2211 public void setId(String value) {
2216 * Gets the value of the hidden property.
2219 * possible object is
2223 public Boolean isHidden() {
2228 * Sets the value of the hidden property.
2235 public void setHidden(Boolean value) {
2236 this.hidden = value;
2240 * Gets the value of the viewreference property.
2243 * possible object is
2247 public Boolean isViewreference() {
2248 return viewreference;
2252 * Sets the value of the viewreference property.
2259 public void setViewreference(Boolean value) {
2260 this.viewreference = value;
2265 * <p>Java class for anonymous complex type.
2267 * <p>The following schema fragment specifies the expected content contained within this class.
2270 * &lt;complexType&gt;
2271 * &lt;complexContent&gt;
2272 * &lt;extension base="{www.jalview.org}pdbentry"&gt;
2273 * &lt;sequence&gt;
2274 * &lt;element name="structureState" maxOccurs="unbounded" minOccurs="0"&gt;
2275 * &lt;complexType&gt;
2276 * &lt;simpleContent&gt;
2277 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2278 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2279 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2280 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2281 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2282 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2283 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2284 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2285 * &lt;/extension&gt;
2286 * &lt;/simpleContent&gt;
2287 * &lt;/complexType&gt;
2288 * &lt;/element&gt;
2289 * &lt;/sequence&gt;
2290 * &lt;/extension&gt;
2291 * &lt;/complexContent&gt;
2292 * &lt;/complexType&gt;
2297 @XmlAccessorType(XmlAccessType.FIELD)
2298 @XmlType(name = "", propOrder = {
2301 public static class Pdbids
2305 @XmlElement(namespace = "www.jalview.org")
2306 protected List<JalviewModel.JSeq.Pdbids.StructureState> structureState;
2309 * Gets the value of the structureState property.
2312 * This accessor method returns a reference to the live list,
2313 * not a snapshot. Therefore any modification you make to the
2314 * returned list will be present inside the JAXB object.
2315 * This is why there is not a <CODE>set</CODE> method for the structureState property.
2318 * For example, to add a new item, do as follows:
2320 * getStructureState().add(newItem);
2325 * Objects of the following type(s) are allowed in the list
2326 * {@link JalviewModel.JSeq.Pdbids.StructureState }
2330 public List<JalviewModel.JSeq.Pdbids.StructureState> getStructureState() {
2331 if (structureState == null) {
2332 structureState = new ArrayList<JalviewModel.JSeq.Pdbids.StructureState>();
2334 return this.structureState;
2339 * <p>Java class for anonymous complex type.
2341 * <p>The following schema fragment specifies the expected content contained within this class.
2344 * &lt;complexType&gt;
2345 * &lt;simpleContent&gt;
2346 * &lt;extension base="&lt;http://www.w3.org/2001/XMLSchema&gt;string"&gt;
2347 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2348 * &lt;attribute name="visible" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2349 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2350 * &lt;attribute name="alignwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2351 * &lt;attribute name="colourwithAlignPanel" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
2352 * &lt;attribute name="colourByJmol" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
2353 * &lt;attribute name="type" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2354 * &lt;/extension&gt;
2355 * &lt;/simpleContent&gt;
2356 * &lt;/complexType&gt;
2361 @XmlAccessorType(XmlAccessType.FIELD)
2362 @XmlType(name = "", propOrder = {
2365 public static class StructureState {
2368 protected String value;
2369 @XmlAttribute(name = "visible")
2370 protected Boolean visible;
2371 @XmlAttribute(name = "viewId")
2372 protected String viewId;
2373 @XmlAttribute(name = "alignwithAlignPanel")
2374 protected Boolean alignwithAlignPanel;
2375 @XmlAttribute(name = "colourwithAlignPanel")
2376 protected Boolean colourwithAlignPanel;
2377 @XmlAttribute(name = "colourByJmol")
2378 protected Boolean colourByJmol;
2379 @XmlAttribute(name = "type")
2380 protected String type;
2381 @XmlAttribute(name = "width")
2382 protected Integer width;
2383 @XmlAttribute(name = "height")
2384 protected Integer height;
2385 @XmlAttribute(name = "xpos")
2386 protected Integer xpos;
2387 @XmlAttribute(name = "ypos")
2388 protected Integer ypos;
2391 * Gets the value of the value property.
2394 * possible object is
2398 public String getValue() {
2403 * Sets the value of the value property.
2410 public void setValue(String value) {
2415 * Gets the value of the visible property.
2418 * possible object is
2422 public Boolean isVisible() {
2427 * Sets the value of the visible property.
2434 public void setVisible(Boolean value) {
2435 this.visible = value;
2439 * Gets the value of the viewId property.
2442 * possible object is
2446 public String getViewId() {
2451 * Sets the value of the viewId property.
2458 public void setViewId(String value) {
2459 this.viewId = value;
2463 * Gets the value of the alignwithAlignPanel property.
2466 * possible object is
2470 public boolean isAlignwithAlignPanel() {
2471 if (alignwithAlignPanel == null) {
2474 return alignwithAlignPanel;
2479 * Sets the value of the alignwithAlignPanel property.
2486 public void setAlignwithAlignPanel(Boolean value) {
2487 this.alignwithAlignPanel = value;
2491 * Gets the value of the colourwithAlignPanel property.
2494 * possible object is
2498 public boolean isColourwithAlignPanel() {
2499 if (colourwithAlignPanel == null) {
2502 return colourwithAlignPanel;
2507 * Sets the value of the colourwithAlignPanel property.
2514 public void setColourwithAlignPanel(Boolean value) {
2515 this.colourwithAlignPanel = value;
2519 * Gets the value of the colourByJmol property.
2522 * possible object is
2526 public boolean isColourByJmol() {
2527 if (colourByJmol == null) {
2530 return colourByJmol;
2535 * Sets the value of the colourByJmol property.
2542 public void setColourByJmol(Boolean value) {
2543 this.colourByJmol = value;
2547 * Gets the value of the type property.
2550 * possible object is
2554 public String getType() {
2559 * Sets the value of the type property.
2566 public void setType(String value) {
2571 * Gets the value of the width property.
2574 * possible object is
2578 public Integer getWidth() {
2583 * Sets the value of the width property.
2590 public void setWidth(Integer value) {
2595 * Gets the value of the height property.
2598 * possible object is
2602 public Integer getHeight() {
2607 * Sets the value of the height property.
2614 public void setHeight(Integer value) {
2615 this.height = value;
2619 * Gets the value of the xpos property.
2622 * possible object is
2626 public Integer getXpos() {
2631 * Sets the value of the xpos property.
2638 public void setXpos(Integer value) {
2643 * Gets the value of the ypos property.
2646 * possible object is
2650 public Integer getYpos() {
2655 * Sets the value of the ypos property.
2662 public void setYpos(Integer value) {
2672 * <p>Java class for anonymous complex type.
2674 * <p>The following schema fragment specifies the expected content contained within this class.
2677 * &lt;complexType&gt;
2678 * &lt;complexContent&gt;
2679 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2680 * &lt;sequence&gt;
2681 * &lt;element name="secondaryStructure" maxOccurs="unbounded"&gt;
2682 * &lt;complexType&gt;
2683 * &lt;complexContent&gt;
2684 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2685 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2686 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2687 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2688 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2689 * &lt;/restriction&gt;
2690 * &lt;/complexContent&gt;
2691 * &lt;/complexType&gt;
2692 * &lt;/element&gt;
2693 * &lt;/sequence&gt;
2694 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
2695 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2696 * &lt;attribute name="viewId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2697 * &lt;attribute name="dividerLocation" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2698 * &lt;attribute name="selectedRna" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
2699 * &lt;/restriction&gt;
2700 * &lt;/complexContent&gt;
2701 * &lt;/complexType&gt;
2706 @XmlAccessorType(XmlAccessType.FIELD)
2707 @XmlType(name = "", propOrder = {
2708 "secondaryStructure"
2710 public static class RnaViewer {
2712 @XmlElement(namespace = "www.jalview.org", required = true)
2713 protected List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> secondaryStructure;
2714 @XmlAttribute(name = "title")
2715 protected String title;
2716 @XmlAttribute(name = "viewId")
2717 protected String viewId;
2718 @XmlAttribute(name = "dividerLocation")
2719 protected Integer dividerLocation;
2720 @XmlAttribute(name = "selectedRna")
2721 protected Integer selectedRna;
2722 @XmlAttribute(name = "width")
2723 protected Integer width;
2724 @XmlAttribute(name = "height")
2725 protected Integer height;
2726 @XmlAttribute(name = "xpos")
2727 protected Integer xpos;
2728 @XmlAttribute(name = "ypos")
2729 protected Integer ypos;
2732 * Gets the value of the secondaryStructure property.
2735 * This accessor method returns a reference to the live list,
2736 * not a snapshot. Therefore any modification you make to the
2737 * returned list will be present inside the JAXB object.
2738 * This is why there is not a <CODE>set</CODE> method for the secondaryStructure property.
2741 * For example, to add a new item, do as follows:
2743 * getSecondaryStructure().add(newItem);
2748 * Objects of the following type(s) are allowed in the list
2749 * {@link JalviewModel.JSeq.RnaViewer.SecondaryStructure }
2753 public List<JalviewModel.JSeq.RnaViewer.SecondaryStructure> getSecondaryStructure() {
2754 if (secondaryStructure == null) {
2755 secondaryStructure = new ArrayList<JalviewModel.JSeq.RnaViewer.SecondaryStructure>();
2757 return this.secondaryStructure;
2761 * Gets the value of the title property.
2764 * possible object is
2768 public String getTitle() {
2773 * Sets the value of the title property.
2780 public void setTitle(String value) {
2785 * Gets the value of the viewId property.
2788 * possible object is
2792 public String getViewId() {
2797 * Sets the value of the viewId property.
2804 public void setViewId(String value) {
2805 this.viewId = value;
2809 * Gets the value of the dividerLocation property.
2812 * possible object is
2816 public Integer getDividerLocation() {
2817 return dividerLocation;
2821 * Sets the value of the dividerLocation property.
2828 public void setDividerLocation(Integer value) {
2829 this.dividerLocation = value;
2833 * Gets the value of the selectedRna property.
2836 * possible object is
2840 public Integer getSelectedRna() {
2845 * Sets the value of the selectedRna property.
2852 public void setSelectedRna(Integer value) {
2853 this.selectedRna = value;
2857 * Gets the value of the width property.
2860 * possible object is
2864 public Integer getWidth() {
2869 * Sets the value of the width property.
2876 public void setWidth(Integer value) {
2881 * Gets the value of the height property.
2884 * possible object is
2888 public Integer getHeight() {
2893 * Sets the value of the height property.
2900 public void setHeight(Integer value) {
2901 this.height = value;
2905 * Gets the value of the xpos property.
2908 * possible object is
2912 public Integer getXpos() {
2917 * Sets the value of the xpos property.
2924 public void setXpos(Integer value) {
2929 * Gets the value of the ypos property.
2932 * possible object is
2936 public Integer getYpos() {
2941 * Sets the value of the ypos property.
2948 public void setYpos(Integer value) {
2954 * <p>Java class for anonymous complex type.
2956 * <p>The following schema fragment specifies the expected content contained within this class.
2959 * &lt;complexType&gt;
2960 * &lt;complexContent&gt;
2961 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
2962 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2963 * &lt;attribute name="annotationId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2964 * &lt;attribute name="gapped" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
2965 * &lt;attribute name="viewerState" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
2966 * &lt;/restriction&gt;
2967 * &lt;/complexContent&gt;
2968 * &lt;/complexType&gt;
2973 @XmlAccessorType(XmlAccessType.FIELD)
2975 public static class SecondaryStructure {
2977 @XmlAttribute(name = "title")
2978 protected String title;
2979 @XmlAttribute(name = "annotationId", required = true)
2980 protected String annotationId;
2981 @XmlAttribute(name = "gapped")
2982 protected Boolean gapped;
2983 @XmlAttribute(name = "viewerState")
2984 protected String viewerState;
2987 * Gets the value of the title property.
2990 * possible object is
2994 public String getTitle() {
2999 * Sets the value of the title property.
3006 public void setTitle(String value) {
3011 * Gets the value of the annotationId property.
3014 * possible object is
3018 public String getAnnotationId() {
3019 return annotationId;
3023 * Sets the value of the annotationId property.
3030 public void setAnnotationId(String value) {
3031 this.annotationId = value;
3035 * Gets the value of the gapped property.
3038 * possible object is
3042 public Boolean isGapped() {
3047 * Sets the value of the gapped property.
3054 public void setGapped(Boolean value) {
3055 this.gapped = value;
3059 * Gets the value of the viewerState property.
3062 * possible object is
3066 public String getViewerState() {
3071 * Sets the value of the viewerState property.
3078 public void setViewerState(String value) {
3079 this.viewerState = value;
3090 * <p>Java class for anonymous complex type.
3092 * <p>The following schema fragment specifies the expected content contained within this class.
3095 * &lt;complexType&gt;
3096 * &lt;complexContent&gt;
3097 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3098 * &lt;sequence&gt;
3099 * &lt;element name="sequencePoint" maxOccurs="unbounded"&gt;
3100 * &lt;complexType&gt;
3101 * &lt;complexContent&gt;
3102 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3103 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3104 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3105 * &lt;/restriction&gt;
3106 * &lt;/complexContent&gt;
3107 * &lt;/complexType&gt;
3108 * &lt;/element&gt;
3109 * &lt;element name="axis" maxOccurs="3" minOccurs="3"&gt;
3110 * &lt;complexType&gt;
3111 * &lt;complexContent&gt;
3112 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3113 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3114 * &lt;/restriction&gt;
3115 * &lt;/complexContent&gt;
3116 * &lt;/complexType&gt;
3117 * &lt;/element&gt;
3118 * &lt;element name="seqPointMin"&gt;
3119 * &lt;complexType&gt;
3120 * &lt;complexContent&gt;
3121 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3122 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3123 * &lt;/restriction&gt;
3124 * &lt;/complexContent&gt;
3125 * &lt;/complexType&gt;
3126 * &lt;/element&gt;
3127 * &lt;element name="seqPointMax"&gt;
3128 * &lt;complexType&gt;
3129 * &lt;complexContent&gt;
3130 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3131 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3132 * &lt;/restriction&gt;
3133 * &lt;/complexContent&gt;
3134 * &lt;/complexType&gt;
3135 * &lt;/element&gt;
3136 * &lt;element name="pcaData" type="{www.jalview.org}PcaDataType"/&gt;
3137 * &lt;/sequence&gt;
3138 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
3139 * &lt;attGroup ref="{www.jalview.org}SimilarityParams"/&gt;
3140 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3141 * &lt;attribute name="scoreModelName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
3142 * &lt;attribute name="xDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3143 * &lt;attribute name="yDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3144 * &lt;attribute name="zDim" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3145 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
3146 * &lt;attribute name="scaleFactor" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
3147 * &lt;attribute name="showLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3148 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
3149 * &lt;/restriction&gt;
3150 * &lt;/complexContent&gt;
3151 * &lt;/complexType&gt;
3156 @XmlAccessorType(XmlAccessType.FIELD)
3157 @XmlType(name = "", propOrder = {
3164 public static class PcaViewer {
3166 @XmlElement(namespace = "www.jalview.org", required = true)
3167 protected List<JalviewModel.PcaViewer.SequencePoint> sequencePoint;
3168 @XmlElement(namespace = "www.jalview.org", required = true)
3169 protected List<JalviewModel.PcaViewer.Axis> axis;
3170 @XmlElement(namespace = "www.jalview.org", required = true)
3171 protected JalviewModel.PcaViewer.SeqPointMin seqPointMin;
3172 @XmlElement(namespace = "www.jalview.org", required = true)
3173 protected JalviewModel.PcaViewer.SeqPointMax seqPointMax;
3174 @XmlElement(namespace = "www.jalview.org", required = true)
3175 protected PcaDataType pcaData;
3176 @XmlAttribute(name = "title")
3177 protected String title;
3178 @XmlAttribute(name = "scoreModelName")
3179 protected String scoreModelName;
3180 @XmlAttribute(name = "xDim")
3181 protected Integer xDim;
3182 @XmlAttribute(name = "yDim")
3183 protected Integer yDim;
3184 @XmlAttribute(name = "zDim")
3185 protected Integer zDim;
3186 @XmlAttribute(name = "bgColour")
3187 protected Integer bgColour;
3188 @XmlAttribute(name = "scaleFactor")
3189 protected Float scaleFactor;
3190 @XmlAttribute(name = "showLabels")
3191 protected Boolean showLabels;
3192 @XmlAttribute(name = "linkToAllViews")
3193 protected Boolean linkToAllViews;
3194 @XmlAttribute(name = "width")
3195 protected Integer width;
3196 @XmlAttribute(name = "height")
3197 protected Integer height;
3198 @XmlAttribute(name = "xpos")
3199 protected Integer xpos;
3200 @XmlAttribute(name = "ypos")
3201 protected Integer ypos;
3202 @XmlAttribute(name = "includeGaps")
3203 protected Boolean includeGaps;
3204 @XmlAttribute(name = "matchGaps")
3205 protected Boolean matchGaps;
3206 @XmlAttribute(name = "includeGappedColumns")
3207 protected Boolean includeGappedColumns;
3208 @XmlAttribute(name = "denominateByShortestLength")
3209 protected Boolean denominateByShortestLength;
3212 * Gets the value of the sequencePoint property.
3215 * This accessor method returns a reference to the live list,
3216 * not a snapshot. Therefore any modification you make to the
3217 * returned list will be present inside the JAXB object.
3218 * This is why there is not a <CODE>set</CODE> method for the sequencePoint property.
3221 * For example, to add a new item, do as follows:
3223 * getSequencePoint().add(newItem);
3228 * Objects of the following type(s) are allowed in the list
3229 * {@link JalviewModel.PcaViewer.SequencePoint }
3233 public List<JalviewModel.PcaViewer.SequencePoint> getSequencePoint() {
3234 if (sequencePoint == null) {
3235 sequencePoint = new ArrayList<JalviewModel.PcaViewer.SequencePoint>();
3237 return this.sequencePoint;
3241 * Gets the value of the axis property.
3244 * This accessor method returns a reference to the live list,
3245 * not a snapshot. Therefore any modification you make to the
3246 * returned list will be present inside the JAXB object.
3247 * This is why there is not a <CODE>set</CODE> method for the axis property.
3250 * For example, to add a new item, do as follows:
3252 * getAxis().add(newItem);
3257 * Objects of the following type(s) are allowed in the list
3258 * {@link JalviewModel.PcaViewer.Axis }
3262 public List<JalviewModel.PcaViewer.Axis> getAxis() {
3264 axis = new ArrayList<JalviewModel.PcaViewer.Axis>();
3270 * Gets the value of the seqPointMin property.
3273 * possible object is
3274 * {@link JalviewModel.PcaViewer.SeqPointMin }
3277 public JalviewModel.PcaViewer.SeqPointMin getSeqPointMin() {
3282 * Sets the value of the seqPointMin property.
3286 * {@link JalviewModel.PcaViewer.SeqPointMin }
3289 public void setSeqPointMin(JalviewModel.PcaViewer.SeqPointMin value) {
3290 this.seqPointMin = value;
3294 * Gets the value of the seqPointMax property.
3297 * possible object is
3298 * {@link JalviewModel.PcaViewer.SeqPointMax }
3301 public JalviewModel.PcaViewer.SeqPointMax getSeqPointMax() {
3306 * Sets the value of the seqPointMax property.
3310 * {@link JalviewModel.PcaViewer.SeqPointMax }
3313 public void setSeqPointMax(JalviewModel.PcaViewer.SeqPointMax value) {
3314 this.seqPointMax = value;
3318 * Gets the value of the pcaData property.
3321 * possible object is
3322 * {@link PcaDataType }
3325 public PcaDataType getPcaData() {
3330 * Sets the value of the pcaData property.
3334 * {@link PcaDataType }
3337 public void setPcaData(PcaDataType value) {
3338 this.pcaData = value;
3342 * Gets the value of the title property.
3345 * possible object is
3349 public String getTitle() {
3354 * Sets the value of the title property.
3361 public void setTitle(String value) {
3366 * Gets the value of the scoreModelName property.
3369 * possible object is
3373 public String getScoreModelName() {
3374 return scoreModelName;
3378 * Sets the value of the scoreModelName property.
3385 public void setScoreModelName(String value) {
3386 this.scoreModelName = value;
3390 * Gets the value of the xDim property.
3393 * possible object is
3397 public Integer getXDim() {
3402 * Sets the value of the xDim property.
3409 public void setXDim(Integer value) {
3414 * Gets the value of the yDim property.
3417 * possible object is
3421 public Integer getYDim() {
3426 * Sets the value of the yDim property.
3433 public void setYDim(Integer value) {
3438 * Gets the value of the zDim property.
3441 * possible object is
3445 public Integer getZDim() {
3450 * Sets the value of the zDim property.
3457 public void setZDim(Integer value) {
3462 * Gets the value of the bgColour property.
3465 * possible object is
3469 public Integer getBgColour() {
3474 * Sets the value of the bgColour property.
3481 public void setBgColour(Integer value) {
3482 this.bgColour = value;
3486 * Gets the value of the scaleFactor property.
3489 * possible object is
3493 public Float getScaleFactor() {
3498 * Sets the value of the scaleFactor property.
3505 public void setScaleFactor(Float value) {
3506 this.scaleFactor = value;
3510 * Gets the value of the showLabels property.
3513 * possible object is
3517 public Boolean isShowLabels() {
3522 * Sets the value of the showLabels property.
3529 public void setShowLabels(Boolean value) {
3530 this.showLabels = value;
3534 * Gets the value of the linkToAllViews property.
3537 * possible object is
3541 public Boolean isLinkToAllViews() {
3542 return linkToAllViews;
3546 * Sets the value of the linkToAllViews property.
3553 public void setLinkToAllViews(Boolean value) {
3554 this.linkToAllViews = value;
3558 * Gets the value of the width property.
3561 * possible object is
3565 public Integer getWidth() {
3570 * Sets the value of the width property.
3577 public void setWidth(Integer value) {
3582 * Gets the value of the height property.
3585 * possible object is
3589 public Integer getHeight() {
3594 * Sets the value of the height property.
3601 public void setHeight(Integer value) {
3602 this.height = value;
3606 * Gets the value of the xpos property.
3609 * possible object is
3613 public Integer getXpos() {
3618 * Sets the value of the xpos property.
3625 public void setXpos(Integer value) {
3630 * Gets the value of the ypos property.
3633 * possible object is
3637 public Integer getYpos() {
3642 * Sets the value of the ypos property.
3649 public void setYpos(Integer value) {
3654 * Gets the value of the includeGaps property.
3657 * possible object is
3661 public Boolean isIncludeGaps() {
3666 * Sets the value of the includeGaps property.
3673 public void setIncludeGaps(Boolean value) {
3674 this.includeGaps = value;
3678 * Gets the value of the matchGaps property.
3681 * possible object is
3685 public Boolean isMatchGaps() {
3690 * Sets the value of the matchGaps property.
3697 public void setMatchGaps(Boolean value) {
3698 this.matchGaps = value;
3702 * Gets the value of the includeGappedColumns property.
3705 * possible object is
3709 public Boolean isIncludeGappedColumns() {
3710 return includeGappedColumns;
3714 * Sets the value of the includeGappedColumns property.
3721 public void setIncludeGappedColumns(Boolean value) {
3722 this.includeGappedColumns = value;
3726 * Gets the value of the denominateByShortestLength property.
3729 * possible object is
3733 public Boolean isDenominateByShortestLength() {
3734 return denominateByShortestLength;
3738 * Sets the value of the denominateByShortestLength property.
3745 public void setDenominateByShortestLength(Boolean value) {
3746 this.denominateByShortestLength = value;
3751 * <p>Java class for anonymous complex type.
3753 * <p>The following schema fragment specifies the expected content contained within this class.
3756 * &lt;complexType&gt;
3757 * &lt;complexContent&gt;
3758 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3759 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3760 * &lt;/restriction&gt;
3761 * &lt;/complexContent&gt;
3762 * &lt;/complexType&gt;
3767 @XmlAccessorType(XmlAccessType.FIELD)
3769 public static class Axis {
3771 @XmlAttribute(name = "xPos")
3772 protected Float xPos;
3773 @XmlAttribute(name = "yPos")
3774 protected Float yPos;
3775 @XmlAttribute(name = "zPos")
3776 protected Float zPos;
3779 * Gets the value of the xPos property.
3782 * possible object is
3786 public Float getXPos() {
3791 * Sets the value of the xPos property.
3798 public void setXPos(Float value) {
3803 * Gets the value of the yPos property.
3806 * possible object is
3810 public Float getYPos() {
3815 * Sets the value of the yPos property.
3822 public void setYPos(Float value) {
3827 * Gets the value of the zPos property.
3830 * possible object is
3834 public Float getZPos() {
3839 * Sets the value of the zPos property.
3846 public void setZPos(Float value) {
3854 * <p>Java class for anonymous complex type.
3856 * <p>The following schema fragment specifies the expected content contained within this class.
3859 * &lt;complexType&gt;
3860 * &lt;complexContent&gt;
3861 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3862 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3863 * &lt;/restriction&gt;
3864 * &lt;/complexContent&gt;
3865 * &lt;/complexType&gt;
3870 @XmlAccessorType(XmlAccessType.FIELD)
3872 public static class SeqPointMax {
3874 @XmlAttribute(name = "xPos")
3875 protected Float xPos;
3876 @XmlAttribute(name = "yPos")
3877 protected Float yPos;
3878 @XmlAttribute(name = "zPos")
3879 protected Float zPos;
3882 * Gets the value of the xPos property.
3885 * possible object is
3889 public Float getXPos() {
3894 * Sets the value of the xPos property.
3901 public void setXPos(Float value) {
3906 * Gets the value of the yPos property.
3909 * possible object is
3913 public Float getYPos() {
3918 * Sets the value of the yPos property.
3925 public void setYPos(Float value) {
3930 * Gets the value of the zPos property.
3933 * possible object is
3937 public Float getZPos() {
3942 * Sets the value of the zPos property.
3949 public void setZPos(Float value) {
3957 * <p>Java class for anonymous complex type.
3959 * <p>The following schema fragment specifies the expected content contained within this class.
3962 * &lt;complexType&gt;
3963 * &lt;complexContent&gt;
3964 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
3965 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
3966 * &lt;/restriction&gt;
3967 * &lt;/complexContent&gt;
3968 * &lt;/complexType&gt;
3973 @XmlAccessorType(XmlAccessType.FIELD)
3975 public static class SeqPointMin {
3977 @XmlAttribute(name = "xPos")
3978 protected Float xPos;
3979 @XmlAttribute(name = "yPos")
3980 protected Float yPos;
3981 @XmlAttribute(name = "zPos")
3982 protected Float zPos;
3985 * Gets the value of the xPos property.
3988 * possible object is
3992 public Float getXPos() {
3997 * Sets the value of the xPos property.
4004 public void setXPos(Float value) {
4009 * Gets the value of the yPos property.
4012 * possible object is
4016 public Float getYPos() {
4021 * Sets the value of the yPos property.
4028 public void setYPos(Float value) {
4033 * Gets the value of the zPos property.
4036 * possible object is
4040 public Float getZPos() {
4045 * Sets the value of the zPos property.
4052 public void setZPos(Float value) {
4060 * <p>Java class for anonymous complex type.
4062 * <p>The following schema fragment specifies the expected content contained within this class.
4065 * &lt;complexType&gt;
4066 * &lt;complexContent&gt;
4067 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4068 * &lt;attGroup ref="{www.jalview.org}position"/&gt;
4069 * &lt;attribute name="sequenceRef" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4070 * &lt;/restriction&gt;
4071 * &lt;/complexContent&gt;
4072 * &lt;/complexType&gt;
4077 @XmlAccessorType(XmlAccessType.FIELD)
4079 public static class SequencePoint {
4081 @XmlAttribute(name = "sequenceRef")
4082 protected String sequenceRef;
4083 @XmlAttribute(name = "xPos")
4084 protected Float xPos;
4085 @XmlAttribute(name = "yPos")
4086 protected Float yPos;
4087 @XmlAttribute(name = "zPos")
4088 protected Float zPos;
4091 * Gets the value of the sequenceRef property.
4094 * possible object is
4098 public String getSequenceRef() {
4103 * Sets the value of the sequenceRef property.
4110 public void setSequenceRef(String value) {
4111 this.sequenceRef = value;
4115 * Gets the value of the xPos property.
4118 * possible object is
4122 public Float getXPos() {
4127 * Sets the value of the xPos property.
4134 public void setXPos(Float value) {
4139 * Gets the value of the yPos property.
4142 * possible object is
4146 public Float getYPos() {
4151 * Sets the value of the yPos property.
4158 public void setYPos(Float value) {
4163 * Gets the value of the zPos property.
4166 * possible object is
4170 public Float getZPos() {
4175 * Sets the value of the zPos property.
4182 public void setZPos(Float value) {
4192 * <p>Java class for anonymous complex type.
4194 * <p>The following schema fragment specifies the expected content contained within this class.
4197 * &lt;complexType&gt;
4198 * &lt;complexContent&gt;
4199 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4200 * &lt;sequence minOccurs="0"&gt;
4201 * &lt;element name="title" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4202 * &lt;element name="newick" type="{http://www.w3.org/2001/XMLSchema}string"/&gt;
4203 * &lt;/sequence&gt;
4204 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4205 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4206 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4207 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4208 * &lt;attribute name="threshold" type="{http://www.w3.org/2001/XMLSchema}float" /&gt;
4209 * &lt;attribute name="showBootstrap" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4210 * &lt;attribute name="showDistances" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4211 * &lt;attribute name="markUnlinked" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4212 * &lt;attribute name="fitToWindow" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4213 * &lt;attribute name="currentTree" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4214 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4215 * &lt;attribute name="linkToAllViews" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4216 * &lt;/restriction&gt;
4217 * &lt;/complexContent&gt;
4218 * &lt;/complexType&gt;
4223 @XmlAccessorType(XmlAccessType.FIELD)
4224 @XmlType(name = "", propOrder = {
4228 public static class Tree {
4230 @XmlElement(namespace = "www.jalview.org")
4231 protected String title;
4232 @XmlElement(namespace = "www.jalview.org")
4233 protected String newick;
4234 @XmlAttribute(name = "fontName")
4235 protected String fontName;
4236 @XmlAttribute(name = "fontSize")
4237 protected Integer fontSize;
4238 @XmlAttribute(name = "fontStyle")
4239 protected Integer fontStyle;
4240 @XmlAttribute(name = "threshold")
4241 protected Float threshold;
4242 @XmlAttribute(name = "showBootstrap")
4243 protected Boolean showBootstrap;
4244 @XmlAttribute(name = "showDistances")
4245 protected Boolean showDistances;
4246 @XmlAttribute(name = "markUnlinked")
4247 protected Boolean markUnlinked;
4248 @XmlAttribute(name = "fitToWindow")
4249 protected Boolean fitToWindow;
4250 @XmlAttribute(name = "currentTree")
4251 protected Boolean currentTree;
4252 @XmlAttribute(name = "id")
4253 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4255 @XmlSchemaType(name = "ID")
4256 protected String id;
4257 @XmlAttribute(name = "linkToAllViews")
4258 protected Boolean linkToAllViews;
4259 @XmlAttribute(name = "width")
4260 protected Integer width;
4261 @XmlAttribute(name = "height")
4262 protected Integer height;
4263 @XmlAttribute(name = "xpos")
4264 protected Integer xpos;
4265 @XmlAttribute(name = "ypos")
4266 protected Integer ypos;
4269 * Gets the value of the title property.
4272 * possible object is
4276 public String getTitle() {
4281 * Sets the value of the title property.
4288 public void setTitle(String value) {
4293 * Gets the value of the newick property.
4296 * possible object is
4300 public String getNewick() {
4305 * Sets the value of the newick property.
4312 public void setNewick(String value) {
4313 this.newick = value;
4317 * Gets the value of the fontName property.
4320 * possible object is
4324 public String getFontName() {
4329 * Sets the value of the fontName property.
4336 public void setFontName(String value) {
4337 this.fontName = value;
4341 * Gets the value of the fontSize property.
4344 * possible object is
4348 public Integer getFontSize() {
4353 * Sets the value of the fontSize property.
4360 public void setFontSize(Integer value) {
4361 this.fontSize = value;
4365 * Gets the value of the fontStyle property.
4368 * possible object is
4372 public Integer getFontStyle() {
4377 * Sets the value of the fontStyle property.
4384 public void setFontStyle(Integer value) {
4385 this.fontStyle = value;
4389 * Gets the value of the threshold property.
4392 * possible object is
4396 public Float getThreshold() {
4401 * Sets the value of the threshold property.
4408 public void setThreshold(Float value) {
4409 this.threshold = value;
4413 * Gets the value of the showBootstrap property.
4416 * possible object is
4420 public Boolean isShowBootstrap() {
4421 return showBootstrap;
4425 * Sets the value of the showBootstrap property.
4432 public void setShowBootstrap(Boolean value) {
4433 this.showBootstrap = value;
4437 * Gets the value of the showDistances property.
4440 * possible object is
4444 public Boolean isShowDistances() {
4445 return showDistances;
4449 * Sets the value of the showDistances property.
4456 public void setShowDistances(Boolean value) {
4457 this.showDistances = value;
4461 * Gets the value of the markUnlinked property.
4464 * possible object is
4468 public Boolean isMarkUnlinked() {
4469 return markUnlinked;
4473 * Sets the value of the markUnlinked property.
4480 public void setMarkUnlinked(Boolean value) {
4481 this.markUnlinked = value;
4485 * Gets the value of the fitToWindow property.
4488 * possible object is
4492 public Boolean isFitToWindow() {
4497 * Sets the value of the fitToWindow property.
4504 public void setFitToWindow(Boolean value) {
4505 this.fitToWindow = value;
4509 * Gets the value of the currentTree property.
4512 * possible object is
4516 public Boolean isCurrentTree() {
4521 * Sets the value of the currentTree property.
4528 public void setCurrentTree(Boolean value) {
4529 this.currentTree = value;
4533 * Gets the value of the id property.
4536 * possible object is
4540 public String getId() {
4545 * Sets the value of the id property.
4552 public void setId(String value) {
4557 * Gets the value of the linkToAllViews property.
4560 * possible object is
4564 public boolean isLinkToAllViews() {
4565 if (linkToAllViews == null) {
4568 return linkToAllViews;
4573 * Sets the value of the linkToAllViews property.
4580 public void setLinkToAllViews(Boolean value) {
4581 this.linkToAllViews = value;
4585 * Gets the value of the width property.
4588 * possible object is
4592 public Integer getWidth() {
4597 * Sets the value of the width property.
4604 public void setWidth(Integer value) {
4609 * Gets the value of the height property.
4612 * possible object is
4616 public Integer getHeight() {
4621 * Sets the value of the height property.
4628 public void setHeight(Integer value) {
4629 this.height = value;
4633 * Gets the value of the xpos property.
4636 * possible object is
4640 public Integer getXpos() {
4645 * Sets the value of the xpos property.
4652 public void setXpos(Integer value) {
4657 * Gets the value of the ypos property.
4660 * possible object is
4664 public Integer getYpos() {
4669 * Sets the value of the ypos property.
4676 public void setYpos(Integer value) {
4684 * <p>Java class for anonymous complex type.
4686 * <p>The following schema fragment specifies the expected content contained within this class.
4689 * &lt;complexType&gt;
4690 * &lt;complexContent&gt;
4691 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4692 * &lt;sequence&gt;
4693 * &lt;element name="UserColourScheme" type="{www.jalview.org/colours}JalviewUserColours"/&gt;
4694 * &lt;/sequence&gt;
4695 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4696 * &lt;/restriction&gt;
4697 * &lt;/complexContent&gt;
4698 * &lt;/complexType&gt;
4703 @XmlAccessorType(XmlAccessType.FIELD)
4704 @XmlType(name = "", propOrder = {
4707 public static class UserColours {
4709 @XmlElement(name = "UserColourScheme", namespace = "www.jalview.org", required = true)
4710 protected JalviewUserColours userColourScheme;
4711 @XmlAttribute(name = "id")
4712 protected String id;
4715 * Gets the value of the userColourScheme property.
4718 * possible object is
4719 * {@link JalviewUserColours }
4722 public JalviewUserColours getUserColourScheme() {
4723 return userColourScheme;
4727 * Sets the value of the userColourScheme property.
4731 * {@link JalviewUserColours }
4734 public void setUserColourScheme(JalviewUserColours value) {
4735 this.userColourScheme = value;
4739 * Gets the value of the id property.
4742 * possible object is
4746 public String getId() {
4751 * Sets the value of the id property.
4758 public void setId(String value) {
4766 * <p>Java class for anonymous complex type.
4768 * <p>The following schema fragment specifies the expected content contained within this class.
4771 * &lt;complexType&gt;
4772 * &lt;complexContent&gt;
4773 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4774 * &lt;sequence&gt;
4775 * &lt;element name="AnnotationColours" type="{www.jalview.org}AnnotationColourScheme" minOccurs="0"/&gt;
4776 * &lt;element name="hiddenColumns" maxOccurs="unbounded" minOccurs="0"&gt;
4777 * &lt;complexType&gt;
4778 * &lt;complexContent&gt;
4779 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
4780 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4781 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4782 * &lt;/restriction&gt;
4783 * &lt;/complexContent&gt;
4784 * &lt;/complexType&gt;
4785 * &lt;/element&gt;
4786 * &lt;element name="calcIdParam" maxOccurs="unbounded" minOccurs="0"&gt;
4787 * &lt;complexType&gt;
4788 * &lt;complexContent&gt;
4789 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
4790 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4791 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4792 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4793 * &lt;/extension&gt;
4794 * &lt;/complexContent&gt;
4795 * &lt;/complexType&gt;
4796 * &lt;/element&gt;
4797 * &lt;/sequence&gt;
4798 * &lt;attGroup ref="{www.jalview.org}swingwindow"/&gt;
4799 * &lt;attribute name="conservationSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4800 * &lt;attribute name="pidSelected" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4801 * &lt;attribute name="bgColour" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4802 * &lt;attribute name="consThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4803 * &lt;attribute name="pidThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4804 * &lt;attribute name="title" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4805 * &lt;attribute name="showFullId" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4806 * &lt;attribute name="rightAlignIds" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4807 * &lt;attribute name="showText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4808 * &lt;attribute name="showColourText" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4809 * &lt;attribute name="showUnconserved" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4810 * &lt;attribute name="showBoxes" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4811 * &lt;attribute name="wrapAlignment" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4812 * &lt;attribute name="renderGaps" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4813 * &lt;attribute name="showSequenceFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4814 * &lt;attribute name="showNPfeatureTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4815 * &lt;attribute name="showDbRefTooltip" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4816 * &lt;attribute name="followHighlight" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4817 * &lt;attribute name="followSelection" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4818 * &lt;attribute name="showAnnotation" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4819 * &lt;attribute name="centreColumnLabels" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4820 * &lt;attribute name="showGroupConservation" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4821 * &lt;attribute name="showGroupConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4822 * &lt;attribute name="showConsensusHistogram" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4823 * &lt;attribute name="showSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4824 * &lt;attribute name="normaliseSequenceLogo" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4825 * &lt;attribute name="ignoreGapsinConsensus" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4826 * &lt;attribute name="startRes" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4827 * &lt;attribute name="startSeq" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4828 * &lt;attribute name="fontName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4829 * &lt;attribute name="fontSize" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4830 * &lt;attribute name="fontStyle" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4831 * &lt;attribute name="scaleProteinAsCdna" type="{http://www.w3.org/2001/XMLSchema}boolean" default="true" /&gt;
4832 * &lt;attribute name="viewName" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4833 * &lt;attribute name="sequenceSetId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4834 * &lt;attribute name="gatheredViews" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
4835 * &lt;attribute name="textCol1" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4836 * &lt;attribute name="textCol2" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4837 * &lt;attribute name="textColThreshold" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
4838 * &lt;attribute name="id" type="{http://www.w3.org/2001/XMLSchema}ID" /&gt;
4839 * &lt;attribute name="complementId" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
4840 * &lt;attribute name="showComplementFeatures" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4841 * &lt;attribute name="showComplementFeaturesOnTop" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
4842 * &lt;/restriction&gt;
4843 * &lt;/complexContent&gt;
4844 * &lt;/complexType&gt;
4849 @XmlAccessorType(XmlAccessType.FIELD)
4850 @XmlType(name = "", propOrder = {
4851 "annotationColours",
4855 public static class Viewport {
4857 @XmlElement(name = "AnnotationColours", namespace = "www.jalview.org")
4858 protected AnnotationColourScheme annotationColours;
4859 @XmlElement(namespace = "www.jalview.org")
4860 protected List<JalviewModel.Viewport.HiddenColumns> hiddenColumns;
4861 @XmlElement(namespace = "www.jalview.org")
4862 protected List<JalviewModel.Viewport.CalcIdParam> calcIdParam;
4863 @XmlAttribute(name = "conservationSelected")
4864 protected Boolean conservationSelected;
4865 @XmlAttribute(name = "pidSelected")
4866 protected Boolean pidSelected;
4867 @XmlAttribute(name = "bgColour")
4868 protected String bgColour;
4869 @XmlAttribute(name = "consThreshold")
4870 protected Integer consThreshold;
4871 @XmlAttribute(name = "pidThreshold")
4872 protected Integer pidThreshold;
4873 @XmlAttribute(name = "title")
4874 protected String title;
4875 @XmlAttribute(name = "showFullId")
4876 protected Boolean showFullId;
4877 @XmlAttribute(name = "rightAlignIds")
4878 protected Boolean rightAlignIds;
4879 @XmlAttribute(name = "showText")
4880 protected Boolean showText;
4881 @XmlAttribute(name = "showColourText")
4882 protected Boolean showColourText;
4883 @XmlAttribute(name = "showUnconserved")
4884 protected Boolean showUnconserved;
4885 @XmlAttribute(name = "showBoxes")
4886 protected Boolean showBoxes;
4887 @XmlAttribute(name = "wrapAlignment")
4888 protected Boolean wrapAlignment;
4889 @XmlAttribute(name = "renderGaps")
4890 protected Boolean renderGaps;
4891 @XmlAttribute(name = "showSequenceFeatures")
4892 protected Boolean showSequenceFeatures;
4893 @XmlAttribute(name = "showNPfeatureTooltip")
4894 protected Boolean showNPfeatureTooltip;
4895 @XmlAttribute(name = "showDbRefTooltip")
4896 protected Boolean showDbRefTooltip;
4897 @XmlAttribute(name = "followHighlight")
4898 protected Boolean followHighlight;
4899 @XmlAttribute(name = "followSelection")
4900 protected Boolean followSelection;
4901 @XmlAttribute(name = "showAnnotation")
4902 protected Boolean showAnnotation;
4903 @XmlAttribute(name = "centreColumnLabels")
4904 protected Boolean centreColumnLabels;
4905 @XmlAttribute(name = "showGroupConservation")
4906 protected Boolean showGroupConservation;
4907 @XmlAttribute(name = "showGroupConsensus")
4908 protected Boolean showGroupConsensus;
4909 @XmlAttribute(name = "showConsensusHistogram")
4910 protected Boolean showConsensusHistogram;
4911 @XmlAttribute(name = "showSequenceLogo")
4912 protected Boolean showSequenceLogo;
4913 @XmlAttribute(name = "normaliseSequenceLogo")
4914 protected Boolean normaliseSequenceLogo;
4915 @XmlAttribute(name = "ignoreGapsinConsensus")
4916 protected Boolean ignoreGapsinConsensus;
4917 @XmlAttribute(name = "startRes")
4918 protected Integer startRes;
4919 @XmlAttribute(name = "startSeq")
4920 protected Integer startSeq;
4921 @XmlAttribute(name = "fontName")
4922 protected String fontName;
4923 @XmlAttribute(name = "fontSize")
4924 protected Integer fontSize;
4925 @XmlAttribute(name = "fontStyle")
4926 protected Integer fontStyle;
4927 @XmlAttribute(name = "scaleProteinAsCdna")
4928 protected Boolean scaleProteinAsCdna;
4929 @XmlAttribute(name = "viewName")
4930 protected String viewName;
4931 @XmlAttribute(name = "sequenceSetId")
4932 protected String sequenceSetId;
4933 @XmlAttribute(name = "gatheredViews")
4934 protected Boolean gatheredViews;
4935 @XmlAttribute(name = "textCol1")
4936 protected Integer textCol1;
4937 @XmlAttribute(name = "textCol2")
4938 protected Integer textCol2;
4939 @XmlAttribute(name = "textColThreshold")
4940 protected Integer textColThreshold;
4941 @XmlAttribute(name = "id")
4942 @XmlJavaTypeAdapter(CollapsedStringAdapter.class)
4944 @XmlSchemaType(name = "ID")
4945 protected String id;
4946 @XmlAttribute(name = "complementId")
4947 protected String complementId;
4948 @XmlAttribute(name = "showComplementFeatures")
4949 protected Boolean showComplementFeatures;
4950 @XmlAttribute(name = "showComplementFeaturesOnTop")
4951 protected Boolean showComplementFeaturesOnTop;
4952 @XmlAttribute(name = "width")
4953 protected Integer width;
4954 @XmlAttribute(name = "height")
4955 protected Integer height;
4956 @XmlAttribute(name = "xpos")
4957 protected Integer xpos;
4958 @XmlAttribute(name = "ypos")
4959 protected Integer ypos;
4962 * Gets the value of the annotationColours property.
4965 * possible object is
4966 * {@link AnnotationColourScheme }
4969 public AnnotationColourScheme getAnnotationColours() {
4970 return annotationColours;
4974 * Sets the value of the annotationColours property.
4978 * {@link AnnotationColourScheme }
4981 public void setAnnotationColours(AnnotationColourScheme value) {
4982 this.annotationColours = value;
4986 * Gets the value of the hiddenColumns property.
4989 * This accessor method returns a reference to the live list,
4990 * not a snapshot. Therefore any modification you make to the
4991 * returned list will be present inside the JAXB object.
4992 * This is why there is not a <CODE>set</CODE> method for the hiddenColumns property.
4995 * For example, to add a new item, do as follows:
4997 * getHiddenColumns().add(newItem);
5002 * Objects of the following type(s) are allowed in the list
5003 * {@link JalviewModel.Viewport.HiddenColumns }
5007 public List<JalviewModel.Viewport.HiddenColumns> getHiddenColumns() {
5008 if (hiddenColumns == null) {
5009 hiddenColumns = new ArrayList<JalviewModel.Viewport.HiddenColumns>();
5011 return this.hiddenColumns;
5015 * Gets the value of the calcIdParam property.
5018 * This accessor method returns a reference to the live list,
5019 * not a snapshot. Therefore any modification you make to the
5020 * returned list will be present inside the JAXB object.
5021 * This is why there is not a <CODE>set</CODE> method for the calcIdParam property.
5024 * For example, to add a new item, do as follows:
5026 * getCalcIdParam().add(newItem);
5031 * Objects of the following type(s) are allowed in the list
5032 * {@link JalviewModel.Viewport.CalcIdParam }
5036 public List<JalviewModel.Viewport.CalcIdParam> getCalcIdParam() {
5037 if (calcIdParam == null) {
5038 calcIdParam = new ArrayList<JalviewModel.Viewport.CalcIdParam>();
5040 return this.calcIdParam;
5044 * Gets the value of the conservationSelected property.
5047 * possible object is
5051 public Boolean isConservationSelected() {
5052 return conservationSelected;
5056 * Sets the value of the conservationSelected property.
5063 public void setConservationSelected(Boolean value) {
5064 this.conservationSelected = value;
5068 * Gets the value of the pidSelected property.
5071 * possible object is
5075 public Boolean isPidSelected() {
5080 * Sets the value of the pidSelected property.
5087 public void setPidSelected(Boolean value) {
5088 this.pidSelected = value;
5092 * Gets the value of the bgColour property.
5095 * possible object is
5099 public String getBgColour() {
5104 * Sets the value of the bgColour property.
5111 public void setBgColour(String value) {
5112 this.bgColour = value;
5116 * Gets the value of the consThreshold property.
5119 * possible object is
5123 public Integer getConsThreshold() {
5124 return consThreshold;
5128 * Sets the value of the consThreshold property.
5135 public void setConsThreshold(Integer value) {
5136 this.consThreshold = value;
5140 * Gets the value of the pidThreshold property.
5143 * possible object is
5147 public Integer getPidThreshold() {
5148 return pidThreshold;
5152 * Sets the value of the pidThreshold property.
5159 public void setPidThreshold(Integer value) {
5160 this.pidThreshold = value;
5164 * Gets the value of the title property.
5167 * possible object is
5171 public String getTitle() {
5176 * Sets the value of the title property.
5183 public void setTitle(String value) {
5188 * Gets the value of the showFullId property.
5191 * possible object is
5195 public Boolean isShowFullId() {
5200 * Sets the value of the showFullId property.
5207 public void setShowFullId(Boolean value) {
5208 this.showFullId = value;
5212 * Gets the value of the rightAlignIds property.
5215 * possible object is
5219 public Boolean isRightAlignIds() {
5220 return rightAlignIds;
5224 * Sets the value of the rightAlignIds property.
5231 public void setRightAlignIds(Boolean value) {
5232 this.rightAlignIds = value;
5236 * Gets the value of the showText property.
5239 * possible object is
5243 public Boolean isShowText() {
5248 * Sets the value of the showText property.
5255 public void setShowText(Boolean value) {
5256 this.showText = value;
5260 * Gets the value of the showColourText property.
5263 * possible object is
5267 public Boolean isShowColourText() {
5268 return showColourText;
5272 * Sets the value of the showColourText property.
5279 public void setShowColourText(Boolean value) {
5280 this.showColourText = value;
5284 * Gets the value of the showUnconserved property.
5287 * possible object is
5291 public boolean isShowUnconserved() {
5292 if (showUnconserved == null) {
5295 return showUnconserved;
5300 * Sets the value of the showUnconserved property.
5307 public void setShowUnconserved(Boolean value) {
5308 this.showUnconserved = value;
5312 * Gets the value of the showBoxes property.
5315 * possible object is
5319 public Boolean isShowBoxes() {
5324 * Sets the value of the showBoxes property.
5331 public void setShowBoxes(Boolean value) {
5332 this.showBoxes = value;
5336 * Gets the value of the wrapAlignment property.
5339 * possible object is
5343 public Boolean isWrapAlignment() {
5344 return wrapAlignment;
5348 * Sets the value of the wrapAlignment property.
5355 public void setWrapAlignment(Boolean value) {
5356 this.wrapAlignment = value;
5360 * Gets the value of the renderGaps property.
5363 * possible object is
5367 public Boolean isRenderGaps() {
5372 * Sets the value of the renderGaps property.
5379 public void setRenderGaps(Boolean value) {
5380 this.renderGaps = value;
5384 * Gets the value of the showSequenceFeatures property.
5387 * possible object is
5391 public Boolean isShowSequenceFeatures() {
5392 return showSequenceFeatures;
5396 * Sets the value of the showSequenceFeatures property.
5403 public void setShowSequenceFeatures(Boolean value) {
5404 this.showSequenceFeatures = value;
5408 * Gets the value of the showNPfeatureTooltip property.
5411 * possible object is
5415 public Boolean isShowNPfeatureTooltip() {
5416 return showNPfeatureTooltip;
5420 * Sets the value of the showNPfeatureTooltip property.
5427 public void setShowNPfeatureTooltip(Boolean value) {
5428 this.showNPfeatureTooltip = value;
5432 * Gets the value of the showDbRefTooltip property.
5435 * possible object is
5439 public Boolean isShowDbRefTooltip() {
5440 return showDbRefTooltip;
5444 * Sets the value of the showDbRefTooltip property.
5451 public void setShowDbRefTooltip(Boolean value) {
5452 this.showDbRefTooltip = value;
5456 * Gets the value of the followHighlight property.
5459 * possible object is
5463 public boolean isFollowHighlight() {
5464 if (followHighlight == null) {
5467 return followHighlight;
5472 * Sets the value of the followHighlight property.
5479 public void setFollowHighlight(Boolean value) {
5480 this.followHighlight = value;
5484 * Gets the value of the followSelection property.
5487 * possible object is
5491 public boolean isFollowSelection() {
5492 if (followSelection == null) {
5495 return followSelection;
5500 * Sets the value of the followSelection property.
5507 public void setFollowSelection(Boolean value) {
5508 this.followSelection = value;
5512 * Gets the value of the showAnnotation property.
5515 * possible object is
5519 public Boolean isShowAnnotation() {
5520 return showAnnotation;
5524 * Sets the value of the showAnnotation property.
5531 public void setShowAnnotation(Boolean value) {
5532 this.showAnnotation = value;
5536 * Gets the value of the centreColumnLabels property.
5539 * possible object is
5543 public boolean isCentreColumnLabels() {
5544 if (centreColumnLabels == null) {
5547 return centreColumnLabels;
5552 * Sets the value of the centreColumnLabels property.
5559 public void setCentreColumnLabels(Boolean value) {
5560 this.centreColumnLabels = value;
5564 * Gets the value of the showGroupConservation property.
5567 * possible object is
5571 public boolean isShowGroupConservation() {
5572 if (showGroupConservation == null) {
5575 return showGroupConservation;
5580 * Sets the value of the showGroupConservation property.
5587 public void setShowGroupConservation(Boolean value) {
5588 this.showGroupConservation = value;
5592 * Gets the value of the showGroupConsensus property.
5595 * possible object is
5599 public boolean isShowGroupConsensus() {
5600 if (showGroupConsensus == null) {
5603 return showGroupConsensus;
5608 * Sets the value of the showGroupConsensus property.
5615 public void setShowGroupConsensus(Boolean value) {
5616 this.showGroupConsensus = value;
5620 * Gets the value of the showConsensusHistogram property.
5623 * possible object is
5627 public boolean isShowConsensusHistogram() {
5628 if (showConsensusHistogram == null) {
5631 return showConsensusHistogram;
5636 * Sets the value of the showConsensusHistogram property.
5643 public void setShowConsensusHistogram(Boolean value) {
5644 this.showConsensusHistogram = value;
5648 * Gets the value of the showSequenceLogo property.
5651 * possible object is
5655 public boolean isShowSequenceLogo() {
5656 if (showSequenceLogo == null) {
5659 return showSequenceLogo;
5664 * Sets the value of the showSequenceLogo property.
5671 public void setShowSequenceLogo(Boolean value) {
5672 this.showSequenceLogo = value;
5676 * Gets the value of the normaliseSequenceLogo property.
5679 * possible object is
5683 public boolean isNormaliseSequenceLogo() {
5684 if (normaliseSequenceLogo == null) {
5687 return normaliseSequenceLogo;
5692 * Sets the value of the normaliseSequenceLogo property.
5699 public void setNormaliseSequenceLogo(Boolean value) {
5700 this.normaliseSequenceLogo = value;
5704 * Gets the value of the ignoreGapsinConsensus property.
5707 * possible object is
5711 public boolean isIgnoreGapsinConsensus() {
5712 if (ignoreGapsinConsensus == null) {
5715 return ignoreGapsinConsensus;
5720 * Sets the value of the ignoreGapsinConsensus property.
5727 public void setIgnoreGapsinConsensus(Boolean value) {
5728 this.ignoreGapsinConsensus = value;
5732 * Gets the value of the startRes property.
5735 * possible object is
5739 public Integer getStartRes() {
5744 * Sets the value of the startRes property.
5751 public void setStartRes(Integer value) {
5752 this.startRes = value;
5756 * Gets the value of the startSeq property.
5759 * possible object is
5763 public Integer getStartSeq() {
5768 * Sets the value of the startSeq property.
5775 public void setStartSeq(Integer value) {
5776 this.startSeq = value;
5780 * Gets the value of the fontName property.
5783 * possible object is
5787 public String getFontName() {
5792 * Sets the value of the fontName property.
5799 public void setFontName(String value) {
5800 this.fontName = value;
5804 * Gets the value of the fontSize property.
5807 * possible object is
5811 public Integer getFontSize() {
5816 * Sets the value of the fontSize property.
5823 public void setFontSize(Integer value) {
5824 this.fontSize = value;
5828 * Gets the value of the fontStyle property.
5831 * possible object is
5835 public Integer getFontStyle() {
5840 * Sets the value of the fontStyle property.
5847 public void setFontStyle(Integer value) {
5848 this.fontStyle = value;
5852 * Gets the value of the scaleProteinAsCdna property.
5855 * possible object is
5859 public boolean isScaleProteinAsCdna() {
5860 if (scaleProteinAsCdna == null) {
5863 return scaleProteinAsCdna;
5868 * Sets the value of the scaleProteinAsCdna property.
5875 public void setScaleProteinAsCdna(Boolean value) {
5876 this.scaleProteinAsCdna = value;
5880 * Gets the value of the viewName property.
5883 * possible object is
5887 public String getViewName() {
5892 * Sets the value of the viewName property.
5899 public void setViewName(String value) {
5900 this.viewName = value;
5904 * Gets the value of the sequenceSetId property.
5907 * possible object is
5911 public String getSequenceSetId() {
5912 return sequenceSetId;
5916 * Sets the value of the sequenceSetId property.
5923 public void setSequenceSetId(String value) {
5924 this.sequenceSetId = value;
5928 * Gets the value of the gatheredViews property.
5931 * possible object is
5935 public Boolean isGatheredViews() {
5936 return gatheredViews;
5940 * Sets the value of the gatheredViews property.
5947 public void setGatheredViews(Boolean value) {
5948 this.gatheredViews = value;
5952 * Gets the value of the textCol1 property.
5955 * possible object is
5959 public Integer getTextCol1() {
5964 * Sets the value of the textCol1 property.
5971 public void setTextCol1(Integer value) {
5972 this.textCol1 = value;
5976 * Gets the value of the textCol2 property.
5979 * possible object is
5983 public Integer getTextCol2() {
5988 * Sets the value of the textCol2 property.
5995 public void setTextCol2(Integer value) {
5996 this.textCol2 = value;
6000 * Gets the value of the textColThreshold property.
6003 * possible object is
6007 public Integer getTextColThreshold() {
6008 return textColThreshold;
6012 * Sets the value of the textColThreshold property.
6019 public void setTextColThreshold(Integer value) {
6020 this.textColThreshold = value;
6024 * Gets the value of the id property.
6027 * possible object is
6031 public String getId() {
6036 * Sets the value of the id property.
6043 public void setId(String value) {
6048 * Gets the value of the complementId property.
6051 * possible object is
6055 public String getComplementId() {
6056 return complementId;
6060 * Sets the value of the complementId property.
6067 public void setComplementId(String value) {
6068 this.complementId = value;
6072 * Gets the value of the showComplementFeatures property.
6075 * possible object is
6079 public boolean isShowComplementFeatures() {
6080 if (showComplementFeatures == null) {
6083 return showComplementFeatures;
6088 * Sets the value of the showComplementFeatures property.
6095 public void setShowComplementFeatures(Boolean value) {
6096 this.showComplementFeatures = value;
6100 * Gets the value of the showComplementFeaturesOnTop property.
6103 * possible object is
6107 public boolean isShowComplementFeaturesOnTop() {
6108 if (showComplementFeaturesOnTop == null) {
6111 return showComplementFeaturesOnTop;
6116 * Sets the value of the showComplementFeaturesOnTop property.
6123 public void setShowComplementFeaturesOnTop(Boolean value) {
6124 this.showComplementFeaturesOnTop = value;
6128 * Gets the value of the width property.
6131 * possible object is
6135 public Integer getWidth() {
6140 * Sets the value of the width property.
6147 public void setWidth(Integer value) {
6152 * Gets the value of the height property.
6155 * possible object is
6159 public Integer getHeight() {
6164 * Sets the value of the height property.
6171 public void setHeight(Integer value) {
6172 this.height = value;
6176 * Gets the value of the xpos property.
6179 * possible object is
6183 public Integer getXpos() {
6188 * Sets the value of the xpos property.
6195 public void setXpos(Integer value) {
6200 * Gets the value of the ypos property.
6203 * possible object is
6207 public Integer getYpos() {
6212 * Sets the value of the ypos property.
6219 public void setYpos(Integer value) {
6225 * <p>Java class for anonymous complex type.
6227 * <p>The following schema fragment specifies the expected content contained within this class.
6230 * &lt;complexType&gt;
6231 * &lt;complexContent&gt;
6232 * &lt;extension base="{www.jalview.org/xml/wsparamset}WebServiceParameterSet"&gt;
6233 * &lt;attribute name="calcId" use="required" type="{http://www.w3.org/2001/XMLSchema}string" /&gt;
6234 * &lt;attribute name="needsUpdate" type="{http://www.w3.org/2001/XMLSchema}boolean" default="false" /&gt;
6235 * &lt;attribute name="autoUpdate" use="required" type="{http://www.w3.org/2001/XMLSchema}boolean" /&gt;
6236 * &lt;/extension&gt;
6237 * &lt;/complexContent&gt;
6238 * &lt;/complexType&gt;
6243 @XmlAccessorType(XmlAccessType.FIELD)
6245 public static class CalcIdParam
6246 extends WebServiceParameterSet
6249 @XmlAttribute(name = "calcId", required = true)
6250 protected String calcId;
6251 @XmlAttribute(name = "needsUpdate")
6252 protected Boolean needsUpdate;
6253 @XmlAttribute(name = "autoUpdate", required = true)
6254 protected boolean autoUpdate;
6257 * Gets the value of the calcId property.
6260 * possible object is
6264 public String getCalcId() {
6269 * Sets the value of the calcId property.
6276 public void setCalcId(String value) {
6277 this.calcId = value;
6281 * Gets the value of the needsUpdate property.
6284 * possible object is
6288 public boolean isNeedsUpdate() {
6289 if (needsUpdate == null) {
6297 * Sets the value of the needsUpdate property.
6304 public void setNeedsUpdate(Boolean value) {
6305 this.needsUpdate = value;
6309 * Gets the value of the autoUpdate property.
6312 public boolean isAutoUpdate() {
6317 * Sets the value of the autoUpdate property.
6320 public void setAutoUpdate(boolean value) {
6321 this.autoUpdate = value;
6328 * <p>Java class for anonymous complex type.
6330 * <p>The following schema fragment specifies the expected content contained within this class.
6333 * &lt;complexType&gt;
6334 * &lt;complexContent&gt;
6335 * &lt;restriction base="{http://www.w3.org/2001/XMLSchema}anyType"&gt;
6336 * &lt;attribute name="start" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6337 * &lt;attribute name="end" type="{http://www.w3.org/2001/XMLSchema}int" /&gt;
6338 * &lt;/restriction&gt;
6339 * &lt;/complexContent&gt;
6340 * &lt;/complexType&gt;
6345 @XmlAccessorType(XmlAccessType.FIELD)
6347 public static class HiddenColumns {
6349 @XmlAttribute(name = "start")
6350 protected Integer start;
6351 @XmlAttribute(name = "end")
6352 protected Integer end;
6355 * Gets the value of the start property.
6358 * possible object is
6362 public Integer getStart() {
6367 * Sets the value of the start property.
6374 public void setStart(Integer value) {
6379 * Gets the value of the end property.
6382 * possible object is
6386 public Integer getEnd() {
6391 * Sets the value of the end property.
6398 public void setEnd(Integer value) {